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Forest Ecologist Suzanne Simard on How She Discovered the Relationships Between Trees and Mycorrhizal Networks.  This Changes Everything!

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Forest Ecologist Suzanne Simard on How She Discovered the Relationships Between Trees and Mycorrhizal Networks.  This Changes Everything!

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Suzanne Simard  |  Mother Trees and the Social Forest

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Forest Ecologist and Mycologist Merlin Sheldrake on his fascinating book Entangled Lives: How Fungi Make Our Worlds, Change our Minds and Shape Our Future.

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Forest Ecologist and Mycologist Merlin Sheldrake on his fascinating book Entangled Lives: How Fungi Make Our Worlds, Change our Minds and Shape Our Future.

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Breakthroughs in Understanding Fungal Networks.  Entangled Lives

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Breakthroughs in Understanding Fungal Networks.  Entangled Lives

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Entangled Life: How Fungi Make Our Worlds, Change Our Minds, and Shape Our Futures — Merlin Sheldrake

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“Entangled Life is a mercurial, revelatory, impassioned, urgent, astounding, and necessary read. It’s fearless in scope, analytically astute, and brimming with infectious joy.” — Helen Macdonald

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Adding Nitrogen Fertiliser Damages the Soil Microbiome and Plant Health.  

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Adding Nitrogen Fertiliser Damages the Soil Microbiome and Plant Health.  

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Do we need nitrogen fertiliser? Or even nitrogen-fixers? Can plants and their microbial partners make enough nitrogen for amino acids and proteins without human intervention? Stupid question! They've been doing it for 100s of millions of years. What are the 4 functional groups and how do we choose the right plants for 'root mingling'?

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"The Nitrogen Solution" with Dr. Christine Jones (Part 3/4)

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Soil scientist Dr Christine Jones: Get the right combination of plants and let nature do the rest!

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Soil scientist Dr Christine Jones: Get the right combination of plants and let nature do the rest!

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Christine Jones translates the most up-to-date science on the soil microbiome for the average lay person's understanding. This is fascinating stuff. This is this-changes-everything-stuff. And our worldview has to change more in the direction of Masanobu Fukuoka's Natural Farming. Plants have been building relationships with microbial life for hundreds of millions of years and we've spent the last 10,000 or so years undoing all that with agriculture. It's time to rethink how we grow food completely and let nature do the work for us. Indigenous peoples already know this. It's fascinating how plants and microbial life communicate through biosignaling and the soil is a very chatty place.

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"Secrets of the Soil Sociobiome" with Dr. Christine Jones (Part 1/4)

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Endophytic microbes and their potential applications in crop management

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Endophytic microbes and their potential applications in crop management

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A short version of James White's work on the rhizophagy cycle. White has a very anthropocentric interpretation, namely that the plants are 'farming' the microbes in the soil.

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The Rhizophagy Cycle: Bacteria Bring Nutrients into Roots

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The Rhizophagy Cycle: Bacteria Bring Nutrients into Roots

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Dr Christine Jones: the latest research on nitrogen.

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Dr Christine Jones: the latest research on nitrogen.

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Plant diversity, four functional plant groups from four different families at least.

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"The Nitrogen Solution" with Dr. Christine Jones (Part 3/4)

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Plant diversity = microbial diversity = carbon storage in the soil

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Plant diversity = microbial diversity = carbon storage in the soil

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Plant diversity strongly influences ecosystem functions and services, such as soil carbon storage...higher plant diversity increases rhizosphere carbon inputs into the microbial community resulting in both increased microbial activity and carbon storage...The present study shows that elevated carbon storage at high plant diversity is a direct function of the soil microbial community, indicating that the increase in carbon storage is mainly limited by the integration of new carbon into soil and less by the decomposition of existing soil carbon.

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Study site of The Jena Experiment

Our study was carried out as a part of The Jena Experiment, a large-scale grassland diversity experiment. The experiment is located on the floodplain of the Saale River near the city of Jena (Thuringia, Germany; 50°57′ N, 11°35′ E). The soil of the field site is classified as Eutric Fluvisol. In spring 2002, 82 experimental grassland plots of 20 × 20 m were established. One monoculture plot was abandoned due to poor establishment, making the total number of plots 81 instead of the 82 originally planned. Plots are arranged in four blocks to account for changes in abiotic factors with distance from the river. Soil texture in the upper soil ranges from sandy loam to silty clay with increasing distance from the river. Sand content declines from 40% near the river to 7% at the furthest plot, while silt content increases from 44 to 69%, respectively. The clay content ranges from 16 to 24%, but is not related to distance from the river. For the 40 years before establishing the experiment, the field site was a cultivated field with mineral fertilizer input. The initial physico-chemical properties, such as pH (7.1-8.4), soil organic carbon (5-33 g C kg −1), and soil nitrogen concentrations (1.0-2.7 g N kg −1), varied across the field site and are considered in the block design of The Jena Experiment.

The plots differed in both the number of plant species (1, 2, 4, 8, 16 and 60 species), randomly chosen from a common pool of 60 plant species, and the number of plant functional groups, that is, grasses, legumes, small herbs and tall herbs, which were classified into four functional groups based on morphological, phenological and physiological traits; for details see ref. 26. Experimental communities are weeded manually twice a year to maintain the levels of diversity and mown twice yearly in June and September as is typical for hay meadows in Central Europe.

Sampling and laboratory analyses

Data included in this paper originated from soil samples taken at a depth of 0-5 cm, where biological activity is at a maximum. Fine root biomass in some cases had to be extrapolated to obtain estimates for the topsoil (0-5 cm), as not all sampling campaigns were set up for stratified sampling (see below).

Soil organic carbon. Soil sampling was performed before sowing in April 2002 and was repeated in April in the years 2004, 2006, 2008 and 2011, as described in more detail in ref. 25. In short, three soil samples were taken per plot (4.8 cm in diameter, 0-30 cm deep) using a split tube sampler (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). In the year 2002, a total of five soil samples were taken per plot. The soil was dried, sieved (2 mm mesh) and milled (4 min, frequency 30 s −1). Total carbon of ground samples was determined by an elemental analyser after combustion at 1,150 °C (Elementaranalysator vario Max CN, Elementar Analysensysteme GmbH, Hanau, Germany). Inorganic carbon concentration was measured by elemental analysis after removing organic carbon for 16 h at 450 °C in a muffle furnace by oxidation. Organic carbon concentration was calculated from the difference between total and inorganic carbon concentrations. Carbon stocks were calculated as the product of bulk soil density and its concentration of carbon. In order to exclude physical aspects of bulk density (for example, inter-annual differences caused by degree of winter freezing), statistical analyses were done with carbon concentrations (g kg −1) and stocks were estimated using the mean of bulk soil density across all years.

Periodic sampling of other data used in this study did not always occur over the same time interval (annual: microbial activity, biannual: soil and root sampling). Thus, the mean of the other variables (basal respiration fine root carbon input) was calculated referring to each biannual soil carbon sampling campaigns.

Fine root standing biomass: root standing biomass was sampled in 2003, 2004, 2006 and 2008, and separated in fine and coarse roots based on root diameter (fine roots ≤2 mm; coarse roots >2 mm). Roots were calculated as grams dry mass per square meter. In the first three sampling campaigns, fine roots were determined to a depth of 30 cm. In 2008, stratified sampling was carried out with a finer resolution of 5 cm increments. On the basis of the fine root ratio of the topsoil (0-5 cm) and entire sampling depth (0-30 cm) in 2008, fine root standing biomass in the topsoil was estimated for each prior sampling year. The carbon content of fine roots was determined using root material from ingrowth cores sampled in 2004 (ref. 29). Fine root biomass comprised on average 80.9% (±16.8 s.d.) of the total root biomass and was highly correlated to the total root biomass ( R ²=0.66, P<0.001).

Basal respiration. It was measured annually from 2003 to 2011, except in 2005. Five soil samples per plot were taken to a depth of 5 cm, pooled and stored at 5 °C. The samples were homogenized, sieved (2 mm) to remove larger roots, animals and stones, and adjusted to a gravimetric soil water content of 25%. Basal respiration was measured using an O ₂ microcompensation apparatus. The microbial respiratory response was measured at hourly intervals for 24 h at 22 °C. Basal respiration (μl O ₂ h −1 per g soil dry mass) was determined without the addition of substrate and measured as the mean of the O ₂ consumption rates 14-24 h after the start of the measurements (for details see ref. 20).

Radiocarbon and soil nitrogen isotope ratios. Radiocarbon concentrations ( ¹⁴C) were measured in soil samples of the years 2002 and 2011 as described in detail by Tefs and Gleixner. Briefly, after decalcification with HCl and graphite production, the ¹⁴C content of the samples was measured with accelerator mass spectroscopy (3 MV Tandetron 4130 AMS, High Voltage Engineering Europa, Amersfoort, The Netherlands). Soil nitrogen isotope ratios ( δ ¹⁵ N) were measured from 50 mg of dried ground soil with an elemental analyser coupled to an isotope-ratio mass spectrometer (EA-IRMS; Delta C prototype IRMS, Finnigan MAT).

Root exudation. Within the experimental setup of The Jena Experiment it is not possible to determine the effects of plant diversity on the amount of root exudation. Therefore, we took advantage of the Ecotron facility in Montpellier (France) to overcome this limitation. Twelve monoliths (2.0 m in depth and 1.6 m in diameter) were excavated from the field site of The Jena Experiment and installed in the macrocosms in the Ecotron in spring 2012. These 12 monoliths reflected the diversity gradient of The Jena Experiment on a smaller scale. Monoliths with high (16 plant species) and low plant diversity (4 plant species) were labelled with ¹³CO ₂ for 4 weeks. We analysed root exudation and the turnover of the exudates by root associated microbes using the phospholipid fatty acid (PLFA) method. Particular specific monounsaturated fatty acids such as PLFA 16:1ω5, 16:1ω7, 17:1ω8 and 18:1ω7 were shown to be highly enriched by root-derived organic carbon in label experiments. We measured the concentration and enrichment in δ ¹³ C of these PLFA markers in the Ecotron to assess the effect of plant diversity on root exudation and the incorporation of the exudates in soil microbes.

Genetic diversity of soil bacteria and fungi. The genetic diversity of soil microbial communities was determined using terminal-restriction fragment length polymorphism. Briefly, total nucleic acids were extracted from 0.25 g fresh weight of soil using the MoBio Powersoil 96 kit. Bacterial 16S rRNA genes were amplified using forward primer 63F (5′-CAGGCCTAACACATGCAAGTC-3′; ref. 56), fluorescently labelled with 6-FAM at the 5′ end, and reverse primer 519r (5′-GTATTACCGCGGCTGCTG-3′; ref. 57). For fungi, we used the primer pair ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) and ITS4 (5′-TCCTCCGCTTATTGATATGC-3′; ref. 59), spanning the ITS1 and ITS2 regions. Amplicons were purified by gel filtration using Sephadex G50 (Sigma-Aldrich, Gillingham, UK) before digestion with restriction endonucleases Msp1 (CCGG) and Taq 1 (TCGA; Promega, Southampton, UK) for bacteria and fungi, respectively. A 3730 DNA analyser (Applied Biosystems, CA, USA) was used for fragment analysis, before binning of individual terminal-restriction fragments using Genemarker software (SoftGenetics, PA, USA). The relative abundance of individual terminal-restriction fragments was calculated by dividing the intensity of each fragment by the total intensity of all fragments before calculation of Simpson's diversity index.

Statistical analyses of main effects of plant diversity

The Jena Experiment is based on a factorial design with different combinations of sown plant species richness and number of functional groups. To assess for the design variables, analyses of variance with sequential sum of squares (type I SS) were applied using R. The 'block effect', mainly accounting for differences in soil texture among the blocks, was included as random factor and fitted first, followed by plant species richness and functional groups. Finally, the presence of each plant functional group (legumes, grasses, small herbs and tall herbs) was included into the model in a series of alternative models.

Path analysis

We applied path analyses (maximum likelihood) to explore the potentially causal relationships between plant diversity and community composition and soil carbon storage using the lavaan package in R. Depending on the results of the analysis of variance approach, all variables with significant effect on changes of soil carbon content were included as exogenous (predictor) variables. As variables potentially mediating plant community effects we included fine root carbon as measure of carbon input and basal respiration as measure of microbial metabolic activity. We tested four different ways how plant diversity can affect carbon storage: due to carbon input from roots, due to microbial activity, due to both root inputs as well as microbial activity, or directly via plant diversity, indicating that other mechanisms than root carbon input and microbial activity underlie the plant diversity effect. Each of the four storage ways comprised a set of models ( Supplementary Fig. 1), differing in the relations from plant diversity to basal respiration and fine root carbon to basal respiration. For all models, the adequacy of the hypothesized structural relationships and the data was verified using χ ²-tests and the residual mean square error of approximation. To test whether carbon storage is a function of the microbial activity or vice versa, we tested all models twice, first with the path from basal respiration towards soil carbon content, as 'sink models' (as described above, Supplementary Note 1) and second with a path from soil carbon content towards basal respiration as 'source models' ( Supplementary Note 2). In the final step, we identified the minimal adequate (most parsimonious) model based on the Bayes Information Criterion. Therefore, all adequate models were compared ( Supplementary Note 3), including nonsignificant pathways and when only significant pathways are contained.

Eisenhauer et al. and Ravenek et al. showed that plant species richness was not closely linked to basal respiration and root standing biomass in the first years of the experiment; therefore, we did not use data from the first 2 years in the present analyses. Missing values were replaced by the mean. All variables were standardized to (0, 1). The total sample size was N=81.

Three-pool ¹⁴C model with serial structure

To describe soil organic carbon dynamics in The Jena Experiment, we implemented a dynamic model of the form

where C f, C s and C p represent carbon storage in the fast, slow and passive pool, respectively. I represents the total amount of carbon input to the first 5 cm of the soil, and k ₁, k ₂ and k ₃ represent first-order decomposition rates for the fast, slow and passive pools, respectively. The transfer coefficients α 2,1 and α 3,2 represent the proportion of the decomposed carbon from each pool that is transferred to a slower cycling pool.

One particular aspect of this model, suggested from the path analysis, is that we represent the effects of the microbial community on decomposition as a control on the transfer rate. That is, we assume

where MB is the microbial biomass and f is a scaling factor. Notice that we do not represent the microbial biomass as an additional pool in our dynamical system because it leads to unrealistic nonlinear behaviour not supported by our own observations.

To account for radiocarbon dynamics, we implemented a model similar to equation (1) representing each pool as a fraction of radiocarbon with respect to an internationally agreed standard. The model has similar form as equation (1) with an additional term accounting for radioactive decay. The model was implemented in the R environment for computing using the SoilR package. The passive pool is mainly needed to account for the low ¹⁴C values in the bulk soil organic matter. As described by other authors, such low ¹⁴ C values are common for arable fields in Europe.

On the basis of our findings in the path analysis, we implemented a measure of soil microbial community activity (basal respiration) as a proxy for the transfer between the fast and slow carbon pool. Unfortunately, no data on basal respiration were available for arable control plots, which would have been needed for the spin up (please see section 'Spin up and parameter estimation for the spin up'). Thus, we took advantage of the microbial biomass (based on the chloroform fumigation extraction analysis) instead. Basal respiration and microbial biomass were highly correlated ( Fig. 3c). For each level of plant species richness, we applied a model with the level specific parameter estimation ( Table 1; Fig. 3b). However, we could neither evaluate the real carbon input (carbon of standing fine root biomass and root exudates, root tips and so on) nor the extent of the transfer coefficient. Thus, we applied a set of different models for each level of plant diversity, modified in the carbon input and transfer coefficient. Implementing the transfer coefficient between the fast and the slow pool depending on soil microbial biomass resulted in good agreement between model predictions and measured data ( Table 3; Supplementary Table 3; and Supplementary Fig. 3).

Table 3 Variations of soil carbon properties and their drivers in The Jena Experiment.

Calculation of new carbon accumulated and loss of old carbon: on the basis of the mass balance and the isotopic mass balance for the isotopic mass ratio (equation (3)), we calculated the yearly (a) amount of new carbon sequestrated ( C new) and loss of the old carbon ( C loss old).

Spin up and parameter estimation for the spin up. The objective of the spin up simulations is to match the carbon stocks and ¹⁴C data for the pre-experimental conditions. We let the spin up simulations run for 10,000 years to assure the modelled pre-experimental conditions are in equilibrium. As there are no comparable data for fine root biomass on the arable control plots, we used the mean fine root carbon of all experimental plots from of all fine root sampling campaigns (mean=149.77 g m −2, s.d.=98.05). Due to ploughing of the soil before the implementation of the experimental plots, a homogeneous distribution of fine root carbon can be assumed as 25 g m −2 in each soil segment of 5 cm. In contrast, after establishment of experimental plots, the fine root biomass distribution was similar to meadows with the main amount of roots in the topsoil, strongly decreasing towards deeper depths. Thus, a fine root carbon input of 67.04 g m −2 (on average) was assumed on experimental plots. The ratio of the assumed fine root inputs between experimental plots and arable land is similar to the ratio of carbon input on meadows and arable lands reported in ref. 68 Furthermore, we applied a fine root turnover of 1.7 years on experimental grassland plots. To meet the measured and the modelled data, a fine root turnover of 1.2 years for arable lands was applied. In the spin up, we set the input factor to 1.7 ( Supplementary Table 3), the transfer coefficient to 0.1 reflecting C mic of 0.22 ng g −1 on the arable control plots (cf. Table 1). This value of the transfer coefficient is within the expected range. The resulting sizes of the three pools and their ages are shown in Supplementary Table 3.

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Plant diversity increases soil microbial activity and soil carbon storage - Nature Communications

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The mechanisms driving soil carbon storage, one of the largest stores of terrestrial carbon, remain poorly understood. Here, the authors present data from the long-term Jena Experiment on grassland biodiversity, showing that elevated carbon storage at high plant diversity is a direct function of increased soil microbial activity.

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Network working to map the Earth's mycorrhizal networks.

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Network working to map the Earth's mycorrhizal networks.

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As this study shows, airborne fungi are literally everywhere.  

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As this study shows, airborne fungi are literally everywhere.  

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State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China

Fungi are ubiquitous in nature; that is, they are present everywhere on the planet; understanding the active state and functional capacity of airborne microbes associated with health of human, animal, and plant is critical for biosafety management. Here, we firstly and directly proved that there were about 40% active fungi in the air via rRNA amplicon sequencing and imaging flow cytometry simultaneously. Amplicon sequencing analysis showed differences between structures of active and total fungal community; Ascomycota were dominant in the active community, while Basidiomycota have low transcriptional activity across all samples. Notably, plant pathogenic fungi were predominant in the air, and more than 50% were active, including not only several common plant pathogens but also biotrophic fungi ( Erysiphe sp. and Microbotryum sp.) and host-specific pathogens, which were generally considered to be inactive after leaving the host. Putative plant pathogens of eight genera were found active across the sampling season, indicating their superior ability to obtain nutrients even in barren nutrient environments. Interestingly, we detected several potentially active unrecorded fungi in China ( Diatrype prominens, Septofusidium herbarum, Pseudomicrostroma glucosiphilum, and Uromycladium tepperianum), which suggested that they spread over a long distance by air and may cause diseases under favorable conditions. Our results suggested that maintaining transmission in air is an essential feature of many fungi including plant pathogens regardless of being a biotrophic, hemibiotrophic, or necrotrophic group. Moreover, two potentially active human pathogens and one animal pathogen were captured, which indicated their potential risks. This study provided a new perspective for more comprehensive understanding of airborne fungi, including their multidimensional lifestyle, state, functioning, and potential pathogenic risk. It also laid the foundation for further prediction and management of airborne microbial communities, which would be of interest for public health and agriculture.

Introduction

Airborne fungi play an important role in the global ecosystem ( Woo et al., 2018), affecting not only precipitation, carbon, and nitrogen cycles ( Pöschl et al., 2010; Haga et al., 2014; Hassett et al., 2015) but also the health of humans, plants, and animals ( Brown and Hovmøller, 2002; Fisher et al., 2012; Golan and Pringle, 2017). The atmosphere is not the most extreme microbial habitat, and most of its features are consistent with other habitats ( Womack et al., 2010). For many microbes, transport in the air is part of their life cycle ( Brown and Hovmøller, 2002). In order to maintain their ability to survive in the atmosphere, they have adapted to the atmospheric environment and evolved survival strategies for long-distance dispersal and/or high-altitude diffusion ( Imshenetsky et al., 1978; Griffin, 2004; Kellogg and Griffin, 2006; Joly et al., 2015). Many fungi including pathogenic fungi of plants and animals can spread over long distances or even intercontinental, causing, or exacerbating diseases ( Brown and Hovmøller, 2002; Fisher et al., 2012; Golan and Pringle, 2017).

It has been found that microbes in air are metabolically active (mainly indicated as bacteria currently), and the residence time in the atmosphere is long enough to reproduce for some microorganisms ( Womack et al., 2010). The function of fungi in the atmosphere depends on the physiological state of cells. Metabolically active vegetative cells have greater potential to transform atmospheric compounds and ultimately alter atmospheric chemistry than dormant spores ( Sussman and Douthit, 1973). The ice nucleation efficiency of fungal cells may also be determined by their physiological state. Potentially active nutrient cells can form ice nucleation more effectively than fungal spores ( Iannone et al., 2011; Després et al., 2012; Morris et al., 2013). Metabolically active fungi were isolated from the atmospheric samples, which could transform carboxylic acid, formaldehyde, and hydrogen peroxide compounds, which play a major role in the atmospheric chemical process ( Ariya et al., 2002; Cote et al., 2008; Vaïtilingom et al., 2013).

In recent years, the application of molecular biology techniques including cloning approaches, qPCR, denaturing gradient gel electrophoresis (DGGE) ( Fröhlich-Nowoisky et al., 2009; Li et al., 2010), and high-throughput sequencing are accelerating the research of atmospheric microbiome ( Yamamoto et al., 2012, 2014; Woo et al., 2013; Cao et al., 2014; Dannemiller et al., 2014; Emerson et al., 2015; Womack et al., 2015; Banchi et al., 2018). Previous studies have shown that fungal spores and other biological particles account for a large proportion of aerosol particles in rain forests and in rural and urban environments. The microorganisms in the atmospheric are as diverse as in the terrestrial environments ( Hughes et al., 2004; Eoin et al., 2007), and their community structure showed significant diurnal dynamics ( Fierer et al., 2008) and seasonal cycles ( Fröhlich-Nowoisky et al., 2009; Du et al., 2018).

Nevertheless, most of culture-independent studies of microbial community diversity only rely on sequence analysis of rDNA, which provides the overall information of living, dead, and dormant cells in a community. However, there may be fundamental differences in structure and composition between active and total communities. For example, it is the rare members of the total community that are dominant in the active community in many environmental systems ( Campbell et al., 2011; Klein et al., 2016); using rDNA data alone may lead to an underestimation of the functional importance of rare taxa ( Campbell et al., 2011; Aanderud et al., 2015). Therefore, sequence analysis based on rRNA in ribosomes and other reliable and efficient technology such as imaging flow cytometry were necessary to uncover the composition of the active community, because ribosomes are more abundant in active than in dormant cells ( Muttray and Mohn, 1988; Prosser, 2002; Lennon and Jones, 2011; Womack et al., 2015). Additionally, imaging flow cytometry is an innovative, high-throughput technology that can provide a clear picture of each microbe cell or particle, as well as the ability to identify dead or live cells by fluorescent staining ( McFarlin et al., 2013; Verma et al., 2018). One of the common methods to investigate total and active communities is to measure the community composition of DNA and RNA in ribosomes ( Chicharo and Chicharo, 2008; Blazewicz et al., 2013; Womack et al., 2015; Denef et al., 2016). This approach has been applied to study active microbial communities on soil and on decaying plant materials ( Rajala et al., 2011; Baldrian et al., 2012; Barnard et al., 2013; Schostag et al., 2015), but there are few reports on the metabolic activity of airborne microbial communities.

Klein et al. (2016) analyzed the metabolic activity of bacteria community in the atmosphere, and they found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from that of the total bacterial community (assayed via rDNA), and rare taxa in the total community were disproportionately active relative to abundant taxa. Amato et al. (2017) studied the active and total microbial community in cloud water, and they uncovered the potential active fungal species mainly composed of saprophytic fungi from terrestrial or aquatic origins known for aerial dispersion, such as Pleosporales, Magnaporthales, Xylariales, and Conioscyphales in Ascomycota; and Pucciniales, Hymenochaetales, and Sporidiobolales in Basidiomycota. Another research about active and total fungal communities in the atmosphere over the Amazon rainforest by Womack et al. (2015) revealed significant differences in the composition of the total and active fungal communities in the atmosphere; and compared with other environments, fungal communities in the atmosphere were most similar to communities found in tropical soils and leaf surfaces. These studies indicate that the combination of rRNA and rDNA sequence analysis not only reveals the diversity of microbial communities in the atmosphere more comprehensively but also can evaluate the species with potential metabolic activity. However, no research focused on both diversity and function of active fungal communities in the atmosphere.

To our best of knowledge, at present, there is no in situ evidence of fungal growth in the air, although fungi can grow in the absence of carbon sources (i.e., fungi could grow on silica gel media as well as in distilled water and liquid culture media without carbon had been added) ( Wainwright, 1987); and Aspergillus, Penicillium, Eupenicillium, and Thysanophora presented with the fastest transformation rate of malonic acid, which is the most abundant in organic aerosols ( Cote et al., 2008) based on the result of previous studies. Therefore, transcriptional activity is more accurate to describe the results based on RNA sequencing at present study, mainly for the following reasons: the cell's total RNA pool is mainly composed of rRNA (82-90%) ( Tissières et al., 1959; Neidhardt and Magasanik, 1960), rRNA is a fundamental constituent of all known microorganisms, most rRNA found in a cell is ribosome associated as an integral structural component of ribosomes ( Lindahl, 1975; Nomura et al., 1984), and rRNA is a product of transcription ( Blazewicz et al., 2013).

In this study, we used comparative rRNA/rDNA amplicon sequencing to study the composition and structure of potentially active and total fungal community in the atmosphere of Kunming city, Yunnan Province of China, an area that is a typical low-latitude plateau with good air quality. We asked the following questions about the fungal communities inhabiting the atmosphere of Kunming: (1) What is the composition of the potentially active and total fungal communities in the atmosphere? Are there differences? (2) What are the major functional groups of the potentially active and total fungal communities in the atmosphere? (3) What are the potential plant pathogenic fungi in the atmosphere? If there are any, what are their potential activities? We aimed to set up a basis, expand the scope of biodiversity and biogeography research, provide information for understanding of diversity and function of atmospheric fungal community, and provide a basis for further studies on the prediction and even management of airborne microbial communities that would be of interest for public health and agriculture.

Materials and Methods

Site Description and Air Sampling

The study site is located within Yunnan Agricultural University, Northern Kunming, China. Air microbial samples were collected from the roof top of the Crop Protection Building (25°7′53.45″N, 102°44′55.36″E, altitude of 1,931 m), about 30 m above the ground; the sampling area is without interference from surroundings, and there are no major pollution sources nearby (see air quality data in Supplementary Table 1). Samples were collected using six independently modified air samplers (KC8704 air sampler, Changzhou Jinfen Instrument Co., Ltd., Jiangsu, China) Ambient air was drawn at an average flow rate of 12.5 L/min; samples were continuously collected from January 1, to July 31, 2018. The filter was changed each week; the filter holder was cleaned with 75% ethanol; and all the tools used for changing new filters, as well as new filters, were packaged separately in aluminum foil, then autoclaved at 121°C, and dried at 55°C previously to avoid contamination. After sampling, the filters were kept in a 50-ml sterile centrifuge tube, 10-ml RNA Later TM (Beyotime, Shanghai, China) in each tube; stored at 4°C for 24 h; and then transferred to be stored at -20°C until downstream analyses.

Nucleic Acid Isolation and cDNA Synthesis

Samples collected of each month were bisected for DNA and RNA extraction. DNA was extracted using QIAGEN DNeasy PowerSoil Kit (Qiagen Inc., Hilden, Germany) according to the manufacturer's instructions. Soil RNA Mini Kit from Omega Bio-Tek (Guangzhu, China) was used for RNA extraction; then cDNA synthesis was performed using 5× all-in-one RT MasterMix (with AccuRT Genomic DNA Removal Kit) from Applied Biological Materials Inc. (Richmond, BC, Canada). All the steps mentioned above were carried out in a clean bench, and all centrifuge tubes and pipette tips were nucleic free. All RNA extraction steps were performed on ice and centrifuged at 4°C. The extracted DNA and samples were stored at -80°C until further use.

Library Preparation and Sequencing

The V4 region of the 18S rRNA genes and transcripts (rRNA which was converted to cDNA) were amplified using the forward primer 528F (5′-barcode-GCGGTAATTCCAGCTCCAA-3′) and reverse primer 706R (5′-barcode-AATCCRAGAATTTCACCTCT-3′). The PCRs were carried out in 50-μl volume reactions with 25 μl 2 ∗taq PCR mix, 1 μl of Primer F (10 μM), 1 μl of Primer R (10 μM), 4 μl of dNTPs, 17 μl of ddH ₂ O, and 2 μl of template DNA. Thermal cycling consisted of initial denaturation at 98°C for 10 min, followed by 30 cycles of denaturation at 95°C for 1 min, annealing at 55°C for 30 s, and elongation at 72°C for 30 s, and finally at 72°C for 5 min. The concentration and purity of DNA and cDNA samples were tested by 1% agarose gel electrophoresis, and samples were diluted with sterile water to 1 ng/μl. Multiplexed sequencing libraries were generated using Ion Plus Fragment Library Kit 48 rxns (Thermo Fisher Scientific, Waltham, MA, United States) following manufacturer's recommendations. The library quality was assessed on the Qubit@2.0 Fluorometer (Thermo Fisher Scientific) and then sequenced on an Ion S5TMXL Ion at Novogene Co. Ltd. (Beijing, China).

Sequence Processing and Data Statistical Analyses

The offline single-end reads were filtered according to the Cutadapt (V1.9.1) quality-controlled process ( Martin, 2011) to obtain raw reads; then raw reads were assigned to samples based on their unique barcode and truncated by cutting off barcode and primer sequence to obtain raw reads. Quality filtering of the raw reads was performed using to QIIME (V1.9.1) ( Caporaso et al., 2010) with the following options: - q ≤ 19, - r = 3, and - p < 0.75. The reads were compared with the reference database (Silva database) ( Quast et al., 2013) using UCHIME algorithm ( Edgar et al., 2011) to detect and remove chimera sequences to obtain clean reads. The operational taxonomic units (OTUs) with a similarity threshold of 97% were selected with the Uparse software package (v7.0.1001) ( Edgar, 2013), singletons were filtered before OTU clustering for improving calculation efficiency, while all clean read sequences (including singleton) were aligned with the representative sequence (the sequence with the highest occurrence frequency), and any matched sequences were retained to calculate the abundance of OTUs. The representative sequence for each OTU was selected for annotation using the Silva Database (SSU rRNA) ( Quast et al., 2013).

α-Diversity indices [Observed Species, Chao1, Shannon, Simpson, abundance-based coverage estimator (ACE), good coverage, and phylogenetic diversity (PD) whole tree] and beta diversity on Bray-Curtis and unweighted_unifrac were calculated with QIIME (Version 1.7.0). The dilution curve, rank abundance curve, species accumulation curve, non-metric multidimensional scaling (NMDS), and hierarchical clustering tree based on UPGMA by unweighted_unifrac distances were performed by Vegan and ggplot2 package in R software (Version 2.15.3). Paired t-test of α-diversity indices were conducted by SPSS 16.0; the average value and standard deviation were used to represent each index in the results; both Bray-Curtis and unweighted_unifrac by t-test were used for analysis of β-diversity differences between active and total fungal communities. Analysis of similarities (Anosim), multiresponse permutation procedure (MRPP) based on Bray-Curtis, and permutational multivariate analysis of variance (Adonis) on Bray-Curtis were performed using Vegan package in R software (Version 2.15.3); and analysis of molecular variance (Amova) based on unweighted_unifrac was performed in Mothur (Version 1.33.3) ( Schloss et al., 2009) to determine whether there were significant differences between active and total fungal communities. Spearman's correlation was used to test the correlation between relative abundance and rRNA:rDNA ratio. p < 0.05 indicates significant correlation.

Ecological Function Assignment and Temporal Dynamics Analysis of Airborne Fungi

To obtain putative ecological functions from fungal OTUs at the genus or species level, the fungal OTU table was submitted to FUNGuild website ( Nguyen et al., 2016) to do ecological function predication. For a more detailed assignment, we also reviewed relevant literatures and allocated known fungal into functional categories. The species distribution status in the world was queried on GBIF ( https://www.gbif.org; March 21-30, 2019). Data of temperature, relative humidity, wind speed, and precipitation were recorded according to the reports of Chinese National Meteorological Center. The air quality data come from a local website.

Core genera were defined as the genus occurring in all samples in the annotation table. All OTUs that had been annotated to species level in the annotation table previously were identified by BLAST matches in National Center for Biotechnology Information (NCBI); the species with the percentage of identification greater than 98% as the putative species (and species with percentage of identification <98% were removed; the alignment result with percentage of identification = 100%, but could not be identified to specific species were marked as "sp.") were selected for functional group division and subsequent analysis based on the latest sequence BLAST in NCBI. The rRNA:rDNA ratio of each was calculated to analyze the temporal dynamics of transcriptional activity.

Air Sampling and Detected by FlowSight® Imaging Flow Cytometry

Samples of PM 2.5 (air fine particulate matter, particulate matter with aerodynamic diameter below 2.5 μm), PM ₁₀ (air coarse particulate matter, particulate matter with aerodynamic diameter below 10 μm), and total suspended particulate (TSP) were collected from the same site as 18S V4 amplicon sequencing samples from April 1 to 3 conducted by three high volume air samplers (Thermo Electron Corp., Waltham, MA, United States): one was equipped with PM 2.5 fractionating inlet, another one was equipped with a PM ₁₀ fractionating inlet, and the third one was without fractionating inlet. All samples were continuously collected for 60 h with an average flow rate of 1.13 m ³/min, resulting in approximately 4,068 m ³ of air flow-through per sample. Particulate matter was collected on 20.32 × 25.4 cm ² Tissuquartz filters (PALL, Port Washington, NY, United States), which was autoclaved at 121°C and dried at 55°C previously. A piece of 1/48 of the filter from each of the samples was cut and placed in 1.5-ml centrifuge tubes filled with sterilized 1× phosphate-buffered saline (PBS), static for 40 min, then centrifuged at 1,000 r/min for 20 min, sucked out precipitation, gentle vortex, and stained using propidium iodide (PI) according to the manufacturer's instructions (Yeasen Co., Ltd, Shanghai, China). Image acquisition was carried out using a 20×objective on a FlowSight ® Imaging Flow Cytometer (Amnis ®, Luminex, Chicago, United States) equipped with a 488-nm laser. A total of 20,000 single, in-focus images were captured on FlowSight ® per sample. PI-stained fluorescence and chlorophyll spontaneous fluorescence were also detected.

The IDEAS ® software (Version 6.2) was used for image analysis and cell counting. At first, the best-focused images were selected from raw images; then cells of best-focused images were gated according to "Area" (0-500 μm ²) and "Aapect Ratio" (0-1) into four gates. Cells were further selected with parameter "Circularity" from 1 to 15 (eliminate debris of plants/animals and fiber, etc.) and "Length" from 0 to 120 μm from the four groups and then classified according to parameter of length and result of fluorescence: the cells with length of ≤5 and ≤20 μm (considered as fungi), the cells with length <5 μm (considered as bacterial), the length of most protozoa is larger than 20 μm; cells/particles successfully stained with PI were considered as dead cells, and chlorophyll auto-fluorescence cells/particles were considered as green plants or algae; the number of each gate was counted for data analyses.

Results

Sequencing Summary

A total of 540,388 and 532,079 qualified reads with average lengths ranging from 304 to 310 nucleotides for 18S rDNA and rRNA sequencing were acquired, respectively, with an average of 76,605 ± 8,786 reads in each sample ( Table 1 and Supplementary Table 3). In total, 1,994 OTUs were obtained by clustering at 97% sequence similarities, including 686 OTUs in rDNA sequencing subset and 1,144 OTUs in rRNA sequencing subset, and 43.1% of the total OTUs (852 OTUs) were common in both subsets. The number of unique OTUs that occurred in rDNA sequencing subset and RNA sequencing subset was 834 and 292, respectively; the proportion of unique OTUs out of total OTUs was 42.2 and 14.8%, respectively. There were 628 OTUs that were assigned to fungi, 48 OTUs belong to metazoans (Animalia), and the remaining 1,247 OTUs were indicated as eukaryotic (Apicomplexa, Chlorophyta, Diatomea, Streptophyta, and other unidentified_Eukaryota) in Silva database. There were 77.7% fungal OTUs (488 OTUs) common in both rDNA and rRNA sequencing subsets, and the unique OTUs in rDNA and rRNA sequencing subset were 89 and 51, accounting for 14.2 and 8.1%, respectively. All of the following data analyses were based on OTUs that were annotated to fungi.

The Composition and Structure of Active Fungal Community Were Significantly Different From Those of Total Community

All of the α-diversity indices such as Richness, Chao1, ACE, Shannon, Simpson, good coverage, and PD whole tree (see Supplementary Figure 4 for hierarchical clustering tree) were not significantly different between total fungal community and the potential active fungal community based on result of t-test ( Supplementary Table 4). Both comparisons of the β-diversity based on Bray-Curtis distance and unweighted_unifrac calculation showed that there were no significant difference between two communities with p = 0.306 (on Bray-Curtis) and p = 0.284 (on unweighted_unifrac).

The NMDS showed distinct clustering with regard to two communities in Figure 1. Algorithm analysis results to test the differences of community structure between groups showed significant differences between total and potentially active fungal communities (Anosim, R = 0.392, p = 0.008; MRPP, A = 0.083, p = 0.06; Adonis, R ² = 0.209 (0.791), p = 0.007; Amova, Fs = 3.162 and p = 0.004).

A total of five phyla, 25 classes, 66 orders, 112 families, 137 genera, and 154 species were identified for the common fungal OTUs in both total and active communities. In the total fungal community (rDNA sequencing subset), Ascomycota and Basidiomycota were dominant with relative abundance of 67.9 ± 23.2% and 29.7 ± 22.5%, respectively; a very low relative abundance was observed in Chytridiomycota (1.3 ± 2.1%), Mucoromycota (1.0 ± 0.7%), and Zoopagomycota (0.1%). In the active fungal community (rRNA sequencing subset), Ascomycota, Basidiomycota, and Mucoromycota dominated with relative abundance with 76.1 ± 12.4, 17.6 ± 13.7%, and 6.0 ± 5.0%, respectively. As shown in Figure 2, the common dominant classes in both the total fungal community and active community were Dothideomycetes (mean relative abundance = 50.5 ± 16.7% in rDNA sequencing subset; 33.5 ± 11.8% in rRNA sequencing subset), Sordariomycetes (13.9 ± 4.9%; 32.5 ± 18.1%), and Eurotiomycetes (7.2 ± 5.7%; 22.2 ± 9.2%) in Ascomycota. In the phylum Basidiomycota, the composition of dominant classes was obviously different in total community and active ones; Agaricomycetes (15.3 ± 14.3%) and Pucciniomycetes (6.9 ± 13.7%) were dominant in total community, while in the active community, only Agaricomycetes dominated with relative abundance of 3.5 ± 3.1%. The average relative abundance of Mucoromycota (mainly was annotated to Mucorales) only accounted for 1% in total community, while it was dominant in the active community with average relative abundance accounting for 10.5 ± 9.9%.

The 10 most dominant orders in total community were Capnodiales (23.1 ± 14.0%) and Pleosporales (19.8 ± 6.4%) of Dothideomycetes; Xylariales (5.9 ± 2.6%) and Hypocreales (2.4 ± 1.5%) of Sordariomycetes; Helotiales (2.8 ± 2.2%) of Leotiomycetes and Chaetothyriales (2.8 ± 2.2%) of Eurotiomycetes, which were in Ascomycota; Agaricales (7.8 ± 8.4%), Polyporales (6.2 ± 4.7%), and Corticiales (2.8 ± 3.6%) of Agaricomycetes; Pucciniales (3.7 ± 6.9%) of Basidiomycota. In the active community, the 10 most dominant orders were Pleosporales (18.1 ± 10.2%), Xylariales (12.8 ± 4.0%), Eurotiales (8.8 ± 5.4%), Capnodiales (7.1 ± 5.9%), Sordariales (7.2 ± 5.0%), Chaetothyriales (3.4 ± 2.2%), Helotiales (3.6 ± 2.5%), Hypocreales (2.8 ± 1.6%), Agaricales (9.0 ± 10.7%), and Mucorales (4.9 ± 6.4%).

The top 10 most abundant genera in total community included Cladosporium (5.5 ± 2.4%), Boeremia (2.9 ± 2.3%), Alternaria (1.5 ± 1.1%), Arthrinium (1.1 ± 0.5%), unidentified_Pleosporales (1.0 ± 0.7%), and Sclerotinia (0.9 ± 0.6%) in Ascomycetes; Psathyrella (2.9 ± 4.3%), Gymnosporangium (2.5 ± 5.7%), and Trametes (1.3 ± 1.3%) in Basidiomycota; and Synchytrium (0.8 ± 2.0%) in Chytridiomycota. The top 10 most abundant genera of the potentially active community included eight genera in Ascomycota, i.e., Arthrinium (4.6 ± 1.7%), Aspergillus (2.9 ± 1.8%), Alternaria (2.8 ± 1.8%), Cladosporium (2.8 ± 2.4%), Sclerotinia (2.0 ± 1.7%), Boeremia (1.7 ± 0.8%), Penicillium (1.0 ± 0.7%) and unidentified_Pleosporales (0.9 ± 0.8%), one genus in Basidiomycota ( Psathyrella, 3.7 ± 4.9%), and Rhizopus (2.3 ± 3.2%) in Mucoromycota.

The community composition varied obviously in different sampling months for both the total and active communities ( Figure 2). In the total fungal community, Ascomycota was predominant from January to April, with an average relative abundance of 86.3%; Basidiomycota has the relative abundance of 11.7%; from May to July, the proportion of Basidiomycota increased gradually and becomes higher than that of Ascomycota (the average relative abundance of Basidiomycota was 53.6%, and that of Ascomycota was 43.5%). In the potentially active fungal community, Ascomycota was predominant across sampling months, average relative abundance was 76% (50.9-92.5%); and the relative abundance of Basidiomycota (6-48.4%, on average of 17.6%) and Mucoromycota (0.6-20%, on average of 5%) was lower.

Putative Species and Their Ecological Functions of Potentially Active Fungi

By combining the results of functional prediction via FUNGuild and description of relevant literatures, 131 fungi, which were further species identified by BLAST matches in NCBI, were grouped into 10 ecological categories (plant pathogen, human pathogen, animal pathogen, mycoparasites, macrofungi (mushroom/wood-rotting fungi), foliar/plant endophytes, lichenized fungi, ectomycorrhizal fungi, saprotroph yeast, and undefined saprotroph) and an additional group of unknown. The species number of transcriptionally active fungi and total number of each category are presented in brackets in Figure 3; the total species number of each category was 31, 4, 1, 3, 41, 8, 7, 1, 9, 20, and 6. In total, 57 putative fungi with potential transcriptional activity (i.e., rRNA:rDNA ratio > 1) were detected ( Supplementary Table 6) including 16 plant pathogens, 16 fungi of saprotroph, two human pathogens, one animal pathogen, five foliar/plant endophytes, seven fungi of macrofungi(mushroom/wood-rotting fungi), two lichenized fungi, one ectomycorrhizal fungi, and one mycoparasites. The proportion of fungi with transcriptional activity varied in different ecological functional categories, i.e., plant pathogen (51.6%), human pathogen (50%), mycoparasites (66.7%), macrofungi (mushroom/wood-rotting fungi, 17.1%), foliar/plant endophytes (62.5%), lichenized fungi (28.5%), ectomycorrhizal fungi (100%), saprotroph yeast (22.2%), and undefined saprotroph (75.0%).

The relative abundance of each ecological category in total and active fungal communities in different months is shown in Figure 4, among which plant pathogen dominated in both total and potentially active fungal communities with average proportions of 65.2% (34.9-85.8%) and 61.1% (42.3-77.2%), respectively. The relative abundance of macrofungi in the total community ranged from 2.4 to 41.5%, which was lower from January to April and then increased significantly from May to July. In addition, the variation trend of the abundance in the potentially active community was the same as that in total community, but with lower proportion (0.5-15.5%). The relative abundance of other categories in total community was very low except for the unknown group, i.e., human pathogen (0.8-8.7%), animal pathogen (0-0.2%), mycoparasites (0.5-2.6%), foliar/plant endophytes (1-2.6%), lichenized fungi (0.2-0.9%), ectomycorrhizal fungi (0-1.3%), saprotroph yeast (0.2-2.5%), undefined saprotroph (1.4-5.5%), and unknown (2.7-15.3%). However, in the potentially active community, the abundance of human pathogen in all months was much higher (6.9-29.1%), and the proportion of mycoparasites was much higher in January (13.6%); the abundance of saprotroph (including saprotroph yeast and undefined saprotroph) changed little in different months (ranged from 1.5 to 8.3%).

Temporal Dynamics of Transcriptional Activity of Airborne Fungi

There were 55 core OTUs (i.e., OTUs shared among all the samples) in the present study, and of them, 27 OTUs were annotated at genus level based on annotation result ( Table 2). Exceptionally, eight genera with transcriptional activity were detected across all the sampling months, including Arthrinium, Aspergillus, Erysiphe, Knufia, Microascus, Penicillium, Torula, and Rhizopus with the rRNA:rDNA ratio ranging from 1.07 to 67. Their transcriptional activity changed dynamically from month to month, and rRNA:rDNA ratios of most genera were the highest in April. In addition, the transcriptional activity of other fungi, such as Boeremia, Cladosporium, Pestalotiopsis, Sclerotinia, Geastrum, and Lactarius, also showed the highest transcriptional activity from March to May.

Potentially Active Fungi Detected by FlowSight® Imaging Flow Cytometry

The FlowSight ® imaging flow cytometry results of air microbial samples with different aerodynamic diameters showed that in the gate of diameter between 5 and 20 μm (considered as fungi), the proportion of dead cells (i.e., cells/particles successfully stained by PI staining) in samples of PM 2.5, PM ₁₀, and TSP was 9.94, 34.71, and 35.54%, respectively, and the proportion of cells with chlorophyll spontaneous fluorescence was 12.60, 41.20, and 42.26%, respectively. Therefore, the proportion of potentially active fungi in samples of PM 2.5, PM ₁₀, and TSP was 77.46, 24.09, and 22.20%, respectively, and the average was 41.25% ( Figure 5).

Figure 5. Potential transcriptional active fungi detected by FlowSight ® imaging flow cytometry. (A,B) Different forms of particles in FlowSight Amnis's working process. (C) The imaging of different particles or fungal spores with propidium iodide (PI) staining. (D) The proportion of potentially active fungi in samples of different aerodynamic diameters.

Discussion

Robust Evidences of Fungal Activity in the Air

Microorganisms are critical to the functioning of terrestrial and aquatic ecosystems; they play a role in the functioning of the atmosphere as well. Due to recent advances in molecular techniques and DNA sequencing capabilities, more and more reports emerged on global microbiomes through cultivation-independent molecular approach ( Bahram et al., 2018; Delgado-Baquerizo et al., 2018; Nayfach et al., 2020). However, studies of the global microbiome are not evenly distributed, and little is known about the biology of the atmosphere relative to aquatic and terrestrial habitats.

In recent years, several studies with short-term and local sampling on diversity of atmospheric microbial via metagenomics have been reported, mainly focused on Europe ( Fröhlich-Nowoisky et al., 2009; Nicolaisen et al., 2017; Banchi et al., 2018), the United States ( Yamamoto et al., 2012), South Korea ( An et al., 2017; Woo et al., 2018), Canada ( Chen et al., 2018), Northern China ( Cao et al., 2014; Yan et al., 2016; Wei et al., 2019), etc. However, there are few reports on atmospheric microbiome in the low-latitude plateau of China.

This is the first study to examine active fungal community in the atmosphere using RNA-based approach and imaging flow cytometry. Both results consistently indicated that more than 40% of airborne fungi have potential transcriptional activity, which is much higher than that in our previous perception. There is robust evidence to directly prove that there are potentially active fungi in the air. Bowsher et al. (2019) demonstrated that 16S rRNA/rRNA gene ratios and cell activity staining reveal consistent patterns of microbial activity in plant-associated soil. They also indicated the 16S ratio and CTC methods report comparable patterns of activity that can be applied to observe ecological dynamics over time, space, or experimental treatment. It is of interest to distinguish active and inactive microbial cells and taxa to understand their functional contributions to ecosystem processes and to understand shifts in microbial activity in response to change. Also, it can contribute to exploring whether the active fungal group can survive and even reproduce in the atmosphere using barren substrates. Is the atmosphere for them, as same as soil and water? Do they play a broader ecological role among different spheres of the Earth? Importantly, the first step in further research is needed to understand if this transcriptional activity equals really metabolic activity or if it is related to spores.

The Structure Between Active and Total Fungal Community Was Significantly Different

In the present study, we firstly conducted long-term sampling analysis in a typical low-latitude plateau region of the northern hemisphere; the result showed that Ascomycota and Basidiomycota were dominant in total fungal community in the atmosphere, with the relative abundance of 30.6-89.9% and 8.2-62.6%, respectively, which is consistent with most previously reported results in the world. On the other hand, a few studies reported Basidiomycota as predominant, rather than Ascomycota ( Fröhlich-Nowoisky et al., 2009; Womack et al., 2015). Different results may be related to sampling season, local environment, sequencing method, and primers used.

The structure between active and total fungal community was significantly different; Ascomycota was predominant with the average relative abundance of 76%, while that of Basidiomycota was only 17.6%. Dothideomycetes, Sordariomycetes, and Eurotiomycetes in Ascomycota and Agaricomycetes in Basidiomycota were dominant in the active community, which was consistent with the result of only previous report of active fungal community in the atmosphere over the Amazon rainforest canopy ( Womack et al., 2015). If these results can be confirmed, Ascomycota predominant in the atmosphere should be a general rule. Ascomycota usually have single-celled or filamentous vegetative growth forms that are small enough to become aerosolized, whereas many of the Basidiomycota are too large to be easily aerosolized other than in the form of metabolically inactive spores ( Womack et al., 2015). The result in present study also indicated Ascomycota and Basidiomycota have different adaptability to the atmosphere. Eight orders including Pleosporales, Capnodiales, Chaetothyriales, Eurotiales, Helotiales, Xylariales, and Hypocreales in Ascomycota; one order (Agaricales) in Basidiomycota; and one order (Mucorales) in Mucoromycota were the top 10 dominant orders. Among which Pleosporales and Xylariales have been reported to be abundant in the active communities in cloud water by Amato et al. (2017).

Furthermore, significant differences in community structure between total and potentially active fungal communities were also in accordance with the previous studies by Baldrian et al. (2012); Womack et al. (2015), and Klein et al. (2016). This emphasizes the importance of diversity and structure of the active microbiome in future research; deeply understanding both structure and function of microbial communities can help to understand their role in the atmosphere and other environment. Previous studies reported significant diurnal dynamics of atmospheric fungal communities ( Fierer et al., 2008) and seasonal cycles ( Fröhlich-Nowoisky et al., 2009; Du et al., 2018). In the present study, the community composition varied obviously in different sampling months for both the total and potentially active community. Basidiomycota increased significantly with the onset of the rainy season, which is consistent with the results of Nicolaisen et al. (2017); abundances of Basidiomycota were significantly higher in autumn than in early spring. This may be due to rainfall, which promotes growth, spore production, and diffusion of Basidiomycetes fungi, especially mushrooms and wood-rotting fungi ( Chen et al., 2018). Our result indicated that the species number and relative abundance of Agaricomycetes were significantly increased with the increase of rainfall; i.e., compared with the average species number of January to April with that of May to July, it rapidly increased from 12.5 to 39.3, and the same trend was found for the average relative abundance, which increased from 0.36 to 9.31%, accordingly. In addition, the relative abundance of Pucciniomycetes and Exobasidiomycetes also increased significantly. Although the proportion of relative abundance of Basidiomycota (0.5-15.5%) was much lower in the potentially active community, the variation trend of the abundance was consistent with that in total community, which indicated that most of them may be dormant since the sampling period is not the abundant sporulation period of native macrofungi.

Temporal Dynamics of Transcriptional Activity of Airborne Fungi

This happens to be the first time to describe the temporal dynamics of potential transcriptional activity of fungi in the air via molecular technique. We speculate that as temperature rises and rainfall increases, along with higher wind speed promoting more fresh spore release into the air from the ground, they may keep transcriptional activity. Additionally, most detected fungi were active in April, suggesting that seasonal variation of fungal activity is caused by the alternation from dry season to rainy season occurring in April ( Supplementary Figure 5).

Rare Taxa in the Airborne Fungal Community Were Disproportionately Active

Some rare taxa may be key species on network in some communities or play important ecological function. Recently, study on estimate of the sequenced proportion of the global prokaryotic genome, which was based on large-scale sequence alignment between Earth Microbiome Project (EMP), released data and the sequenced genomes in the public database, and the result highlighted that there were a large number of rare taxa that are not deeply explored ( Zhang et al., 2020).

The results of the present work reveal significant negative correlation between the relative abundance of the fungi in total community and rRNA:rDNA ratio ( R ² = 0.305, p < 0.001) indicates that some of potentially transcriptional active species could occur with very low relative abundance in the total community. In addition, by comparing the top 35 abundant putative species in the potentially active community with those of total community, it was found that only five putative species (i.e., Arthrinium sp., Aspergillus sp., Rhizopus oryzae, Knufia petricola, and Penicillium sp.) were in the top 20% abundant group of the active community, but the relative abundance of the remaining 30 species in the active community only ranged from 0.001 to 0.05%.

Both results indicate that rare taxa in the airborne fungal community were disproportionately active, a phenomenon also observed in the atmosphere ( Klein et al., 2016), soil ( Dlott et al., 2015), marine ( Campbell et al., 2011), and wastewater anaerobic digester ( Jia et al., 2019) for bacterial communities. There may be fundamental differences in the structure and composition of active and total communities. Using rDNA data alone is limited in determining the diversity and activity state of the microbial community, which may underestimate the potential transcriptional activity of the rare groups ( Campbell et al., 2011; Aanderud et al., 2015). They may play an important role in the biosphere; however, little research has been done on them, and their important ecological functions remain undiscovered until now.

Ecological Functions of Potentially Active Fungi

To the best of our knowledge, published research has rarely focused on the function of airborne microbes with traits particularly well-suited for survival and potential activities in extreme environments, although it has been proposed by Womack et al. (2015). We allocated 131 putative species of fungi into 10 ecologically functional categories referring to literatures and functional annotation result in FUNGuild, as well as activity ability evaluation based on rRNA:rDNA ratio for each category. The results indicated that different functional groups of fungi have different adaptability to the atmosphere: some groups may be able to survive in the air for long time, while others may only stay for a short time and settle to the ground very fast.

Transcriptionally Active Plant Pathogenic Fungi in the Air

Our results showed that plant pathogenic fungi are the dominant group in the air, which is consistent with the study on the community characteristics of PM 2.5 atmospheric bacteria and fungi after biomass combustion disturbance in a rural area of the north China plain. The abundant species were Alternaria spp., Bipolaris spp., Botrytis spp., Fusarium spp., and other plant pathogens, which may survive in the form of hypha or spore ( Wei et al., 2019). A study by Nicolaisen et al. (2017) reported Botrytis cinerea, Sclerotinia sclerotiorum, Blumeria graminis, Microdochium nivale, Venturia spp., Pyrenophora teres, Pyrenophora bromii, Phoma spp., Claviceps purpurea, Phaeosphaeria sp., Tilletia walkeri, etc., as the major plant pathogenic fungi in the atmosphere. Chen et al. (2018) in the Canadian agricultural experimental station showed that the genera of plant pathogenic fungi with high abundance were Cladosporium, Alternaria, Fusarium, Pestalotiopsis, Ophiognomonia, Erysiphe, Entyloma, Ustilago, etc., which also appeared in the present study.

There is no report focus on diversity of plant pathogenic fungi with potential transcriptional activity in the atmosphere previously. According to our result, about 50% of putative plant pathogens have potential transcriptional activity in the atmosphere. Firstly, the group of common plant pathogens has a wide host range, such as genera of Alternaria, Fusarium, and Rhizopus. The species most commonly associated with plant disease are, e.g., Alternaria alternata, which causes wheat black spot, sorghum grain mold, and black spot of soybean; Alternaria solani causes early blight on potato and tomato; Fusarium graminearum causes seedling blight on rice and maize, wheat scab, maize Fusarium ear rot, sorghum Fusarium stem rot, soybean root rot, etc., which not only cause loss of crop yield but also seriously reduce the quality of crops by producing toxins; Rhizopus oryzae can cause soft rot of jackfruit; Rhizopus stolonifer usually causes post-harvest disease of peach, grape, jujube, strawberry, etc. ( Guo et al., 2015). rRNA:rDNA ratios of these genera were greater than 1, i.e., Alternaria (1.86), Fusarium (1.45), and Rhizopus (9.81), which indicated they have potential transcriptional activity; probably as a result of long-term adaptive evolution in the air, the atmosphere could be a reservoir for them.

Surprisingly, typical biotrophic airborne pathogens such as Erysiphe sp. have rRNA:rDNA ratio >1 across all sampling months, and probably the most important reason may be due to the wide distribution of host plant (including peas, broad beans, alfalfa, Melilotus, and Astragalus; Guo et al., 2015), which provided wide hyphae or spore sources. Our results showed that some biotrophic fungi can be detected in the air year-round, suggesting that these fungi have alternative ways of survival and dispersal in air for long time. Many fungi with long-distance wind dispersal patterns are pathogens on major crop disease outbreaks worldwide, such as Puccinia spores, which are spread by wind over long distances in the air and cause stem rust in North America ( Eversmeyer and Kramer, 2000), wheat leaf rust ( Nagarajan and Singh, 1990), sugarcane rust, wheat stem rust, and stripe rust ( Wellings and Mcintosh, 2010) from the Indian subcontinent, resulting in the yield loss of global cereal crops ( Narayanasamy, 1997). Other important pathogenic fungi, such as Hemileia vastatrix, cause coffee leaf rust ( Bowden et al., 1971), and Phakopsora pachyrhizi causes soybean rust ( Pan et al., 2006), which can spread from Africa and Asia to North America, respectively. Another typical biotrophic genus, Microbotryum, which is a smut fungus, showed transcriptional activity as well with rRNA:rDNA ratio equal to 3.91 in present study. The same as rust fungi, powdery mildew fungi and smut fungi are obligate parasites and mainly spread through the air; therefore, we believe that both of them remain transcriptional activity when spread in the air, which deserves high attention and more research in the future.

In addition, several putative plant pathogens have not been reported or distributed in China; for example, Diatrype prominens (average rRNA:rDNA ratio = 2.37), mainly distributed in North America according to the record of GBIF, is a host of Arbutus menziesii ( Tedersoo et al., 2014). According to the previous study, Ophiognomonia clavigignenti-juglandacearum is mainly distributed in the United States and Canada, causing walnut canker, and are also parasitic to other species of Juglans ( Nair et al., 1979). It was first found in Wisconsin and then spread to other states and Canada; was identified as an invasive species in North America in 1967; and may pose a serious threat to survival of white walnut. Trechispora alnicola can cause yellow ring disease on Poa pratensis ( Wilkinson, 1987), distributed in over 24 countries or regions in Asia, Africa, South America, North America, and Oceania. Uromycladium tepperianum causes gall rust of Acacia saligna, which is native to Australia, and was used to prevent the expansion of A. saligna in South Africa ( Wood and Morris, 2007). Currently, it is mainly distributed in Australia, South Africa, New Zealand, Indonesia, and New Caledonia based on the record on GBIF. Among the above pathogenic fungi, there were five species with potential transcriptional activity, i.e., D. prominens (average rRNA:rDNA ratio = 2.37) and Septofusidium herbarum (2.53) in Ascomycota, and Pseudomicrostroma glucosiphilum (1.55) and U. tepperianum (15.41), which suggest that they may be have spread over long distances in the air and may cause diseases in favorable conditions.

Altogether, our results indicated that survival in air is a common feature of plant pathogenic fungi; it covers all biotrophic, hemibiotrophic, and necrotrophic groups. While about 50% of the fungi were indicated in dormancy, the seasonal variation of the dormancy of the fungi needs to be investigated to understand whether a dormant group can last longer in the air or lacks a host.

Nevertheless, the limitation of compared rRNA/rDNA analysis must be considered, although it is useful for potential transcriptional activity research ( Blazewicz et al., 2013). Due to differences in sample processing and/or insufficient sampling, deviation of rRNA:rDNA ratio calculation will result, and therefore, other unknown reasons will cause the appearance of "phantom taxa," which only exist in rRNA sequencing subset but not observed in rDNA sequencing subset ( Klein et al., 2016), or active populations as will be misclassified as dormant ( Steven et al., 2017). Additionally, quantification and direct metabolic activity analysis of major pathogenic fungi should be conducted to carry out risk assessment in future research.

Potentially Transcriptionally Active Human Pathogens and Animal Pathogens in the Air

In our complex changing world, some environmental health problems are not straightforward to identify until a very serious health impact occurs ( Lai et al., 2009). We identified human pathogenic and animal pathogenic fungi in the atmosphere in present study: four human pathogens, i.e., genera Candida and Microascus. Candida normally lives on the skin and inside the body and can cause infections if it grows out of control or if it enters deep into the body ( Fotos and Hellstein, 1992). Microascus species have emerged as significant invasive pathogens in the immunocompromised patient. They are also frequently recovered as the Scopulariopsis anamorph in more superficial settings and as agents of onychomycosis. For example, the best-matched species is Microascus cirrosus (Per. Ident = 99.67% by BLAST in NCBI), which causes onychomycosis ( De Vroey et al., 1992) and postoperative fungal infection ( Krisher et al., 1995; Miossec et al., 2011). There are other two putative fungi: Rhizomucor pusillus (with Per. Ident = 99.3-100%, but highest Per. Ident with Rhizomucor miehei was only 96.52%) is a conditionally pathogenic fungus that causes inflammation and tissue degeneration and necrosis, which can spread directly in the organism and spread in blood ( Ma et al., 1992); Lichtheimia corymbifera causes mucormycosis, which can spread widely to the brain, lungs, gastrointestinal tract, and heart ( Lu et al., 2008; Garcia-Hermoso et al., 2009; Bellanger et al., 2010). Among which, rRNA:rDNA ratios of M. cirrosus and L. corymbifera were 4.56 and 4.36, respectively, which probably indicated their high risk of infection as they have high transcriptional activity, especially for M. cirrosus, which was active across the whole sampling season.

Similarly, the putative species Acaromyces ingoldii (Per. Ident = 99.04% by BLAST in NCBI, but Per. Ident of other matches were lower than 90%), as an animal pathogen, is currently distributed in Brazil, Panama, China, Israel, Japan, Philippines, Vietnam, and other countries or areas according to records on GBIF, with potential transcriptional activity (rRNA:rDNA ratio = 35.81) indicating the risk to some extent. As a result, we suggest that it is a necessity to strengthen the research on the potential active human/animal pathogens in the air and to improve the awareness of risk control before health hazards.

Other Fungi With Potential Transcriptional Activity

There were 36 putative species of Basidiomycota and five putative species of Ascomycota in macrofungi (mushroom/wood-rotting fungi). However, only seven of them were transcriptionally active, which was the lowest proportion of all categories, suggesting that spores of macro-fungi in air were dormant. Other potential active species of different functional categories, including lichenized fungi and saprophytic fungi, probably play broad and important roles on Earth such as affecting precipitation, carbon, and nitrogen cycles. While there are few studies focusing on them, so far, results in them having an important ecological function have not been discovered yet.

Conclusion

In the present study, we revealed that there are considerable amount of active fungi via RNA-based approach and imaging cytometry simultaneously. RNA-based amplicon showed that Ascomycota dominated the active community, while Basidiomycota have low transcriptional activity in the active community. The structure of the active community of atmospheric fungi was significantly different from that of total community. For the first time, we deeply analyzed the potential transcriptional activity of airborne fungi from different ecological and functional categories and figured out that plant pathogenic fungi are the dominant group in the air, and more than 50% were potentially active. Our results further indicated that survival in air is a common feature of plant pathogenic fungi regardless of biotrophic, hemibiotrophic, and necrotrophic groups. Moreover, it is essential to strengthen the research on the potential active pathogens of humans and animals in the air to prevent risks before health hazards; also, rare species with potential transcriptional activity in the atmosphere should not be underestimated and/or ignored, which may play an important role in the biosphere, while little research has been done and their important ecological functions remain largely undiscovered. Considering the genetic and species diversity of pathogenic fungi in the air, resistant crop and varieties should be selected for distribution based on local and seasonal variations of pathogenic fungi dynamics across a broader geographic region in agricultural production. This study provides a new perspective for more comprehensive understanding of the atmospheric fungal community, as well as the scope of biodiversity and biogeography extension, and to help to establish awareness of microbial function and safety.

Data Availability Statement

The amplicon sequencing reads have been deposited in the NCBI SAR with the accession number SUB9585712 and the Bioproject number PRJNA727682.

Author Contributions

YC, YW, and LL conceived and designed the experiments. ZH, YZ, and LW contributed to the sample collection and species information query for annotation. YC, XZ, and JD carried out all the laboratory work. YC and XZ contributed in the data analysis and writing. CL contributed in the funding acquisition and supervision. SJ contributed to the writing-reviewing and editing. All authors contributed to the article and approved the submitted version.

Funding

This research was supported by the National Key R&D Program of China (2017YFD0200400) to CL and the opening foundation of the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan (gzkf2020-01). The FlowSight ® Imaging Flow Cytometry process was technically supported by Luminex Corporation (Shanghai) Co. Ltd.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Publisher's Note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Acknowledgments

Special thanks to Yun Li (Senior File Application Scientist of Luminex Corporation).

Supplementary Material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2021.683266/full#supplementary-material

Footnotes

References

Fotos, P. G., and Hellstein, J. W. (1992). Candida and Candidosis. epidemiology, diagnosis and therapeutic management. Dent. Clin. North Am. 36, 857-878.
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Garcia-Hermoso, D., Hoinard, D., Gantier, J. C., Grenouillet, F., Dromer, F., and Dannaoui, E. (2009). Molecular and phenotypic evaluation of Lichtheimia corymbifera (formerly Absidia corymbifera) complex isolates associated with human mucormycosis, rehabilitation of L. ramosa. J. Clin. Microbiol. 47, 3862-3870. doi: 10.1128/JCM.02094-08

Wood, A. R., and Morris, M. J. (2007). Impact of the gall-forming rust fungus Uromycladium tepperianum on the invasive tree Acacia saligna in South Africa, 15 years of monitoring. Biol. Control 41, 68-77. doi: 10.1006/bcon.1997.0560

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RNA-Based Analysis Reveals High Diversity of Plant-Associated Active Fungi in the Atmosphere

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Fungi are ubiquitous in nature; that is, they are present everywhere on the planet; understanding the active state and functional capacity of airborne microbes associated with health of human, animal, and plant is critical for biosafety management. Here, we firstly and directly proved that there were about 40% active fungi in the air via rRNA amplicon sequencing and imaging flow cytometry simultaneously.

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This artistic video explains the crux of microbiologist Lynn Margulis's work on the origins of cells with a nucleus. Single-celled organisms started cooperating, as the species in lichen do, for mutual benefit. In this way, some cells ingested another cell that became the nucleus and eukaryotic cells came into being. These are the cells that make up multi-cellular species. In the same way, mitochondria became part of eukaryotic cells, and chloroplasts, the photosynthesizing cells in plants, were incorporated into the organism. Cooperation is an evolutionary strategy.

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Dr Elaine Ingham is the world-renowned expert on the soil food web.  Her courses are aimed at farmers and are therefore expensive (there are grants), but her primer, with the basic concepts and the species is downloadable for free.

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Fungi are everywhere, inside and out, and there is a wide diversity of fungi species inside leaf tissue that performs functions for the plant. They can protect agains herbivores and pathogens, droughts, flooding and salinity, extreme temperatures and low soil nutrients.

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Fungi matter | Dr. Demetra Kandalepas | TEDxLSU

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A molecule made by trees can seed clouds, suggesting that pre-industrial skies were less sunny than thought.

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Neil McAllister / Alamy Stock Photo

Molecules released by trees can seed clouds, two experiments have revealed. The findings, published on 25 May in Nature and Science, run contrary to an assumption that the pollutant sulphuric acid is required for a certain type of cloud formation - and suggest that climate predictions may have underestimated the role that clouds had in shaping the pre-industrial climate.

If the results of the experiments hold up, predictions of future climate change should take them into account, says Reto Knutti, a climate modeller at the Swiss Federal Institute of Technology (ETH Zurich). For 20 or more years, clouds have been the largest source of uncertainty in understanding how manmade emissions affect the atmosphere, he says.

In addition to releasing carbon dioxide, burning fossil fuels indirectly produces sulphuric acid, which is known to seed clouds. So, climate scientists have assumed that since pre-industrial times, there has been a large increase in cloud cover, which is thought to have an overall cooling effect by reflecting sunlight back into space. And they have assumed that this overall cooling effect has partially masked the climate's underlying sensitivity to rising carbon dioxide levels.

The latest experiments suggest that it may have been cloudier in pre-industrial times than previously thought. If this is so, then the masking effect, and in turn the warming effects of carbon dioxide, might have been overestimated, says Jasper Kirkby, a physicist at the CERN, Europe's particle-physics laboratory near Geneva, Switzerland, who led one of the experiments.

But Kirkby adds that itis too early to say whether this is true in practice, or by how much, because there are so many factors that play into such projections."There are many uncertainties; we are only talking about one," says Kirkby. Knutti says the results will probably not affect the most likely projections of warming, as laid out by the Intergovernmental Panel on Climate Change. "Our best estimate is probably still the same," he says.

Aerosols needed

Clouds are made of microscopic droplets of liquid water or, in some cases, of small ice crystals. But in the atmosphere, water vapour cannot simply turn into a cloud: it needs solid or liquid particles, known as aerosols, on which to condense.

About half of these aerosols originate, already in solid form, from Earth's surface: for instance, dust from deserts, salt crystals from the oceans or soot from combustion. The other half forms anew in the atmosphere from gaseous impurities. The individual gas molecules capture more molecules from the air to form solid particles. If they grow to 50-100 nanometres, water vapour can condense on them.

Maximilien Brice/ CERN

Until recently, atmospheric scientists thought that only sulphuric acid vapour, which can be produced by volcanic emissions or by burning fossil fuels, could trigger this process. As a result, it was thought that pre-industrial skies were somewhat less cloudy than present ones because they contained less of this pollutant, says Kirkby.

To investigate the process, he turned to the Cosmics Leaving Outdoor Droplets (CLOUD) experiment, which he founded. A three-metre tall stainless steel tank that can reproduce a vast range of atmospheric conditions, CLOUD can be hooked up to the beams of particles that feed the Large Hadron Collider (LHC) at CERN. This simulates the effects of cosmic rays - high-energy subatomic particles that come from outside the Solar System and are thought to have a role in cloud formation - in the atmosphere.

Cosmic-ray starter kit

In the two Nature papers, Kirkby and his co-authors report that aerosols can form and grow to the size needed to seed a cloud from compounds emitted by trees - without any sulphuric acid and accelerated by simulated cosmic rays. In these experiments, the team used α-pinene, a molecule that helps to give fir forests their characteristic smell, but compounds from other types of vegetation might show a similar effect, the scientists say.

In the third paper, published in Science, a team that includes some of Kirkby's co-authors reported a similar finding using a different experiment. Federico Bianchi, a chemist now at the University of Helsinki, and his collaborators measured the composition of air and monitored the weather at the Jungfraujoch Research Station in the Swiss Alps at around 3,500 metres in altitude. They found that molecules similar to α-pinene that could also originate from vegetation can seed clouds without much sulphuric acid.

Jungfrau Railways

In addition to feeding into climate predictions, the findings have another potential implication, says atmospheric scientist Bjorn Stevens of the Max Planck Institute for Meteorology in Hamburg, Germany. Some scientists have warned that measures such as scrubbing sulphur dioxide from coal-plant emissions could remove some of the beneficial cooling effect of clouds and boost global warming, but this may now be less of a concern because trees can seed clouds too. "What it means is, we don't have to fear clean air," says Stevens.

It is also interesting to speculate whether trees emit these compounds in part because there is a benefit to them in making their own climate, Kirkby says. "This really does touch on the Gaia hypothesis," he says, referring to the theory that Earth's life behaves as a single organism that tends to preserve itself. " It's a beautiful mechanism for trees to control their environment."

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Cloud-seeding surprise could improve climate predictions

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Neil McAllister / Alamy Stock Photo Molecules released by trees can seed clouds, two experiments have revealed. The findings, published on 25 May in Nature and Science, run contrary to an assumption that the pollutant sulphuric acid is required for a certain type of cloud formation - and suggest that climate predictions may have underestimated the role that clouds had in shaping the pre-industrial climate.

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Bacteria live 6 miles above the earth and play a role in regulating climate.

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This is a very clear and concise (5 mins) explanation of the soil microbiome-plant relationship that ensures nutrient uptake so that we have healthy, nutrient-dense food (as well as carbon sequestration and water retention in soil).

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David R. Montgomery on Symbioses in the Soil

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Only 10% of the genetic make-up in and on our body is human. The other 90% is microbial. In this book, Martin J. Blaser, director of the Human Microbiome Project explains how we acquire our gut microbiome, what it does for us and what happens when it is compromised.

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Martin J. Blaser MD has studied the role of bacteria in human disease for more than thirty years. He is the director of the Human Microbiome Program at New York University, served as the chair of medicine at NYU and as the president of the Infectious Diseases Society of America, and has had major advisory roles at the U.S. National Institutes of Health. He cofounded the Bellevue Literary Review and his work has been written about in publications that include The New Yorker, Nature, The New York Times, The Economist, The Washington Post, and The Wall Street Journal. His more than one hundred media appearances include the BBC, CNN, NPR, The Today Show, Good Morning America, and The O'Reilly Factor. He lives in New York City.

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A clarion call to save humanity's most essential fellow creatures - and our health Far beneath our skin exists an unfathomable, ancient universe - an internal ecosystem that is critical to our health. Dr Martin Blaser invites us into the wilds of the human 'microbiome', unfurling its inner workings and evolution.

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Martin J. Blaser is the director of the Human Microbiome Project. In this talk he explains how we are colonised by our gut microbes and what happens when they go missing due to over-use of antibiotics in childhood (for example).

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The IPBES report and agriculture. Subsidies have lead to the degradation of the soil microbiome.

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On May 6 th, a summary of the Global Assessment on Biodiversity was released, and it is harrowing. The report finds that 23 percent of our agricultural lands are less productive than five years ago. In refreshingly bold terms, the report comments on the role agricultural subsidies play in catalyzing soil health degradation and biodiversity loss. Agricultural subsidies are problematic because, too often, subsidy policies do not consider the impacts of the farming practices used to grow the crops that are subsidized. The United States Government provides subsidies through the Federal Crop Insurance Program (FCIP) regardless of the practices used to grow crops. This payment-for-production structure ignores the environmental and public health externalities of producing commodity crops intensively and provides no incentive for farmers to change their on-farm behavior and employ farming techniques that build soil health.

Almost one third of the 320 million acres of harvested cropland in the United States is used to grow corn, and another one third is used to grow soybeans. Most of these corn and soybean crops are not grown for human consumption, they're exported or used as feedstock for livestock, but they are two of the most heavily subsidized crops in the United States.

The Global Assessment states "harmful economic incentives...associated with unsustainable practices of fisheries, aquaculture, agriculture (including fertilizer and pesticide use) ...are often associated with [the] overexploitation of natural resources...(B5)." Chemicals and synthetic fertilizers promise short-term boosts in crop yields, but the overapplication and reliance on chemicals and synthetic fertilizers on commodity farms create soil conditions that are inhospitable for the soil microbiome.

Healthy soil is alive. 1 teaspoon of healthy soil can support a microbiome of 1 billion organisms like bacteria, fungi, and earthworms. The microbes in our soil provide nutrients, carbon, and water to plants, which means when our soil microbiome is well-fed and supported, our soil and our plants are healthier. Our soil ecosystem is the greatest concentration of biomass anywhere on the planet, but when the federal government pays crop insurance without considering the practices that are used to grow those crops, our soil microbiome pays the price. Microbes matter, because:

The microbes in our soil help sequester carbon. The microbes in our soil all need one thing to live: carbon. Our plants pump excess carbon from the atmosphere into the soil to support microbial health and biodiversity. When soil is contaminated by toxic pesticides, fungicides, and insecticides, the harsh chemicals reduce microbial populations in the soil. Fewer microbes in the soil mean fewer organisms to consume and sequester carbon in the soil. By spraying crops with harmful chemicals, we reduce the soil's capacity to act as a carbon sink.

The microbes in our soil help retain water and use it more efficiently. Mycorrhizal fungi, a critical component of the soil microbiome, provide nutrients and water to plant roots. Mycorrhizal fungi are only found on living plant roots, and they build intricate nutrient and water highways through soil so that plants can access nutrients and water from faraway places (see image to the right). Not only do the highways transmit water, when the mycorrhizal fungi build their highways, they puncture the soil and create pockets of space for additional water to be stored. Healthy soil can hold up to 20 times its weight in water, and the highways that mycorrhizal fungi grow provide water security for plants during droughts. Mycorrhizal fungi only grow near living roots. When industrial agricultural practices encourage farmers to till, to rip living roots out from the soil so that their crop rows look "clean," or when farmers fallow their fields and skip a growing season, mycorrhizal fungi populations are not supported. When mycorrhizal fungi populations are not supported, soil cannot sequester as much water, and our crops are less resilient during drought.

The microbes in our soil keep our food healthy. When plants photosynthesize, they break down water and convert the energy from the sun to form sugars. Whatever sugars the plant doesn't use, it pumps into the soil to feed the microbes and fungi. In return, the fungi provide nutrients like organic nitrogen, phosphorous, calcium, and zinc to the plant. Diverse fungi species help plants access a variety of nutrients, and this nutrient exchange keeps our plants healthy and nutrient-rich. Monocropping, an industrial agriculture practice supported by agricultural subsidies, does not support mycorrhizal fungi diversity, and the nutrient density of our fruits and vegetables is suffering. The lack of biodiversity above ground affects the biodiversity below ground.

The Global Biodiversity Assessment is clear: We need to reconsider what types of agricultural systems are supported by taxpayer dollars. Every year for the last ten years, the federal government has paid farmers an average of $8 billion in crop insurance payments through the FCIP, and a significant portion of these federal subsidies go to commodity farms that employ agricultural practices that degrade soil health, like nondiverse crop rotations, heavy fertilizer and pesticide use, and tillage. The billions of dollars of subsidies paid by the federal government should not support degenerative agricultural practices. For the sake of biodiversity protection and soil health, we should reward farmers for treating their farms as biodiverse, microbe-rich ecosystems. Policy should incentivize soil building practices like crop diversity, cover crops, crop rotations, integrated livestock management, and no-till.

NRDC advocates for regenerative agricultural systems that support microbial biodiversity and soil health, and our campaign to reform the FCIP involves making it easier for farmers who practice soil-building techniques to access the FCIP. We also worked with a diverse coalition of agricultural and business groups to successfully pass a new Soil Health Demonstration Trial provision in the last Farm Bill. This provision will reward farmers for adopting soil-building practices that sequester carbon in the soil.

The Global Biodiversity Assessment calls out the dangerous trajectory of current agricultural subsidies. We've hit the snooze button too many times on subsidy reform, and it's time for our policymakers to wake up to biodiversity losses perpetuated by this broken system.

About the Authors

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Microbes Matter: What the Biodiversity Report Means for Soil

# data[].attributes.attachment_link.description
On May 6 th, a summary of the Global Assessment on Biodiversity was released, and it is harrowing. The report finds that 23 percent of our agricultural lands are less productive than five years ago. In refreshingly bold terms, the report comments on the role agricultural subsidies play in catalyzing soil health degradation and biodiversity loss.

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The Health of the Soil Microbiome and the Human Microbiome.

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The Health of the Soil Microbiome and the Human Microbiome.

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If there is just one form of ecological knowledge we need to understand the relationship between the health of the biosphere and the health of humans it is surely in this excellent, informative interview with husband and wife team David R. Montgomery (geomorphologist) and Anne Biklé (biologist). Here they discuss the research findings for their book The Hidden Half of Nature: The Microbial Roots of Life and Health to make it accessible to the average person. Biklé talks about her research into the relationship between the soil microbiome and the human gut microbiome and the way it impacts on the human immune system to protect us against cancers and modern lifestyle diseases. Montgomery explains the plant-soil microbiome symbiosis and why we need to transition to agriculture that nurtures it.

And, of course, the plant-microbiome relationship is the way we sequester carbon drawn from the atmosphere in the soil. It's the way we restore the carbon cycle, and, therefore, the hydrological cycle. It's a win-win for the planet and humans.

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Microbes Matter! From Healthy Soil to Your Healthy Gut

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Nutrient-dense, non-toxic food and the soil microbiome.

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Nutrient-dense, non-toxic food and the soil microbiome.

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Soil microbiologist Walter Jehne explains pedogensis, the formation of soil by microbial life and the symbiosis with plants that ensure nutrient rich foods.

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NutriSoil a New Agriculture, Walter Jehne presentation

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Research shows that fungi can chose to strengthen cell walls (and therefore store carbon) or to decompose organic matter (which could release CO2 through oxidisation). This should be included in climate modules used by the IPCC to predict further emissions and responses to climate conditions.

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January 27, 2020 by Adityarup "Rup" Chakravorty, American Society of Agronomy

Fungi play an important role in the ecosystem by decomposing plant and animal debris into nutrients and simpler compounds. Credit: Susan V. Fisk

When we think of climate change, we tend to think about greenhouse gases, fossil fuels and pollution. Most of us don't think about fungi.

But Kathleen Treseder does. Treseder, an ecologist at the University of California, Irvine, studies how fungi can affect climate and vice-versa.

"Fungi are important to consider," she says. "They can influence nearly every aspect of ecosystems, especially processes that occur in soils."

New research from her lab shows that fungi can have different lifestyles in response to climate change. These findings can be incorporated into computational models that simulate ecosystems.

"We may be able to better predict shifts in atmospheric carbon dioxide levels and climate change," says Treseder. "That can help us estimate how much, when and where climate change will affect human societies."

It's important to be able to forecast which places will be hit by climate change and how quickly. These early warnings can help preparations, such as building sea walls or flood channels, or direct the development of new crop varieties.

Fungi are terrific decomposers. They break down organic material to get nutrients and energy. In doing so, they turn complex chemicals into simpler elements, such as carbon. In fact, "fungi are an integral part of the global carbon cycle," says Treseder. "They can move carbon from decomposing material into the atmosphere as carbon dioxide."

By studying how fungi respond to climate change in Alaskan forests like this, we can better understand how much carbon dioxide they will release to the atmosphere. This knowledge will help us improve predictions of future climate change. Credit: Kathleen Treseder

But fungi don't just release carbon. They can also store it. For example, environmental stress can cause fungi to strengthen their cell walls. They do so by using organic compounds that contain carbon. These carbon compounds can stay in soils for years to decades or even longer.

Treseder's research explores how fungi decide whether to use limited energy and resources to decompose material or for other processes. "No one can do everything well, and the same goes for fungi," says Treseder. "If fungi invest resources into one activity like decomposition, then those resources won't be available to support another activity like tolerating environmental stress."

These resource allocation decisions become even more important in a world with changing climate. "For example, will more extreme climates select for fungi that tolerate stress well, but cannot decompose dead material as efficiently?" says Treseder. "If so, then their production of carbon dioxide might decrease, slowing climate change."

To answer these questions, Treseder traveled to Alaska and Costa Rica. Experiments were set up in Alaskan Boreal forests and the cloud forests of Costa Rica. "

"We chose these locations because they are both endangered by climate change," says Treseder. "Northern ecosystems are warming particularly fast. Clouds are disappearing from the mountaintops of Costa Rica."

Treseder and colleagues exposed areas of the forests to drought-like conditions or more mellow environments. They collected soil samples from the different experimental areas.

Fungi are particularly abundant in northern ecosystems like Alaska, where warming is occurring quickly. Credit: Kathleen Treseder

Then they analyzed products made by fungal genes. These gene products served as indicators for whether the fungi were investing more resources toward decomposition or strengthening cell walls.

"We found that where drought stress increased, the amount of fungi that invested more in strengthening cell walls and less in decomposition tended to increase," says Treseder. In contrast, in more moderate conditions, the reverse occurred. Fungi that decomposed more efficiently became more common.

These findings suggest that fungi might store more carbon as global climate becomes more extreme. On the other hand, they might release more carbon dioxide in moderate climates. "These opposing feedbacks would not have been apparent without examining trade-offs among fungal traits," says Treseder.

Treseder is working to incorporate these findings into new and existing models of climate change. One particular area of focus are Earth system models that the Intergovernmental Panel on Climate Change uses for its official predictions. "We hope our research improves predictions of future trajectories of climate change," says Treseder.

Provided by American Society of Agronomy

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January 27, 2020 by Adityarup "Rup" Chakravorty, American Society of Agronomy When we think of climate change, we tend to think about greenhouse gases, fossil fuels and pollution. Most of us don't think about fungi. But Kathleen Treseder does. Treseder, an ecologist at the University of California, Irvine, studies how fungi can affect climate and vice-versa.

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Microbial Life on Earth is Threatened by Human Activities and Global Warming

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Microbial Life on Earth is Threatened by Human Activities and Global Warming

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This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.

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Introduction

Human activities and their effects on the climate and environment cause unprecedented animal and plant extinctions, cause loss in biodiversity and endanger animal and plant life on Earth5. Losses of species, communities and habitats are comparatively well researched, documented and publicized6. By contrast, microorganisms are generally not discussed in the context of climate change (particularly the effect of climate change on microorganisms). While invisible to the naked eye and thus somewhat intangible7, the abundance (~10 ³⁰ total bacteria and archaea)8 and diversity of microorganisms underlie their role in maintaining a healthy global ecosystem: simply put, the microbial world constitutes the life support system of the biosphere. Although human effects on microorganisms are less obvious and certainly less characterized, a major concern is that changes in microbial biodiversity and activities will affect the resilience of all other organisms and hence their ability to respond to climate change9.

Microorganisms have key roles in carbon and nutrient cycling, animal (including human) and plant health, agriculture and the global food web. Microorganisms live in all environments on Earth that are occupied by macroscopic organisms, and they are the sole life forms in other environments, such as the deep subsurface and 'extreme' environments. Microorganisms date back to the origin of life on Earth at least 3.8 billion years ago, and they will likely exist well beyond any future extinction events.

Although microorganisms are crucial in regulating climate change, they are rarely the focus of climate change studies and are not considered in policy development. Their immense diversity and varied responses to environmental change make determining their role in the ecosystem challenging. In this Consensus Statement, we illustrate the links between microorganisms, macroscopic organisms and climate change, and put humanity on notice that the microscopic majority can no longer be the unseen elephant in the room. Unless we appreciate the importance of microbial processes, we fundamentally limit our understanding of Earth's biosphere and response to climate change and thus jeopardize efforts to create an environmentally sustainable future6 (Box 1).

Box 1 Scientists' warning

Scope of the Consensus Statement

In this Consensus Statement, we address the effects of microorganisms on climate change, including microbial climate-active processes and their drivers. We also address the effects of climate change on microorganisms, focusing on the influences of climate change on microbial community composition and function, physiological responses and evolutionary adaptation. Although we focus on microorganism-climate connections, human activities with a less direct but possibly synergistic effect, such as via local pollution or eutrophication, are also addressed.

For the purpose of this Consensus Statement, we define 'microorganism' as any microscopic organism or virus not visible to the naked eye (smaller than 50 μm) that can exist in a unicellular, multicellular (for example, differentiating species), aggregate (for example, biofilm) or viral form. In addition to microscopic bacteria, archaea, eukaryotes and viruses, we discuss certain macroscopic unicellular eukaryotes (for example, larger marine phytoplankton) and wood-decomposing fungi. Our intent is not to exhaustively cover all environments nor all anthropogenic influences but to provide examples from major global biomes (marine and terrestrial) that highlight the effects of climate change on microbial processes and the consequences. We also highlight agriculture and infectious diseases and the role of microorganisms in climate change mitigation. Our Consensus Statement alerts microbiologists and non-microbiologists to address the roles of microorganisms in accelerating or mitigating the impacts of anthropogenic climate change (Box 1).

Marine biome

Marine biomes cover ~70% of Earth's surface and range from coastal estuaries, mangroves and coral reefs to the open oceans (Fig. 1). Phototrophic microorganisms use the sun's energy in the top 200 m of the water column, whereas marine life in deeper zones uses organic and inorganic chemicals for energy10. In addition to sunlight, the availability of other energy forms and water temperature (ranging from approximately −2 °C in ice-covered seas to more than 100 °C in hydrothermal vents) influence the composition of marine communities11. Rising temperatures not only affect biological processes but also reduce water density and thereby stratification and circulation, which affect organismal dispersal and nutrient transport. Precipitation, salinity and winds also affect stratification, mixing and circulation. Nutrient inputs from air, river and estuarine flows also affect microbial community composition and function, and climate change affects all these physical factors.

In marine environments, microbial primary production contributes substantially to CO ₂ sequestration. Marine microorganisms also recycle nutrients for use in the marine food web and in the process release CO ₂ to the atmosphere. In a broad range of terrestrial environments, microorganisms are the key decomposers of organic matter and release nutrients in the soil for plant growth as well as CO ₂ and CH ₄ into the atmosphere. Microbial biomass and other organic matter (remnants of plants and animals) are converted to fossil fuels over millions of years. By contrast, burning of fossil fuels liberates greenhouse gases in a small fraction of that time. As a result, the carbon cycle is extremely out of balance, and atmospheric CO ₂ levels will continue to rise as long as fossil fuels continue to be burnt. The many effects of human activities, including agriculture, industry, transport, population growth and human consumption, combined with local environmental factors, including soil type and light, greatly influence the complex network of microbial interactions that occur with other microorganisms, plants and animals. These interactions dictate how microorganisms respond to and affect climate change (for example, through greenhouse gas emissions) and how climate change (for example, higher CO ₂ levels, warming, and precipitation changes) in turn affect microbial responses. OMZ, oxygen minimum zone.

The overall relevance of microorganisms to ocean ecosystems can be appreciated from their number and biomass in the water column and subsurface: the total number of cells is more than 10 ²⁹ (refs) and the Census of Marine Life estimates that 90% of marine biomass is microbial. Beyond their sheer numbers, marine microorganisms fulfil key ecosystem functions. By fixing carbon and nitrogen, and remineralizing organic matter, marine microorganisms form the basis of ocean food webs and thus global carbon and nutrient cycles13. The sinking, deposition and burial of fixed carbon in particulate organic matter to marine sediments is a key, long-term mechanism for sequestering CO ₂ from the atmosphere. Therefore, the balance between regeneration of CO ₂ and nutrients via remineralization versus burial in the seabed determines the effect on climate change.

In addition to getting warmer (from increased atmospheric CO ₂ concentrations enhancing the greenhouse effect), oceans have acidified by ~0.1 pH units since preindustrial times, with further reductions of 0.3-0.4 units predicted by the end of the century. Given the unprecedented rate of pH change, there is a need to rapidly learn how marine life will respond22. The impact of elevated greenhouse gas concentrations on ocean temperature, acidification, stratification, mixing, thermohaline circulation, nutrient supply, irradiation and extreme weather events affects the marine microbiota in ways that have substantial environmental consequences, including major shifts in productivity, marine food webs, carbon export and burial in the seabed19,23,24,25,26,27,28,29.

Microorganisms affect climate change

Marine phytoplankton perform half of the global photosynthetic CO ₂ fixation (net global primary production of ~50 Pg C per year) and half of the oxygen production despite amounting to only ~1% of global plant biomass30. In comparison with terrestrial plants, marine phytoplankton are distributed over a larger surface area, are exposed to less seasonal variation and have markedly faster turnover rates than trees (days versus decades)30. Therefore, phytoplankton respond rapidly on a global scale to climate variations. These characteristics are important when one is evaluating the contributions of phytoplankton to carbon fixation and forecasting how this production may change in response to perturbations. Predicting the effects of climate change on primary productivity is complicated by phytoplankton bloom cycles that are affected by both bottom-up control (for example, availability of essential nutrients and vertical mixing) and top-down control (for example, grazing and viruses). Increases in solar radiation, temperature and freshwater inputs to surface waters strengthen ocean stratification and consequently reduce transport of nutrients from deep water to surface waters, which reduces primary productivity. Conversely, rising CO ₂ levels can increase phytoplankton primary production, but only when nutrients are not limiting.

Some studies indicate that overall global oceanic phytoplankton density has decreased in the past century39, but these conclusions have been questioned because of the limited availability of long-term phytoplankton data, methodological differences in data generation and the large annual and decadal variability in phytoplankton production. Moreover, other studies suggest a global increase in oceanic phytoplankton production44 and changes in specific regions or specific phytoplankton groups45,46. The global sea ice ( Sea Ice Index) is declining, leading to higher light penetration and potentially more primary production47; however, there are conflicting predictions for the effects of variable mixing patterns and changes in nutrient supply and for productivity trends in polar zones34. This highlights the need to collect long-term data on phytoplankton production and microbial community composition. Long-term data are needed to reliably predict how microbial functions and feedback mechanisms will respond to climate change, yet only very few such datasets exist (for example, the Hawaii Ocean Time-series and the Bermuda Atlantic Time-series Study). In this context, the Global Ocean Sampling Expedition51, transects of the Southern Ocean52,53, and the Tara Oceans Consortium11,54,55,56,57,58,59 provide metagenome data that are a valuable baseline of marine microorganisms.

Diatoms perform 25-45% of total primary production in the oceans, owing to their prevalence in open-ocean regions when total phytoplankton biomass is maximal63. Diatoms have relatively high sinking speeds compared with other phytoplankton groups, and they account for ~40% of particulate carbon export to depth62,64. Physically driven seasonal enrichments in surface nutrients favour diatom blooms. Anthropogenic climate change will directly affect these seasonal cycles, changing the timing of blooms and diminishing their biomass, which will reduce primary production and CO ₂ uptake65. Remote sensing data suggest a global decline of diatoms between 1998 and 2012, particularly in the North Pacific, which is associated with shallowing of the surface mixed layer and lower nutrient concentrations46.

In addition to the contribution of marine phytoplankton to CO ₂ sequestration, chemolithoautotrophic archaea and bacteria fix CO ₂ under dark conditions in deep ocean waters69 and at the surface during polar winter70. Marine bacteria and archaea also contribute substantially to surface ocean respiration and cycling of many elements18. Seafloor methanogens and methanotrophs are important producers and consumers of CH ₄, but their influence on the atmospheric flux of this greenhouse gas is uncertain71. Marine viruses, bacteriovorous bacteria and eukaryotic grazers are also important components of microbial food webs; for example, marine viruses influence how effectively carbon is sequestered and deposited into the deep ocean57. Climate change affects predator-prey interactions, including virus-host interactions, and thereby global biogeochemical cycles72.

Oxygen minimum zones (OMZs) have expanded in the past 50 years as a result of ocean warming, which reduces oxygen solubility. OMZs are global sinks for reactive nitrogen, and microbial production of N ₂ and N ₂ O accounts for ~25-50% of nitrogen loss from the ocean to the atmosphere. Furthermore, OMZs are the largest pelagic methane reservoirs in the ocean and contribute substantially to open ocean methane cycling. The observed and predicted future expansion of OMZs may therefore considerably affect ocean nutrient and greenhouse gas budgets, and the distributions of oxygen-dependent organisms.

The top 50 cm of deep-sea sediments contains ~1 × 10 ²⁹ microorganisms8,16, and the total abundances of archaea and bacteria in these sediments increase with latitude (from 34° N to 79° N) with specific taxa (such as Marine Group I Thaumarchaeota) contributing disproportionately to the increase76. Benthic microorganisms show biogeographic patterns and respond to variations in the quantity and quality of the particulate matter sinking to the seafloor77. As a result, climate change is expected to particularly affect the functional processes that deep-sea benthic archaea perform (such as ammonia oxidation) and associated biogeochemical cycles76.

Aerosols affect cloud formation, thereby influencing sunlight irradiation and precipitation, but the extent to which and the manner in which they influence climate remains uncertain78. Marine aerosols consist of a complex mixture of sea salt, non-sea-salt sulfate and organic molecules and can function as nuclei for cloud condensation, influencing the radiation balance and, hence, climate79,80. For example, biogenic aerosols in remote marine environments (for example, the Southern Ocean) can increase the number and size of cloud droplets, having similar effects on climate as aerosols in highly polluted regions. Specifically, phytoplankton emit dimethylsulfide, and its derivate sulfate promotes cloud condensation79,84. Understanding the ways in which marine phytoplankton contribute to aerosols will allow better predictions of how changing ocean conditions will affect clouds and feed back on climate84. In addition, the atmosphere itself contains ~10 ²² microbial cells, and determining the ability of atmospheric microorganisms to grow and form aggregates will be valuable for assessing their influence on climate8.

Vegetated coastal habitats are important for carbon sequestration, determined by the full trophic spectrum from predators to herbivores, to plants and their associated microbial communities85. Human activity, including anthropogenic climate change, has reduced these habitats over the past 50 years by 25-50%, and the abundance of marine predators has dropped by up to 90%. Given such extensive perturbation, the effects on microbial communities need to be evaluated because microbial activity determines how much carbon is remineralized and released as CO ₂ and CH ₄.

Climate change affects microorganisms

Climate change perturbs interactions between species and forces species to adapt, migrate and be replaced by others or go extinct28,88. Ocean warming, acidification, eutrophication and overuse (for example, fishing, tourism) together cause the decline of coral reefs and may cause ecosystems shifts towards macroalgae and benthic cyanobacterial mats94,95. The capacity for corals to adapt to climate change is strongly influenced by the responses of their associated microorganisms, including microalgal symbionts and bacteria. The hundreds to thousands of microbial species that live on corals are crucial for host health, for example by recycling the waste products, by provisioning essential nutrients and vitamins and by assisting the immune system to fight pathogens99. However, environmental perturbation or coral bleaching can change the coral microbiome rapidly. Such shifts undoubtedly influence the ecological functions and stability of the coral-microorganism system, potentially affecting the capacity and pace at which corals adapt to climate change, and the relationships between corals and other components of the reef ecosystem99,100.

Generally, microorganisms can disperse more easily than macroscopic organisms. Nevertheless, biogeographic distinctions occur for many microbial species, with dispersal, lifestyle (for example, host association) and environmental factors strongly influencing community composition and function. Ocean currents and thermal and latitudinal gradients are particularly important for marine communities104,105. If movement to more favourable environments is impossible, evolutionary change may be the only survival mechanism88. Microorganisms, such as bacteria, archaea and microalgae, with large population sizes and rapid asexual generation times have high adaptive potential22. Relatively few studies have examined evolutionary adaptation to ocean acidification or other climate change-relevant environmental variables22,28. Similarly, there is limited understanding of the molecular mechanisms of physiological responses and the implications of those responses for biogeochemical cycles18.

However, several studies have demonstrated effects of elevated CO ₂ levels on individual phytoplankton species, which may disrupt broader ecosystem-level processes. A field experiment demonstrated that increasing CO ₂ levels provide a selective advantage to a toxic microalga, Vicicitus globosus, leading to disruption of organic matter transfer across trophic levels106. The marine cyanobacterial genus Trichodesmium responds to long-term (4.5-year) exposure to elevated CO ₂ levels with irreversible genetic changes that increase nitrogen fixation and growth107. For the photosynthetic green alga Ostreococcus tauri, elevated CO ₂ levels increase growth, cell size and carbon-to-nitrogen ratios108. Higher CO ₂ levels also affect the population structure of O. tauri, with changes in ecotypes and niche occupation, thereby affecting the broader food webs and biogeochemical cycles108. Rather than producing larger cells, the calcifying phytoplankton species Emiliania huxleyi responds to the combined effects of elevated temperature and elevated CO ₂ levels (and associated acidification) by producing smaller cells that contain less carbon109. However, for this species, overall production rates do not change as a result of evolutionary adaptation to higher CO ₂ levels109. Responses to CO ₂ levels differ between communities (for example, between Arctic phytoplankton and Antarctic phytoplankton110). A mesocosm study identified variable changes in the diversity of viruses that infect E. huxleyi when it is growing under elevated CO ₂ levels, and noted the need to determine whether elevated CO ₂ levels directly affected viruses, hosts or the interactions between them111. These examples illustrate the need to improve our understanding of evolutionary processes and incorporate that knowledge into predictions of the effects of climate change.

Ocean acidification presents marine microorganisms with pH conditions well outside their recent historical range, which affects their intracellular pH homeostasis18,112. Species that are less adept at regulating internal pH will be more affected, and factors such as organism size, aggregation state, metabolic activity and growth rate influence the capacity for regulation112.

Lower pH causes bacteria and archaea to change gene expression in ways that support cell maintenance rather than growth18. In mesocosms with low phytoplankton biomass, bacteria committed more resources to pH homeostasis than bacteria in nutrient-enriched mesocosms with high phytoplankton biomass. Consequently, ocean acidification is predicted to alter the microbial food web via changes in cellular growth efficiency, carbon cycling and energy fluxes, with the biggest effects expected in the oligotrophic regions, which include most of the ocean18. Experimental comparisons of Synechococcus sp. growth under both present and predicted future pH concentrations showed effects not only on the cyanobacteria but also on the cyanophage viruses that infect them113.

Environmental temperature and latitude correlate with the diversity, distribution and/or temperature optimum ( T opt) of certain marine taxa, with models predicting that rising temperatures will cause a poleward shift of cold-adapted communities. However, T opt of phytoplankton from polar and temperate waters was found to be substantially higher than environmental temperatures, and an eco-evolutionary model predicted that T opt for tropical phytoplankton would be substantially higher than observed experimental values116. Understanding how well microorganisms are adapted to environmental temperature and predicting how they will respond to warming requires assessments of more than T opt, which is generally a poor indicator of physiological and ecological adaptation of microorganisms from cold environments119.

Many environmental and physiological factors influence the responses and overall competitiveness of microorganisms in their native environment. For example, elevated temperatures increase protein synthesis in eukaryotic phytoplankton while reducing cellular ribosome concentration120. As the biomass of eukaryotic phytoplankton is ~1 Gt C (ref.13) and ribosomes are phosphate rich, climate change-driven alteration of their nitrogen-to-phosphate ratio will affect resource allocation in the global ocean120. Ocean warming is thought to favour smaller plankton types over larger ones, changing biogeochemical fluxes such as particle export121. Increased ocean temperatures, acidification and decreased nutrient supplies are projected to increase the extracellular release of dissolved organic matter from phytoplankton, with changes in the microbial loop possibly causing increased microbial production at the expense of higher trophic levels122. Warming can also alleviate iron limitation of nitrogen-fixing cyanobacteria, with potentially profound implications for new nitrogen supplied to food webs of the future warming oceans123. Careful attention needs to be paid to how to quantify and interpret responses of environmental microorganisms to ecosystem changes and stresses linked to climate change124,125. Key questions thus remain about the functional consequences of community shifts, such as changes in carbon remineralization versus carbon sequestration, and nutrient cycling.

Terrestrial biome

There is ~100-fold more terrestrial biomass than marine biomass, and terrestrial plants account for a large proportion of Earth's total biomass15. Terrestrial plants perform roughly half of net global primary production30,67. Soils store ~2,000 billion tonnes of organic carbon, which is more than the combined pool of carbon in the atmosphere and vegetation126. The total number of microorganisms in terrestrial environments is ~10 ²⁹, similar to the total number in marine environments8. Soil microorganisms regulate the amount of organic carbon stored in soil and released back to the atmosphere, and indirectly influence carbon storage in plants and soils through provision of macronutrients that regulate productivity (nitrogen and phosphorus)126,127. Plants provide a substantial amount of carbon to their mycorrhizal fungal symbionts, and in many ecosystems, mycorrhizal fungi are responsible for substantial amounts of nitrogen and phosphorus acquisition by plants128.

Plants remove CO ₂ from the atmosphere through photosynthesis and create organic matter that fuels terrestrial ecosystems. Conversely, autotrophic respiration by plants (60 Pg C per year) and heterotrophic respiration by microorganisms (60 Pg C per year) release CO ₂ back into the atmosphere126,129. Temperature influences the balance between these opposing processes and thus the capacity of the terrestrial biosphere to capture and store anthropogenic carbon emissions (currently, storing approximately one quarter of emissions) (Fig. 1). Warming is expected to accelerate carbon release into the atmosphere129.

Forests cover ~30% of the land surface, contain ~45% of terrestrial carbon, make up ~50% of terrestrial primary production and sequester up to 25% of anthropogenic CO ₂ (refs130,131). Grasslands cover ~29% of the terrestrial surface132. Non-forested, arid and semiarid regions (47%) are important for the carbon budget and respond differently to anthropogenic climate change than forested regions132,133. Lakes make up ~4% of the non-glaciated land area134, and shallow lakes emit substantial amounts of CH ₄ (refs135,136). Peat (decomposed plant litter) covers ~3% of the land surface and, due to plant productivity exceeding decomposition, intact peatlands function as a global carbon sink and contain ~30% of global soil carbon137,138. In permafrost, the accumulation of carbon in organic matter (remnants of plants, animals and microorganisms) far exceeds the respiratory losses, creating the largest terrestrial carbon sink. Climate warming of 1.5-2 °C (relative to the global mean surface temperature in 1850-1900) is predicted to reduce permafrost by 28-53% (compared with levels in 1960-1990)142, thereby making large carbon reservoirs available for microbial respiration and greenhouse gas emissions.

Evaluations of the top 10 cm of soil143 and whole-soil profiles to 100 cm deep, which contain older stocks of carbon144, demonstrate that warming increases carbon loss to the atmosphere. Explaining differences in carbon loss between different soil sites will require a greater range of predictive variables (in addition to soil organic matter content, temperature, precipitation, pH and clay content)145,146. Nevertheless, predictions from global assessments of responses to warming indicate that terrestrial carbon loss under warming is causing a positive feedback that will accelerate the rate of climate change143, particularly in cold and temperate soils, which store much of the global soil carbon147.

Microorganisms affect climate change

Higher CO ₂ levels in the atmosphere increase primary productivity and thus forest leaf and root litter, which leads to higher carbon emissions due to microbial degradation151. Higher temperatures promote higher rates of terrestrial organic matter decomposition152. The effect of temperature is not just a kinetic effect on microbial reaction rates but results from plant inputs stimulating microbial growth.

Several local environmental factors (such as microbial community composition, density of dead wood, nitrogen availability and moisture) influence rates of microbial activity (for example, fungal colonization of wood) necessitating Earth system model predictions of soil carbon losses through climate warming to incorporate local controls on ecosystem processes155. In this regard, plant nutrient availability affects the net carbon balance in forests, with nutrient-poor forests releasing more carbon than nutrient-rich forests156. Microbial respiration may be lower in nutrient-rich forests as plants provide less carbon (for example, as root exudates) to rhizosphere microorganisms157.

Plants release ~50% of fixed carbon into the soil, which is available for microbial growth. In addition to microorganisms using exudates as an energy source, exudates can disrupt mineral-organic associations, liberating organic compounds from minerals that are used for microbial respiration, thereby increasing carbon release159. The relevance of these plant-mineral interactions illustrates the importance of biotic-abiotic interactions, in addition to biotic interactions (plant-microorganism) when one is evaluating the influence of climate change159. Thermodynamic models that incorporate the interactions of microorganisms and secreted enzymes with organic matter and minerals have been used to predict soil carbon-climate feedbacks in response to increasing temperature; one study predicted more variable but weaker soil carbon-climate feedbacks from a thermodynamic model than from static models160.

The availability of soil organic matter for microbial degradation versus long-term storage depends on many environmental factors, including the soil mineral characteristics, acidity and redox state; water availability; climate; and the types of microorganisms present in the soil161. The nature of the organic matter, in particular substrate complexity, affects microbial decomposition. Furthermore, the microbial capacity to access organic matter differs between soil types (for example, with different clay content)162. If access is taken into account, increasing atmospheric CO ₂ levels are predicted to allow greater microbial decomposition and less soil retention of organic carbon162.

Elevated CO ₂ concentrations enhance competition for nitrogen between plants and microorganisms163. Herbivores (invertebrates and mammals) affect the amount of organic matter that is returned to soil and thereby microbial biomass and activity164. For example, grasshoppers diminish plant biomass and plant nitrogen demand, thereby increasing microbial activity163. Climate change can reduce herbivory, resulting in overall alterations to global nitrogen and carbon cycles that reduce terrestrial carbon sequestration163. Detritivores (for example, earthworms) influence greenhouse gas emissions by indirectly affecting plants (for example, by increasing soil fertility) and soil microorganisms165. Earthworms modify soils through feeding, burrowing and deposition of waste products. The anaerobic gut environment of earthworms harbours microorganisms that perform denitrification and produce N ₂O. Earthworms enhance soil fertility, and their presence can result in net greenhouse gas emissions165, although the combined effects of increased temperature and decreased rainfall on detritivore feeding and microbial respiration may reduce emissions166.

In peatlands, decay-resistant litter (for example, antimicrobial phenolics and polysaccharides of Sphagnum mosses) inhibits microbial decomposition, and water saturation restricts oxygen exchange and promotes the growth of anaerobes and release of CO ₂ and CH ₄ (refs137,167). Increased temperature and reduced soil water content caused by climate change promote the growth of vascular plants (ericaceous shrubs) but reduce the productivity of peat moss. Changes in plant litter composition and associated microbial processes (for example, reduced immobilization of nitrogen and enhanced heterotrophic respiration) are switching peatlands from carbon sinks to carbon sources137.

Melting and degradation of permafrost allows microbial decomposition of previously frozen carbon, releasing CO ₂ and CH ₄ (refs). Coastal permafrost erosion will lead to the mobilization of large quantities of carbon to the ocean, with potentially large CO ₂ emissions occurring through increased microbial remineralization170, causing a positive feedback loop that accelerates climate change139,140,141,168,169,170,171. Melting of permafrost leads to increases in water-saturated soils172, which promotes anaerobic CH ₄ production by methanogens and CO ₂ production by a range of microorganisms. Production is slow compared with metabolism in drained aerobic soils, which release CO ₂ rather than CH ₄. However, a 7-year laboratory study of CO ₂ and CH ₄ production found that once methanogen communities became active in thawing permafrost, equal amounts of CO ₂ and CH ₄ were formed under anoxic conditions, and it was predicted that by the end of the century, carbon emissions from anoxic environments will drive climate change to a greater extent than emissions from oxic environments172.

A 15-year mesocosm study that simulated freshwater lake environments determined that the combined effects of eutrophication and warming can lead to large increases in CH ₄ ebullition (bubbles from accumulated gas)135. As small lakes are susceptible to eutrophication and tend to be located in climate-sensitive regions, the role of lake microorganisms in contributing to global greenhouse gas emissions needs to be evaluated135,136.

Climate change affects microorganisms

Shifts in climate can influence the structure and diversity of microbial communities directly (for example, seasonality and temperature) or indirectly (for example, plant composition, plant litter and root exudates). Soil microbial diversity influences plant diversity and is important for ecosystem functions, including carbon cycling173,174.

Both short-term laboratory warming and long-term (more than 50 years) natural geothermal warming initially increased the growth and respiration of soil microorganisms, leading to net CO ₂ release and subsequent depletion of substrates, causing a decrease in biomass and reduced microbial activity175. This implies that microbial communities do not readily adapt to higher temperatures, and the resulting effects on reaction rates and substrate depletion reduce overall carbon loss175. By contrast, a 10-year study found that soil communities adapted to increased temperature by changing composition and patterns of substrate use, leading to less carbon loss than would have occurred without adaptation176. Substantial changes in bacterial and fungal communities were also found in forest soils with a more than 20 °C average annual temperature range177, and in response to warming across a 9-year study of tall-grass prairie soils178.

Two studies assessed the effects of elevated temperatures on microbial respiration rates and mechanisms and outcomes of adaptation179,180. The studies examined a wide range of environmental temperatures (−2 to 28 °C), dryland soils (110 samples) and boreal, temperate and tropical soils (22 samples), and evaluated how communities respond to three different temperatures (~10-30 °C). Thermal adaptation was linked to biophysical characteristics of cell membranes and enzymes (reflecting activity-stability trade-offs180) and the genomic potential of microorganisms (with warmer environments having microbial communities with more diverse lifestyles179). Respiration rates per unit biomass were lower in soils from higher-temperature environments, indicating that thermal adaptation of microbial communities may lessen positive climate feedbacks. However, as respiration depends on multiple interrelated factors (not just on one variable, such as temperature), such mechanistic insights into microbial physiology need to be represented in biogeochemical models of possible positive climate feedbacks.

Microbial growth responses to temperature change are complex and varied181. Microbial growth efficiency is a measure of how effectively microorganisms convert organic matter into biomass, with lower efficiency meaning more carbon is released to the atmosphere182,183. A 1-week laboratory study found that increasing temperature led to increases in microbial turnover but no change in microbial growth efficiency, and predicted that warming would promote carbon accumulation in soil183. A field study spanning 18 years found microbial efficiency was reduced at higher soil temperature, with decomposition of recalcitrant, complex substrates increasing by the end of the period along with a net loss of soil carbon182.

Similarly, in a 26-year forest-soil warming study, temporal variation occurred in organic matter decomposition and CO ₂ release184, leading to changes in microbial community composition and carbon use efficiency, reduced microbial biomass and reduced microbially accessible carbon184. Overall, the study predicted anthropogenic climate change to cause long-term, increasing and sustained carbon release184. Similar predictions arise from Earth system models that simulate microbial physiological responses185 or incorporate the effects of freezing and thawing of cold-climate soils186.

Climate change directly and indirectly influences microbial communities and their functions through several interrelated factors, such as temperature, precipitation, soil properties and plant input. As soil microorganisms in deserts are carbon limited, increased carbon input from plants promotes transformation of nitrogenous compounds, microbial biomass, diversity (for example, of fungi), enzymatic activity and use of recalcitrant organic matter133. Although these changes may enhance respiration and net loss of carbon from soil, the specific characteristics of arid and semiarid regions may mean they could function as carbon sinks133. However, a study of 19 temperate grassland sites found that seasonal differences in rainfall constrain biomass accumulation132. To better understand aboveground plant-biomass responses to CO ₂ levels and seasonal precipitation, we also need improved knowledge of microbial community responses and functions.

Metagenome data, including metagenome-assembled genomes, provide knowledge of key microbial groups that metabolize organic matter and release CO ₂ and CH ₄ and link these groups to the biogeochemistry occurring in thawing permafrost. Tundra microbial communities change in the soil layer of permafrost after warming192. Within 1.5 years of warming, the functional potential of the microbial communities changed markedly, with an increasing abundance of genes involved in aerobic and anaerobic carbon decomposition and nutrient cycling. Although microbial metabolism stimulates primary productivity by plants, the balance between microbial respiration and primary productivity results in a net release of carbon to the atmosphere192. When forests expand into warming regions of tundra, plant growth can produce a net loss of carbon, possibly as a result of root exudates stimulating microbial decomposition of native soil carbon153,193. Although there are reports of carbon accumulating owing to warming (for example, ref.183), most studies describe microbial community responses that result in carbon loss.

Rapid warming of the Antarctic Peninsula and associated islands resulted in range expansion of Antarctic hair grass ( Deschampsia antarctica), as it outcompetes other indigenous species (for example, the moss Sanionia uncinata) through the superior capacity of its roots to acquire peptides and thus nitrogen194. The ability of the grass to be competitive depends on microbial digestion of extracellular proteins and generation of amino acids, nitrate and ammonium194. As warmer soils in this region harbour greater fungal diversity, climate change is predicted to cause changes in the fungal communities that will affect nutrient cycling and primary productivity195. Cyanobacterial diversity and toxin production within benthic mats from both the Antarctic Peninsula and the Arctic increased during 6 months of exposure to high growth temperatures196. A shift to toxin-producing species or increased toxin production by existing species could affect polar freshwater lakes, where cyanobacteria are often the dominant benthic primary producers196.

Climate change is likely to increase the frequency, intensity and duration of cyanobacterial blooms in many eutrophic lakes, reservoirs and estuaries197,198. Bloom-forming cyanobacteria produce a variety of neurotoxins, hepatotoxins and dermatoxins, which can be fatal to birds and mammals (including waterfowl, cattle and dogs) and threaten the use of waters for recreation, drinking water production, agricultural irrigation and fisheries198. Toxic cyanobacteria have caused major water quality problems, for example in Lake Taihu (China), Lake Erie (USA), Lake Okeechobee (USA), Lake Victoria (Africa) and the Baltic Sea.

Climate change favours cyanobacterial blooms both directly and indirectly198. Many bloom-forming cyanobacteria can grow at relatively high temperatures201. Increased thermal stratification of lakes and reservoirs enables buoyant cyanobacteria to float upwards and form dense surface blooms, which gives them better access to light and hence a selective advantage over nonbuoyant phytoplankton organisms202,203. Protracted droughts during summer increase water residence times in reservoirs, rivers and estuaries, and these stagnant warm waters can provide ideal conditions for cyanobacterial bloom development204.

The capacity of the harmful cyanobacterial genus Microcystis to adapt to elevated CO ₂ levels was demonstrated in both laboratory and field experiments205. Microcystis spp. take up CO ₂ and HCO ₃− and accumulate inorganic carbon in carboxysomes, and strain competitiveness was found to depend on the concentration of inorganic carbon. As a result, climate change and increased CO ₂ levels are expected to affect the strain composition of cyanobacterial blooms205.

Agriculture

According to the World Bank ( World Bank data on agricultural land), nearly 40% of the terrestrial environment is devoted to agriculture. This proportion is predicted to increase, leading to substantial changes in soil cycling of carbon, nitrogen and phosphorus, among other nutrients. Furthermore, these changes are associated with a marked loss of biodiversity206, including of microorganisms207. There is increasing interest in using plant-associated and animal-associated microorganisms to increase agricultural sustainability and mitigate the effects of climate change on food production, but doing so requires a better understanding of how climate change will affect microorganisms.

Microorganisms affect climate change

Methanogens produce methane in natural and artificial anaerobic environments (sediments, water-saturated soils such as rice paddies, gastrointestinal tracts of animals (particularly ruminants), wastewater facilities and biogas facilities), in addition to the anthropogenic methane production associated with fossil fuels208 (Fig. 2). The main sinks for CH ₄ are atmospheric oxidation and microbial oxidation in soils, sediments and water208. Atmospheric CH ₄ levels have risen sharply in recent years (2014-2017) but the reasons are unclear so far, although they involve increased emissions from methanogens and/or fossil fuel industries and/or reduced atmospheric CH ₄ oxidation, thereby posing a major threat to controlling climate warming209.

Agricultural practices influence microbial communities in specific ways. Land usage (for example, plant type) and sources of pollution (for example, fertilizers) perturb microbial community composition and function, thereby altering natural cycles of carbon, nitrogen and phosphorus transformations. Methanogens produce substantial quantities of methane directly from ruminant animals (for example, cattle, sheep and goats) and saturated soils with anaerobic conditions (for example, rice paddies and constructed wetlands). Human activities that cause a reduction in microbial diversity also reduce the capacity for microorganisms to support plant growth.

Rice feeds half of the global population210, and rice paddies contribute ~20% of agricultural CH ₄ emissions despite covering only ~10% of arable land. Anthropogenic climate change is predicted to double CH ₄ emissions from rice production by the end of the century210. Ruminant animals are the largest single source of anthropogenic CH ₄ emissions, with a 19-48 times larger carbon footprint for ruminant meat production than plant-based high-protein foods211. Even the production of meat from non-ruminant animals (such as pigs, poultry and fish) produces 3-10 times more CH ₄ than high-protein plant foods211.

The combustion of fossil fuels and the use of fertilizers has greatly increased the environmental availability of nitrogen, perturbing global biogeochemical processes and threatening ecosystem sustainability212,213. Agriculture is the largest emitter of the potent greenhouse gas N ₂O, which is released by microbial oxidation and reduction of nitrogen214. The enzyme N ₂O reductase in rhizobacteria (in root nodules) and other soil microorganisms can also convert N ₂O to N ₂ (not a greenhouse gas). Climate change perturbs the rate at which microbial nitrogen transformations occur (decomposition, mineralization, nitrification, denitrification and fixation) and release N ₂O (ref.213). There is an urgent need to learn about the effects of climate change and other human activities on microbial transformations of nitrogen compounds.

Climate change affects microorganisms

Crop farming ranges from extensively managed (small inputs of labour, fertilizer and capital) to intensively managed (large inputs). Increasing temperature and drought strongly affect the ability to grow crops215. Fungal-based soil food webs are common in extensively managed farming (for example, grasslands) and are better able to adapt to drought than bacterial-based food webs, which are common in intensive systems (for example, wheat)216,217. A global assessment of topsoil found that soil fungi and bacteria occupy specific niches and respond differently to precipitation and soil pH, indicating that climate change would have differential impacts on their abundance, diversity and functions218. Aridity, which is predicted to increase owing to climate change, reduces bacterial and fungal diversity and abundance in global drylands219. Reducing soil microbial diversity reduces the overall functional potential of microbial communities, thereby limiting their capacity to support plant growth173.

The combined effects of climate change and eutrophication caused by fertilizers can have major, potentially unpredictable effects on microbial competitiveness. For example, nutrient enrichment typically favours harmful algal blooms, but a different outcome was observed in the relatively deep Lake Zurich220. Reducing phosphorus inputs from fertilizers reduced eukaryotic phytoplankton blooms but increased the nitrogen-to-phosphorus ratio and thus the non-nitrogen-fixing cyanobacterium Planktothrix rubescens became dominant220. In the absence of effective predation, annual mixing has an important role in controlling cyanobacterial populations. However, warming increased thermal stratification and reduced mixing, thereby facilitating the persistence of the toxic cyanobacteria220.

Infectious diseases

Climate change affects the occurrence and spread of diseases in marine and terrestrial biota221 (Fig. 3), depending on diverse socioeconomic, environmental and host-pathogen-specific factors222. Understanding the spread of disease and designing effective control strategies requires knowledge of the ecology of pathogens, their vectors and their hosts, and the influence of dispersal and environmental factors223 (Table 1). For example, there is a strong link between increasing sea surface temperatures and coral disease and, although the disease mechanisms are not absolutely clear for all the different syndromes, associations with microbial pathogens exist. Peaks in disease prevalence coincide with periodicities in the El Niño Southern Oscillation (ENSO)227. In particular, in some coral species, ocean warming can alter the coral microbiome, disrupting the host-symbiont equilibrium, shifting defensive mechanisms and nutrient cycling pathways that may contribute to bleaching and disease99. Ocean acidification may also directly cause tissue damage in organisms such as fish, potentially contributing to a weakened immune system that creates opportunities for bacterial invasion228.

Anthropogenic climate change stresses native life, thereby enabling pathogens to increasingly cause disease. The impact on aquaculture, food-producing animals and crops threatens global food supply. Human activities, such as population growth and transport, combined with climate change increase antibiotic resistance of pathogens and the spread of waterborne and vector-borne pathogens, thereby increasing diseases of humans, other animals and plants.

Table 1 Transmission response of pathogens to climatic and environmental factors

Sea star species declined by 80-100% along an ~3000 km section of the North American west coast, with peak declines occurring during anomalous increases in sea surface temperatures229. As sea stars are important predators of sea urchins, loss of predation can cause a trophic cascade that affects kelp forests and associated marine biodiversity229,230. Given the effects of ocean warming on pathogen impacts, temperature monitoring systems have been developed for a wide range of marine organisms, including corals, sponges, oysters, lobsters and other crustaceans, sea stars, fish and sea grasses231.

Forest die-off caused by drought and heat stress can be exacerbated by pathogens232. For crops, a variety of interacting factors are important when one is considering response to pathogens, including CO ₂ levels, climatic changes, plant health and species-specific plant-pathogen interactions233. A broad range of microorganisms cause plant diseases (fungi, bacteria, viruses, viroids and oomycetes) and can, therefore, affect crop production, cause famines (for example, the oomycete Phytophthora infestans caused the Irish potato famine) and threaten food security233. An assessment of more than 600 crop pests (nematodes and insects) and pathogens since 1960 found an expansion towards the poles that is attributable to climate change233. The spread of pathogens and the emergence of disease are facilitated by transport and introduction of species and are influenced by effects of weather on dispersal and environmental conditions for growth233.

Climate change can increase the disease risk by altering host and parasite acclimation234. For ectotherms (such as amphibians), temperature can increase susceptibility to infection, possibly through perturbation of immune responses234,235. Monthly and daily unpredictable environmental temperature fluctuations increase the susceptibility of the Cuban tree frog to the pathogenic chytrid fungus Batrachochytrium dendrobatidis. The effect of increasing temperature on infection contrasts with decreased growth capacity of the fungus in pure culture, illustrating the importance of assessing host-pathogen responses (rather than extrapolating from growth rate studies of isolated microorganisms) when evaluating the relevance of climate change234.

Climate change is predicted to increase the rate of antibiotic resistance of some human pathogens236. Data from 2013-2015 suggest that an increase of the daily minimum temperature by 10 °C (which is conceivable for some parts of the USA by the end of the century) will lead to an increase in antibiotic resistance rates of Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus by 2-4% (up to 10% for certain antibiotics)236. Potential underlying mechanisms include elevated temperatures facilitating horizontal gene transfer of mobile genetic elements of resistance, and increased pathogen growth rates promoting environmental persistence, carriage and transmission236. Population growth, which amplifies climate change, is also an important factor in contributing to the development of resistance236.

Vector-borne, foodborne, airborne, waterborne and other environmental pathogens may be particularly susceptible to the effects of climate change (Table 1). For vector-borne diseases, climate change will affect the distribution of vectors and hence the range over which diseases are transmitted, as well as the efficiency with which vectors transmit pathogens. Efficiency depends on the time between a vector feeding on an infected host and the vector becoming infectious itself. At warmer temperatures, this time can be reduced substantially, providing more opportunity for transmission within the vector's lifespan. Certain vector-borne diseases, such as bluetongue, an economically important viral disease of livestock, have already emerged in Europe in response to climate change, and larger, more frequent outbreaks are predicted to occur in the future241. For certain waterborne infections by pathogenic Vibrio spp., poleward spread correlates with increasing global temperature and lower salinity of aquatic environments in coastal regions (such as estuaries) caused by increased precipitation242. These changed conditions can promote the growth of Vibrio spp. in the environment242. Increasing sea surface temperatures also correlate with increases in Vibrio cholerae infections in Bangladesh243, infections with several human-pathogenic Vibrio spp. in the Baltic Sea region242 and the abundance of Vibrio spp. (including human pathogens) in the North Atlantic and North Sea244.

Malaria and dengue fever are two vector-borne diseases that are known to be highly sensitive to climate conditions, and thus their spatial distributions are expected to shift in response to climate change. Climate change can facilitate the spread of vector-borne pathogens by prolonging the transmission season, increasing the rate of replication of pathogens in the vector and increasing the number and geographic range of mosquitoes. This is especially the case for Aedes aegypti, the major vector of dengue, Zika, chikungunya and yellow fever viruses, which is currently limited to tropical and subtropical regions because it cannot survive cold winters. In combination with other mosquito-borne diseases (such as West Nile fever and Japanese encephalitis) and tick-borne diseases (such as Lyme disease), millions of people are predicted to be newly at risk under climate change.

Many infectious diseases, including several vector-borne and waterborne diseases, are strongly influenced by climate variability caused by large-scale climate phenomena such as the ENSO, which disrupts normal rainfall patterns and changes temperatures in about two thirds of the globe every few years. Associations with ENSO have been reported for malaria, dengue fever, Zika virus disease, cholera, plague, African horse sickness and many other important human and animal diseases.

Adaptation of species to their local environment has been studied less in microorganisms than in animals (including humans) and plants, although the mechanisms and consequences of adaptation have been studied in natural and experimental microbial populations255. Viral, bacterial and fungal pathogens of plants and animals (such as crops, humans and livestock) adapt to abiotic and biotic factors (such as temperature, pesticides, interactions between microorganisms and host resistance) in ways that affect ecosystem function, human health and food security255. The cyclic feedback between microbial response and human activity is well illustrated by the adaptation patterns of pathogenic agricultural fungi256. Because agricultural ecosystems have common global features (for example, irrigation, fertilizer use and plant cultivars) and human travel and transport of plant material readily disperse crop pathogens, 'agro-adapted' pathogens have a higher potential to cause epidemics and pose a greater threat to crop production than naturally occurring strains256. The ability of fungal pathogens to expand their range and invade new habitats by evolving to tolerate higher temperatures compounds the threat fungal pathogens pose to both natural and agricultural ecosystems257.

Microbial mitigation of climate change

An improved understanding of microbial interactions would help underpin the design of measures to mitigate and control climate change and its effects (see also ref.7). For example, understanding how mosquitoes respond to the bacterium Wolbachia (a common symbiont of arthropods) has resulted in a reduction of the transmission of Zika, dengue and chikungunya viruses through the introduction of Wolbachia into populations of A. aegypti mosquitoes and releasing them into the environment258. In agriculture, progress in understanding the ecophysiology of microorganisms that reduce N ₂O to harmless N ₂ provides options for mitigating emissions214,259. The use of bacterial strains with higher N ₂O reductase activity has lowered N ₂O emissions from soybean, and both natural and genetically modified strains with higher N ₂O reductase activity provide avenues for mitigating N ₂O emissions214. Manipulating the rumen microbiota260 and breeding programmes that target host genetic factors that change microbial community responses261 are possibilities for reducing methane emission from cattle. In this latter case, the aim would be to produce cattle lines that sustain microbial communities producing less methane without affecting the health and productivity of the animals261. Fungal proteins can replace meat, lowering dietary carbon footprints262.

Biochar is an example of an agricultural solution for broadly and indirectly mitigating microbial effects of climate change. Biochar is produced from thermochemical conversion of biomass under oxygen limitation and improves the stabilization and accumulation of organic matter in iron-rich soils263. Biochar improves organic matter retention by reducing microbial mineralization and reducing the effect of root exudates on releasing organic material from minerals, thereby promoting growth of grasses and reducing the release of carbon263.

A potentially large-scale approach to mitigation is the use of constructed wetlands to generate cellulosic biofuel using waste nitrogen from wastewater treatment; if all waste in China were used, it could supply the equivalent of 7% of China's gasoline consumption264. Such major developments of constructed wetlands would require the characterization and optimization of their core microbial consortia to manage their emissions of greenhouse gases and optimize environmental benefits265.

Microbial biotechnology can provide solutions for sustainable development266, including in the provision (for example, of food) and regulation (for example, of disease or of emissions and capture of greenhouse gases) of ecosystem services for humans, animals and plants. Microbial technologies provide practical solutions (chemicals, materials, energy and remediation) for achieving many of the 17 United Nations Sustainable Development Goals, addressing poverty, hunger, health, clean water, clean energy, economic growth, industry innovation, sustainable cities, responsible consumption, climate action, life below water, and life on land6 (Box 1). Galvanizing support for such actions will undoubtedly be facilitated by improving public understanding of the key roles of microorganisms in global warming, that is, through attainment of microbiology literacy in society7.

Conclusion

Microorganisms make a major contribution to carbon sequestration, particularly marine phytoplankton, which fix as much net CO ₂ as terrestrial plants. For this reason, environmental changes that affect marine microbial photosynthesis and subsequent storage of fixed carbon in deep waters are of major importance for the global carbon cycle. Microorganisms also contribute substantially to greenhouse gas emissions via heterotrophic respiration (CO ₂), methanogenesis (CH ₄) and denitrification (N ₂ O).

Many factors influence the balance of microbial greenhouse gas capture versus emission, including the biome, the local environment, food web interactions and responses, and particularly anthropogenic climate change and other human activities (Figs 1- 3).

Human activity that directly affects microorganisms includes greenhouse gas emissions (particularly CO ₂, CH ₄ and N ₂ O), pollution (particularly eutrophication), agriculture (particularly land usage) and population growth, which positively feeds back on climate change, pollution, agricultural practice and the spread of disease. Human activity that alters the ratio of carbon uptake relative to release will drive positive feedbacks and accelerate the rate of climate change. By contrast, microorganisms also offer important opportunities for remedying human-caused problems through improved agricultural outcomes, production of biofuels and remediation of pollution.

Addressing specific issues involving microorganisms will require targeted laboratory studies of model microorganisms (Box 2). Laboratory probing of microbial responses should assess environmentally relevant conditions, adopt a 'microbcentric' view of environmental stressors and be followed up by field tests. Mesocosm and in situ field experiments are particularly important for gaining insight into community-level responses to real environmental conditions. Effective experimental design requires informed decision-making, involving knowledge from multiple disciplines specific to marine (for example, physical oceanography) and terrestrial (for example, geochemistry) biomes.

To understand how microbial diversity and activity that govern small-scale interactions translate to large system fluxes, it will be important to scale findings from individuals to communities and to whole ecosystems. Earth system modellers need to include microbial contributions that account for physiological and adaptive (evolutionary) responses to biotic (including other microorganisms, plants and organic matter substrates) and abiotic (including mineral surfaces, ocean physics and chemistry) forcings.

We must improve our quantitative understanding of the global marine and soil microbiome. To understand biogeochemical cycling and climate change feedbacks at any location around the world, we need quantitative information about the organisms that drive elemental cycling (including humans, plants and microorganisms), and the environmental conditions (including climate, soil physiochemical characteristics, topography, ocean temperature, light and mixing) that regulate the activity of those organisms. The framework for quantitative models exists, but to a large extent these models lack mechanistic details of marine and terrestrial microorganisms. The reason for this omission has less to do with how to construct such a model mathematically but instead stems from the paucity of physiological and evolutionary data allowing robust predictions of microbial responses to environmental change. A focused investment into expanding this mechanistic knowledge represents a critical path towards generating the global models essential for benchmarking, scaling and parameterizing Earth system model predictions of current and future climate.

Extant life has evolved over billions of years to generate vast biodiversity, and microbial biodiversity is practically limitless compared with macroscopic life. Biodiversity of macroscopic organisms is rapidly declining because of human activity, suggesting that the biodiversity of host-specific microorganisms of animal and plant species will also decrease. However, compared with macroscopic organisms, we know far less about the connections between microorganisms and anthropogenic climate change. We can recognize the effects of microorganisms on climate change and climate change on microorganisms, but what we have learned is incomplete, complex and challenging to interpret. It is therefore not surprising that challenges exist for defining causes and effects of anthropogenic climate change on biological systems. Nevertheless, there is no doubt that human activity is causing climate change, and this is perturbing normal ecosystem function around the globe (Box 1). Across marine and terrestrial biomes, microbially driven greenhouse gas emissions are increasing and positively feeding back on climate change. Irrespective of the fine details, the microbial compass points to the need to act (Box 2). Ignorance of the role of, effects on and feedback response of microbial communities to climate change can lead to our own peril. An immediate, sustained and concerted effort is required to explicitly include microorganisms in research, technology development, and policy and management decisions. Microorganisms not only contribute to the rate of climate change but can also contribute immensely to its effective mitigation and our adaptation tools.

Box 2 A call to action

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Scientists' warning to humanity: microorganisms and climate change - Nature Reviews Microbiology

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The microbial majority with which we share Earth often goes unnoticed despite underlying major biogeochemical cycles and food webs, thereby taking a key role in climate change. This Consensus Statement highlights the importance of climate change microbiology and issues a call to action for all microbiologists.

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Monsanto's Bt cotton, genetically modified to contain a gene from Bacterium Thurlingensis, has been a huge failure and farmers who have used it see decreasing yields and increasing costs. This article about a recent study into the issue, explains why, and at the same time is highly informative about the role played by fungi that collaborate with 94% of plants in nutrient uptake.

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A new study finds that transgenic cotton genetically modified to express a Bt ( Bacillus thuringiensis) insect toxin inhibits the development of the beneficial soil organism Rhizophagus irregularis, a common arbuscular mycorrhizal (AM) fungus.

The study, which examined three separate genetically modified (GM) cotton lines and three non-GM lines, also found that the GM varieties disrupt the ability of the fungus to form a symbiotic association with the GM crop.

The fungus, when grown with GM cotton, displays fewer reproductive spores, fewer associations with GM cotton roots and increased fungal degeneration.

While the specific mechanism requires further study, the statistical analysis carried out in the study demonstrates that the "Bt-trait significantly contributes to the inhibition of pre-symbiotic development and AM fungal colonization, which might be attributed to either Bt toxin toxicity or interference of signal perception between AM fungi and the hosts."

Analysing three commercialised Bt cotton crops grown in China, the investigators found a reduction of fungal colonisation of roots by 44.4%, 25.0% and 51.3% for each line when compared with their isogenic parental controls.

Branching of the AM fungi was also significantly reduced, with shortened hyphae and reduced arbuscule frequency - tuft-like structures that help colonise roots on the Bt lines, which were reduced by up to 68.2% for one of the lines. This was consistent with a significant reduction in shoot biomass (Bt lines having a biomass of 0.34, 0.33 and 0.30 grams for each line) compared to controls (0.27, 0.27 and 0.25 g).

Crucially, the GM cotton plants appeared to suffer from their reduced ability to associate with the mycorrhizal fungus: they showed reduced shoot growth when compared with non-GM parental lines.

This highlights the importance of maintaining a living, healthy soil - which our industrial agricultural practices are destroying.
Unanticipated and wide reaching effects on the health of our soils
It is increasingly apparent that Bt crops are a failing technology, unable to withstand the pests they are designed to ward off. Burkina Faso, the first African nation to cultivate Bt cotton has now pulled it from the market due to the low quality of cotton it produces. India is seeing farmers revert to conventional varieties due to dire failures in Bt cotton yields that have pushed farmers further into debt and suicide.

Admitting Bt crop failures, the GM industry have since marketed crops with multiple Bt toxins in an effort to delay their futility. However, as this latest study, performed by researchers in Huazong Agricultural University under the Chinese Ministry of Agriculture shows, there are many ways in which Bt crops can have unanticipated and wide reaching effects on the health of our soils and wider environment, some of which go beyond the inability of Bt toxins to target pests.

Some problems seen with Bt crops - including the spread of crop disease and rise of secondary pest attacks - may well be exacerbated by the damage to soil biology.

Living soil is essential to life, moderating climate, storing and recycling water and nutrients, biodegrading pollutants, with humans utterly dependent on its survival for food production, and also serves as an important mitigating factor in an era of unpredictable climate change.

The sacred properties of soil have long been recognised by human cultures, but this knowledge has been eroded by the advent of industrial agriculture that has resulted in declining soil health. In the last 40 years, we have lost an estimated third of all arable land to soil infertility, reflected in plateauing and even declining crop yield gains in the last decade, despite continued increases in economic investments.

This study is the latest warning that a decisive shift from industrial / GMO practices to sustainable, agroecological methods is needed to undo the damage, and ensure food security and health of people and planet for the future.
AM fungi act as 'underground highways' supplying nutrients, information
AM fungi form associations with an estimated 94% of plant species, an ancient mutualism believed to have originated some 450 million years ago that facilitated the colonisation of land by early plants.

They are a vital component of the living soil, supplying plants with key nutrients including phosphate, as well as water, supporting plants' ability to deal with biotic and abiotic stresses such as drought, salinity, disease and pest attacks. In return, plants supply sugars to the fungi.

While mushrooms are familiar to us all, scientists are continuing to reveal the intricacies and complexities of this relationship hidden underground, performed by a vast network of fungal threads, the mycelial network, that make up most of the fungal body. Interacting with many plants, they work as a communication web, or underground 'highway' through which plants can relay information, such as the presence of pests to its plant neighbours.

Recent findings tell of the remarkable ability of AM fungi to relay warnings of aphid pest attacks from one pea plant to its neighbours, allowing them to produce the necessary aphid-deterring chemicals to protect themselves. A 2016 study has introduced the concept that trees are not only in competition with each other for nutrients, but can share them. Carbon is supplied to neighbouring trees, even those of a different species, via AM fungal networks.

Indeed the soil, and mycorrhizae themselves, are important mediators of the wider ecosystem function, with mycorrhizal biodiversity correlating with ecosystem variability, nutrient capture and plant productivity.

Harvesting the potential for AM fungi to improve food production and maintain the health of the environment is an ongoing field of research and has great potential to mitigate some of abiotic and biotic stresses that limit yield.

Examples of recent gains in the field include a study citing a 20% increase in cassava yields in Colombian fields. Low phosphate bioavailability in tropical soils suggests an opportunity for using AM fungi to improve yields in such regions. Fivefold differences in rice growth was obtained when the soils were inoculated with different isolates of one AM fungi species.

Such studies raise questions on the extent population genetic diversity and species diversity in crop growth, and also whether such effects are direct or indirect. Care must also be given in understanding how introduction of AM fungi to soils will affect existing fungal populations as well as the wider ecological soil and plant community.

What is already understood is that any loss to mycorrhizal biodiversity and abundance is a threat to the stability, productivity and sustainability of crop cultivation. Further, effects on climate change cannot be disentangled from the dynamics of the soil; the soil contains more carbon than plants and air combined.

Whole ecosystems - including agro-ecosystems - must be protected in order to nullify this threat, and that includes reversing the roll out of GM crops and their associated pesticides.
AM fungal damage by Bt toxins contributing to yield failures?
The latest evidence that Bt crops damage this symbiotic relationship may provide an explanation for the failure of the GM crops to thrive. They are increasingly failing to yield, to effectively ward of pests as they are designed to do, and to resist plant attacks, drought and other stresses. These problems are afflicting both Bt cotton as well as maize in various regions of the world.

While this study by Chen et al., is the first to show a direct effect of Bt crops on the early stages of the AM fungal life cycle, it builds on previous reports of altered relationships between Bt crops and AM fungi, including reduced colonisation of crop roots by AM fungi, as well as lower density of fungi spores in agricultural plots.

The spread of previously unseen diseases such as root rot in cotton plants in India may well be, at least in part, the result of damaged AM fungal symbiosis. Root rot was not seen until the introduction of Bt cotton in India in 2002-2003, affecting 2-3% of crops in one region of Andhra Pradesh, which spread to 40% by 2008.

Studies in bean plants have shown that AM fungi are able to inhibit disease progression by the same fungal pathogen ( Rhizoctonia solani) responsible for root rot in cotton. Bt Bringal (aubergine), piloted in Bangledesh over the last couple of seasons has also been a complete failure according to reports citing a variety of problems afflicting the crop including fungal infections (including root and stem rot, wilt, leaf spot and fruit spot), viruses and pest attacks.

Farmers have therefore had to use additional pesticides, increasing costs and pollution of food and land.
The failure of reductionist approaches
As highlighted in various contexts, the reductionist approach to food production is proviing top be a failure, with the science clouded by short-term fixes and economic incentives.

Even Monsanto now realise that maintaining a healthy soil is key - if only for them to investigate ways in which they can manipulate individual factors in the 'creation' of microbial fertilizers. As ever, the warping of science to suit ideology means that addressing the issue from a holistic point of view is again lost to the pursuit of patentable intellectual property and corporate profit..

We move one step at a time, addressing each crop stress singularly, only for it to have knock on effects on all other interrelated factors. Increasing tolerance to one stress through genetic modification or chemical manipulation will not solve the multiple stressors that likely impact a crop at any one time.

AM fungi and the rest of the soil community, on the other hand, should be harnessed on a 'whole ecosystem' basis for their ability to improve resistance to multiple stresses, from nutrient depletion to climate change, many of which are difficult for us to predict.

The study: ' Evidences of inhibited arbuscular mycorrhizal fungal development and colonization in multiple lines of Bt cotton' is by Xiu-Hua Chen at al and and published by Agriculture, Ecosystems & Environment.
Dr Eva Sirinathsinghji is a writer, and scientist and independent consultant working on biosafety concerns of scientific technologies. Her main focus is agricultural sustainability and the protection of human health and the environment at the Institute of Science in Society (ISIS). Recent publications include Banishing Glyphosate.

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Vital soil fungi damaged by GMO Bt cotton

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A study of GMO cotton varieties shows they disrupt an important beneficial soil fungus, writes Eva Sirinathsinghji, apparently due to the Bt insecticide they are engineered to express. Disruption caused by the transgenic cotton to mycorrhizal fungi, and the wider soil ecosystem, may underlie the low yields and poor pest resistance now endemic among Bt GM crops.

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Geomorphologist David Montgomery discusses soil erosion in this excellent lecture.

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Dave Montgomery - Dirt: The Erosion of Civilizations

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Dr Christine Jones.

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Christine Jones -- Nitrogen: The double-edged sword

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Urban greenness influences airborne bacterial community composition

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Urban greenness influences airborne bacterial community composition

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JavaScript is disabled on your browser. Please enable JavaScript to use all the features on this page.

Highlights

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We compared airborne bacterial samples from parks and parking lots with 16S sequencing.

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Bacterial communities from parks and parking lots were compositionally distinct.

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Proportion of vegetated area within 50 m explained 15% of the variation among samples.

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Parking lots had similar bacterial signatures, but parks tended to be unique.

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Passive and active collection methods gave comparable results.

Abstract

Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p = 0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50 m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing neighborhoods and open space systems that foster better human health.

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Urban greenness influences airborne bacterial community composition

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JavaScript is disabled on your browser. Please enable JavaScript to use all the features on this page. * We compared airborne bacterial samples from parks and parking lots with 16S sequencing. * Bacterial communities from parks and parking lots were compositionally distinct. * Proportion of vegetated area within 50 m explained 15% of the variation among samples.

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The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems

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The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems

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Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny.

Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities.

Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.

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The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems

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Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins.

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Microbial diversity determines the invasion of soil by a bacterial pathogen

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Microbial diversity determines the invasion of soil by a bacterial pathogen

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Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling'?

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Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling'?

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The Jena Experiment: Recommended by Dr Christine Jones.

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The Jena Experiment: Recommended by Dr Christine Jones.

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A short but informative video about the Jena Experiment's research into the symbiotic relationships between plant diversity above ground and microbial diversity below ground and the wide biodiversity this relationship fosters.

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Christine Jones with probably the most important information about soil microbes we'll ever hear. When there is sufficient microbial species richness and abundance in the soil, microbial communities sequester carbon rapidly and can also switch plant genes on and off.

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Changes in soil aggregation and glomalin-related soil protein content as affected by the arbuscular mycorrhizal fungal species Glomus mosseae and Glomus intraradices

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Changes in soil aggregation and glomalin-related soil protein content as affected by the arbuscular mycorrhizal fungal species Glomus mosseae and Glomus intraradices

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Abstract

Arbuscular mycorrhizal (AM) fungi are key organisms of the soil/plant system, influencing soil fertility and plant nutrition, and contributing to soil aggregation and soil structure stability by the combined action of extraradical hyphae and of an insoluble, hydrophobic proteinaceous substance named glomalin-related soil protein (GRSP). Since the GRSP extraction procedures have recently revealed problems related to co-extracting substances, the relationship between GRSP and AM fungi still remains to be verified. In this work the hypothesis that GRSP concentration is positively correlated with the occurrence of AM fungi was tested by using Medicago sativa plants inoculated with different isolates of Glomus mosseae and Glomus intraradices in a microcosm experiment. Our results show that (i) mycorrhizal establishment produced an increase in GRSP concentration - compared to initial values - in contrast with non-mycorrhizal plants, which did not produce any change; (ii) aggregate stability, evaluated as mean weight diameter (MWD) of macroaggregates of 1-2 mm diameter, was significantly higher in mycorrhizal soils compared to non-mycorrhizal soil; (iii) GRSP concentration and soil aggregate stability were positively correlated with mycorrhizal root volume and weakly correlated with total root volume; (iv) MWD values of soil aggregates were positively correlated with values of total hyphal length and hyphal density of the AM fungi utilized.

The different ability of AM fungal isolates to affect GRSP concentration and to form extensive and dense mycelial networks, which may directly affect soil aggregates stability by hyphal enmeshment of soil particles, suggests the possibility of selecting the most efficient isolates to be utilized for soil quality improvement and land restoration programs.

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Changes in soil aggregation and glomalin-related soil protein content as affected by the arbuscular mycorrhizal fungal species Glomus mosseae and Glomus intraradices

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JavaScript is disabled on your browser. Please enable JavaScript to use all the features on this page. Arbuscular mycorrhizal (AM) fungi are key organisms of the soil/plant system, influencing soil fertility and plant nutrition, and contributing to soil aggregation and soil structure stability by the combined action of extraradical hyphae and of an insoluble, hydrophobic proteinaceous substance named glomalin-related soil protein (GRSP).

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AMP shows better results than LCG (Light Continuous Grazing) and HCG (Heavy Continuous Grazing) for improved soil function, improved forage biomass and increased litter cover and water infiltration. AMP sequesters more carbon than LCG and HCG.

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Highlights

*

We assess outcomes of holistic planned grazing by bison in shortgrass prairie.

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AMP grazing improved soil function by limiting overstocking and overgrazing.

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AMP grazing improved forage biomass and species composition over continuous grazing.

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AMP grazing increased litter cover and infiltration while decreasing bare ground.

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Total soil carbon stocks improved with AMP and LCG grazing vs. HCG grazing.

Abstract

We assess holistic planned grazing outcomes in shortgrass prairie of the Northern Great Plains of North America. We compared key ecosystem functions on the ranch managed using adaptive multi-paddocks (AMP) grazing by bison with those on neighboring ranch paddocks managed using set stocked light continuous (LCG) and heavy continuous grazing (HCG) grazed by cattle. Sites on the neighboring ranches in each grazing category were paired for sampling by soil type and landscape position. In all paddocks, management practices had been constant for more than a decade. Positive results with AMP grazing include increased fine litter cover ( P <  0.05), improved water infiltration ( P <  0.06), two to three times the available forage biomass ( P <  0.001), improved plant composition ( P <  0.05), decrease in invasive plants ( P <  0.05), and decrease in bare ground ( P <  0.05). Higher infiltration occurred with AMP on soils having higher permeability but not on soils having a high clay content. Differences were greatest between AMP and HCG management with LCG being intermediate. Counterintuitively, herbaceous biomass in LCG was less than that of the more heavily stocked HCG ( P <  0.05). This was due to decades of heavy continuous grazing resulting in HCG being dominated by invasive herbaceous plants of no forage value in contrast to LCG paddocks that had a greater proportion of palatable forages. The HCG paddocks were dominated by unpalatable invasive plants that were avoided by cattle. Soil carbon stocks increased under the AMP grazing but not on all soils. Total carbon stocks (TC), summing organic carbon and inorganic carbon, were not different between the AMP and LCG grazing strategies ( P >  0.63) but both had higher TC values across all soils than HCG ( P <  0.001). There were no differences in TC among grazing treatments on the different soils ( P >  0.46) except on the Norrest silty clay loam soil that had the highest permeability. On this soil there were differences between AMP and HCG ( P < 0.0001) and LCG and HCG ( P <  0.0001). There were significantly lower TC levels at all soil depths with HCG than with AMP and LCG ( P  <  0.05). Using holistic planned grazing protocols with AMP grazing effectively limited overstocking and overgrazing by adjusting animal numbers to match available forage amounts and grazing for short periods followed by adequate recovery after grazing. This study indicated ecological improvements by AMP grazing on the 777 Bison Ranch compared to HCG pastures is contributing to improvements in this semi-arid short grass ecosystem.

Keywords

Regenerative ecosystem management

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Today we are going to examine the role arbuscular mycorrhizal (AM) fungi play in providing phosphorus and other benefits to plants and the impact of chemical fertilizers on plant-fungi symbiosis.

Nutrient Cycles

You often hear about the P-cycle (phosphorus) or the N-cycle (nitrogen) and have probably seen all sorts of graphics demonstrating how these nutrients move in the environment. I am going to focus on phosphorus (P) because it is generally the most limiting nutrient for plants. The reality however is that these cycles are interlinked and altering one cycle will impact other things. All plants need three basic macro-nutrients: N, P and K (nitrogen, phosphorus and potassium).

When you buy fertilizer those are the elements you look for. However when you saturate your agriculture system with these nutrients, carbon becomes the limiting factor, not to plants, but to the microbes in the soil that can serve as storage devices for nutrients, keeping them from leaching out of the system. Increases in P also lead to increases in utilization of other nutrients that are necessary for plant growth.

Because P is a highly reactive element it can occur as a constituent of many different kinds of molecules. This makes it very difficult to accurately measure, because testing methods tend to focus on a specific source of P, bound in a specific substrate. The two most commonly used methods for testing P in soil are the Bray and Olsen methods. The Bray method measures acid soluble forms of P bound mostly to aluminum and iron in the soil.

The Olsen test is used for more alkaline soils that typically contain a lot of calcium-bound phosphates. This method frees P from calcium carbonate and iron oxides and then measures the amount of P in solution.

Both the Bray and Olsen P tests target inorganic P (Pi). This is because plants can uptake Pi directly from the soil when it is dissolved in water; hence the effectiveness of phosphate fertilizers. Get enough P into solution at the right time and your plants get bigger. Pi, however, has a fleeting life in soil. It is quickly bound to other things, runs off, or leaches away. It leaves the system and exits the natural cycles that keep the phosphorus where you want it, which is within your field. If you run these tests on soil from natural ecosystems you will discover that there is very little inorganic phosphorus available. Yet these systems produce more plant biomass than our carefully cultivated and heavily fed cropping systems. How is this possible?

P is hoarded in natural ecosystems by living organisms. It's a limiting nutrient so nearly every little bit is scavenged and incorporated into living cells. This system is highly efficient and leaves very little Pi lying around waiting to wash away and get lost from the system. This is the organic side of the equation, and our current testing methods tend to ignore organic phosphorus (Po). Why? Because plants can't uptake Po directly. Organisms in the soil however, can make Po available to plants.

As those billions of microbes in a handful of soil go through their life cycles living and dying, they are providing a constant source of nutrients. Some bacteria mineralize Po, turning it into Pi, which makes it directly available to plants. Arbuscular mycorrhizal fungi are capable of passing both organic and inorganic forms of phosphate to plants. One of the huge differences between our cropland soils and natural ecosystems is the abundance of arbuscular mycorrhizal fungi. When I extract spores from cropland soil, most of what I see is literally black, dead or unhealthy looking spores. The extractions are starkly different than those from natural ecosystems, which are full of plump, brightly colored, healthy looking spores.

We found that 50 ml of soil (slightly less than 1/4 cup) from a remnant of native prairie contained over 1,300 AM fungal spores, while the same amount of cropland soil, from the same area, averaged fewer than 200 AM fungal spores ( Figure1). Furthermore, non-AM fungal spores found in the extractions were the dominant fungi in agricultural soils, while they were a very small percentage of the spores found in native prairie soil ( Figure 2). In agricultural soils there were nearly three times more non-AM fungal spores than there were AM fungal spores, while in native prairie soil AM fungal spore production outnumbered non-AM fungal spores by nearly five to one. This is a very important difference because non-AM fungi may compete with AM fungi for resources, while providing little or no benefit to crops.

What are we doing that is killing them?

Probably, the largest contributor to this situation is the application of inorganic phosphate fertilizers. When we saturate the soil with plant-available phosphate, plants reject their symbiotic partners. Under natural conditions, plants pay these fungi for phosphorus. They exchange sugars, which they can efficiently acquire through photosynthesis, to the AM fungi for harder to get phosphorus. Both organisms are specialized in this regard. When we provide a ton of phosphate, the plant rejects colonization. AM fungi are obligate symbionts. This means they cannot survive and reproduce without a host.

Deny them a host for very long and they soon begin to die. Eventually you have the situation we see in our croplands. But they are not all gone. So who are the survivors?

Those species that are the most highly infective have managed to hold on. With all that fertilizer in the soil, they don't have to work very hard either. We are literally selecting for less beneficial microbes in our soil. But we don't stop there. We also coat our seeds with both fungicides and other pesticides. In fact, it's getting harder and harder to find uncoated seeds. Since most of the microorganisms in soil fall into the "good" category, this sort of indiscriminate poisoning is likely to kill more good things than bad things. If you are combating a specific problem in your field, you treat for it. Prophylactic treatments to protect seeds "just in case" are not only an invitation to resistance, but it kills things that you want living in your soil.

Let's consider the shift in fungal populations from AM fungi to non-AM fungi. Try to imagine the root system of a plant as the streets in a gated community. The street is lined with houses. Each house represents a niche in an ecological community.

A niche is where something can live and flourish. A plant's root system provides a home for a wide range of organisms. Now we apply a pesticide and suddenly a large percentage of those houses are empty. Nature abhors a void.

Something else is now going to move into those empty houses. Will you get a good neighbor or a bad neighbor in each of those houses? Well, that is something of a craps shoot - it just depends on what is nearby. Every time you go through a pesticide cycle, you roll the dice again.

Eventually, something you really don't want is going to move in. This is yet another reason why pesticides should be used sparingly.

How do you beat the odds?

You choose management techniques that favor the most beneficial organisms.

Remember, every organism living in the soil is competing with every other organism for resources. If you throw the balance to favor the beneficial organisms their populations can increase. This means when chemical intervention is necessary the odds are better of getting a good neighbor after you wipe out half the neighborhood. It also means during periods when intervention is not required, what the neighborhood is full and there's little room for something else to move in. You stack the deck in your favor. It is much easier to jump into an empty house than it is to try and evict the current resident - so fill those houses with good neighbors.

We've told you most of what's in the soil falls into the good zone. However some things are better than others for your plants, and you can't manage for everything when there are literally billions of organisms in the soil. You need to manage for the support of the most beneficial group of organisms for plants.

This group is undoubtedly the arbuscular mycorrhizal fungi. Don't get me wrong, there are a host of bacteria and fungi out there that promote plant growth, but nothing out there has shown the diverse benefits and defense capabilities that arbuscular mycorrhizal fungi demonstrate overall. Furthermore, managing for them is unlikely to seriously threaten other beneficial organisms, unlike chemical applications.

So let's talk about these mysterious organisms so few people have ever seen and take a realistic look at what they can do for plants.

Arbuscular Mycorrhizal Fungi

AM fungi are plant symbionts. Symbiotic organisms are generally interdependent upon one another. In the case of AM fungi and plants, it is an obligate relationship for the fungi. The degree of plant dependency upon these organisms varies widely and some plants are unable to live without them, while others are completely non-mycorrhizal and do not act as hosts for AM fungi. It is estimated that 80-90 percent of all flowering plants are mycorrhizal. Most of our crops fall into this group.

The mycorrhizal symbiosis is the oldest symbiosis known to science. Fossil evidence suggests plants first colonized land with the help of AM fungi. That means this intimate relationship has been evolving for over 400 million years. It is a biologically complex relationship that we don't fully understand yet.

It begins when a seed germinates. The young plant produces hormones called strigolactones that attract AM fungi to it. The plant wants to be colonized. In fact, it prepares channels for the AM fungi that run between the cells in its roots. The fungi penetrate plant roots with a filament called a hyphae, and grow through these channels. Along the way it occasionally penetrates individual cells where it produces a structure called an arbuscule. The plant grows a special membrane to surround the arbuscule.

The interface between these structures is where nutrients and minerals are exchanged between plant and AM fungi. Once colonization has occurred, the fungus sends its hyphae into the soil. They are finer than the smallest roots and can penetrate pores in the soil that roots are too large to access, collecting water and nutrients which would otherwise be unavailable to the plant. Because the hyphae grow out from the plant's roots, extending beyond them into the soil, they also extend the total volume of soil available to the plant for nutrient uptake.

Benefits of AM Fungi

First and foremost among the benefits of AM fungi is the uptake of phosphorus. Literally every species of AM fungi known provide this crucial service to plants. Phosphorus and sugar are the currency of this symbiosis. AM fungi are so specialized they can only feed on sugars obtained through their arbuscules.

If you try to grow them in a Petri dish with sugar in the agar, they germinate, go looking for a host and die when they don't find one. They don't start taking up sugar through their hyphae and growing independent of a host plant. This gives the plant a measure of control. It can dissolve arbuscules that are not providing phosphorus and deny the fungi carbohydrates.

However if the plant is not providing sugar, the fungi can stop providing phosphorus, or meter it out based upon how well the plant feeds it. Since both partners have control over metering an essential nutrient to the other partner, it becomes hard to cheat. This also demonstrates how saturating the system with phosphate fertilizer interferes with the relationship.

The plant suddenly no longer needs the AM fungi. And if that were the sum total of what AM fungi did, replacing them with chemical phosphate might be a good idea. However, AM fungi are complex organisms that do much more than just mine and meter phosphate.

Unfortunately for the fungi, the mechanism that regulates how plants respond to them depends on phosphate concentrations in the soil. Heavy applications of chemical phosphate destroy the symbiosis, and a host of other benefits are lost with it. These benefits include: drought tolerance, salt tolerance, improved plant nutrition, defense against pathogens including nematodes, improved soil quality and aggregation, tolerance to herbivory, increased fecundity (more seeds, fruits and flowers), reduced compaction stress, and reduced transplant shock. That is the short list, emphasizing only the benefits of particular interest to farmers and horticulturists.

Defending Your Home

If the plants are not strong and healthy they can't afford the cost of supporting a population of AM fungi. The fungi want a healthy host - if their host dies they may also die. That plant is their home and they actively defend it against invaders. They don't want to live in a derelict home, and they don't want bad neighbors. Imagine the population of AM fungi populating your plant's roots as a complex biological monitoring system. That fungus is making sure the plant has everything it needs.

It senses water stress, it provides more water. It senses a nutrient deficiency and it provides that nutrient. It senses nematodes approaching and it signals the plant to produce defensive chemicals. There is absolutely no product on the market available anywhere that can monitor every plant in your field and attempt to compensate for whatever stress factors the environment throws its way. Yet this is what AM fungi are doing for your plants every day, and we are killing them all off with our current and most common agricultural practices, the most basic of which is how we fertilize our fields. We have pushed so much Pi through our fields over the years that they are now rich in unavailable phosphorus. Remember much of the phosphate fertilizer we apply winds up bound to soil particles. Only something between 5-20 percent of the fertilizer you spent those hard earned dollars on, ever reaches your plants. However that untapped reserve of bound Pi and Po tied up in the microbial community and decomposing litter could be made available to plants through AM fungi.

The Conundrum

It has been demonstrated on average that AM fungi can replace up to 25 percent of the phosphorus we currently utilize without a decline in yield. However this generalization is not crop specific. Many experiments utilizing AM fungi depend on only a few easy to grow species that do well under greenhouse conditions.

Furthermore, these studies are often conducted in low P soils. If you suddenly stopped applying phosphate fertilizers to your fields, with a resident population of AM fungi that are now adapted to being highly infective and "lazy" (because they haven't had to work hard with you providing the phosphorus) you would probably have trouble maintaining your yields. Natural ecosystems don't rely upon 75 percent of the recommended amount of P. Theoretically, we should be able to replace most if not all of our P requirements with appropriate management techniques and restoration of AM fungal communities.

Transition studies in high P soils are needed to determine how long it will take for AM fungal populations to rebound, and to measure how effective those populations are at taking up phosphorus, and maintaining or increasing yields.

By Dr. Wendy Taheri. This article appeared in the September 2012 issue of Acres U.S.A. magazine.

Dr. Wendy Taheri is a mycorrhizal ecologist currently employed as a research microbiologist for the USDA Agricultural Research Service at the North Central Agricultural Research Laboratory in South Dakota. If you have specific questions about arbuscular mycorrhizal fungi, or about these articles, contact her at wendy.taheri@ars.usda.gov.

Read more

Learn more about mycorrhizal fungi and its impact on soil health with this article, from the May 2018 issue of Acres U.S.A. magazine.

Read an interview with fungi guru and microbiologist/professional mycologist Trad Cotter here.

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The Role of AM Fungi in Agricultural Ecosystems

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The land-sparing argument is mostly flawed when it promises to save land for wildlife or for carbon sequestration. Continued intensification of the food system will lead to increased pressure on nature as well as the continued erosion of food culture. A regenerative food system and landscapes with multiple uses are both means and ends by themselves.

Since 1960 the global population has more than doubled, but the total production of crop farming increased three and a half times, measured in calories. Meanwhile, agriculture area increased with less than ten percent and grasslands even less (grasslands are now shrinking quite rapidly according to FAOSTAT). The increase of production has been driven by irrigation, multiple cropping and the green revolution technology packet of artificial fertilizers, pesticides and new varieties. By far, the most spectacular development in farming is not yield per area unit however, but the increased productivity of farm labor. Instead of catering for the need of the family and a smaller surplus extracted by lords of various sorts, a farmer or farm worker today often produce food for hundreds of people. If we look at staple foods in the most mechanized farm regions, one worker may actually "feed" thousand person.

Through this extraordinary increase in land and labor productivity, cost of grains, oilseeds and soybeans have plummeted while production has quadrupled. The net effect is a great increase in food energy available to humans. In addition, the rapidly increasing use of crops as animal feed and biofuel feed stock have swallowed an even larger share. Meanwhile, the continued intensification of farming is the root cause of the huge environmental impact from the food system, the destruction of habitats, the broken cycles of nutrients such as nitrogen and phosphorus and the huge effect on the climate.

Some (such as the Breakthrough Institute) are using the land use efficiency argument to promote a continuation of the increased intensification of farming. By doing so we could spare land to "wild nature". Lately, some researcher concluded that
Undoubtedly, humans are outcrowding other species at an alarming pace. Superficially, the land-sparing argument has some appeal. However, there is very limited evidence, if any, that intensification of land use actually saves land, neither locally nor globally. Some marginal agriculture lands have been converted to conservation purpose (such as in the US
In addition, humans demand land for many other things than farming and farm land will often be used for highways, electric grid, hydro dams, lawns, golf courses, malls, urban sprawl, logistic centers, mines or oil wells. So even if our modern civilization limits its use of land for agricultural purposes, the whole system of which it is part is constant putting a bigger share of land into our direct use. Conservation Reserve Program), but as long as land is productive enough it will be used for commercial purposes, be it for animal feed, biofuel or industrial feedstock or forest monocultures (a common fate of abandoned agriculture land).
To allocate land uniquely for carbon sequestration means that we will just increase our demand on the rest of nature, and give us yet another excuse not to tackle the root cause of our predicament, the burning of fossil fuels and the constantly increasing consumption of nature resources, living or dead. Maximized carbon sequestration within the industrial paradigm will most likely mean that even more ecosystems will be devastated and reduced to productive factors. organic farming was much worse for the climate than conventional. Again, land use was the key argument. In his view all land has an alternative use for natural carbon sequestration, which means that land that has a low yield will be very damaging for the climate.
Food and farming are examples of Jevon's paradox; increased efficiency leads to more consumption, not less. It has provided the masses with more calories and a huge increase in consumption of luxury foods such as meat, exotic fruits and soft vegetables. Global chicken consumption increased 13 times between 1960 and 2017, and chicken is now the most consumed meat in the world. Access to cheap staple feeds and the successful industrialization of chicken breeding combined with its short life span - perfect for quarterly capitalism - were key factors for success. The author surveyed the cost of various protein sources in the Swedish retailers and came to the conclusion that the only source of protein that could compete with chicken in price per gram of protein were dried beans. Cheap food has also caused increasing waste and waists.

The intensification is part and parcel of a globalized and homogenized food system and the transformation of whole landscapes into uniform production of soybeans, wheat, asparagus, corn or palmoil. It is the cause of a tremendous loss of local food culture, meaning, biodiversity and nutrient cycling. It also has devastating effects on rural landscapes which no longer are places to live, love and die for and in, but just commodity deserts.

Of course, if we really want to be "efficient", we can easily feed 10 billion people on a diet of monoculture soy, palm oil, sugar, wheat and rice, on the existing agriculture land. To make the whole chain even more efficient we mill them into a powder or process into a liquid which we distribute to the households according to subscription ( it is already happening you know!). In this way we can save a lot by reducing peoples' cooking, their expensive private kitchens and household appliances. Perhaps solar powered drones can deliver? There are alternatives of course. Instead of looking into one commodity or one "ecosystem service" at a time we need to develop the food and agriculture system so that we combine the production of good and nutritious food with carbon sequestration, soil fertility, bio-diversity, human relations and culture in the same regenerative landscape. Such a landscape can host vibrant rural communities instead of being a supplier of raw materials to the cities or a dump. A re-localized food system will become both the means and the end in such a bright future.

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A regenerative food system is both a means and an end

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The land-sparing argument is mostly flawed when it promises to save land for wildlife or for carbon sequestration. Continued intensification of the food system will lead to increased pressure on nature as well as the continued erosion of food culture. A regenerative food system and landscapes with multiple uses are both means and ends by themselves.

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Holistic Regeneration of our Lands: a Producer's Perspective

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Holistic Regeneration of our Lands: a Producer's Perspective

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Gabe Brown and his Keys To Building a Healthy Soil, filmed on Nov. 18th 2014 at the Idaho Center for Sustainable Agriculture's annual symposium

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Gabe Brown: Keys To Building a Healthy Soil

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Soil as Carbon Storehouse: New Weapon in Climate Fight?

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Soil as Carbon Storehouse: New Weapon in Climate Fight?

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The degradation of soils from unsustainable agriculture and other development has released billions of tons of carbon into the atmosphere. But new research shows how effective land restoration could play a major role in sequestering CO2 and slowing climate change

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Soil as Carbon Storehouse: New Weapon in Climate Fight?

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The degradation of soils from unsustainable agriculture and other development has released billions of tons of carbon into the atmosphere. But new research shows how effective land restoration could play a major role in sequestering CO2 and slowing climate change.

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New study charts the entire network of soil microbes for the first time.

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New study charts the entire network of soil microbes for the first time.

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'Relationships' in the soil become stronger during the process of nature restoration. Although all major groups of soil life are already present in former agricultural soils, they are not really 'connected' at first. These connections need time to (literally) grow, and fungi are the star performers here. A European research team led by the Netherlands Institute of Ecology (NIOO-KNAW) has shown the complete network of soil life for the first time. This Wednesday, the results of the extensive study are published in Nature Communications.

Earthworms, fungi, nematodes, mites, springtails, bacteria: it's very busy underground! All soil life together forms one giant society. Under natural circumstances, that is. A large European research team discovered that when you try to restore nature on grasslands formerly used as agricultural fields, there is something missing. Lead author Elly Morriën from the Netherlands Institute of Ecology explains: "All the overarching, known groups of soil organisms are present from the start, but the links between them are missing. Because they don't 'socialise', the community isn't ready to support a diverse plant community yet."

When nature restoration progresses, you'll see new species appearing. But those major groups of soil life remain the same and their links grow stronger. "Just like the development of human communities", says Morriën. "People start to take care of each other. In the soil, you can see that organisms use each other's by-products as food." In this way, nature can store and use nutrients such as carbon far more efficiently.

Fungi as drivers

"Fungi turn out to play a very important role in nature restoration, appearing to drive the development of new networks in the soil." In agricultural soils, the thready fungal hyphae are severely reduced by ploughing for example, and therefore the undamaged soil bacteria have an advantage and rule here. The researchers studied a series of former agricultural fields that had changed use 6 to 30 years previously. With time, there is a strong increase in the role of fungi.

Earlier, researchers did look at fungal biomass, but that won't show you the whole story. "After six years, about 10% is fungal biomass and 90% is from bacteria. Still, we discovered that already at that stage, about half the carbon - being the food - goes to the fungi. After 30 years, that share has risen to three quarters of the carbon stored. Fungi really are the drivers in natural soils."

From steppe to savannah

The international team compared grassland soils from all over Europe. In the Netherlands, research fields on the Veluwe were included. "Worldwide, you find many types of grassland ecosystems. Think of steppes, tundras, prairies and savannahs."

A unique opportunity, Morriën calls it. Because of the European consortium EcoFINDERS, data for many species of soil organisms from many different locations could be studied. By labelling the carbon atoms, the research team was able to follow the food flow throughout the whole soil ecosystem. In this way, they could link the organisms to their corresponding functions in the community. Morriën: "This linking has never been done at such a large scale before. Now we can finally get an advanced view of a complete and intricate soil community." And who knows: "We might be able to help the fungi restore the missing links, which will speed up nature restoration considerably."

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With more than 300 staff members and students, NIOO is one of the largest research institutes of the Royal Netherlands Academy of Arts and Sciences (KNAW). The institute specialises in water and land ecology. As of 2011, the institute is located in an innovative and sustainable research building in Wageningen, the Netherlands. NIOO has an impressive research history that stretches back 60 years and spans the entire country and beyond.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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'Relationships' in the soil become stronger during nature restoration. Although all major groups of soil life are already present in former agricultural soils, they are not really 'connected'. These connections need time to (literally) grow, and fungi are the star performers.

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The full documentary about the soil food web. Microbes galore!

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Study of childhood exposure to farm microbes and raw milk with regard to later development of allergies, asthma etc.

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Exposure to farming in early life and development of asthma and allergy: a cross-sectional survey. - PubMed - NCBI

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December 20, 2018 by Lisa Zyga, Phys.org

TSP solutions obtained by the amoeba-based computing system for 4, 5, 6, 7, and 8 cities. Credit: Zhu et al. ©2018 Royal Society Open Science

Researchers have demonstrated that an amoeba-a single-celled organism consisting mostly of gelatinous protoplasm-has unique computing abilities that may one day offer a competitive alternative to the methods used by conventional computers.

The researchers, led by Masashi Aono at Keio University, assigned an amoeba to solve the Traveling Salesman Problem (TSP). The TSP is an optimization problem in which the goal is to find the shortest route between several cities, so that each city is visited exactly once, and the start and end points are the same.

The problem is NP-hard, meaning that as the number of cities increases, the time needed for a computer to solve it grows exponentially. The complexity is due to the large number of possible solutions. For example, for four cities, there are only three possible routes. But for eight cities, the number of possible routes increases to 2520.

In the new study, the researchers found that an amoeba can find reasonable (nearly optimal) solutions to the TSP in an amount of time that grows only linearly as the number of cities increases from four to eight. Although conventional computers can also find approximate solutions in linear time, the amoeba's approach is completely different than traditional algorithms. As the scientists explain, the amoeba explores the solution space by continuously redistributing the gel in its amorphous body at a constant rate, as well as by processing optical feedback in parallel instead of serially.

Although a conventional computer can still solve the TSP much faster than an amoeba, especially for small problem sizes, the new results are intriguing and may lead to the development of novel analogue computers that derive approximate solutions of computationally complex problems of much larger sizes in linear time.

How it works

The particular type of amoeba that the scientists used was a plasmodium or "true slime mold," which weighs about 12 mg and consumes oat flakes. This amoeba continually deforms its amorphous body by repeatedly supplying and withdrawing gel at a velocity of about 1 mm/second to create pseudopod-like appendages.

In their experiments, the researchers placed the amoeba in the center of a stellate chip, which is a round plate with 64 narrow channels projecting outwards, and then placed the chip on top of an agar plate. The amoeba is confined within the chip, but can still move into the 64 channels.

In order to maximize its nutrient absorption, the amoeba tries to expand inside the chip to come in contact with as much agar as possible. However, the amoeba does not like light. Since each channel can be selectively illuminated by light, it's possible to force the amoeba to retreat from the illuminated channels.

In order to model the TSP, each channel in the stellate chip represents an ordered city in the salesman's route. For example, in the case with four cities labeled A-D, if the amoeba occupies channels A4, B2, C1, and D3, then the corresponding solution to the TSP is C, B, D, A, C.

In order to guide the amoeba toward an optimal or nearly optimal solution, the key lies in controlling the light. To do this, the researchers use a neural network model in which every six seconds the system updates which channels are illuminated. The model incorporates information about the distance between each pair of cities, as well as feedback from the amoeba's current position in the channels.

The model ensures that the amoeba finds a valid solution to the TSP in a few ways. For example, once the amoeba has occupied a certain fraction of a particular channel, say A3, then channels A1, A2, and all other "A" channels are illuminated in order to prohibit city A from being visited twice. Also, B3, C3, D3, and all other "3" channels are illuminated to prohibit simultaneous visits to multiple cities.

The model accounts for the distances between cities by making it easier to illuminate channels that represent cities with longer distances than with shorter distances. For instance, say the amoeba occupies channel B2, and has begun to encroach into channels C3 and D3 in equal amounts, and the distance between cities B and C is 100 while the distance between cities B and D is 50. The longer distance between B and C eventually causes the system to illuminate channel C3, causing the amoeba to retreat from that channel but allowing it to continue moving into D3.

Overall, modeling the TSP with an amoeba harnesses the amoeba's natural tendency to seek out a stable equilibrium. As channels representing shorter routes are less likely to be illuminated, the amoeba may spread out in those channels and continue to explore other non-illuminated channels in order to maximize its surface area on the agar plate.

The researchers also developed a computer simulation called AmoebaTSP that mimics some of the main features of how the amoeba addresses the problem, including the continuous movement of gel as it is supplied at a constant rate and withdrawn from various channels.

"In our stellate chip for solving the n- city TSP, the total area of the body of the amoeba becomes n when the amoeba finally finds an approximate solution," Aono told Phys.org. "There seems to be a 'law' that the amoeba supplies its gelatinous resource to expand in the non-illuminated channels at a constant rate, say, x. This law would be kept even when some resources bounce back from illuminated channels. Then the time required to expand the body area n to represent the solution becomes n/ x. This mechanism would be the origin of the linear time, and it was reproduced by our computer simulation model.

"But still, the mechanism by which how the amoeba maintains the quality of the approximate solution, that is, the short route length, remains a mystery. It seems that spatially and temporally correlated movements of the branched parts of the amoeba located at distant channels are the key. Each of these branches is oscillating its volume with some temporal 'memory' on illuminated experiences. Groups of the branches perform synchronization and desynchronization for sharing information even though they are spatially distant."

In the future, the researchers plan to further improve the amoeba's computing abilities.

"We will investigate further how these complex spatiotemporal oscillatory dynamics enhance the computational performance in finding higher-quality solutions in shorter time," said coauthor Song-Ju Kim at Keio University. "If it could be clarified, the knowledge will contribute to create novel analogue computers that exploit the spatiotemporal dynamics of electric current in its circuit.

"Of course, running some other algorithms on traditional digital computers for linear time, we can derive approximate solutions to TSP. On the other hand, when running our simulation models (AmoebaTSP or its developed versions) on the traditional computers as we did in this study, the analogue and parallel spatiotemporal dynamics require nonlinear time for simulating them as digital and serial processes. So we are trying to obtain much higher-quality solutions than those derived from the traditional ones by running our models on the analogue computers for linear time or shorter."

The researchers also expect that, by fabricating a larger chip, the amoeba will be able to solve TSP problems with hundreds of cities, although this would require tens of thousands of channels.

More information: Liping Zhu, Song-Ju Kim, Masahiko Hara, and Masashi Aono. "Remarkable problem-solving ability of unicellular amoeboid organism and its mechanism." Royal Society Open Science. royalsocietypublishing.org/doi/10.1098/rsos.180396

© 2018 Science X Network

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Amoeba finds approximate solutions to NP-hard problem in linear time

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December 20, 2018 by Lisa Zyga, Phys.org Researchers have demonstrated that an amoeba-a single-celled organism consisting mostly of gelatinous protoplasm-has unique computing abilities that may one day offer a competitive alternative to the methods used by conventional computers. The researchers, led by Masashi Aono at Keio University, assigned an amoeba to solve the Traveling Salesman Problem (TSP).

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As big as the Vatican City and dating back to the time of the Battle of Thermopylae -- it could only be a fungal network!

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As big as the Vatican City and dating back to the time of the Battle of Thermopylae -- it could only be a fungal network!

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Generally speaking, the idea of a spreading fungus-they make a cream for that-is a pretty revolting concept. But a fungus that spreads across 90 acres? That's almost inspiring.

That's the estimate for the size of the famed Armillaria gallica fungus in Crystal Falls,* Michigan, deemed the world's single largest organism when it was discovered in the late 1980s. At that time, researchers believed that the fungus-which is mostly composed of an underground network of tendrils and emerges from the ground in clumps of honey mushrooms-weighed 110 tons and was about 1,500 years old. The same team of Canadian and American researchers recently revisited the fungus to conduct genetic tests, only to find that their initial assessment had been way, way off. In a new paper under review and posted to , the authors posit that the titanic organism weighs four times as much and is about 1,000 years older. For reference, that makes this single individual more massive than three large blue whales, and just a little smaller than Vatican City.

To come to the revised estimate, the researchers studied the genetic makeup of 245 samples and studied the growth rates of the hyphae filaments that help the fungus spread. Genetic sequencing of 15 samples also revealed that just 163 of its genome's 100 million bases have changed over all that time. That's remarkably steady from a genetic-mutation point of view. Maybe that shouldn't be surprising for something that's been around since the Battle of Thermopylae.

The new measurements may be exciting, but it's worth remembering that honey mushrooms are parasitic, and can take out surrounding trees and plants. And this individual is still overshadowed by its cousin, an Armillaria ostoyae fungus in Oregon's Blue Mountains. Discovered in 1998, the Oregonian fungus covers 2,200 acres and could be thousands of years older.
Correction: An earlier version of this story misidentified the town of Crystal Falls as Crystal Creek.

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The Original 'Humungous Fungus' Is Even Bigger and Older Than We Thought

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Generally speaking, the idea of a spreading fungus-they make a cream for that-is a pretty revolting concept. But a fungus that spreads across 90 acres? That's almost inspiring. That's the estimate for the size of the famed Armillaria gallica fungus in Crystal Falls,* Michigan, deemed the world's single largest organism when it was discovered in the late 1980s.

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And international and interdisciplinary team of researchers discover microbial life deep below the Earth's surface living in a different timeframe entirely, with metabolisms so slow some of them might be a thousand years old.

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Scientists identify vast underground ecosystem containing billions of micro-organisms

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Global team of scientists find ecosystem below earth that is twice the size of world's oceans

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Soil microbiota and immuno-deficiency treatment.

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Soil microbiota and immuno-deficiency treatment.

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Nature-derived microbiota exposure as a novel immunomodulatory approach | Future Microbiology

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This work is supported by the Finnish Funding Agency for Innovation TEKES under the Large Strategic Opening project 'ADELE' (grant number 40333/14). A patent application 'Immunomodulatory compositions' related to methods for modifying human microbiota has been filed on behalf of A Sinkkonen, H Hyöty, O Laitinen, M Grönroos, S Oikarinen and N Nurminen.

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Study/Literature Review of the links between the gut microbiota and environmental factors such as soil.  

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Study/Literature Review of the links between the gut microbiota and environmental factors such as soil.  

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The study of environmental influences on gut microbiota structure and function is especially pertinent because the human living environment is becoming rapidly urbanized. Such drastic changes to the human environment may interrupt the healthy development of the microbiota and increase risk of inflammatory diseases.

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Abstract

Global comparisons reveal a decrease in gut microbiota diversity attributed to Western diets, lifestyle practices such as caesarian section, antibiotic use and formula-feeding of infants, and sanitation of the living environment. While gut microbial diversity is decreasing, the prevalence of chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma is on the rise in Westernized societies. Since the immune system development is influenced by microbial components, early microbial colonization may be a key factor in determining disease susceptibility patterns later in life. Evidence indicates that the gut microbiota is vertically transmitted from the mother and this affects offspring immunity. However, the role of the external environment in gut microbiome and immune development is poorly understood. Studies show that growing up in microbe-rich environments, such as traditional farms, can have protective health effects on children. These health-effects may be ablated due to changes in the human lifestyle, diet, living environment and environmental biodiversity as a result of urbanization. Importantly, if early-life exposure to environmental microbes increases gut microbiota diversity by influencing patterns of gut microbial assembly, then soil biodiversity loss due to land-use changes such as urbanization could be a public health threat. Here, we summarize key questions in environmental health research and discuss some of the challenges that have hindered progress toward a better understanding of the role of the environment on gut microbiome development.

Keywords: gut microbiome, immunity, environment, human health, immune tolerance, microbial colonization, biodiversity, microbe-rich environments

Introduction

Human health is closely linked to the diverse set of microorganisms in the intestine collectively known as the gut microbiota (Hooper and Gordon, 2001). This population of microorganisms and their genetic potential, or the gut microbiome, has been linked to human metabolism, intestinal homeostasis, immune development (Lynch and Pedersen, 2016), and brain processes and behavior (Mayer et al., 2015). A stable and diverse gut microbiota, optimal for maintaining health, produces metabolites that fuel physiological and metabolic processes. The gut microbiota also tunes local and systemic immune responses to confer protective immunity against pathogens while simultaneously maintaining immune tolerance toward commensals (Cerf-Bensussan and Gaboriau-Routhiau, 2010). Other functions of the gut microbiota include fermentation of indigestible dietary components (Flint et al., 2012), breakdown of environmental pollutants and pharmaceuticals (Claus et al., 2017), and pathogen competitive exclusion (Kamada et al., 2013). Alterations to the gut microbiota, known as dysbiosis, can disrupt these essential health-promoting services and are associated with gastrointestinal, cardiovascular, autoimmune and metabolic diseases (Carding et al., 2015). Therefore, the gut microbiome is a microbial ecosystem that operates much like a microbial organ that functions to promote health and prevent disease.

We are only beginning to understand the ecological processes that lead to the growth and development of a stable and diverse gut microbiome that promotes host-health. The gut microbiota is a diverse ecosystem comprised of bacteria, archaea, fungi and viruses including a diverse bacteriophage community (Manrique et al., 2016). Bacteria dominate the microbiota in abundance and diversity, with commensal members from seven phyla (Firmicutes, Bacteriodetes, Actinobacteria, Fusobacteria, Proteobacteria, Verrucomicrobia, and Cyanobacteria), the majority of which are uncultivated and novel phylotypes (Eckburg et al., 2005). Members of the microbiota can be permanent "residents," transmitted through close contact between individuals, or transient "hitchhikers" from ingested food, water and various components of the environment (Ley et al., 2006; Harmsen and de Goffau, 2016). These transmission routes are important for establishing and maintaining microbial diversity in the gut (Browne et al., 2017). The mechanism of transmission can determine the pattern of colonization which shapes the gut microbial community of the host, but these patterns of transmission are poorly understood. Colonization that leads to the establishment of a stable and diverse adult gut microbiome lays the foundation for a homeostatic host-microbial relationship maintained by balanced immune responses. Colonizing gut microbes provide signals known as microbe-associated molecular patterns (MAMPs) that affect the maturation of the immune system and gut associated lymphoid tissue (GALT) (Wopereis et al., 2014). The development of the GALT is associated with bacterial activation of Toll-like receptors (TLRs) and downstream signaling pathways involved in maintaining host-microbial homeostasis, regulated through cytokines and chemokines (Hooper et al., 2015). Germ free animals have defects in the development of GALT, as well as cellular defects such as decrease in the number of lymphocytes, and molecular immune deficiencies such as reduced antibody production (Round and Mazmanian, 2009; Torrazza and Neu, 2011). Thus, colonization of the gut by microbes is not only important for the development of gut tissue, but also for the establishment of immune tolerance.

Gut bacterial community assembly begins pre-birth (Blaser and Dominguez-Bello, 2016), but rapid colonization takes place at birth and continues for the first 3 years of life (Lozupone et al., 2013). Two key factors that could influence the successful transmission of beneficial gut microbes to the infant are the mother and the external environment. Various studies that have sampled infant fecal microbiota have revealed that early gut microbial settlers that colonize the gut are derived from maternal vaginal, fecal, milk, mouth and skin microbiota during both gestation and birth through vertical transmission, and from the environment through horizontal transmission (Inoue and Ushida, 2003). Therefore, the infant gut microbiome is transmitted from a gut microbial species pool, comprised of gut symbionts from both the mother and the environment (Figure ). The effect of the environment on the diversity and richness of the human gut bacterial species pool and gut microbiota transmission has yet to be explored. If the transmission of gut microbes is primarily parent-child, then environmental factors such as standards of hygiene, contamination of food and water by fecal microbes, delivery mode and hospitalization after birth can alter transmission mechanisms. On the other hand, if colonization patterns and gut microbiota diversity is linked to transmission of microbes from the external environment, then additional factors such as place of birth, geography, urban vs. rural living environment may also alter colonization of the gut microbiota affecting the human health. In this review, we discuss what is known about the role of environmental factors on the gut microbiota composition, diversity and assembly, identify major research challenges for research aiming to elucidate gut microbiota transmission patterns, and make suggestions for future studies that integrate the gut microbiome with environmental health research.

Influence of environment on variations in gut microbiota diversity

The composition and diversity of gut microbiota varies between individuals. Under germ free conditions, gut microbiota transplantation experiments between model organisms such as zebrafish and mice have shown that gut microbiota composition is host-specific (Rawls et al., 2006). In humans, many other factors contribute to variation, such as diet, host genetics and metabolism, familial relationships, culture (Dominguez-Bello and Blaser, 2011), and demographics (Lozupone et al., 2013). According to global surveys of fecal microbiota from healthy populations, variation between individuals in richness of gut microbiota is largely explained by age, ethnicity (Huttenhower et al., 2012), geography (Torrazza and Neu, 2011), medication exposure, blood parameters, bowel, diet, health, anthropometrics and lifestyle (Falony et al., 2016). Of particular interest is the observation that healthy adults from rural societies such as Papua New Guinea (Martínez et al., 2015), Amerindia and Malawi (Clemente et al., 2015), and hunter-gatherers from Tanzania and Amazon (Schnorr et al., 2014) have higher gut bacterial species richness compared to urban populations in Italy and US. Similarly, children (between ages 1 to 5) from rural communities have more diverse gut microbiotas compared to children from Western populations (De Filippo et al., 2010). These host-specific differences in gut microbiota may arise from distinct selective pressures within the host gut habitat including genetics and diet but also may be due, at least in part, to their unique environments.

Role of the environment on gut community assembly and immunoregulation

The role of the environment in the assembly of the gut microbiota has yet to be elucidated, although there is good reason to believe they are linked. Urbanization leads to changes in living conditions such as increased sanitation and antibiotic use (Popkin, 1999), separation from the outdoors (Turner et al., 2004), and poor land management practices that may reduce soil microbial biodiversity (Wall et al., 2015). Accordingly, studies show that infants born via caesarian section have altered colonization patterns and lower total gut microbiota diversity (Biasucci et al., 2010), and individuals who grow up in city environments have a less diverse gut microbiome (Sjögren et al., 2009). Further, urbanites are more prone to inflammatory disorders like diabetes and multiple sclerosis (Kay, 2000) as well as allergic diseases such as asthma (Rook, 2012) during both infancy and adulthood (Garn and Renz, 2007). Although host genetics may in large part determine the composition of the adult gut microbiome, it has been shown that alien microbes from diverse habitats like soil can colonize the germ-free gut (Seedorf et al., 2014). Therefore, horizontal transmission of environmental microbes may be contributing commensal microbes to the gut ecosystem, altering patterns of colonization to increase variation in gut microbiota diversity.

Early-life exposure to microbe-rich environments may be beneficial for human health by increasing the gut bacterial species pool. The "microbial old friends" hypothesis, posits microbe-rich environments are a source of beneficial microbes that promote gut microbiota diversity (Zhou et al., 2015) reducing inflammatory disease risk (Rook et al., 2013). Indeed, growing up in microbe-rich environments, like traditional farms, result in healthier children (Mosca et al., 2016). Therefore, the prevalence of inflammatory disorders may be higher in modern cities because of reduced exposure to beneficial microbes from the environment, such as microbes from house dust or zoonotic microbes from animals. Indeed, exposure to household pets has been shown to alter the infant gut microbiota and reduce allergic disease (Tun et al., 2017). Reduced exposure to pathogenic microorganisms, largely as a result of modern hygienic practices, can also result in defective immunoregulation (Garn and Renz, 2007). The "hygiene hypothesis" makes the argument that infectious stressors are particularly important during early childhood (Wills-karp et al., 2001; Garn and Renz, 2007) and is supported by epidemiological studies showing rural children have reduced asthma (Ege et al., 2011), hay fever (Strachan, 1989) and ectopic eczema (Isolauri et al., 2000). Such allergic diseases are chronic inflammatory disorders caused by a decrease in immune tolerance (Garn and Renz, 2007). Decrease in tolerance is associated with a decrease in Treg cells expressing the transcription factor forkhead box P3 (FOXP3+ Treg cells) (Simon et al., 2015). FOXP3+ Treg cells produce anti-inflammatory cytokines such as interleukin 10 (IL-10) and transforming growth factor-β (TGF-β) which help to suppress exacerbating inflammatory responses and balance CD4+ helper T (Th) Th1 and Th2 cells. In allergic diseases, cytokine stimulation of naïve T cells from IL-4, IL-5 and IL-13 tilt the balance of Th cells toward the Th2 phenotype (Kay, 2000). In infants, there may be a normal Th2 bias observed in both mice (1-3 weeks old) and humans (0-2 years old) (Marchant and Goldman, 2005; Dowling and Levy, 2014). As the infant ages, the Th2 skew is balanced by Th1 responses and induced memory responses through mucosal-associated invariant T cells and interleukin-8 (CXCL8) secreting naïve T cells (Simon et al., 2015). In contrast, allergic infants have a persistent Th2 phenotype, resulting in long term Th2-skewed immunity (Barrios et al., 1996). Therefore, early life exposure to a broad range of immunoregulation-inducing commensal and pathogenic environmental microorganisms can provide a Th1 stimulus, conferring protection against immune disorders.

What is it about urban environments that reduces healthy gut microbiome functioning? Both "old friends" and the "hygiene hypothesis," are contingent on microbial biodiversity. Urban development leading to the loss of local habitats and biodiversity may be detrimental to human health by depleting or otherwise altering the reservoirs of environmental microbes including bacteria, fungi and viruses that may play a role in gut microbiota-mediated immune health. The "biodiversity hypothesis" posits that clinical diseases, caused by poor microbiome, immune dysfunction and inflammation, are linked to biodiversity loss (Anderson et al., 2013). Biodiversity loss due to industrialization is associated with adverse health effects, including inflammatory diseases (Haahtela et al., 2013). Environmental biodiversity and immune function have been linked in epidemiological studies, which show individuals living in built environments have lower diversity of microbiota and higher allergic disposition (Wardle et al., 2004). The World Allergy Organization has proposed that loss of biodiversity is linked to loss of microbial diversity, resulting in microbial deprivation and ultimately, inflammatory disorders (Haahtela et al., 2013). This proposal extends the "old friends" and hygiene hypothesis to include environmental biodiversity as being important in the development of the immune system and gut microbiome (von Hertzen et al., 2011). A biodiverse environment that is microbe-rich may promote the development of healthy gut microbiota and lower disease risk.

Extending the "biodiversity hypothesis" to include soil biodiversity has the potential to provide more insight into the role of the environment and gut mediated immune health. Soils contain a dynamic reservoir of biodiversity (Torsvik and Øvreås, 2002) and this diversity is essential for maintaining biogeochemical processes and ecosystem functioning (Wardle et al., 2004). In this way, soil biodiversity provides benefits to human health indirectly through suppression of soil-borne pathogens, provision of clean air, water and food, and exposure to immunoregulation-inducing soil microorganisms (Wall et al., 2015). Although unknown, we ask if there is a direct link between soil microbial diversity and human health? Certainly, soil microbial diversity varies in taxonomic composition between biomes (Fierer et al., 2012b), physical and chemical gradients (Fierer et al., 2012a; Lauber et al., 2013), and anthropogenic activity (Ramirez et al., 2010). Whether it is species richness that is important, or the composition of key taxa has not been determined. There is some indirect evidence that soil biodiversity and human microbiota are interrelated (Hanski et al., 2012), to provide "natural immunity" (von Hertzen et al., 2011). Further, exposure to soil microbes has been experimentally shown to increase gut microbiota diversity (Zhou et al., 2015). There is also some evidence to suggest that exposure to possible soil pathogens could contribute to immune tolerance (Wall et al., 2015). However, little is known about the impact of soil exposure on gut microbiota transmission and colonization patterns in humans.

Exploration of the connections between soil microbial communities and gut microbial communities

For soil biodiversity to be relevant to human health requires microbes from local soil to be transmitted horizontally to humans and then established in the gut. If so, then people exposed to similar soil microbial communities should have more similar gut communities. We analyzed soil and gut studies from publicly available datasets on Qiita ( http://qiita.microbio.me), to investigate the link between soil and gut microbial diversity, in terms of richness, diversity and species identity. We combined OTU (operational taxonomic unit) tables from 7 gut studies ( n = 2,497 human fecal samples) and 4 soil studies ( n = 1,123 soil samples) that used 16 s amplicon sequencing to study bacterial communities (Figures ). The human fecal samples were collected from 14 countries, although the vast majority of samples were from USA ( n = 1,062), Malawi ( n = 1,042) and Venezuela ( n = 99). These samples were collected from a range of ages (0-77 years). A small proportion of adult humans were diagnosed with obesity, atherosclerosis ( n = 52). Soil studies were from 17 different locations and most samples were from North America ( n = 1062). Soil samples ranged from wetland to garden soil from tundra to tropical biomes.

US studies dominate

Although our dataset was diverse, we lacked sufficient data to explore global variation in soil-gut microbiota. At the time of analysis, there were 244 studies on Qiita of which we picked four large-scale soil and seven gut studies to pool into a combined dataset (Figure ). Most studies on soil and human bacterial communities were located in the US. Future efforts should survey populations from different countries and physiographic regions to provide global geographical gut microbial datasets.

There is little overlap between soil and gut microbes at lower taxonomic levels

We performed downstream analysis to compare the relative proportion of bacterial phyla in human gut and soil samples (Figure ). We visualized the OTUs in human gut and soil samples using taxa summary plots. Samples were grouped and averaged by sample type (gut or soil) and taxonomic composition was summarized on multiple taxonomic levels (e.g., phylum, order, etc.) (Navas-Molina et al., 2013). We found that human fecal samples were dominated by Bacteriodetes and Firmicutes phyla, whereas soil samples were dominated by Proteobacteria and Verrucomicrobia. These differences in taxonomic composition between soil and gut samples were also consistent at lower taxonomic levels (see Figure table).

Study effects account for variation

Differences in DNA extraction protocol, primer selection, sequencing platform and sequence analysis pipelines introduce bias to datasets known as study effects. To evaluate the influence of study effects, we pooled all human gut studies from a single investigator (Rob Knight, University of California), and excluded all studies outside the US resulting in four studies. We tested for study effects ( n = 935) by considering research group (Figure ) and primer subfragment (Figure ). We found that primer target region or research group contributed to strong study-based clustering, similar to clustering patterns found in other meta-analyses of the human microbiota (Lozupone et al., 2013). Our results indicate that soil and gut bacterial communities have few overlapping taxa, but because most gut and soil studies survey North American cohorts, we were not able to determine whether local soil microbial communities influence the composition of gut microbial communities of individuals from different geographical locations.

Challenges for studying environment-gut microbiota interactions in health and disease

Global surveys on the relationships between environment, gut microbiota and inflammation are yet to be explored, such as how traditional diets consumed in a region may contribute to the gut microbial community or how local soil influences diversity of the gut microbiota of the population through horizontal transmission. The mechanism of horizontal transmission of environmental microbes, whether inhalation, ingestion or cutaneous, also remains to be elucidated. The rate of urbanization and soil degradation may be related to changes in the composition of the gut microbiota, such as an increase abundance of bacterial indicators of dysbiosis such as Proteobacteria (Shin et al., 2015). We cannot begin to understand the link between soil microbial diversity and gut microbial assembly until studies adopt standardized collection, extraction and sample preparation procedures with complete and transparent metadata reporting and appropriate analysis platforms. Some additional challenges for study design and analysis of environment-gut studies are outlined below.

Challenge 1: quantifying microbe-richness and diversity of the environment

To link gut microbiota to environmental microbial diversity, it will be important for future studies to develop standardized methods that reliably reflect microbial biodiversity in the environment. In addition to microbial diversity of the direct environment (home, air, soil, water, etc.), biodiversity of the surrounding environment should be estimated by recording information about the landscape, including land use type and predominant vegetation structure, abiotic factors such as climatic factors and information about the biodiversity of resident communities (i.e., plants, animals, etc.; as described by Hanski et al., 2012). Given the logistical challenges associated with such efforts, we recommend choosing sampling locations strategically in relation to desired environmental (Metzger et al., 2013) and other characteristics. This approach will help elucidate associations between microbial exposure, environmental biodiversity, and gut microbiota assembly.

Together, these parameters will help elucidate direct effects of microbial exposure and environmental biodiversity on gut microbiota assembly.

Challenge 2: collection, storage and analysis of host-microbiome-environment interactions

Developing analysis tools and platforms that are able to store and analyze large datasets will be critical to link gut microbiota assembly to external factors. Currently, limitations in sample collection, processing and storage (Gorzelak et al., 2015), as well as systems of reporting, study design, sample size, variation in demographics and statistical approaches prevent cross study comparisons (Hunter, 2005). The two publicly-available platforms for microbiome-environment studies are Qiita and SourceTracker (Knights et al., 2011), yet these have had little uptake by the community as a whole. To fully understand demographic factors in gut microbial assembly, this will need to be a globally coordinated effort. The utility of the NIH Human Microbiome Project ( http://www.hmpdacc.org/) could be enhanced by including protocols and repositories for environmental biodiversity (microbial and otherwise). Applications such as SourceTracker could then be easily used to investigate source-sink dynamics of the microbiota, to investigate microbiome-exposure interactions on the ecology of the microbiome. Once the challenge of data collection, handling and analysis are met, microbiome changes can be used as biomarkers to indicate individual health and disease outcome (Segata et al., 2011).

Conclusion

The study of environmental influences on gut microbiota structure and function is especially pertinent because the human living environment is becoming rapidly urbanized. Such drastic changes to the human environment may interrupt the healthy development of the microbiota and increase risk of inflammatory diseases. Moving forward, we must incorporate gut microbiota surveys into a broader framework of environmental exposure, for a thorough understanding of how ecosystem processes contribute to gut microbiota development, and affect the quality of human health.

Author contributions

NT: data collection and analysis; statistical analysis; intellectual design; writing and editing of the manuscript. NA: data collection and analysis; statistical analysis. JP: data analysis; statistical analysis oversight; editing of the manuscript. MH: data analysis; intellectual design; writing and editing of the manuscript; funding support. DG: intellectual design; writing and editing of the manuscript; funding support.

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Footnotes

Funding. JP and MH are funded through grants from the Natural Sciences and Engineering Research Council. DG is funded through grants from the Natural Sciences and Engineering Research Council and Crohn's and Colitis Canada.

References

Anderson P. M. L., Okereke C., Rudd A., Parnell S. (2013). Urbanization, Biodiversity and Ecosystem Services: Challenges and Opportunities. Dordrecht: Springer.

Biasucci G., Rubini M., Riboni S., Morelli L., Bessi E., Retetangos C. (2010). Mode of delivery affects the bacterial community in the newborn gut. Early Hum. Dev. 86 (Suppl. 1), 13-15. 10.1016/j.earlhumdev.2010.01.004

Dominguez-Bello M. G., Blaser M. J. (2011). The human microbiota as a marker for migrations of individuals and populations. Ann. Rev. Anthropol. Anthropol. 40, 451-474. 10.1146/annurev-anthro-081309-145711

Harmsen H. J. M., de Goffau M. C. (2016). The human gut microbiota, in Microbiota of the Human Body: Implications in Health and Disease, ed Schwiertz A., editor. (Cham: Springer International Publishing; ), 95-108.

Metzger M. J., Brus D. J., Bunce R. G. H., Carey P. D., Gonçalves J., Honrado J. P., et al. (2013). Environmental stratifications as the basis for national, European and global ecological monitoring. Ecol. Indic. 33(Suppl. C), 26-35. 10.1016/j.ecolind.2012.11.009

Popkin B. M. (1999). Urbanization, lifestyle changes and the nutrition transition. World Dev. 27, 1905-1916. 10.1016/S0305-750X(99)00094-7

Turner W. R., Nakamura T., Dinetti M. (2004). Global urbanization and the separation of humans from nature. Bioscience 54, 585-590. 10.1641/0006-3568(2004)054[0585:GUATSO]2.0.CO;2

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Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

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Global comparisons reveal a decrease in gut microbiota diversity attributed to Western diets, lifestyle practices such as caesarian section, antibiotic use and formula-feeding of infants, and sanitation of the living environment. While gut microbial diversity is decreasing, the prevalence of chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma is on the rise in Westernized societies.

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In boreal forests fungi deep in the soil sequester carbon in the soil.

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Study finds fungi, not plant matter, responsible for most carbon sequestration in northern forests

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(Phys.org) -A new study undertaken by a diverse group of scientists in Sweden has found that contrary to popular belief, most of the carbon that is sequestered in northern boreal forests comes about due to fungi that live ...

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Are you a multi-species organism or a symbiotic host?  Either way, we are all holiobionts.

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Are you a multi-species organism or a symbiotic host?  Either way, we are all holiobionts.

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Evolutionary biology and ecology regard the symbiosis between species differently. Is it important? Yes!

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Cicadas might be a pest, but they're special in a few respects. For one, these droning insects have a habit of emerging after a prime number of years (7, 13, or 17). They also feed exclusively on plant sap, which is strikingly low in nutrients. To make up for this deficiency, cicadas depend on two different strains of bacteria that they keep cloistered within special cells, and that provide them with additional amino acids. All three partners - the cicadas and the two types of microbes - have evolved in concert, and none could survive on its own.

These organisms together make up what's known as a holobiont: a combination of a host, plus all of the resident microbes that live in it and on it. The concept has taken off within biology in the past 10 years, as we've discovered more and more plants and animals that are accompanied by a jostling menagerie of internal and external fellow-travellers. Some of the microorganisms kill each other with toxins, while others leak or release enzymes and nutrients to the benefit of their neighbours. As they compete for space and food, cohabiting microbes have been found to affect the nutrition, development, immune system and behaviour of their hosts. The hosts, for their part, can often manipulate their resident microbiota in many ways, usually via the immune system.

You yourself are swarming with bacteria, archaea, protists and viruses, and might even be carrying larger organisms such as worms and fungi as well. So are you a holobiont, or are you just part of one? Are you a multispecies entity, made up of some human bits and some microbial bits - or are you just the human bits, with an admittedly fuzzy boundary between yourself and your tiny companions? The future direction of medical science could very well hinge on the answer.

The American evolutionary theorist Lynn Margulis, who popularised the theory of symbiosis, first coined the term 'holobiont' in 1991. She was interested in long-term, tightly integrated associations such as those evident in lichens - the crusty-looking growths found on rocks and trees, made up of fungus conjoined with algae. Margulis thought that there was a tight analogy between an egg and a sperm coming together to form a new organism, and the coming together of two species to form a new symbiotic consortium, which she called a holobiont.

Margulis argued that the interactions within a holobiont aren't too different from the life cycle of sexually reproducing organisms. The partners are integrated wholes that die and reproduce as one. But instead of sending out tiny cells to reproduce, holobionts send out individual organisms of different species.

With this framing in mind, when biologists began to use the term in the 1990s, they applied it to a few (usually two) organisms. But the word took on a very different cast in the hands of the American coral reef biologist Forest Rohwer and his colleagues, who defined a holobiont as a host and all of its associated microorganisms.

Two protagonists just aren't enough when it comes to explaining the evolutionary success of corals. They are made up of clusters of polyps, tiny wiggling things that get by with just a few tentacles and a toothless maw. Coral polyps reproduce by cloning themselves, and then sticking together to form large colonies, supported by a jointly fashioned skeleton. The most spectacular corals work hand-in-hand with photosynthetic algae that they host within their own cells. The algae provide nutrients via photosynthesis, while the coral gives the algae both food and protection. And those simple little polyps don't end their symbiotic relationships there. Corals don't possess a complicated immune system to fend off pathogens; instead, they seem to selectively cultivate helpful or benign bacteria, which crowd out the harmful microbes. Corals also produce mucus that appears to be able to trap phages, viruses that infect and kill only bacteria. An enemy of an enemy is a friend, after all.

Rohwer and colleagues, unaware of Margulis's idea, introduced the term holobiont to capture the dynamics of coral physiology. As a result, by the early 2000s, the scientific literature contained two contrasting definitions. One picked out an organism-like symbiotic pair that reproduced, while the other identified an ecological community of microbes indexed to a host.

For a time, the ecological account prevailed. But Margulis's physiological conception of holobionts was revitalised in the late 2000s as part of a new theory: what's known as the hologenome theory of evolution. Advocates merged both versions of holobiont into something a bit more conceptually loaded. On this view, the ecological notion of holobiont (the host and all its resident microbes) is given additional properties. It's an entity that's coherent enough to have its own hologenome, made up of the host genome plus all the microbial genomes. A major implication of this theory is that natural selection doesn't just act on the genome of individual organisms: it acts on the hologenome of holobionts, which are seen as single units that can evolve at the level of the holobiont.

Today, researchers engage in fierce debate over which forces shape holobionts and host-microbiome systems. They can be roughly split into two factions, the ecological and the evolutionary. On the ecological side, holobionts are seen as complex and dynamic ecosystems, in constant flux shaped by individual interactions from the bottom up. So you are part of a holobiont. But this stands in opposition to the evolutionary account, which casts holobionts as higher-level entities akin to organisms or units of selection, and believes that they are shaped as a whole from the top down. On this view, you are a holobiont.

The ecological and evolutionary views make for very different predictions about how a holobiont will change over time. Evolutionary theory predicts that the parts of a unit of selection will tend to cooperate: to sacrifice their own interests for the good of the whole. Ecological theory, by contrast, predicts competition and exploitation: parts will cooperate only insofar as it benefits them. Think of the differences between an ant colony and a motley assortment of insects fighting over scarce resources.

A dominant view in medicine treats the body as a battleground where any invaders are bad and must be exterminated. But in an ecosystem, there are no bad guys, just species playing different roles. If the ecological account of holobionts is true, a human host is more like a habitat to be managed, with the right balance and competition between different kinds of microbes being an important consideration. What counts as healthy can depend on what kinds of services we want out of our attendant ecosystem. If the microbes in a holobiont are more like ants in a colony, or genes in a genome, they are parts of a larger integrated whole. So we might expect stable co-adapted partners living in concert across holobiont generations.

However, the evolutionary version of holobionts gives us reason to stick to an expanded version of the 'us versus them' picture of medicine. It's just that now we have a few more allies on our side that we need to take care of. The evolutionary framework might also provide some justification for the calls for a return to a palaeomicrobiome that existed before the modern diet - for that would literally help to return a missing part of ourselves.

As things stand, the evidence leans heavily towards a more ecological interpretation of holobionts. Most of the partners come together anew each generation, and don't interact in the ways that are necessary for higher-level integration into organismic wholes. The theoretical bar for making that transition is high, and getting over it is going to be rare. But it potentially varies from holobiont to holobiont. There is still a long and exciting scientific road ahead, as researchers begin to unravel the secret lives and complex effects of microbes on the development, behaviour and evolution of their hosts.

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I, holobiont. Are you and your microbes a community or a single entity? - Derek J Skillings | Aeon Ideas

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Cicadas might be a pest, but they're special in a few respects. For one, these droning insects have a habit of emerging after a prime number of years (7, 13, or 17). They also feed exclusively on plant sap, which is strikingly low in nutrients.

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Drylands agriculture with microbial teas.

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Drylands agriculture with microbial teas.

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Very interesting and explained briefly.

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i have done 10 trials with nothing but microbe teas and rock dust and/or some other small amount of mineral supplement on more than 40 acres (meaning all together the plots totaled 40+ acres). the soils were extremely poor, compacted soil, soil stripped of top soil, one with a long history of chemical fertilizer and all but one had been tilled repeatedly. the results in all but one where there was almost no water (1 inch a month) were immediate and spectacular. there were results on the less water one but much slower. it is NOT a long term process. the microbe partners are the quickest way to get great results on any soil, including poor and depleted soils. they have for eons taken the nutrients out of the soil and turned them into fantastic plants.
people in our current paradigm enforced in our mindset by agribusiness and colonialism believe that you cannot restore poor soils without adding something (usually a lot of somethings). they do not believe that nature knows how to do it. it ain't true and we need to open up our minds.
this paradigm was initially named for me by toby hemenway in his video why agriculture will never be sustainable.
elaine ingham has done soil analyses around the world including saudi arabia and found every soil has what plants need to thrive. indeed, whatever soil analyses you have done show you what is available. (you can ask for the analysis which shows what is actually there). everything in the soil becomes available with the plants microbe partners.
the question is how to get the microbe partners of the plants to go to work. my observations show (from digging on more than 30 pieces of land where i consult) that when you use compost, a lot of amendments of any kind, especially chemical fertilizer, the microbe partners do not do their job as they are not needed.
what does work according to me is microbe teas, along with a great deal of respect for our microbe friends who have been turning earth into paradise for 4 billion years. microbe teas can be made on the farm with little expense. see korean natural farming on facebook and on google. you can also use compost teas. in permaculture people have been using mulch and this does work, it is a slower process and on large acreage until your chop and drop get big enough is very expensive to bring in large amounts of mulch. cover crops also work, but tilling them in takes away the biological advantage (meaning after the huge input of oxygen the available microbes digest all the materials and then die). what many people in permaculture do, however, is add soil amendments to their mulch, again this is topping the microbe partners. feeding the plants and not the soil as m. fukuoka san would say.

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i have done 10 trials with nothing but microbe teas and rock dust and/or some other small amount of mineral supplement on more than 40 acres (meaning all together the plots totaled 40+ acres). the soils were extremely poor, compacted soil, soil stripped of top soil, one with a long history of chemical fertilizer and all but one had been tilled repeatedly.

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The 2018 State of the World's Fungi Report

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The 2018 State of the World's Fungi Report

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Fungi are more important to the entire web of life than previously thought.

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Fascinating study on the relationship between fertiliser and the plant microbiome.

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Fascinating study on the relationship between fertiliser and the plant microbiome.

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Does fertilising plant reduce their ability to fight off disease?

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A growth chamber packed with tomato plants sprayed with bacteria to simulate different leaf microbiomes and then challenged with a plant pathogen to measure how well the microbiomes protect the plant from disease. Credit: Britt Koskella

A new study of the role microbial communities play on the leaves of plants suggests that fertilizing crops may make them more susceptible to disease.

University of California, Berkeley, biologists found that spraying tomatoes with microbes from healthy tomatoes protected them from disease-causing bacteria, but that fertilizing the tomatoes beforehand negated the protection, leading to an increase in the population of pathogenic microbes on the plants' leaves.

While the researchers don't yet know whether the increased number of bad bacteria on the leaves actually makes the tomatoes sick, the study clearly shows that fertilizer throws the community of microbes on the leaves off-balance. That potentially could allow disease-causing organisms to enter the plant.

"When we change the nutrient environment that plants are in, we are fundamentally altering the plant- microbiome interaction and also, importantly, the microbiome-mediated protection of natural plant/microbe interactions," said senior author Britt Koskella, a UC Berkeley assistant professor of integrative biology.

The fertilizer effect was not the only surprise from the study, Koskella said. She and co-author Maureen Berg, a graduate student, were investigating how the density of the microbial community on the leaves affected the plants' resistance to disease and discovered that a lower dose of beneficial microbes sprayed on the leaves was often more effective in protecting the plants from infection than higher doses. Berg sprayed leaves with an artificial microbial community composed of 12 species of bacteria taken from the natural microbiome of healthy tomatoes.

"We found that the most protective community was the most dilute, the least concentrated, the lowest dose," she said. "This was completely nonintuitive. A medium dose gave medium protection and the highest dose was the least protective."
Probiotics for plants
The reasons are unclear, but the findings are important because organic farmers are talking about spraying crops with probiotics to encourage better growth and disease protection, in the same way that humans consume probiotics containing "good" microbes in hopes of improving their health.

A representative agar plate illustrating the great diversity of bacteria that colonize tomato leaves in an agricultural field. Each spot is a growing colony of bacteria that was washed off a tomato leaf. Credit: Elijah Mehlferber, Koskella lab, UC Berkeley

"The fact that we saw this lower-dose/higher-protection effect suggests it is not as simple as just throwing on more microbes," Koskella said. "There is a lot of work to be done understanding how to apply a plant probiotic."

She and Berg will report their findings in the Aug. 6 print edition of the journal Current Biology; the article will be posted online July 26.

Koskella focuses on plants' above-ground microbiomes, or the phyllosphere, a poorly understood community compared to the well-studied below-ground microbiome associated with plant roots, the rhizosphere. Researchers are finding unsuspected activity within phyllosphere microbes, including that some of the bacteria fix nitrogen from the air like root-associated bacteria. Many studies have demonstrated that microbial communities in the roots can promote plants' nutrient uptake, growth and resistance to disease, and Koskella is investigating whether this also holds true for the above-ground microbiome.

Her experiments are relevant to the issue of treating crops with probiotics, and could help answer questions such as: What is the right mix of bacteria for a given plant? What is the best way to apply this proper mix?

To investigate these questions, Koskella and Berg began by sampling the natural leaf microbes of healthy tomatoes grown in outdoor fields at UC Davis.

They then sprayed the mix on sterile tomato plants in growth chambers at UC Berkeley and, one week later, injected the leaves with Pseudomonas syringae bacteria, which cause tomato speck, a major problem that's treated with pesticides. The new microbial community on the tomatoes did, in fact, protect the plants from colonization by pathogens, though the microbial communities obtained from some tomato fields worked better than the microbiomes from other fields.

"This phyllosphere microbial community, much like our own skin, is a first line of defense against disease, so we expected to see protection, though we didn't know for sure," Koskella said.

Signs of tomato speck on a leaf lacking a protective microbiome and subsequently invaded by a pathogenic microbe, Pseudomonas syringae. Credit: Norma Morella, Koskella lab, UC Berkeley

Artificial microbial communities
Surprisingly, when they varied the concentration of microbes sprayed on the leaves, they found that in many cases low dosages worked better than high dosages.

To find out why, they constructed an artificial microbial community composed of 12 of the species found on natural plants-basically, the 12 that grew best in culture. When they sprayed various dosages of the synthetic community on tomatoes, they got the same result: low, diluted doses were more protective against Pseudomonas than were high, concentrated doses.

Berg repeated the experiment to confirm the puzzling findings, but during one subsequent trial she decided to fertilize the droopy plants first. In that trial, none of the microbiome doses were protective against Pseudomonas. When they repeated the trial with and without fertilization, they confirmed that application of fertilizer abolished the protective effects previously observed.

In each experiment, they judged protection against pathogens by recording the relative population of Pseudomonas compared to the other, mostly beneficial microbes, since a healthy microbiome should effectively compete with a pathogen and knock it down to low levels.

Koskella has suspicions about why fertilizer alters the microbiome, top among them the possibility that the nutrients make healthier leaves, which keeps all the microbes happy and obviates the need for the good microbes to out-compete the bad microbes. She and her group are now pursuing experiments to test that hypothesis.

They still have no idea why probiotic treatment at low dosages works better than high doses, but hope that future research can solve this mystery and help guide the suitable application of probiotics in agriculture.

Nevertheless, Koskella and Berg said, the impact of fertilizer on the leaf and stem microbiome should lead biologists to explore fertilizer's effect on the root microbiome as well, and on the general health of the plant.

"We have been fertilizing crops for so long it would surprise me if we haven't already seen consequences of long-term fertilization on how plants interact with their microbes," she said. "There are a lot of studies that show domesticated plants tend to have very different microbial communities than their wild relatives."

The big questions are, does that affect the plant's overall health, and why?

More information: Current Biology (2018). DOI: 10.1016/j.cub.2018.05.085

Provided by: University of California - Berkeley

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Fertilizer destroys plant microbiome's ability to protect against disease

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A new study of the role microbial communities play on the leaves of plants suggests that fertilizing crops may make them more susceptible to disease. University of California, Berkeley, biologists found that spraying tomatoes with microbes from healthy tomatoes protected them from disease-causing bacteria, but that fertilizing the tomatoes beforehand negated the protection, leading to an increase in the population of pathogenic microbes on the plants' leaves.

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How nutrients are transferred from symbiotic microbes to plant roots: the rhizophagy cycle.

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How nutrients are transferred from symbiotic microbes to plant roots: the rhizophagy cycle.

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Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes

Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA

Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP 221005, India

U.S. Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105-2807, USA

Author to whom correspondence should be addressed.

Received: 22 August 2018 / Accepted: 5 September 2018 / Published: 17 September 2018

endobiome; endophyte; nutrient transport; reactive oxygen; rhizosphere; symbiosis

1. Introduction

It is widely known and accepted that most plants obtain nutrients generally through absorption of dissolved inorganic nutrients from soils [ 1]. However, it is also known that some plants engage in nitrogen-transfer symbioses where plants associate with prokaryotes that fix nitrogen in association with roots and transfer that nitrogen to plants [ 2, 3]. Among these nitrogen-transfer symbioses are actinorhizal symbioses that occur in three orders of plants (Fagales, Rosales and Cucurbitales) where roots may become inter-cellularly and intra-cellularly colonized by diazotrophic actinomycetes of the genus Frankia that inhabit nodules in roots [ 2]. Families of plants where actinorhizal symbioses are common include: Betulaceae, Elaeagnaceae, Fagaceae, Myricaceae, Rosaceae and so forth [ 4]. Other nitrogen-transfer symbioses are the rhizobial symbioses where certain diazotrophic bacteria infect root hairs and move into the root cortex where they become intracellular and stimulate formation of nodules; bacteria then situate in the cytoplasm of nodule cells in vesicles and transfer nitrogen to plants in the form of ammonia [ 5, 6]. Rhizobial symbioses are limited principally to legumes (family Fabaceae) [ 5]. In some plants, diazotrophic cyanobacteria form nitrogen transfer associations with plant tissues where they fix nitrogen and transfer it to the plant [ 4]. Among these are species of the genus Gunnera that possess specialized glands that secrete polysaccharides to attract cyanobacteria, which enter into tissues of the stem and become intracellular within host cell vesicles where they fix nitrogen that is subsequently transferred to the host plant [ 4].

In all the previously discussed nitrogen-transfer symbioses, hosts evolved ways to internalize and engage in prolonged symbiosis with diazotrophic prokaryotes using specialized plant symbiosis organs or tissues. All of these associations are restricted to specific families that evolved specialized symbiosis organs (nodules or glands); however, all species of plants internalize microbial endophytes into plant tissues that do not involve specialized organs [ 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]. Microbial endophytes have been shown to provide a plurality of benefits to host plants, including growth promotion, improved biotic and abiotic stress tolerance and increased disease protection [ 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]. One logical means of plant growth promotion by plant endophytes is improved nutrient acquisition by plants. However, mechanisms for direct nutrient transfer from endophytic bacteria to plants have been elusive [ 30, 31]. In some cases, bacteria that have not been found to be capable of fixing atmospheric nitrogen are nevertheless found to scavenge nitrogen and other nutrients from the rhizosphere and transfer them to plants [ 32]. In other cases, endophytes have been shown to increase solubilization of bound phosphates in the rhizosphere, and thus have been hypothesized to function by increasing plant phosphate supply in the rhizosphere [ 17]. In absence of a mechanism for direct transfer of nutrients from microbes to plants, many scientists attribute growth promotion largely or partially to effects of microbe-produced phytohormones, disease control, or other non-nutritive benefits [ 33, 34, 35, 36, 37, 38].

Evidence for a mechanism for direct transference of nutrients from symbiotic microbes to plant roots was provided by Paungfoo-Lonhienne et al. [ 39]. Through a series of experiments, these investigators showed that plant roots (Lycopersicum esculentum and Arabidopsis thaliana) internalized bacteria and yeasts into root cells where microbes appeared to be degraded in time. Paungfoo-Lonhienne et al. [ 40] later denominated this microbe internalization and degradation process 'rhizophagy' to denote that roots appeared to be 'eating' microbes. Adamczyk et al. [ 41] and Paungfoo-Lonhienne et al. [ 42] demonstrated that plants had the capacity to employ secreted proteases in order to degrade proteins, further supporting the hypothesis that plants actively degrade microbes and their protein products associated with roots. White et al. [ 43] documented degradation of bacteria on root surfaces as a result of the action of root-secreted reactive oxygen and proposed that through the action of reactive oxygen roots may be scavenging nitrogen from bacteria that colonize roots. White et al. [ 44] later documented internalization of bacteria into periplasmic spaces of root cells and their oxidative degradation within cells through use of a reactive oxygen staining technique. Collectively, these observations have suggested that plants are engaging in a process of microbivory in order to extract nutrients from microbes that colonize roots [ 45, 46].

Over the past several years, we have conducted experiments using various host species and endophytic bacteria to elucidate how the plant microbivory process works in plant roots [ 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]. In this paper, we describe features of the microbivory process and hypotheses with regard to how the process works. We hypothesize that many plants, perhaps all plants, acquire some nutrients directly from symbiotic microbes by a process we term the 'rhizophagy cycle' ( Figure 1). In the rhizophagy cycle symbiotic microbes (often seed transmitted bacteria) alternate between an intracellular/endophytic phase and a free-living soil phase. We hypothesize that microbes acquire soil nutrients in the free-living soil phase and that those nutrients are extracted from microbes oxidatively in the intracellular/endophytic phase. We also discuss proposed mechanisms plants employ to manipulate symbiotic microbes to transport nutrients from the soil into root cell periplasmic spaces, extract nutrients through oxidation and deposit surviving microbes exhausted of their nutrients back into the rhizosphere through the tips of elongating root hairs ( Figure 2, Figure 3, Figure 4, Figure 5, Figure 6, Figure 7, Figure 8, Figure 9, Figure 10, Figure 11, Figure 12, Figure 13, Figure 14, Figure 15, Figure 16, Figure 17 and Figure 18).

2. The Symbiotic Bacteria

In our experiments, we employed microbes that were transmitted within or on the surfaces of seeds of several species of plants [ 46, 47, 48, 56, 57]. The bacteria that functioned in the rhizophagy cycle in in vitro experiments include species of genera of Gram-negative bacteria: Alpha-proteobacteria Bosea, Methylobacterium; Beta-proteobacteria Achromobacter and Burkholderia; Gamma-proteobacteria Acinetobacter, Klebsiella, Pantoea, Pseudomonas and Micrococcus; and Gram-positive Bacilli Bacillus and Paenibacillus; and Actinobacteria Curtobacterium and Microbacterium. Bacteria that function in the rhizophagy cycle belong to diverse classes of bacteria and it seems likely that any bacterium that colonizes roots and can be induced to enter root cells may be involved in the process [ 46, 47, 48, 50, 55].

3. Plant 'Farming' of Rhizosphere Microbes

Plants produce a root exudate zone adjacent to and just behind root tip meristems [ 58]. Plants secrete carbohydrates, amino acids, vitamins and organic acids into this zone [ 59]. The literature suggests that plants alter numbers and diversity of microbes on root surfaces and in the rhizosphere through secretion of exudates [ 60]. Plants are known to increase secretion of exudates in nutrient limiting soils, likely leading to increased microbial activity around roots and increased 'microbial mining' for nutrients [ 59]. Root exudates attract microbes that will grow in the root exudates [ 58, 61]. In this sense root exudates act as signal molecules that attract a diverse community of microbes to the exudate zone and biofilm around the root tip meristem [ 61, 62, 63]. Through the continued secretion of root exudates plants are cultivating microbes and when nutrients are scarce plants increase cultivation of microbes by producing more exudates [ 59]. The response of plants to increase density and diversity of the microbial community around roots by secreting more root exudates in nutrient limiting situations is consistent with the hypothesis that the root associated microbes function in nutrient acquisition. Through the secretion of root exudates, plants may be considered to be 'farming' microbes.

4. Nutrients Transferred to the Host Plant

Some of the bacteria (e.g., Burkholderia and Klebsiella) involved in the rhizophagy cycle have been frequently found to fix atmospheric nitrogen, while others are sometimes or rarely reported as nitrogen fixing [ 64]. For bacteria involved in the rhizophagy cycle, it is unlikely that any nitrogen fixation occurs while they are in tissues of plant roots because bacteria are exposed to high levels of reactive oxygen in roots and nitrogenases are rapidly degraded by oxygen [ 43, 44, 64, 65]. Any nitrogen fixation activities by rhizophagy cycle bacteria would likely occur in the free-living soil phase where bacteria grow in the rhizosphere in low oxygen conditions. Consistent with this, Roley et al. [ 31] found that a nitrogen-fixing Burkholderia only showed evidence of active nitrogen fixation in roots of switchgrass (Panicum virgatum) after root tissues senesced. On the other hand, it seems logical that bacteria could deliver nutrients to plants via the rhizophagy cycle without nitrogen fixation occurring; instead bacteria need only be capable of obtaining nutrients in the rhizosphere by scavenging of nutrients from soils, bacteria, fungi or plants. The capacity of some bacteria (including species of Bacillus) to produce and secrete resistant proteases may enable these bacteria to scavenge nitrogen from other microbes by degrading and absorbing their proteins in the rhizosphere [ 66]. Irizarry and White [ 57] showed that addition of Bacillus amyloliquefaciens to cotton seedlings growing in soil resulted in increased growth and an increased expression of nitrate transporter genes. In isotope tracking experiments using grass seedlings both with and without bacteria, grown in agarose amended with 15N-labeled proteins, White et al. [ 55] showed that presence of the bacteria on seedlings resulted in acquisition of approximately 30% more nitrogen by grass seedlings than in seedlings without bacteria. However, in that experiment, it was not possible to determine what proportion of the nitrogen was obtained from absorption of microbe-mineralized nitrogen in media around roots, versus from direct degradation of microbes within or on surfaces of roots. Hill, Marsden and Jones [ 67] conducted isotope-tracking experiments to assess the flow of nitrogen into wheat plants from direct consumption of microbes versus inorganic soluble nitrogen. These authors concluded that plant consumption of microbes was occurring but that the rate of movement of nitrogen through rhizophagy was one to two orders of magnitude slower than soluble inorganic nitrogen. Hill, Marsden and Jones [ 67] did not examine nutrient transfer to plants other than nitrogen. Thus, no work has been done to date to identify the particular nutrients that plants acquire from rhizophagy. It seems probable that plants would not be internalizing and degrading symbiotic microbes unless critical nutrients were being obtained from consumption of those microbes.

5. Rhizophagy Microbes as Carriers of Micronutrients

Through the activities of some symbiotic microbes, nutrients (e.g., phosphates, organic nitrogen) may be solubilized in the rhizosphere [ 68]. Solubilized nutrients may be absorbed by root hairs into roots. However, bacteria also efficiently scavenge nutrients in the rhizosphere (soil) and sequester difficult to obtain micronutrients (including boron, cobalt, copper, iron, manganese, magnesium and zinc) using biogenic ligands with a high affinity for metals called siderophores [ 69]. Root associated bacteria are often motile and capable of moving out away from the plant root in order to acquire soil nutrients-and of returning to the plant to acquire additional carbon and other root exudate nutrients. Bacteria would appear to be ideal carriers of micronutrients that are required for plant growth and development. Through the process of rhizophagy, all of the nutrients acquired or produced by bacteria could be oxidatively extracted from them. Bar-Ness et al. [ 70] showed that a pseudomonad was responsible for transporting iron from soil to dicot and monocot roots to support plant growth. Bar-Ness et al. [ 71] showed that in cotton (Gossypium sp.) iron was acquired directly from bacteria at the root tip meristems. In the process of rhizophagy, it is at the root tip meristems that bacteria enter plant cells and are exposed to reactive oxygen that likely extracts nutrients from the intracellular bacteria-inducing electrolyte leakage of bacteria and making nutrients available for absorption into plant root cells. Further work is needed to determine precisely which nutrients may be obtained by plants from the direct consumption/oxidation of microbes.

6. Balance between Microbe-Oxidation Susceptibility and Resistance

Experiments using bacterial endophytes Pseudomonas spp. (from seeds of grass Phragmites australis) and Micrococcus luteus (from seeds of Lycopersicum esculentum) that differed in resistance to reactive oxygen degradation due to their relative capacities to produce antioxidants (carotenoids, catalases, peroxidases and superoxide dismutase) have suggested that bacteria that participate in the rhizophagy cycle may be matched to their particular host plants. More specifically, rhizophagy bacteria must be degradable by levels of reactive oxygen produced by their hosts. Pseudomonas spp. that stimulated growth of several grasses [ 47, 49] were observed entering root cells and then swelling and losing protein content as they were degraded. These same bacteria were not observed to degrade when they were put into the seedlings of dandelion (Taraxacum officionale) [ 47, 49]. Micrococcus luteus, a tomato endophyte, was shown to stimulate growth of seedlings of tomato ( Figure 2). However, inoculation of Micrococcus luteus into the seedlings of several other plant species, including grasses (Festuca arundinaceae and Poa annua), carrot (Daucus carota), curly dock (Rumex crispus) and Japanese knotweed (Fallopia japonica) resulted in internal colonization of root cells and suppression of root growth. Examination of roots of these species bearing Micrococcus luteus showed that bacteria colonized the interior of root cells, and elicited reactive oxygen production, but did not degrade within root cells, instead copiously replicating in seedling roots ( Figure 4, Figure 5, Figure 6, Figure 7, Figure 8, Figure 9, Figure 10 and Figure 11) to exit seedlings and accumulate en masse around roots. This could be explained by the increased capability of Micrococcus luteus to withstand reactive oxygen levels in hosts other than tomato. Mohana, Thippeswamy and Abishek [ 72] showed that carotenoids produced by Micrococcus luteus protect the bacterium from oxidation. Ohwada et al. [ 73] showed that Micrococcus luteus has 91 times more catalase activity and 20 times more peroxidase activity than Pseudomonas. The results of our experiments with pseudomonads and Micrococcus seem to indicate that microbes that establish a symbiosis with plants in the rhizophagy cycle must be susceptible to degradation by the host in the intracellular phase. In this study, the pseudomonads were compatible with their grass hosts and were degraded (or some of them were degraded) within roots. The degradable pseudomonads may thus provide a source of nutrients to their grass host plants, resulting in growth stimulation. Micrococcus was resistant to degradation by several hosts and likely did not provide nutrients. Further, because Micrococcus luteus was resistant to degradation in the root several hosts, the numbers of bacteria in cells could not be regulated and likely overwhelmed the seedlings due to bacterial overload. This emphasizes that plants and their symbiotic microbes may be adapted optimally to maximize benefits of the symbiosis. In an optimal rhizophagy cycle relationship, microbes would enter plant roots and some would be degraded oxidatively, keeping intracellular microbe numbers in check, while survivors would exit roots to rejoin soil populations.

7. Mechanisms for Microbe Entry into Roots

7.1. Endocytosis Hypothesis to Explain Microbe Entry into Root Meristem Cells

Paungfoo-Lonhienne et al. [ 39] proposed that movement of microbes into plant cells is a form of endocytosis where plant derived cell-wall degrading enzymes play a role in loosening cell walls to permit entry of microbes into plant root cells. Experiments using Arabidopsis thaliana and Lycopersicon esculentum inoculated with Escherichia coli showed that plants expressed higher levels of cellulases than un-inoculated controls. These authors also found that bacteria on surfaces of root cells were sometimes covered by a matrix composed of cellulose fibers as evidenced by immuno-histochemical experiments. It was proposed that coating microbes in a matrix could be an early stage of endocytosis into root cells. Further, Paungfoo-Lonhienne et al. [ 39] reasoned that movements in the root cell cytoskeleton were consistent with the hypothesized active endocytosis of microbes by root cells. An active endocytosis mechanism for internalizing microbes into root cells is logical and cannot be ruled out; however, another mechanism involving manipulation of microbe virulence is possible based on experiments that we have conducted.

7.2. Hypothesized Role of Short-Chain Fatty Acids in Induction of Bacteria to Enter into Root Meristem Cells

Bacteria growing in biofilms on the root surface and in the rhizosphere anaerobically ferment carbohydrates present in root exudates to form short-chain fatty acids (SCFAs). Butyric and propionic acids are among the SCFAs fermented by bacteria associated with roots [ 74]. In other research [ 75, 76], butyric and propionic acids in animal intestines have been shown to act as signal molecules or inhibitors of some bacteria and yeasts. When SCFAs are in high concentration in biofilms, bacteria and yeasts (e.g., Salmonella spp. and Candida spp.) remain in the biofilm phase but when butyric and propionic acid concentrations fall, virulence genes in microbes are up-regulated and microbes parasitize epithelial tissues in the walls of the animal's gut [ 75, 76]. Butyric acid and its derivatives are now widely being used to suppress gut parasitism by bacteria in agricultural/industrial animal production [ 77, 78]. In isotope tracking experiments, Tramontano and Scanlon [ 79] showed that root meristem cells absorbed butyric and propionic acids and transported these compounds to the cell nucleus where the root cell responded by slowing cell division. Lanzagorta, de la Torre and Aller [ 80] found the 2 mM concentration of butyrate reversibly slowed the cell cycle of Allium cepa root tip meristem cells. Why plant cell division in the meristem slows is unknown, but it shows that the plant may respond to presence of the microbes around the meristem. The active absorption of these SCFAs by root meristem cells, may stimulate bacteria in the biofilm around the root meristem to infect the thin-walled meristem cells in a comparable way microbes in intestines infect intestinal epithelial tissues. Thus, absorption of SCFAs by the root meristem is a possible 'rhizophagy trigger,' essentially inducing microbes to parasitize the meristem cells. In this sense, the removal of organic acids from the microbial biofilm around root meristems may represent part of the symbiotic 'cross talk' between plant and microbe, comparable to interactions that occur in establishment of rhizobial symbioses [ 5].

7.3. Propionic Acid and Butyric Acid Experiment to Test SCFA Removal-Induced Infection of Meristem Cells

To test whether absorption of propionic and butyric acids from the bacterial biofilm by the root tip meristem is the trigger to initiate entry of bacteria into root meristem cells, we conducted experiments in which we grew seedlings of the grass Poa annua (inoculated with Pseudomonas fluorescens) on agarose (Sigma, Burlington, MA, USA) that contained 0, 2, 4, 6, 8, or 10 mM of butyric or propionic acids (Sigma, Burlington, MA, USA). After approximately 10 days, seedlings were stained for 15 h in a solution of 3,3-diaminobenzidine (DAB) (Sigma, Burlington, MA, USA) and counterstained using aniline blue (0.01%, aqueous; Sigma, Burlington, MA, USA), then examined microscopically for evidence of intracellular bacteria using a compound light microscope (Zeiss, Axioskop; Carl Zeiss Microscopy, Thornwood, NY, USA) [ 44]. In these experiments, we found that concentrations of SCFAs from 0-4 mM gradually reduced entry of bacteria into root cells and at 4 mM no bacteria could be seen within root cells [ 46, 51, 53]. These experimental results are consistent with the hypothesis that absorption of SCFAs from the bacterial biofilm around the root tip meristem is a trigger for intracellular invasion of bacteria into meristem cells. In our experiments, at 4 mM/L of SCFAs in the agarose, the root meristem cells could not remove the SCFAs from the bacterial biofilm due to its constant replacement by additional SCFAs from the agarose. However, whether a mechanism of root cell endocytosis, as suggested by Paungfoo-Lonhienne et al. [ 39], or active infection by microbes triggered by removal of bacterial fermentation products by the root meristem, a combination of the two mechanisms, or another mechanism entirely, accounts for internalization of microbes into root cells will require additional investigation.

8. Loss of Cell Walls by Bacteria on Entry into the Periplasmic Space of Root Cells

Microscopic examination ( Figure 4, Figure 5, Figure 6, Figure 7, Figure 8, Figure 9, Figure 10 and Figure 11) of a diverse selection of seedlings of grasses (Cynodon dactylon and Poa annua) and dicots (Rumex crispus, Daucus carota, Fallopia japonica and other species) infected by Pseudomonas spp. or Micrococcus luteus shows that bacteria initially enter root meristem cells as walled cells-pseudomonads are rod-shaped and Micrococcus luteus cells are spherical and in tetrads. In the periplasmic space of root cells, bacteria lose cell walls and form spherical L-forms ( Figure 12, Figure 13 and Figure 14) [ 81]. Likely, it is exposure of bacteria to reactive oxygen, constitutively produced in the meristematic cells, that triggers bacteria to become wall-less L-form bacteria [ 82]. The reactive oxygen may damage bacterial membrane wall synthesis enzymes that results in formation of the wall-deficient bacteria. L-forms can also be induced experimentally in bacteria by exposure to antibiotics that inhibit cell wall synthesis by bacteria [ 81], or spontaneously in plant and animal tissues [ 81]. L-form bacteria have been shown to occur in both animal and plant tissues and have been associated with symbiosis and disease [ 83, 84, 85]. In the L-form phase bacteria do not divide regularly or possess defined cell sizes. Instead, bacteria often form chains of spherical cells that 'bleb' or 'bud' to smaller and smaller sizes.

9. Intracellular Bacteria Exit Roots to Re-Enter Soil Populations

Our previous observations suggest that bacteria exit root hairs at the elongating root hair tips ( Figure 8, Figure 9, Figure 10 and Figure 11). When all bacteria have exited the hair through the tip, hair elongation stops. This suggests that root hair growth, at least in some cases, is a function of intracellular bacteria. It also suggests that root hairs may function as a mechanism to deposit bacteria exhausted of nutrients back out into the rhizosphere where they can acquire additional nutrients before returning to the root exudate zone. Confirmation of movement back into the soil is significant because it completes the cyclic process of 'rhizophagy'-with the potential that intracellular bacteria may re-enter soil and eventually return to roots with nutrients that could support plant growth. A 'rhizophagy cycle' where roots continuously extract small amounts of minerals, vitamins, or other growth factors from endosymbiotic bacteria could be an important source of nutrients for plants that has been largely overlooked by plant scientists. The occurrence of a rhizophagy process that is widespread in plants could explain how some bacteria that are not able to fix nitrogen themselves nevertheless may show significant enhancements in plant growth promotion [ 32].

10. Do Fungi Also Function in the Rhizophagy Cycle?

In a recent study, we isolated the fungus Aureobasidium pullulans (Ascomycota) from seeds and seedlings of the plant Froelichia gracilis (Amaranthaceae). We also isolated the endophytic yeast Rhodotorula sp. from Abrus precatora (Fabaceae). Experiments using A. pullulans and Rhodotorula sp. demonstrated that these yeasts internally colonized seedling roots of several plant species, entering into root cells and locating in the periplasmic spaces of root parenchyma [ 46]. Initial colonization appears to occur at the root tip meristem based on presence of fungal cells in periplasmic spaces of parenchyma cells in outer cell layers of the root behind the tip meristem and in root hairs at all stages of development. The fungi also have the capability to form wall-less protoplasts called 'mycosomes' that can bud sequentially to form chains within plant cells [ 86]. In our experiments, we observed both walled fungal cells ( Figure 18) and apparent wall-less mycosomes ( Figure 15 and Figure 17) within seedling root cells. The fungi were also seen to exit root cells at the tips of elongating root hairs ( Figure 16), accumulating around hair tips as masses of yeast cells, often forming caps on tip of the hairs ( Figure 18). Our experiments using both yeasts show that fungi follow the same path through plant roots as seen in bacteria involved in the rhizophagy cycle. These yeasts appear to cycle between an intracellular endophytic phase and a free-living soil phase. It seems reasonable to hypothesize that nutrients could be extracted from fungi oxidatively when they are in the protoplast mycosome phase. Atsatt and Whiteside [ 86] observed mycosome formation in several additional species of fungi in phyla Ascomycota, Basidiomycota and Zygomycota, suggesting that other fungi may also possess the capability to become internalized in plant root cells. Much more work is needed to evaluate the potential benefits of intracellular fungi to their host plants.

11. Non-Nutritive Functions of Rhizophagy Microbes

11.1. Modulation of Plant Development

Experiments using seedlings of grasses and other plant species have demonstrated that some, or perhaps all, microbes that internalize in plant cells modulate development of the seedlings. Seedlings from rigorously surface-disinfected seeds using sodium hypochlorite to remove all surface microbes invariably are diminished developmentally, often showing loss of root gravitropic response (roots fail to grow downward) and reduced or no root hair formation. Re-inoculation of the symbiotic bacteria onto axenic seeds restores normal root growth in seedlings [ 43, 48, 49, 50]. Thus, it is evident that plants appear to rely on symbiotic microbes to modulate development. Modulation of plant development may be considered to be a basic function of microbes in the rhizophagy cycle. The hypothesized mechanisms for modulation of plant development may relate to microbial production, or removal of, plant hormones [ 36, 38, 53, 87, 88].

11.2. Enhancement in Oxidative Stress Tolerance in Host Plants

Entry of microbes into root cells is generally accompanied by increased production of defensive reactive oxygen by the root cells [ 47]. Increased production of reactive oxygen may cause the host to increase production of antioxidants (e.g., superoxide dismutase, peroxidases, catalases) and oxidative stress-related genes to reduce the negative effects of reactive oxygen on the host itself. The direct association between the amount of reactive oxygen secreted by the host and its resistance to oxidative stress has not been verified but endophytic microbe colonization of plants frequently provides hosts with increased tolerance to abiotic stresses (e.g., drought, heavy metals, salinity and high temperatures) and biotic stresses (e.g., diseases, herbivory) and the underlying mechanism in many cases has been resistance to oxidative stress [ 20, 21, 22, 56, 57, 89, 90, 91, 92].

11.3. Enhanced Disease Resistance Due to Endophytic Microbes

Some of the microbes that become intracellular in plant roots have been shown to inhibit pathogenic fungi in the soil or in the plant [ 25, 26, 49, 50, 93, 94]. Disease protection may be the result of induced systemic resistance (ISR) where the endophyte causes the plant to up-regulate its disease resistance genes making plants more resistant to pathogens [ 26, 95]. However, some of these microbes also have direct inhibitory activity on pathogenic fungi. Soares et al. [ 27] showed that a Bacillus endophyte of English ivy (Hedera helix) produced antifungal lipopeptides that directly inhibited growth of the pathogenic fungus Alternaria tenuisima and protected the host from disease. Pseudomonad endophytes of plants also venture into the soil and colonize potential fungal pathogens, repressing their growth and reducing virulence [ 47]. Pseudomonads are known to produce antifungal compounds including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin and hydrogen cyanide; these and/or other compounds may inhibit growth of potential pathogens and/or alter their behavior in reducing growth and virulence [ 96].

11.4. Endophyte-Mediated Suppression of Competitor Plant Species

Microbes involved in the rhizophagy cycle intimately associate with plant root tissues and cells, growing around the root tip meristems and passing through cell walls where they come into direct contact with root cell plasma membranes. We hypothesize that this intimate association requires that the microbe must be subject to control by the plant cells. If the intracellular microbes are resistant to degradation by host-produced reactive oxygen due to production of antioxidants the microbe may replicate itself excessively at the expense of the host cell and host growth may be reduced. If microbes produce metabolites such as hydrogen cyanide or other compounds that restrict respiration or other functions of the host cell, plant growth may again be compromised. Thus, it seems reasonable that hosts and rhizophagy cycle endophytes are adapted to maximize benefits to both hosts and microbes. Colonization of rhizophagy cycle endophytes into hosts to which they are not adapted may result in 'endobiome interference,' where endophytes reduce growth and competitiveness of hosts and perhaps interfere with the growth promotional activities of native endophytes [ 53]. In some of our experiments 'endobiome interference' may have occurred. For example, experiments we conducted using seed-transmitted pseudomonads from the grass Phragmites australis showed that the bacteria stimulated growth of several grasses but suppressed growth and increased mortality in seedlings of dandelion (Taraxacum officionale) and curly dock (Rumex crispus) [ 47]. In other experiments [ 53], we showed that endophytic yeasts Rhodotorula sp. and Aureobasidium pullulans and bacteria Micrococcus luteus and Paenibacillus sp. from seedlings of plant species Abrus precatorius, Froelichia gracilis, Lycopersicum esculentum and Poa annua, respectively, suppressed root growth and increased mortality of seedlings of dandelion (Taraxacum officionale), curly dock (Rumex crispus) and clover (Trifolium repens). Here, microbes that were most inhibitory to seedling growth were those that were resistant to reactive oxygen due to production of antioxidants-and likely internal replication of microbes could not be controlled by the inhibited seedlings, resulting in replication of endophytes at the expense of host growth. We do not know the mechanisms by which endophytic colonization of non-hosts led to increased seedling mortality. Endobiome interference could be a factor that affects competition between plant species in natural plant communities-with endophytes serving as a means to suppress the growth of competitor plant species [ 47]. Additional experiments are needed to determine whether 'endobiome interference' occurs in natural plant communities.

12. Conclusions

The 'rhizophagy cycle' is a process where microbes alternate between an endophytic phase and a free-living soil phase. Rhizophagy microbes become intracellular in root cells by infecting cells at the root tip meristem. Microbes exist primarily as wall-less protoplasts ('L-forms' for bacteria and 'mycosomes' for fungi) in close association with host cell plasma membranes in roots. Root cell plasma membranes secrete reactive oxygen onto microbes and this may reduce replication of intracellular microbes and cause leakage of nutrients from microbes. Intracellular microbes trigger formation of root hairs on roots and they exit cells at the elongating root tips, reforming cell walls as they exit from root hairs. Plants appear to manipulate microbes in the rhizophagy cycle by: (1) stimulating bacterial growth around root tip meristems of seedlings by secretion of root exudates around the root tip; (2) triggering bacteria to enter into periplasmic spaces in root cells at the root-tip meristem by absorbing bacterial fermentation products including butyric acid, causing bacteria to up-regulate virulence/endoparasitism genes; (3) subjecting bacteria in periplasmic spaces to superoxide formed on root cell plasma membranes to extract nutrients from bacteria, and (4) depositing surviving intracellular bacteria back into the rhizosphere from the tips of elongating root hairs to maximize new nutrient acquisition by bacteria. Microbes engage in the rhizophagy symbiosis likely because they also benefit from the nutrients provided by host plants in terms of root exudates and nutrients that leak from root cells during the endophytic/intracellular phase. The rhizophagy symbiosis may be viewed as a mutualism involving an exchange of nutrients between the plant and microbe participants. Much of our research to date on the rhizophagy cycle has been done on seedlings, however future research is needed to confirm that the rhizophagy cycle also occurs at root tips of more mature plants. While 'rhizophagy' has been shown to increase movement of nitrogen into plants, we hypothesize that the real benefit of the rhizophagy cycle may be in acquisition of iron and other micronutrients from symbiotic microbes that sequester these soil nutrients using siderophores, although this must be proven. The biological implications of the rhizophagy cycle and microbes that are involved in it in terms of plant growth promotion and plant-plant interactions via symbiotic microbes are topics that require much additional research.

Author Contributions

All authors contributed equally in research and writing of this manuscript.

Funding

S.K.V. was supported on a Raman Post-Doctoral fellowship (No.-F 5-11/2016 IC) for the year (2016-17) to conduct research in USA. Funding support was also provided from USDA-NIFA Multistate Project W3157, the New Jersey Agricultural Experiment Station, the Rutgers University Turf Science Center, and from a Cooperative Ecosystems Studies Unit CESU G16AC00433 grant between Rutgers University and the U.S. Geological Survey for control of invasive Phragmites australis. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Conflicts of Interest

The authors have no conflict of interest to declare.

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Figure 1. Diagrammatic representation of the rhizophagy cycle. ( A) Diagram of the rhizophagy cycle showing microbes entering root cells at the root tip meristem and exiting root cells at the tips of elongating root hairs. Rhizophagy cycle microbes alternate between an intracellular endophytic phase and a free-living soils phase; soil nutrients are acquired in the free-living soil phase and extracted oxidatively in the intracellular endophytic phase; ( B) Shows bacteria (arrow) in the periplasmic space of parenchyma cell near root tip meristem of an Agave sp. seedling (bar = 20 µm; stained with 3,3-diaminobenzidine followed by aniline blue); ( C) Bacteria (arrow) emerging from root hair tip of grass seedling (bar = 20 µm; stained with fluorescent nucleic stain SYTO 9).

Figure 3. Root parenchyma cells of axenic tomato seedling showing absence of bacteria in cells (bar = 25 µm; stained with 3,3-diaminobenzidine followed by aniline blue).

Figure 14. Tomato seedling root hair tip showing spherical L-forms of bacteria (arrows; bar = 20 µm; stained with 3,3-diaminobenzidine followed by aniline blue).

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Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes

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In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase.

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A series of short videos on testing soil for microbial life and for nutrients, structure etc.

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Working in partnership, the Innovation for Agriculture (IfA), Catchment Sensitive Farming (CSF) and Ernest Cook Trust have produced a series of 'Learning fro...

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Using polycultures, ground cover and animals to restore the living soil.

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Using polycultures, ground cover and animals to restore the living soil.

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And excellent article, an example of transition to agriculture that regenerates soil by the EU.

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Benefits of Mycorrhizal Fungi for Plant Growth

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Benefits of Mycorrhizal Fungi for Plant Growth

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Use of arbuscular mycorrhizal fungi and organic farming 

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Use of arbuscular mycorrhizal fungi and organic farming 

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In one chapter, Pollan looks at how fermentation played a role in human evolution and food cultures, storage economies and health.  He learns to make cheese, beer, sourdough bread, sauerkraut and other foods that are preserved for us by microbes.

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A Natural History of Transformation

In Cooked, Michael Pollan explores the previously uncharted territory of his own kitchen. Here, he discovers the enduring power of the four classical elements-fire, water, air, and earth- to transform the stuff of nature into delicious things to eat and drink. Apprenticing himself to a succession of culinary masters, Pollan learns how to grill with fire, cook with liquid, bake bread, and ferment everything from cheese to beer. In the course of his journey, he discovers that the cook occupies a special place in the world, standing squarely between nature and culture. Both realms are transformed by cooking, and so, in the process, is the cook. Each section of Cooked tracks Pollan's effort to master a single classic recipe using one of the four elements. A North Carolina barbecue pit master tutors him in the primal magic of fire; a Chez Panisse-trained cook schools him in the art of braising; a celebrated baker teaches him how air transforms grain and water into a fragrant loaf of bread; and finally, several mad-genius "fermentos" (a tribe that includes brewers, cheese makers, and all kinds of picklers) reveal how fungi and bacteria can perform the most amazing alchemies of all. The reader learns alongside Pollan, but the lessons move beyond the practical to become an investigation of how cooking involves us in a web of social and ecological relationships: with plants and animals, the soil, farmers, our history and culture, and, of course, the people our cooking nourishes and delights. Cooking, above all, connects us.

The effects of not cooking are similarly far reaching. Relying upon corporations to process our food means we consume large quantities of fat, sugar, and salt; disrupt an essential link to the natural world; and weaken our relationships with family and friends. In fact, Cooked argues, taking back control of cooking may be the single most important step anyone can take to help make the American food system healthier and more sustainable. Reclaiming cooking as an act of enjoyment and self-reliance, learning to perform the magic of these everyday transformations, opens the door to a more nourishing life.

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In Cooked, Michael Pollan explores the previously uncharted territory of his own kitchen. Here, he discovers the enduring power of the four classical elements-fire, water, air, and earth- to transform the stuff of nature into delicious things to eat and drink.

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Another EU funded research project and a remarkably resource. Downloadable for free.

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A very useful resource and can be downloaded for free.

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Soil Atlas of Europe - ESDAC - European Commission

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The atlas is the result of a collective effort by more the 40 National soil surveys and soil science institutions cooperating across Europe within the European Soil Bureau Network (ESBN).

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Paul Stamet's 'manual for the mycological rescue of the planet'.

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Mycelium Running is a manual for the mycological rescue of the planet. That's right: growing more mushrooms may be the best thing we can do to save the environment, and in this groundbreaking text from mushroom expert Paul Stamets, you'll find out how.

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Fungi matter | Dr. Demetra Kandalepas | TEDxLSU

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Suzanne Simard Talks About The Wood Wide Web

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Suzanne Simard Talks About The Wood Wide Web

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Dr Suzanne Simard gives a seminar on the mycorrhizal network (the wood wide web) that is essential for healthy soil and nutrient uptake.

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Wood Wide Web: Dr. Suzanne Simard on the Secret Life of Tree and the Importance of Networks

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Humus - the essential ingredient: Graeme Sait at TEDxNoosa

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This website has quite a few articles about soil microbes.

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An inquiry came my way, some years ago, from a worried homeowner who had second thoughts about instructing his gardener to remove thirty yards of newly spread compost because it was full of what appeared to be tiny hopping insects. Springtails, the tiny arthropods that precipitated the hasty compost removal, are ubiquitous in gardens and play an essential role in decomposition of organic materials. They are seldom noticed but can be present in great abundance in leaf litter, compost, and other organic materials. Although the homeowner was relieved to learn that the compost was safe, the gardener may have been less pleased about having moved so much compost three times.

The soil food web includes many species of tiny arthropods, known collectively as "microarthropods." In an earlier article (see Pacific Horticulture, October 2010), we explored the almost invisible world of soil microorganisms: bacteria, actinomycetes, protozoans, algae, and others. Microarthropods and other small soil animals are visible (sometimes barely so) but miniscule; most require some level of magnification for identification. Many microarthropods, especially springtails and soil mites, are responsible for breaking down organic material into a form that bacteria can consume, and are fundamental to the creation of humus and the formation of soil.
Biodiversity below Ground
Biodiversity in the soil food web supports above-ground biodiversity. The thin layer where soil and litter meet is especially crucial to this process. This layer of soil is the most biologically active; many species of microarthropods thrive only in the interface between soil and litter. Others are found in deeper layers; these are often thinner, wormlike in form, with shorter legs than their counterparts in leaf litter. The distribution of differently adapted species in soil layers is a good reason to avoid disturbing soil layers whenever possible. For instance, in his book, Life in the Soil, James Nardi points out that springtail species may be separated by only a thin layer of soil, yet have an appearance and behavior distinctly different from one another.

Soil mites are the most abundant soil microarthropods in all but arid and semi-arid environments (where ants play a leading role). About half of all mite species are soil dwellers; some are predatory, but most are scavengers. One scavenger is the tiny oribatid mite, the most abundant soil mite in the upper layers of soil. Sometimes called "seed mites," they are able to close their "shells" and resemble small dark shiny beetles. Other mites dwell deep in the soil; little is known of their role. Pseudoscorpions are tiny, harmless arachnids (unless you are a springtail, their preferred prey) that look like miniature stingless scorpions. They often travel by "hitch-hiking" on larger organisms, such as daddy-long-legs and insects, a relationship known as "phoresy." Many small species of spiders also inhabit leaf litter and the top layers of soil.

Some species of centipedes and millipedes are found in soil; the tiny individuals may be juvenile forms of larger species. Symphylans are occasionally farm and garden pests. Symphylans generally eat decomposing matter; if populations increase dramatically, however, they can also eat roots. To avoid symphylan issues, compost that is not fully decomposed should be applied only as a surface treatment and not mixed into the soil. Crustaceans such as pillbugs and sowbugs have several miniscule relatives that may be found in water features; among these are copepods and daphnia. Look closely at a backyard pond, and you may see some of these interesting kinds of crustaceans swimming about.
Insects, Too
Numerous species of insects may be included with microarthropods. Even a seasoned beetle collector may be surprised at the diversity of tiny beetle species found in the soil. Ants, true bugs, crickets, and termites are all found in the soil and leaf litter. Several groups of arthropods with three pairs of legs, once classified as insects, have recently been moved into their own groups, based on differences in their mouthparts. In addition to the springtails, diplurans and proturans (blind, pale soil predators) have been moved into their own respective groups.

Besides arthropods, other miniscule soil organisms are present. Rotifers are so small that they are often mistaken for single-celled protozoa, but they are actually complex animals. Although usually found in water, a few species are soil dwellers, and may be found in moss or lichen, navigating through a film of water in search of prey. If the soil dries out, rotifers may survive drought in the form of cysts and reanimate when conditions are suitable. Tardigrades can also reanimate; they are commonly found in soil, moss, and lawns, where they prey on protozoa and other organisms, and feed on algae and fungi.

The health and sustainability of any landscape begins with intelligent stewardship of its most valuable resource: the soil underfoot. Soil is not simply a canvas on which we paint our beautiful plant pictures, but rather a living substrate. A good gardener, before anything else, tends the soil-the foundation of the landscape. We believe that we are growing plants, but we are really growing soil. When we proudly show off our prize tomatoes, we might, just as proudly, show off a handful of the soil from whence they came.
Nutshell:
Popular Names:
Soil microarthropods include chelicerates (mites, spiders, and pseudoscorpions), myriapods (centipedes, millipedes, and symphylans), crustaceans (small aquatic forms often found in water features), springtails, and insects. Many groups do not have popular names; proturans and diplurans, for instance, are small soil arthropods related to insects.

Common Groups:
The most easily spotted microarthropods are oribatid mites and other soil mites, springtails (Collembola), minute beetles, pseudoscorpions, and aquatic crustaceans. Minute centipedes, millipedes, and symphylans are also common; proturans and diplurans, less so. Other minute non-arthropod soil organisms include tardigrades (water bears) and rotifers. (Nematodes will be discussed in a future article.)

Distribution:
Worldwide. Many species of microarthropods have not yet been described.

Life Cycle:
Some microarthropods are capable of parthenogenic (asexual) reproduction; for instance, orobatid mites have no need for males to reproduce. Rotifers and tartigrades share this efficient means of reproduction.

Appearance:
Varied and diverse; although many can be spotted with the naked eye, magnification is an essential gardening tool for clear viewing of these tiny organisms.

Life Span:
Varied. Most are short-lived. Microarthropods may have multiple generations annually. Those that can form cysts may be able to endure years of drought; these include some crustaceans, rotifers, and tardigrades.

Diet:
Varied. Some microarthropods function as decomposers; many are predators of other small organisms.

Benefits:
Microarthropods contribute to a healthy soil ecology, especially to decomposition of organic matter in soils and mulches; many control populations of injurious organisms.

Problems:
Symphylans may eat roots if an excess of poorly decomposed organic material is mixed into the soil.

Interesting facts:
Tardigrades share an exoskeleton in common with arthropods. They are able to dehydrate and "shut down" their metabolism, forming a cyst resistant to extremes of humidity and temperature (a process called cryptobiosis). They have been revived from dry specimens of museum moss after over a hundred years.

Sources:
When sufficient organic matter and moisture are present, an abundance of microarthropods is sure to be present.
More information:
Life in the Soil: A Guide for Naturalists and Gardeners, James B Nardi. An essential text on soil; engaging and informative, with wonderful illustrations.

Dirt: The Ecstatic Skin of the Earth, William Bryant Logan. A natural history of soil; shares a great appreciation for the world beneath our feet.

Dirt: The Movie. Narrated by Jamie Lee Curtis, a wonderful, eye-opening look at soil.

http://www.uni.illinois.edu/~dstone/microarthcollectionandexam.html. This university website is lesson based, with great links for those who wish to further explore microarthropods.

http://www.magiscope.com/ A magiscope is a wonderful little field microscope for use in identifying both macro- and microarthropods. Far more than a child's toy, it is useful for gardeners and amateur naturalists looking for affordable, sturdy magnification.

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Pacific Horticulture Society | Garden Allies: Soil Microarthropods

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An inquiry came my way, some years ago, from a worried homeowner who had second thoughts about instructing his gardener to remove thirty yards of newly spread compost because it was full of what appeared to be tiny hopping insects.

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The best book so far for gardeners and farmers about the soil food web with lots of pictures of those microscopic life forms and everything visible that lives in, on and around your soil. Fascinating and very informative.

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Healthy soil teems with life-not just earthworms and insects, but a staggering multitude of bacteria, fungi, and other microorganisms. Chemical fertilizers injure the microbial life that sustains healthy plants, and the soil becomes increasingly dependent on artificial, often toxic, substances.

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Compare the sterile patch on the left with the leaf litter transformed into humus on the right by microbes, worms and insects.

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Bioturbation with and without soil fauna

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Soil bacteria can be used to clean glyphosate from the soil.

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Mapping soil microbes: Earth Microbiome Project study

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Mapping soil microbes: Earth Microbiome Project study

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Scientists at the University of Colorado, Boulder have created the first worldwide atlas of soil microbes, mapping 500 of the most common kinds of bacteria found in soil across the globe, from deserts to grasslands to wetlands.

"It is amazing how much we still don't know about even the most dominant microorganisms found in soil," Noah Fierer, co-author of the new study and a research fellow at CU Boulder, said in a statement. "Now that we have this list, we can really focus our research efforts to categorize these major groups and see where they are and what they do."

For the study, which was published this week in the journal Science, researchers collected soil samples from 237 locations on six continents and in 18 countries. They then analyzed the microbes' DNA to track similarities and differences and created a list of 500 bacteria that account for almost half of all soil microbes. They then used computer models to map the organisms' predicted distribution and abundance.

"Most of the microorganisms that made our most-wanted list - they don't have a species name," Fierer told NPR. "They're un-described."

The work was done as part of the Earth Microbiome Project, a consortium of scientists from across the globe studying soil microbes.

The newly mapped organisms "probably play an important role, because they are dominant and ubiquitous," Janet Jansson, a microbiologist at the Pacific Northwest National Laboratory in Washington and one of the leaders of the Earth Microbiome Project, told NPR. "So I think that's what the next step has to be: Characterizing what they do, and how they are impacted by change - climate change, for example."

For more on how climate change is impacting the world's microbiomes, click here.

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Scientists Unlock Key Information About the World's Soil Microbes

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Scientists at the University of Colorado, Boulder have created the first worldwide atlas of soil microbes, mapping 500 of the most common kinds of bacteria found in soil across the globe, from deserts to grasslands to wetlands.

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But those studies have been associational and could not show whether exercise actually altered microbes or how any microbial changes might later affect health.

So for the new study, which was published in November in Medicine & Science in Sports & Exercise, scientists from the University of Illinois at Urbana-Champaign decided to track the guts of people who undertook an unfamiliar exercise routine.

The study was designed, in fact, as a follow-up to an earlier, interesting animal study by the same scientists. In that work, the researchers had allowed some lab mice to run and others to sit around for most of their adult lives. Gut material from the mice was then transplanted into animals that had been bred to be germ-free, so that their guts would easily incorporate these new tribes of bacteria. After the animals' microbiomes were established, the scientists exposed the mice to a substance that can cause tissue irritation and inflammation in the colon.

The scientists found that the animals with gut bugs from the runners were better able to resist and heal tissue damage and tamp down inflammation than those whose microbes had come from sedentary mice.

Now the scientists wished to see if exercise would likewise affect the functioning of microbes in people.

They began by recruiting 32 men and women who did not exercise. About half were obese and the rest of normal weight.

The scientists took blood and fecal samples and tested everyone's aerobic fitness. Then they had the men and women begin supervised workouts, during which their efforts increased over time from about 30 minutes of easy walking or cycling to about an hour of vigorous jogging or pedaling three times per week.

The volunteers were asked not to change their normal diets.

After six weeks, the scientists collected more samples and retested everyone, and then asked the volunteers to stop exercising altogether.

Six weeks later, the tests were once again repeated.

The subsequent analysis showed that the volunteers' gut bugs had changed throughout the experiment, with some increasing in numbers and others declining. The researchers also found changes in the operations of many microbes' genes. Some of those genes were working harder now, while others had grown silent.

Most of these changes were not shared from one person to the next. Everyone's gut responded uniquely to exercise.

But there were some similarities, the researchers found. In particular, they noted widespread increases in certain microbes that can help to produce substances called short-chain fatty acids. These fatty acids are believed to aid in reducing inflammation in the gut and the rest of the body. They also work to fight insulin resistance, a precursor to diabetes, and otherwise bolster our metabolisms.

Most of the volunteers had larger concentrations of these short-chain fatty acids in their intestines after exercise, along with the microbes that produce them.

These increases were greatest, though, among the volunteers who had begun the experiment lean compared to those who were obese, the scientists found.

And perhaps not surprisingly, almost all of the changes in people's guts dissipated after six weeks of not exercising. By and large, their microbiomes reverted to what they had been at the study's start.

Still, the study's overall results suggest that even a few weeks of exercise can alter the makeup and function of people's microbiomes, says Jeffrey Woods, a professor of kinesiology and community health at the University of Illinois who conducted the study, along with his doctoral student Jacob Allen (now a postdoctoral researcher at Ohio State University) and others.

In theory, Dr. Woods continues, these changes could contribute to some of the broader health benefits of exercise, such as its ability to reduce inflammation throughout the body.

"But more studies need to be done to prove this," he says.

He also hopes that future research can explain why the obese volunteers showed smaller gains in their fatty-acid producing microbes than the leaner men and women. Additional study could also help to determine whether and how people's microbiomes might continue to change if they exercise for longer than six weeks - a goal that all of us, of course, have resolved to do in the coming year, right?

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Exercise Alters Our Microbiome. Is That One Reason It's So Good for Us?

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But those studies have been associational and could not show whether exercise actually altered microbes or how any microbial changes might later affect health. So for the new study, which was published in November in Medicine & Science in Sports & Exercise, scientists from the University of Illinois at Urbana-Champaign decided to track the guts of people who undertook an unfamiliar exercise routine.

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Excellent talk on the basics of our gut microbiome and what we can do to maintain it.

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Excellent talk on the basics of our gut microbiome and what we can do to maintain it.

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Speaker for the Microbes: Emma Allen-Vercoe at TEDxWaterloo 2013

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She's a Microbial Ecologist with a Robogut. You're home to trillions of bacteria. Have we killed all the goods ones? Home is where the microbes are, especially if you're talking about the human digestive system. With 10 times more non-human cells than human ones, each person is literally more microbial than they thought - up to three pounds worth!

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Earth Microbiome Project: Rick Stevens at TEDxNaperville

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Plant and soil microbes: EM (Effective Microbes). 

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Plant and soil microbes: EM (Effective Microbes). 

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Dee Eggers tends to focus on a good microbe/bad microbe scenario, but it remains a fascinating view of human and plant health.

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Biohacking the microbiome: Dee Eggars at TEDxUNCAsheville

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In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience. At a TEDx event, TEDTalks video and live speakers combine to spark deep discussion and connection in a small group.

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Always listen to an Irish Granny: you are what you eat

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Always listen to an Irish Granny: you are what you eat

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Feed Your Microbes - Nurture Your Mind | John Cryan | TEDxHa'pennyBridge

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Fascinating!

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Mind-altering microbes: how the microbiome affects brain and behavior: Elaine Hsiao at TEDxCaltech

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Who are we, or what are we?  What is the self?

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Who are we, or what are we?  What is the self?

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We are an ecosystem. In the future, health will require diversity and community.

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Our Germs, Our Future.  Human Microbiome as a Community of Self. | Miriam Lueck Avery | TEDxMarin

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This talk was given at a local TEDx event, produced independently of the TED Conferences. What are we really?. Our bodies aren't really self-contained machines - they're more like ecosystems. The recent explosion of research into our body's microbial universe will change 21c treatment of metabolic, immune and psycho-emotional disorders.

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Studying the role of microbes in digestion

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Studying the role of microbes in digestion

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Studying how gut microbes work in pets is a way to understand the human microbiome and how it functions.

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The Microbiome | Daniel P. Beiting | TEDxPeddieSchool

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The Microbiome Dr. Daniel Beiting was born and raised in Ohio. After attending college at Appalachian State University, Dan moved on to pursue his doctorate in Immunology at Cornell University, where his studies focused on understanding how the immune system copes with chronic parasitic infections.

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Hygiene might have altered the development of our immune system, the collection of organs that fight infections and internal threats to our health.

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by Asu Erden + BIO

Parasitic hookworms. Photo by Getty

Between the mid-1990s and the mid-2000s alone, the likelihood of having a classmate with a food allergy increased by 20 per cent in the United States. In fact, over the past five decades, the incidence of all allergies and autoimmune diseases - caused by your body attacking itself - has skyrocketed. What could explain our sudden hypersensitivity to our surroundings and ourselves? Since evolution operates on the timescale of millennia, the culprits lie not in our genes but somewhere within our environment.

One thing that has changed in public health is our awareness of germs and how they spread. In response to that insight, over the past half-century our implementation of hygiene practices has spared us from debilitating infections and enormous human misery. But the new vigilance might have altered the development of our immune system, the collection of organs that fight infections and internal threats to our health.

The idea that too clean an environment might be harmful has been dubbed 'the hygiene hypothesis'. The concept has been perverted by some to suggest that the less clean the environment, the better. But its meaning is different: it is not dirt that we are missing but exposure to certain microbes that normally contribute to the development of our immune system. 'It's not that we aren't exposed enough to microbes but that we're not exposed to the right types of microbes,' says the immunobiologist Ruslan Medzhitov at the Yale School of Medicine, also head of the Food Allergy Science Initiative at the Broad Institute.

So what has changed? In short, it's the standard for what constitutes a good microbe versus a bad one. 'Take bacterial species that increase nutrient absorption from food,' Medzhitov says. These were immensely beneficial at a time where you had to go days without eating. Today in the parts of the world with an overabundance of food, having such bacteria in your intestine contributes to obesity. 'Microbes that cause intestinal inflammation are another example of what we call bad microbes because they induce [detrimental immune] responses. But in the past, these microbes could have protected you from intestinal pathogens,' he adds.

The most common such foes are helminths (commonly known as intestinal worms). While they have been eradicated in most of the economic West, their absence from our environment might be contributing to the increase in allergic and autoimmune diseases by diverting our immune system's attention towards our food and ourselves. This is what Ken Cadwell, a microbiologist at New York University (NYU), contends. He is interested in better understanding Crohn's, an autoimmune disease caused by our immune system attacking our gastrointestinal tract.

Cadwell's team discovered that the bacterium Bacteroides vulgatus causes reduced mucus secretion in mice, something that results in the condition. In collaboration with the parasitologist P'ng Loke, also at NYU, Cadwell then decided to treat mice that had Crohn's disease with helminths, known to trigger mucus secretions in the intestine. And it worked! The two researchers identified that the ensuing establishment of Clostridiales bacteria in the gut cured the mice.

But would it work in humans? Loke collected stool samples from populations living in helminth-endemic areas in Malaysia before and after deworming treatment, and he noticed something intriguing. People from these regions had abundant Clostridiales in their gut before treatment and a lower incidence of autoimmune bowel diseases. After successful deworming, the protective bacteria disappeared, setting the stage for autoimmune illness to rear its head.

Yet treating humans with worms will not work as a public-health measure. Worm treatment is beneficial only for those Crohn's patients with a genetic make-up causing reduced mucus-secretion and lacking Clostridiales bacteria. For everybody else, it is just a harmful infection. Now scientists are trying to better understand how to reap the benefits of worm therapy while avoiding its downsides. 'I am more in favour of an alternative that gives the same [health] effect without having to give somebody a live parasite,' says Cadwell. 'That would be ideal.'

Besides the change in our exposure to microbes, our modern lives include diets much higher in sugar, salt and carbs. Now a team from Harvard and Yale has discovered that even moderate increases in salt consumption trigger activation of immune actors, known as Th17 cells, especially prevalent in such autoimmune diseases as arthritis and multiple sclerosis, to name just two. 'Recent studies found that if you have the right [genes], your likelihood of developing rheumatoid arthritis goes up 10-fold from the average risk in the population. But if you combine that with smoking, it leads to an increased risk of 100-fold. Now a recent study also showed that if you have the right [genes], you smoke, but you also consume a high-salt diet, the risk goes up 500-fold,' says the immunologist Vijay Kuchroo at Harvard, who did the work with his colleague, the neurologist David Hafler of Yale.

We are forced to conclude that the explosion of allergies and autoimmune diseases results from a mismatch between genes selected by pressures of our evolutionary past and the reality of modern life. While we have adapted in the past, we might not be able to adapt again by relying on biology alone. There is no going back - the old world is gone. To curtail the increase in allergies and autoimmunity, we have to evolve our social, political and scientific regimes, providing healthier food options at lower cost and improving our understanding of the underlying immunological mechanisms at play.

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The very microbes that helped us evolve now make us sick | Aeon Ideas

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by Asu Erden + BIO Parasitic hookworms. Photo by Getty Between the mid-1990s and the mid-2000s alone, the likelihood of having a classmate with a food allergy increased by 20 per cent in the United States. In fact, over the past five decades, the incidence of all allergies and autoimmune diseases - caused by your body attacking itself - has skyrocketed.

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Microbiologist Claire Fraser explains clearly and comprehensively the importance of the human microbiome.

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Microbiologist Claire Fraser explains clearly and comprehensively the importance of the human microbiome.

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Are we too clean? How changing a body's microbes leads to illness | Claire Fraser | TEDxMidAtlantic

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Nutitionist and acupunturist Melissa Ramos talks about poop!

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Nutitionist and acupunturist Melissa Ramos talks about poop!

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The answer to your health is in your poop | Melissa Ramos | TEDxDistilleryDistrictWomen

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As a Nutritionist and Acupuncturist, Ramos' high-heeled approach to health helps people feel sexy from the inside out and focuses on digestive imbalances, mental health and hormone-related issues. Her topic will be "The answer to your health is in your poop" and it is inspired by her work at at www.sexyfoodtherapy.com.

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Naturopath Mark Davis talks about the history and the success of fecal transplants as a treatment for many diseases.

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Naturopath Mark Davis talks about the history and the success of fecal transplants as a treatment for many diseases.

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Fecal transplants & why you should give a crap | Mark Davis | TEDxSalem

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How swallowing someone else's poop could save your life! Dr. Mark Davis is a Portland-based naturopath who specializes in stomach and intestinal health. He is an expert in fecal transplantation, having successfully administered it for patients of many conditions. Davis cofounded Microbiomes, LLC, which was the first group in the U.S.

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Intelligence in nature and the power of microbes.

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Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves.

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Are we compromising our health by shutting outside microbes out of buildings. Jessica Green thinks we need newly trained architects and building managers who will design, create and maintain polycultural interior microbial landscapes

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Managing the magic of microbes | Jessica Green | PhD at TEDxPortland

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Many thanks to our Presenting Sponsor, The University of Oregon - White Stag Block. Jessica-aka "Thumper Biscuit" in roller derby circles-is a professor at both the University of Oregon and the Santa Fe Institute. She's a TED Fellow whose current goal is to help people visualize the invisible world of microorganisms to foster a world full of buildings that limit infectious disease and maximize energy.

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With trillions of microbial friends you should never need to feel lonely again.

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With trillions of microbial friends you should never need to feel lonely again.

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The gut flora: You and your 100 trillion friends: Jeroen Raes at TEDxBrussels

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Jeroen Raes is a bionaut, he researches the human microbiome. What he's discovered in his lab at the Flanders Institute of Biology could herald a major breakthrough not just in gastro-intestinal medicine, but in our fundamental knowledge of the human biology.

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Ruari Robertson on the basic paradigm shift in understanding microbes in our gut.

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Food for thought: How your belly controls your brain | Ruairi Robertson | TEDxFulbrightSantaMonica

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Rob Knight: How our microbes make us who we are

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Rob Knight is a pioneer in studying human microbes, the community of tiny single-cell organisms living inside our bodies that have a huge - and largely unexplored - role in our health. "The three pounds of microbes that you carry around with you might be more important than every single gene you carry around in your genome," he says.

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On the importance of cooking for human evolution, development, health, and well-being.