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Plant interaction with friendly bacteria gives pathogen their break

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Plant interaction with friendly bacteria gives pathogens their break

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Professor Giles Oldroyd of the John Innes Centre explains how plant roots form beneficial interactions with microbes in the soil. Almost all plants associate with mycorrhizal fungi to help in the uptake of nutrients such as phosphate. Some plants, particularly legumes, also associate with bacteria that 'fix' atmospheric nitrogen into a form the plant can use as fertiliser.

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Fungal-plant symbiosis

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Sustainable Soil Management for Strawberries

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Plants engage in important symbiotic relationships with both bacteria and fungi that involve exchanges of nutrients; their encounters with nitrogen-fixing bacteria and mycorrhizal fungi activate the same required symbiosis pathway despite totally different outcomes. In this video, Oldroyd and colleagues describe how they identified genes that, while apparently functioning downstream of the common symbiosis pathway, are specifically required for mycorrhizal symbiosis.

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Mycorrhiza II – what is it and how does it work?

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Methods of Applying Mycorrhizal Fungi Inoculants

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Dr. Michael Amaranthus Mycorrhiza Lecture

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Mycorrhizae & Mycorrhizal Soil Amendments

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Mycorrhiza II – what is it and how does it work?

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The word „mycorrhiza" refers to the symbiosis of the roots of many plants with various fungi. This symbiosis occurs almost ubiquitously in our environment and facilitates plant life under stressful conditions. This video shows how the partners of the interaction are recognizing each other, which structures they are forming for exchanging nutrients and which plants are colonized by which group of fungi.

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microbial interaction in plant.

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yeast interaction and wine flavour

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Evolution coevolution of ant and fungus

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Evolution coevolution of the ant and fungi

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evolution antibiotics ants http://www.pbs.org/wgbh/evolution/library/01/3/l_013_01.html This segment from Evolution: "Evolutionary Arms Race," illustrates the coevolution of the leafcutter ant and the fungi on which it feeds. Leafcutters have been "farming" this fungus for millions of years, feeding, fertilizing, weeding, and harvesting it.

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Interactions between species are what define ecological communities, and community ecology studies these interactions anywhere they take place.

Table of Contents
1) Competitive Exclusion Principle 2:02
2) Fundamental vs. Realized Niche 3:48
3) Eco-lography / Resource Partitioning 5:25
4) Character Displacement 7:29
5) Mutualism 9:15
6) Commensalism 9:55

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Community Ecology: Feel the Love - Crash Course Ecology #4

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The interactions between the two populations are classified as above according to whether both populations or one of them benefit from the associationship, or one or both populations are negatively affected
Mutualism and parasitism have been most extensively studied in microbial relationships.In view of their enormous biological, medical, and agricultural implications, the mutualism and parasitism will attract greater concentration in this chapter though other will be considered briefly.
Mutualism

Mutualism describes a relationship in which both associated partners derive some benefit, often a vital one, from their living together. Attempt to summarise the main kinds of mutualistic associations; some of which are trivial and of scientific interest only but others such as Rhizobium legume association, mycorrhizae, coral-microbial association, herbivore-microbial association and lichens are very important, or indispensable, both to the local ecosystem and on a world scale.

Kinds of Mutualistic Associations Involving Microorganisms

Mycorrhizae (Sing. Mycorrhiza)
Mycorrhizae represent a mutualistic symbiosis between the root system of higher plants and fungal hyphae. Frank, who first noted the existence of such a characteristic association in the roots of Cupulifereae in 1885, coined the term 'mycorrhiza'. Over the last 20 years, basic works conducted by hundreds of researchers from different countries has shown that this association is fundamental and universally occurring. Among the different symbiotic associations between the soil microorganisms and root of plants, mycorrhizae are the most prevalent as they occur on more than 90% of the vascular plants. However, Kumar and Mahadevan (1984) have studied a large number of mycorrhizal associations are found that they are highly influenced by the toxic substances that, when present, are essentially concentrated in the root of plants. Such substances may be alkaloids, phenolics, terpenoids, tannis, stilbenes, etc.
Advantages

1. The fungus derives nutrients via the root of the plant. Sugars formed in the leaves move down the stem as sucrose. Sucrose itself never accumulates in the fungus; it is converted into isomers such as 'trehalose' thus resulting in the low sugar concentration.
2. The fungal hyphae act like a massive root hair system, scavenging minerals from the soil and supplying them to the plant.
3. Because of this associationship the plant partner, in addition to the nutritional benefits, develops drought resistance, tolerance to pH and temperature extremes, and greater resistance to pathogens due to 'phytoalexins' released by the fungus.
Classification

Mycorrhizae are generally divided into two types, although a third type that is more or less a combination of the first two is recognized by some.
The two major types are termed Ectomycorrhizae and Endomycorrhizae while the third one, however, is referred to as Ectendomycorrhizae.

Ectomycorrhizae (Ectotrophic mycorrhizae) Ectomycorrhizae are common on many forest trees, particularly pines, beech and birch which are of much economic value.The fungal hyphae form a sheath over the outside of the roots which is generally called 'mantle of hyphae'. From this mantle, a hyphal network called hartignet extends into the first few layers of the cortex or rarely deeper and then reaches the endodermis.Root hair formation is suppressed in the infected root and the root morphology is changed by the repeated formation of short branches with blunt tips and limited growth. Common ectomycorrhizal genera are Basidiomycetes, particularly Agaricales such as Amanita, Tricholoma, Russula, Lactarious, Suillus, leccinum and Cortinarius; some Ascomycetes such as the truffles have also been reported.

The fungi of Ectomycorrhizae secrete various growth promoting substances such as auxins, cytokinins and gibberellic acids. Nevertheless, they produce some antimicrobial substances which protect the host plant against soil-borne pathogens. Fungi derive their carbon from the host in the form of glucose, fructose or sucrose which is ultimately converted to mannitol, trehalose, and glycogen. These mycorrhizae are known to stimulate plant growth and nutrient uptake in soils of low to moderate fertility.

Vesicular-arbuscular (VA) mycorrhizae
Vesicular-arbuscular (VA) mycorrhizae represent associations between fungi, mostly the members of Zygomycetes, and a great number of angiosperms such as trophical forest trees, almost all agricultural crops (except rice in paddy fields) and most of the herbs and grasses of trophical and temperate natural ecosystems. Fungi forming VA mycorrhizae are restricted to only one family, Endogonaceae, of Zygomycetes with two genera, Endogone and Glomus, forming associations with a huge variety of distantly related plants. VA mycorrhizae are especially important because of their widespread occurrence and association with agricultural crops. In VA mycorrhizae the fungal hyphae develop some special organs, called vesicles and arbuscules, within the root cortical cells. Vesicles are thick walled, spherical to oval in shape, borne on the tip of the hyphae either in intercellular spaces or in the cortical cells of the root. These vesicles are food storage organs of the fungus. However, the arbuscules are brush-like dichotomously branched (extensively) haustoria developed within the cortical cells. Though widely distributed geographically, the VA mycorrhizae are not of usual occurrence in continuously flooded sites (Keeley, 1980).

VA Mycorrhiza

The importance of VA mycorrhizae is in the effects that they have on plant nutrition, especially the immobile elements such as phosphorus. The external hyphae greatly increase the volume of soil and translocated the phosphorus to the roots. Plants are heavily infected with VA mycorrhizal fungi in phosphorus-deficient soils and myucorrhizae are poorly developed when the phosphorus supply is adequate. It is thus a self-regulating system, increasing, phosphorus uptaken when this element is in short supply. The phosphorus so absorbed is converted into polyphosphate granules in the hyphae and passed to the arbuscules for ultimate transfer to host plant.

Orchidaceous mycorrhizae
Orchidaceous mycorrhizae are very different from VA mycorrhizae. Here the higher plant is temporarily or permanently parasitic on the fungus; the later are mostly from the genus Rhizoctonia with the perfect stages occurring in basidiomyetes and ascomycetes. Orchid seeds are minute (0.3-14 mg), without any significant food reserve. Some fail to germinate at all unless infected by fungus; others germinate, but, development soon ceases unless the seedling becomes infected by the fungus (Hardley, 1975). The hyphae of the fungus penetrate the cells of the cortex and form coils within the cortical cells. These nutrient rich hyphal coils, generally called peletons, then break down making food available to the plant. How the orchid persuades the fungus to undergo this bizarre self-sacrifice is not known, though the role of "Phytoalexin orchinol" has been implicated. However, the degenerating peletons supply the orchid with carbohydrate and probably vitamins and hormones obtained by saprophytic action of fungus outside the root. most orchids eventually become green, and so the association between the orchid and the fungus may shift from parasitism to mutualism. Other orchids, e.g., Neottia nidus-avis (bird's nest orchid) remain acholorophyllus and parasitic on the fungus throughout their life

Ericaceous mycorrhizae
Ericaceous mycorrhizae are associated with the two families, ericaceae and epacridaceae, in which the fungus forms dense intracellular coil in the outer cortical cells.Earlier, it was believed that the fungus was Phoma sp. but cultural studies proved that it is Pezizella ericae (an ascomycete). This fungus has trememdous capacity of mineralization and absorption of organic nitrogen, thus it greatly stimulates nitrogen uptake and plant growth even in infertile peat soil. Englander and Hull (1980) have suggested Clavaria spp. as the mycorrhizal fungus of Rhidodendron spp. and Azalea spp. However, this mycorrhizal association result in no development of root hairs as well as the absence of epidermal cells of the root.

Ericaceous Mycorrhiza; Ectendomycorrhizae (Ectendotrophic mycorrhizae) The mycorrhizae which bear the characteristic of both, ecto- and endomycorrhizae, are categorised by some as Ectendomycorrhizae. The fungal partner established mantle of hyphae on the surface of the root as well as hyphal coils and haustoria within the invaded cortical cells of the root. In the forests, 'Conifer-Boletus-Monotropa' association represents a well studied example of Ectendomycorrhizae. Monotropa, a nonchlorophyllous plant, usually grows near the roots of the conifers in the forests. It is now well established that a fungus called Boletus forms a common mycorrhizal association between the conifer and Monotropa, though the nature of the association differs with the two plants. Boletus forms ectomycorrhiza with Monotropa and endomycorrhiza with the conifer. The fungus forms a bridge between the two plants.
Syntrophy

Syntrophy (Gr. syn=together; trophe-nourishment) is such mutualistic interrelationship between two different microorganisms which together degrade some substances (and conserve energy doing it) that neither could degrade separately. In most cases of syntrophism the nature of a syntrophic reaction involves H2 gas being produced by one partner and being consumed by the other. Thus, Syntrophy has also been called interspecies hydrogen transfer. Following are some examples of syntrophic associations:

(i) Ethanol fermentation to acetate and eventual production of methane is a good example. Ethanol oxidizing bacterium ferments ethanol producingH2 which is a valuable electron donor for methanogenesis hence used by a methanogen. When both these reactions are summed, the overall reaction is exergonic (i.e., energy releasing). Actually, the oxidation of ethanol to acetate plus H2 is energetically unfavourable, the reaction becomes favourable when H2 produced during it is consumed by the methanogens. In this way, both partners thus use the energy released in the coupled reaction of syntrophic association.
Ethanol Fermentation to Methane and Acetate By Syntrophic Association

(iii) Syntrophobacter degrades low molecular weight fatty acids (e.g., propionic acid) to produce H2 which, if not consumed, inhibits the growth of the producer. When this hydrogen is immediately consumed by Methanospirillum, the syntrophic partner, the growth rates of both Syntrophobacter and Methanospirillum is stimulated, i.e., both partners are benefited.

Microbial Action in the Rumen of Ruminants

The cellulases hydrolyse the cellulose to glucose, and the microorganisms then ferment the glucose to a variety of organic acids such as acetic acid (ethanoate), butyric acid (butyrate) and propionic acid (propionate), so providing energy for their own growth. About 103 dm3 per day of Co2 and CH4 are produced as waste products, which are burped out by the animal. Thus the microorganisms present in rumen convert largely indigestible plant material into low molecular weight carbon compounds which can be utilized by the herbivore.

Microbial Action in the Rumen of the Ruminants

Microbes in herbivore-rumen
Though less in number than the bacteria, the protozoa may be 50% of the biomass and they include isotrichia, Diplodinium, Dasytrichia and Epidinium. Generally, these protoza have been assigned a role in increasing bacterial turn over rate by their feeding; they remove about 1% of the bacteria per minute. Some of the protozoa can also degrade cellulose but probably not significantly when compared with the bacteria.Many bacteria have been isolated from the rumen but the main ones are Rumenococcus flavifaciens. R. albus, Bacteroids succinogenes. B. amylophilus and Butyrovibrio. These and others degrade cellulose and starch and generate, as earlier described, organic acids. Methane is formed by Methanobacterium ruminnantium, using hydrogen and carbon dioxide produced by the degradation.The fungi in rumen have only been reported recently; they include some yeasts but more especially there are anaerobic chytrid-like fungi with multiflagellate zoospores which are apparently widely distributed. These fungi may be significant in the digestion of lignocellulose.
Alimentary Canal of Ruminants
Herbivore-Microbial Association
Plants contain about 30% cellulose (dry weight), the large insoluble inert polysaccharide. It would be very much to the advantage of any herbivore to digest the chemical but, however, the only herbivore to possess the appropriate digestive enzyme, cellulose, is snails. All others, from insects to mammals, do not possess this enzyme and they establish mutualistic associationship with cellulose splitting bacteria and protozoa. These microorganisms generally occupy one of the several sites in the gut, the most advanced condition being that in ruminants. Ruminants, such as cow and sheep, have evolved a unique four chambered 'stomach' that has helped establish them as extremely successful herbivores. The rumen volume is large compared with size of the mammal (in the cow it is 80-100 L) so that there being a long resistance time for cellulose decomposition. Plant material is chewed, mixed with saliva and passed to rumen. The rumen contains very numerous microorganisms of which about 90% are cellulose secretors. These may be 104 to 105 protozoa. 1010 - 1011 bacteria and 4 × 104 fungi. The contents of the rumen are continually mixed by slow contractions of the wall at 1-2 minute intervals.

Bioluminescence by Marine Invertebrates and Fish
Some luminescent bacteria (e.g., Photobacterium, Beneckea) establish mutualistic association with marine invertebrates and fish (e.g., Anomalops katoptron). If oxygen is available, these bacteria that normally inhabit some specific organ of the partner, emit blue-green light. The production of light is due to luciferase enzyme that mediates the reaction of reduced flavin mononucleotide (FMNH2), molecular oxygen, and a long-chain aldehyde that produces flavin mononucleotide (FMN) in an electronically excited state. The return of the excited FMN to its ground state results in the emission of light. In turn, the animal partners supply the bacteria with nutrients and protein from competing microorganisms. However, the light emitted by bacteria is used in various ways like sexual mating rituals, search of food sources, warding-off predators, etc.

Coral-Microbial Association
Corals are highly productive and yet live in waters that are very poor in nutrients; the open ocean may have a net productivity of 50 g cm-2 year-1 whereas coral reefs may produce up to 2500 g cm-2 year-1. The reasons for this are still not clear. It is considered that the dinoflagellate symbionts, Gymnodinium microadriaticum and Amphidinium species, are ubiquitous in reed-building corals and they pass atleast 25%, and probably as much as 60 to 70% of their fixed carbon to the animal as glycerol and glucose. They may also take up nitrate from the water and pass it to the coral in a utilizable form alanine. Cyanobacteria are important on reefs in fixing nitrogen, and they may be free living or symbiotic. Bacterial symbionts living on the outside of the coral in mucilage layer have also been implicated in the conservation and rapid recycling of phosphorus and nitrogen to the corals. There are, therefore, a number of potential or actual symbiotic microorganisms which could account for the productivity of coral reefs. Apart from the productivity aspects, Gymnodinium is also very important in depositing skeletal calcium as a result of photosynthesis. The dinoflagellates apparently have to reinfect each generation of corals for they are not passed on during reproduction. How they do this is not known for they have never been found free living in the environment, though they can grow independently in culture.

Lichens are remarkable in that under natural conditions the algal-fungal or cyanobacterial-fungal association behaves as a single organism. The fungus (mycobiont) is usually an ascomycete and about 20,000 lichen fungi have been described which is approximately 25% of all known fungi.
There are only some 30 genera of algae (Phycobiont) and cyanobacteria (cyanobiont) known to form lichens. The relationship between the two associates of the lichen thallus is still not fully confirmed, though lichens have been the classic material for the study of microbial mutualistic symbiosis. The Phycobiont/cyanobiont supplies carbohydrate to the mycobiont and the latter may supply minerals to the former. We have no experimental confirmation that the mycobiont supplies minerals to its associates; also, the Phycobiont may be able to absorb its own minerals from the substrate. 'Good' laboratory conditions cause the association to break down, whilst adverse conditions help to maintain it. This indicates that the association probably enables the associates to exploit habitat which would be unsuitable when they grow apart. Lichens are considered the 'pioneer organisms'. They have been claimed to be important in increasing the rate of soil formation from bare rock (Seaward, 1977). They may accelerate physical destruction of the rock by shrinkage and expansion of the thallus, may decompose the rock by wide range of chemical substances such as carbon dioxide (acting as H2CO3), various organic acids, and chelating agents. Lichens may accumulate minerals and nitrogen which are eventually released to the primitive soil when the lichen thallus is decayed. Lichens are greatly affected (even killed) by the level of SO2 present in the atmosphere; their abundance can be used as an indicator of atmospheric pollution. They or their products may be used as food dyes, and indicators (litmus).
Lichens Classifications
Taking mycobionts into consideration, the lichens are classified into three categories:

(a) Ascolichens: Those having ascomycetous mycobiont. Examples: Paltigera, Parmelia, Collema, Graphis, Physcia, Cladonia, etc.
(b) Basidiolichens: Those having basidiomycetous mycobiont. Examples: Cora, Omphalina, etc.

(c) Deuterolichens: Those having deuteromycetous mycobiont. These lichens are very few in number and are mostly sterile in the sense that their fungal associates do not produce spores

Taking, phycobionts into consideration, the lichens are classified into two categories:

(a) Chlorophycophilous: Those having green algal Phycobiont.
(b) Diphycophilous: Those having green algae as well as cyanobacteria in the same thallus.Those lichens that have only blue green bacteria (cyanobacteria) and fungal partner in their thalli are called cyanophillous.
Taking morphology into account, lichens are classified into three forms:

(a) Crustose: Crust-like, the crusts are so closely attached to the substratum by the whole of its lower surface that is very difficult to dissociate them without breaking. Example - Lecidea, Graphis, Verrucaria, etc.
(b) Foliose: Leaf-like; adhere to the substratum only at definite points by means of certain outgrowths called 'rhizines'. Ex-Gyrophora. Peltigera, Parmelia, Physcia, Collema, etc.
(c) Fruticose: Shrubby, generally upright in habit; some are pendent, i.e., hang from the twigs and branches of the trees. Examples - Cladonia, Ramalina, Evernia, etc. 9shrubby) and Usnea barbata (pendent).

Anatomically, lichens can be classified into two types:
Parasitism
(a) Homolomerous: When algal/cyanobacterial counterpart scattered irregularly but uniformly among the fungal counterparts within the thallus; no any definite cortical layer.
(b) Heteromerous: Thallus with remarkable differentiation into zones: algal/cyanobacterial counterpart contained to a particular zone or layer.
Mycoparasitism
Parasitism represents the symbiotic associationship between two living organisms and is of advantage to one of the associates (parasite) but is harmful to the other (host) to a greater or lesser extent. The parasites may be destructive or balanced. The former destroy the host cells in their later stages of development whereas the latter fulfil their demands from the host in such a way that the host cells are not destroyed but continue to live.
Facultative and Obligate Parasites
Associations would be easy to describe if organisms always behaved in the same way. Unfortunately, they do not. Many microorganisms, for instance, can survive as both parasites and saprophytes. The fungus Ceratocytstis ulmi, which causes Dutch elm disease, kills the tree and then lives saprophytically on its dead remains. Such an organism which mostly lives as saprophyte but seldom holds the charge of a parasite is referred to as facultative parasite. In contract, downy mildews, powdery mildews, etc. only grow on live protoplasm of the host plant in nature. Such as organism which cannot live elsewhere except on the living protoplasm of its host in nature is called obligate parasite (biotroph). Facultative and obligate parasites often differ in their pathogenic effects, i.e., in their ability to injure the host. Since obligates are restricted to living organisms, their effects on the host are often less severe, although the host may show less vigorous growth. In contrast, facultative parasites which have only recently acquired a host, tend to be more damaging.

When one fungus parasitizes the other, the act is referred to as 'mycoparasitism'. This term has been generally used interchangeably with 'hyperperasitism'. 'direct parasitism' or 'interfungus parasitism'. This incitant is generally called 'mycoparasite' or 'hyperparasite'. Mycoparasitism has been classified into two main groups on the basis of nutritional relationship of parasite with host : necrotrophic and biotrophic.

(a) Necrotrophic Mycroparasitism
The necrotrophic (destructive) parasite makes contact with its host, excretes a toxic substance which kills the host cells and utilizes the nutrients that are released.

(b) Biotrophic Mycoparasitism
The Biotrophic (balanced) parasite is able to obtain its nutrients from the living host cells, a relationships that normally exists in Nature. The Mycroparasitism is of common occurrence and examples can be found among all the groups of fungi from chytrids to higher basidiomycetes (Sneh et al., 1977; Dwivedi and Mishra, 1982; El-Shafie and Webster, (1979).
(b) Few examples are as follows:

A three member mycoparasitic associationship has also been reported in which chytridium parasiticum is parasite on Chytridium subercrelatum which, too parasitizes Rhizidium richmondense, another chytrid (Willoughby 1956).
The biological control of plant diseases has recently become an area intensive research in view of the hazardous impact of pesticides and other agro-chemical on the ecosystem. Amongst the biological agents, the mycoparasites have attained a significant position. It has been suggested that efforts should be made to investigate the biological control of plant diseases through parasitism and predation. Therefore, the mycologists and plant pathologists are searching for new mycoparasites because the greater number of these the greater would be the chance of exploiting them as agents for biological control. Trichoderma is an important example.
Hemibiotroph
New terms for parasites
The belief that the obligate parasites cannot be grown in laboratory on artificial culture media came at stake when after reports poured in recent years in which there are claims to grow successfully some obligate parasites on culture media. This has prompted the biologists to propose new terminologies in this respect.
BlotrophA parasite which always obtains its food from living tissues regardless of the ease with which it can be cultured in the laboratory on artificial media, is referred to as a biotroph.The term 'biotroph' is now being used for obligate parasites because some of them have been successfully cultured in the laboratory during past few decades.

A parasite is called Hemibiotroph if it attacks living in the same way as the biotroph but continues growing and reproducing even after the living tissues are dead. Hemibiotroph, infact represent facultative saprophytes.
Amensalism
A parasite, when it kills living of the host in advance of penetration during infection and then obtains its food as a saprophyte, is called a nectotroph. Necrotrophs represent the facultative parasites and are also referred to as perthotrophs or perthophytes.

Amensalism (from the Latin for not at the same table) refers to such an interaction in which one microorganism releases a specific compound has a negative effect on another microorganism. That is, the Amensalism is a negative microbe-microbe interaction. Some important examples are:

(i) Antibiotic Production by a microorganism and inhibiting or killing of other microorganism susceptible to that antibiotic is the important example of Amensalism. Concentrations of such antibodies in the bulk of soil or water are certainly small, though there could be a large enough quantity on a micro-habitat scale to give inhibition of nearby microorganisms. The antibiotics reduce the saprophytic survival ability of pathogenic microorganism in soil. The attini ant-fungal mutualistic relationship is promoted by antibiotic producing bacteria (e.g., Streptomyces) that are maintained in the fungal gardens (see box). In this case, streptomyces produces an antibiotic which controls Escovopsis, a persistent parasitic fungus, which can destroy the ant's fungal garden.
(ii) Production of ammonia by some microbial population is deleterious to other microbial population. Ammonia is produced during the decomposition of proteins and amino acids. A high concentration of ammonia is inhibitory to nitrate oxidizing populations of Nitrobacter.

A Schematic Diagram Showing the Use of Antibiotic Producing Streptomyces by Attini ants to control the growth of fungal parasite in their fungal Garden

Competition

In contrast to the positive interactions of mutualism and synergism, competition represents a negative relationship between two populations in which both populations are adversely affected with respect to their survival and growth. In this case, the microbial populations compete for a substance which is in short supply. Competition results in the establishment of dominant microbial population and the exclusion of population of unsuccessful competitors.During decomposition of organic matter the increase in number and activity of microorganisms put heavy demand on limited supply of oxygen, nutrients, space etc. The microbes with weak saprophytic survival ability are unable to compete with other soil saprophytes for these requirements and either perish or become dormant by forming resistant structures.
Predation

Predation typically occurs when one microorganism, the predator, engulfs and digests other microorganisms, the prey, and the former derives nutrition from the latter. In microbial fraternity, however, the distinction between predation and parasitism is not sharp. The interaction between Bdellovibrio bacteria and other small gram-negative bacteria is considered by some as predation but by others as parasitism. Bdellovibrio is apparently quite widespread in aquatic habitats and attacks other bacteria, normally gram-negative ones by boring a hole in the wall, entering the bacterium and causing lysis with the eventual release of many small Vibrio-shaped bacteria. The major microbial predators are the protozoa which may engulf bacteria and more rarely algae and other protozoa. These systems have been used extensively in models and simulations of predator prey-relationship. In the simplest from the protozoan population (e.g., Tetrahymena) is limited by its bacterial food (e.g., Klebsiella) and numbers of both prey and predator show cyclic oscillations. Another such example is of Didinium-paramecium (both protozoa) relationships. Didinium preys on the paramecium until the population of the later becomes extinct. Lacking a food source, the Didinium population also becomes extinct. If a few members of the paramecium population are able to hide and escape predation by the Didinium, then the paramecium population recovers following the extinction of the Didinium. Thus a cyclic oscillation can occur in the population of these two protozoans. Predatory fungi exist and have been considered as possible biocontrol agents for some diseases of plants caused by soil microorganism. Nematodes and protozoa may be trapped by a variety of net-like-hyphae, sticky surface and nooses. The organism is the invaded by hyphae and digested.

Protocooperation (synergism)

Protocooperation (or synergism), like mutualism, represents an association between two microbial population in which both population benefit from each other, but it differs from the mutualism in that the association is not 'obligatory'. Both synergistic populations of microbes are able to survive in their natural environment on their own. Protocooperation or synergism allows microbial population to perform metabolic activities such as synthesis of a product which neither population could perform alone.
Following are few examples:

(i) The Desulfolvibrio bacteria supply H2S and CO2 to Chlorobium bacteria and, in turn, the Chlorobium bacteria make sulphate (SO4) and organic material available to Desulfovibrio. Thus the mixture of the two bacterial populations produce much more cellular material than either alone.
(ii) Nocardia population metabolizes cyclohexane resulting in degradation products that are used by Pseudomonas population. The Pseudomonas population. The pseudomonas species produce biotin and growth factors that are required for the growth of Nocardia.

(iii) Azotobacter population present in soil fixes atmospheric nitrogen if they have a sufficient source of organic compounds. Other soil bacterial populations such as cellulomones are able to utilize the fixed form of nitrogen and provide the Azotobacter population with needed organic compounds.
Commensalism

Commensalism represents a relationship between two microbial populations in which one is benefit and the other remains unaffected (i.e., neither benefit nor harmed). Thus the commensalism is a unidirectional relationship between two microbial populations, It is quite common, frequently based on physical or chemical modifications of the habitat, and is usually not 'obligatory' for the two population involved. Commensalistic association is often established when one microbial population, during the course of its normal growth metabolism, modifications the habitat in such a way that the other population is benefited.
Following are some examples:
(i) A disease causing microbial population when a lesion on the surface, it creates an entry-passage for other microbial population that otherwise could not enter and grow in the host tissues. For convenience, Mycobacterium leprae, the causative agent of leprosy, open lesions on the body-surface and thus allow other pathogens to establish secondary infections.

(ii) When facultative anaerobes utilize oxygen and lower the oxygen content, they create anaerobic habitat which suits the growth of obligate anaerobes because the latter benefit from the metabolic activities of the facultative anaerobes in such a habitat. On the contrary, the facultative anaerobes remain unaffected. The occurrence of obligate anaerobes within habitats of predominantly aerobic character, such as the oral cavity, is dependent on such commensal relationship.
(iii) Population of Mycobacterium vaccae, while growing on propane cometabolizes (gratuitously oxidizes) cyclohexane to cyclohexane which is then used by other bacterial population, e.g., Pseudomonas. The latter population is thus benefited since it is unable to oxidise cyclohexane to cyclohexanone. Mycobacterium remains unaffected since it does not assimilate the cyclohexanone.

Cometabolism

Cometabolism is the process in which one organism growing on a particular substrate gratuitously oxidizes (i.e., oxidizes without any motive) a second substrate which is of no use for it. The oxidation products, however, are well used by other organism.
An Example of Commensalism based on cometabolism

Some microbial populations create Commensalistic habitat by detoxifying compounds by immobilization. Leptothrix bacteria deposite manganese on their surface. In this way, they reduce manganese concentration in the habitat thus permitting the growth of other microbial populations. If Leptothrix do not act so, the manganese concentration would be toxic to other microbial population.

Fungal Gardens
The fungal gardens of ants (e.g., attini ants, Acromyrmex), ambrosia beetles, and some termites are excellent mutualistic examples of an insect helping fungi to grow in pure culture.Attini ants macerate leaf material, mix it with saliva and faecal matter, and inoculate the prepared substrate with fungus. After the fungus flourishes, the ants harvest a portion of the fungal biomass and the byproducts they ingest. Ambrosia beetles and some termites develop fungal pure-culture in their habitat and rely on the cellulolytic enzymes of the microbial populations to convert plant remains into habitat sources that they can use. The insect provides an optimal habitat for growth of the fungus.

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The interactions between the two populations are classified as above according to whether both populations or one of them benefit from the associationship, or one or both populations are negatively affectedMutualism and parasitism have been most extensively studied in microbial relationships.In view of their enormous biological, medical, and agricultural implications, the mutualism and parasitism will attract greater concentration in this chapter though other will be considered briefly.

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This video share about role of microorganism interaction especially in our environment

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Metabolic Resource Allocation in Microbes Determines Ecosystem Interactions and Spatial Dynamics

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Modeling the complex nature of microbial cooperation and competition in spatially structured environments. http://www.cell.com/cell-reports/abstract/S2211-1247(14)00280-0 Authors: William R. Harcombe, William J. Riehl, Ilija Dukovski, Brian R. Granger, Alex Betts, Alex H. Lang, Gracia Bonilla, Amrita Kar, Nicholas Leiby, Pankaj Mehta, Christopher J.

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You are your microbes - Jessica Green and Karen Guillemin

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The story of symbiosis with zooxanthellae, or how they enable their host to thrive in a nutrient poor environment.

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Fungus-related parasitic microspodium that infects benthic nematodes at methane seeps on the Pacific Ocean floor

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Interaction of Rhizobia sp. which is a soil bacteria that fix nitrogen after becoming established inside root nodules of legumes.

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An animation I made for "What's Organic About Organic" about the symbiotic relationship between legumes and rhizobia and the role they play in adding nitrogen to the soil

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Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture.the article is descibe the interactions between arbuscular mycorrhizal fungi and other microorganisms is necessary for the development of sustainable management of soil fertility and crop production.

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Abstract

1 Introduction

Soil microorganisms have an important influence on soil fertility and plant health [1]. Symbiotic mycorrhizal fungi, such as arbuscular mycorrhizal (AM) fungi form a key component of the microbial populations influencing plant growth and uptake of nutrients. In addition to increasing the absorptive surface area of their host plant root systems, the hyphae of these symbiotic fungi provide an increased area for interactions with other microorganisms, and an important pathway for the translocation of energy-rich plant assimilates to the soil.

Traditionally, the influence of plant assimilates on microbial communities has been defined in relation to the rhizosphere, the narrow zone of soil surrounding living roots [ 2]. The rhizosphere is characterised by increased microbial activity stimulated by the leakage and exudation of organic substances from the root [ 3]. However, since plant roots in natural and semi-natural ecosystems are commonly mycorrhizal, the rhizosphere concept has been widened to include the fungal component of the symbiosis, resulting in the term "mycorrhizosphere"[ 4] ( Fig. 1). The mycorrhizosphere is the zone influenced by both the root and the mycorrhizal fungus, and includes the more specific term "hyphosphere", which refers only to the zone surrounding individual fungal hyphae. Since mycorrhizas and fungal hyphae are more or less ubiquitous in natural soils, it could be argued that all soil could be included in the term "mycorrhizosphere".

The natural roles of mycorrhizosphere organisms may have been marginalised in intensive agriculture, since microbial communities in conventional farming systems have been modified due to tillage [ 5, 6] and high inputs of inorganic fertilisers, herbicides and pesticides [ 1, 7] ( Fig. 2). Microbial diversity in these systems has been reduced [ 8] and the functional consequences of this loss of diversity are still uninvestigated. Increased environmental awareness has progressively led to a shift from conventional intensive management to low-input, sustainable crop production in Europe. In low-input cropping systems the natural activities of microorganisms may contribute to the biocontrol of pathogens and improved supply of nutrients, thus maintaining crop health and production. A better understanding of the interactions of soil microorganisms with each other and with plants is therefore crucial for the development of sustainable management of soil fertility and crop production.

The purpose of this review is to outline the current knowledge on microbial interactions in the mycorrhizosphere of AM plants and the potential influence of agricultural practices on the microbial communities. The review focuses on interactions between fungi and bacteria. In addition, we include a brief discussion on how this knowledge is currently used and how the understanding of microbial interactions could prove important to sustainable agriculture in the future. It does not provide a complete review of biological control research, but rather concentrates on aspects of the interactions in the mycorrhizosphere, which may have practical applications. Future perspectives of AM mycorrhizosphere research are also discussed.

2 The arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis is the oldest (>460 million years BP) and most widespread type of mycorrhizal association. It is estimated that 250,000 species of plants worldwide, including many arable crops, are capable of forming the symbiosis [ 9]. The plant hosts include angiosperms, gymnosperms and pteridophytes, all having true roots [ 10]. Approximately 160 fungal taxa of the order Glomales (Glomeromycota) have been described on the basis of their spore morphology [ 11], although recent molecular analyses indicate that the actual number of AM taxa may be much higher [ 12, 13].

During the formation of AM symbiosis the fungus penetrates the root cortical cell walls and forms haustoria-like structures (arbuscules or coils) that interface with the host cytoplasm [ 9]. These fungal structures (especially the highly branched arbuscules) provide an increased surface area for metabolic exchanges between the plant and the fungus. Some AM fungi also produce vesicles, which are structures, believed to function as storage organs [ 9]. It has been estimated that in natural ecosystems plants colonised with AM may invest 10-20% of the photosynthetically fixed carbon in their fungal partners [ 14]. Clearly, this represents a significant input of energy into the soil ecosystem and this carbon may be crucial to microorganisms associated with the mycorrhizosphere.

Arbuscular mycorrhizal fungi also interface directly with the soil by producing extraradical hyphae that may extend several centimetres out into the soil [ 15]. Extraradical hyphae can have a total surface area of several orders of magnitude greater than that of roots alone, which increases the potential for nutrient uptake, and possibly also water uptake, although results concerning the latter are still conflicting [[ 15, 16]. Hyphae of AM fungi have been shown to play an important role in soil stabilisation through formation of soil aggregates [ 17]. Additionally, the extraradical hyphae are generally believed to be important to the plants for acquisition of phosphorus (P) and other mineral nutrients [ 18]. The extraradical mycelium of AM fungi can also enhance mobilisation of organically bound nitrogen from plant litter [ 19].

Arbuscular mycorrhizal symbiosis can also alleviate negative effects of plant pathogens [ 20-23] and toxic levels of metals [ 24]. In addition, the extraradical hyphae may interact with other soil organisms either indirectly by changing host plant physiology, including root physiology and patterns of exudation into the mycorrhizosphere, or directly by physically and/or metabolically interacting with other organisms in the mycorrhizosphere.

3 Effects of AM fungi on mycorrhizosphere bacteria

Colonisation of plant roots by AM fungi can affect bacterial communities associated with the roots in both direct and indirect ways (Fig. 1). Direct interactions include provision of energy-rich carbon compounds derived from host assimilates, which are transported to the mycorrhizosphere via fungal hyphae, changes in pH of the mycorrhizosphere induced by the fungus, competition for nutrients, and fungal exudation of other inhibitory or stimulatory compounds. Indirect interactions can also take place in the form of mycorrhiza-mediated effects on host plant growth, root exudation, and soil structure.

Using a simple dilution plate technique, Ames et al. [ 25] demonstrated that a single bacterial isolate significantly increased in the mycorrhizosphere of Glomus mosseae inoculated plants compared with the rhizosphere of non-mycorrhizal plants, even though AM colonisation never exceeded 5.5%. Meyer and Linderman [ 26] also demonstrated selective differences in populations of naturally occurring taxonomic and functional groups of bacteria in the rhizosphere and the rhizoplane of mycorrhizal and non-mycorrhizal sweet corn ( Zea mays) and subterranean clover ( Trifolium subterraneum) plants. Secilia and Bagyaraj [ 27] showed that total bacterial populations in the rhizosphere of guinea grass ( Panicum maximum) were greater in plants colonised by Glomus fasciculatum, Gigaspora margarita and Sclerocystis dussi than in non-mycorrhizal plants. These authors suggested that increased amino acid exudation by P-deficient mycorrhizal plants might have stimulated the growth of amino acid-requiring bacteria.

Organic compounds produced by extraradical hyphae and the hyphae themselves play a role in aggregation of soil particles [ 17], which could provide microsites for microbial colonisation and growth. Forster and Nicolson [ 28] analysed the microbial composition of such aggregates and identified a range of bacteria, actinomycetes and algae. Andrade et al. [ 29] used compartmented systems in which roots and hyphae were separated by fine mesh in order to investigate the qualitative and quantitative effects of AM on microbial communities in the mycorrhizosphere and the stability of soil aggregates associated with it. They found that total bacteria and P-solubilising bacteria isolated from the water-stable soil-aggregate (WSA) fraction tended to be more numerous than from the unstable fraction. Schreiner et al. [ 30] found increases in WSA in mycorrhizal soybean ( Glycine max), which were dependent on the mycorrhizal fungal species involved. Differences in the bacterial communities were also found among the fungal species, suggesting that AM species may influence both WSA and bacterial composition.

Andrade et al. [ 31] examined bacteria associated with the mycorrhizosphere and the hyphosphere of the AM fungal species, Glomus etunicatum, G. intraradices and G. mosseae. The observed changes in the bacterial community in the hyphosphere were not due to the amount of AM mycelium per se, suggesting that qualitative effects (e.g., composition of exudates) of the fungal species on the hyphosphere are more important to the composition and proliferation of rhizobacteria than the quantitative development of AM mycelia in the soil.

While many studies have demonstrated qualitative and quantitative effects of AM fungi on bacterial communities, the underlying mechanisms are unclear. There are still few or no studies concerning the total amounts or spectrum of compounds released from AM mycelium. Further experiments employing spatial compartmentation of roots and mycelium are needed to distinguish between direct and indirect effects of mycorrhiza on bacterial populations. Although changed bacterial community structure has been shown in association with the mycorrhizosphere, there are no direct demonstrations of compounds produced by AM fungi, which stimulate or inhibit bacteria. There is some evidence from studies using PLFA (phospholipid fatty acid) analysis and BIOLOG™ that the effect on the bacterial populations is influenced by the mycorrhizal dependency of plants [32], however, the issue of culturability remains a general problem in studies on bacterial community structure.

4 Effects of AM fungi on fungal pathogens and N-transforming bacteria

AM fungi may also interact with other root-associated microorganisms, such as pathogenic fungi. The possible mechanisms of interaction are the same as those mentioned in the previous section. In a study by Filion et al. [ 33], the differential effects in vitro of a crude extract from the growth medium of the AM fungus G. intraradices on the sporulation of two pathogenic fungi and on the growth of two bacterial species were investigated. Conidial germination of the mycoparasitic fungus Trichoderma harzianum and the growth of Pseudomonas chlororaphis were stimulated, whereas conidial germination of the plant root pathogen Fusarium oxysporum was reduced, and the growth of Clavibacter michiganensis was unaffected. The measured effects were correlated with extract concentration and no significant influence of pH on growth or germination was detected. The authors concluded that the release of unspecified substances by the AM fungus into the growth medium was the main factor explaining the differential growth of the tested microorganisms. In other studies Citernesi et al. [ 34] screened bacteria isolated from 17 year old G. mosseae pot cultures. They found that many of the bacterial isolates within the different zones of the mycorrhizosphere were actively antagonistic against in vitro growth of the soil-borne pathogens, Fusarium and Phytophthora. Their results also suggest the possibility of integrated use of AM fungi and their associated bacteria in biological control of soil-borne pathogens.

Many authors have suggested that the ability of AM-colonised plants to better withstand an attack from root pathogens can be ascribed to an increased nutritional status in the host plant due to the presence of the AM fungus. However, there are reports which contradict this theory. In field experiments, Newsham et al. [ 22] transplanted Glomus sp.-inoculated and non-inoculated seedlings of the annual grass Vulpia ciliata into a natural population, and found that AM inoculation did not affect P concentrations in the plants. However, the mycorrhiza protected the plants from the deleterious effects of Fusarium oxysporum infection on shoot and root growth. Apparently, the AM suppressed pathogen development in the roots. Following transplantation, comparison of root-infecting mycofloras of AM and non-AM plants revealed that AM plants had fewer naturally occurring infections of F. oxysporum and Embellisia chlamydospora[ 22]. It was proposed that the main benefit supplied by AM fungi to V. ciliata is the protection from pathogenic fungi, rather than improved P uptake. This theory was also proposed by Niemira et al. [ 20], who used a peat-based medium containing the AM fungus G. intraradices to test whether it could suppress the tuber dry rot ( Fusarium sambucinum) in minitubers of potato ( Solanum tuberosum). Minitubers grown in this medium had significantly less (20-90%) tuber dry rot. They were also able to demonstrate these effects in a high-input commercial greenhouse, despite the fact that AM colonisation was very low and no evidence of enhanced plant P nutrition could be found. In addition, St-Arnaud et al. [ 23] demonstrated that the presence of Tagetes patula plants colonised by the AM fungus G. intraradices can inhibit root pathogen development in soil and thereby reduce disease severity in co-cultured non-mycorrhizal carnation ( Dianthus caryophyllus). In other experiments, Caron [ 35] observed a reduction in Fusarium populations in the soil surrounding mycorrhizal tomato ( Lycopersicon esculentum) roots, and suggested that there was a potential role for AM fungi in biocontrol of soil-borne diseases.

The presence of AM fungi is known to enhance nodulation and N fixation by legumes. Mycorrhizal and nodule symbioses often act synergistically on infection rate, mineral nutrition and plant growth [ 36]. The increased P uptake conferred by the AM symbiosis is beneficial for the functioning of the nitrogenase enzyme of the bacterial symbiont, leading to increased N fixation and consequently promotion of root and mycorrhizal development [ 37]. Amora-Lazcano et al. [ 36] studied the response of other N-transforming microorganisms to two different Glomus species. The occurrence of autotrophic nitrifying bacteria in pot cultures of sweet corn colonised by the AM fungi G. mosseae and G. fasciculatum was significantly higher than in non-mycorrhizal cultures, whereas ammonifying and denitrifying bacterial populations significantly decreased in pot cultures of mycorrhizal plants. Evidently, the presence of AM fungi can modify populations of N-transforming microorganisms and these interactions may affect nutrient availability in soils [ 36].

Although qualitative effects of AM fungi on fungal pathogens have been repeatedly demonstrated, there is still a lack of information concerning direct effects on these pathogens. There are few or no studies on interactions of AM fungi with bacterial pathogens and, as in the case of fungal pathogens, it is often difficult to distinguish between direct effects on the pathogens and indirect effects brought about by the improved nutritional status of the mycorrhizal plants.

5 Effects of mycorrhizosphere bacteria on AM fungi

Mycorrhizosphere bacteria may affect AM fungi and their plant hosts through a variety of mechanisms ( Fig. 1). Some of these have been more fully studied in ectomycorrhizal fungi [ 38], but possibilities include (1) effects on the receptivity of the root; (2) effects on the root-fungus recognition; (3) effects on the fungal growth; (4) modification of the chemistry of the rhizospheric soil; and (5) effects on the germination of the fungal propagules.

In an early study, Mosse [ 39] observed that glomalean spores germinated better on agar when bacteria were present. Later, Daniels and Trappe [ 40] showed that Glomus versiforme germinated in non-sterile soils, but not in autoclaved or irradiated soils. Germination was also enhanced following addition of kaolin or activated charcoal, indicating that the spores contained self-inhibitors, which were possibly inactivated by soil bacteria, or were immobilised by substances with a high ion exchange capacity. Similarly, Mayo et al. [ 41] showed that surface-sterilised spores of G. versiforme germinated less frequently than non-surface sterilised spores. Isolation of bacteria from these spores showed that several genera, including Pseudomonas and Corynebacterium, enhanced spore germination. Carpenter-Boggs et al. [ 42] tested the stimulatory effects of actinomycetes and Streptomyces orientalis on Gigaspora margarita spore germination and found that amounts of volatile compounds produced by the isolates correlated well with AM spore germination. Conversely, other studies using pasteurisation, fumigation or sterilisation of soils have demonstrated that the presence of some soil bacteria may also inhibit spore germination [ 43] or AM sporulation [ 44, 45].

Nitrogen fixing bacteria clearly have the potential to influence AM fungi. The presence of genes for N fixation has been shown in endosymbiotic Burkholderia sp. [ 46], but expression of this activity at levels significantly influencing the growth of the mycorrhizal association has yet to be demonstrated. Rhizobium spp. may act synergistically with AM fungi on their plant hosts. Nodulation and N fixation are commonly increased in legumes following AM colonisation, probably because the mycorrhiza supplies the plant and the rhizobacteria with P, which is essential for the enzymes involved in the N fixation process. Nitrogen fixation further promotes mycorrhizal development [ 37]. Some mycorrhizosphere bacteria may be able to promote mycorrhizal establishment through improved spore germination [ 39], but so far there are no direct demonstrations of this in the field. The colonisation enhancement may also be mutual between associated microorganisms and this has been reported following dual inoculation of Pseudomonas sp. and Glomus sp., which additionally increased the growth of the host plant in an additive manner [ 47].

A central problem in characterising effects of bacteria on AM fungi is the difficulty of identifying the active bacteria against a biological background of immense diversity (see Section 10). Clearly, mycorrhizosphere bacteria have a number of potential effects on AM fungi. A central remaining challenge is to determine whether effects demonstrated under laboratory conditions can be reproduced in the field.

6 Endosymbiotic bacteria of AM fungi

Many soil microorganisms are difficult to culture. Since non-culturable microorganisms may account for a large part of the soil microflora [ 48], the ability to identify and isolate them is important for understanding the function of these organisms in soil ecosystems. The cytoplasm of some AM fungi harbours structures called bacterium-like organisms (BLOs), however, the identification of these has been hampered since they cannot be grown on cell-free media [ 49]. Bianciotto et al. [ 50] used a combined morphological and molecular approach to demonstrate that the cytoplasm of the AM fungus Gigaspora margarita contains bacterial endosymbionts. Analysis of the small-subunit rRNA gene sequence of the BLOs in G. margarita spores led to the conclusion that these endosymbionts were closely related to the genus Burkholderia. In order to determine whether intracellular bacteria occur sporadically in individual AM fungal isolates or as a common feature in the family Gigasporaceae, Bianciotto et al. [ 51] investigated two geographically separated isolates of the species G. margarita and five other species in the genera Gigaspora and Scutellospora. The results showed that all investigated species except G. rosea contained endosymbiotic bacteria closely related to the genus Burkholderia. Further studies by Minerdi et al. [ 46] demonstrated that Burkholderia spp. in G. margarita contain genes involved in N fixation. The function and distribution of these endosymbionts remain to be explored, however, the findings suggest that these bacteria constitute a component of the fungal cytoplasm and that they must be taken into account when considering the extent of microbial diversity in ecosystems [ 50, 51].

7 Interactions at the cellular level

Many of the mycorrhizosphere microbial interactions discussed above may involve cellular interactions that are not yet understood. Bianciotto et al. [ 52] demonstrated that rhizobia and pseudomonads, commonly considered to be plant growth promoting rhizobacteria (PGPR), may attach to spores and hyphae of the AM fungus Gigaspora margarita germinated under sterile conditions in vitro. Their results showed that the degree of attachment to fungal hyphae and inorganic surfaces was clearly different between bacterial strains. However, the bacteria that did show a higher degree of attachment did not show specificity for either fungal or inorganic surfaces. It was therefore suggested that the first stages of attachment to a surface are governed by general physiochemical parameters, such as electrostatic attraction. In contrast, cell surface structures or extracellular material of bacterial origin produced around the attached bacteria provide the mechanism for a more secure, permanent attachment to the fungal structures. This suggestion was later confirmed by Bianciotto et al. [ 53], who used bacterial mutants inhibited in extracellular polysaccharide production in adhesion assays in vitro to demonstrate that such mutants were strongly impaired in the attachment to mycorrhizal structures and hyphae. Using gfp-labelled microorganisms, Lagopodi et al. [ 54] observed that the biocontrol bacteria Pseudomonas fluorescens WCS365 and P. chlororaphis PCL1391 applied to tomato seedlings occupy the same sites (the groves along the junctions of the epidermal cells) on the tomato root, as does the pathogenic fungus Fusarium oxysporum. The biocontrol bacteria occupied these sites more rapidly than the pathogenic fungus and this could be a crucial aspect of their biocontrol ability. The use of bacterial strains with increased ability to attach to roots and hyphae, and to form protective biofilms, could have useful applications in biocontrol [ 53, 55].

Filippi et al. [ 56] used transmission electron microscopy to show that bacteria were associated with the surfaces of peridium-covered spore clusters (referred to as "sporocarps"), surfaces of spores, surfaces of hyphae, and in micro-niches formed by peridial hyphae of Glomus mosseae. Bacterial cells were found embedded in spore walls, possibly by tunnels produced in the walls by the bacteria. The study determined that large numbers of bacteria, actinomycetes, and non-mycorrhizal fungi, some of which displayed chitinolytic abilities, occurred on the sporocarp surfaces and in the sporocarp homogenate.

In the past 10 years several attempts have been made to investigate possible physical interactions between AM fungi and bacteria in the hyphosphere [ 52, 53, 57]. Ravnskov et al. [ 57] studied the influence of Glomus intraradices on Pseudomonas fluorescens DF57 bacteria in hyphosphere and rhizosphere soil. They used P. fluorescens DF57 strain (DF57-P2) containing a chromosomal insertion of Tn 5::luxAB gene in a phosphate starvation-inducible locus, in combination with a control strain (DF57-40E7) with a constitutively expressed luxAB gene, to measure P starvation and metabolic activity. It was evident that the presence of AM neither induced P starvation response, nor affected the metabolic activity of the bacterium. Additionally, they found that constitutively gfp-labelled P. fluorescens did not attach to G. intraradices hyphae and could not use the hyphae as a carbon substrate. It was proposed that G. intraradices can negatively influence the growth and survival of P. fluorescens DF57, not only in the presence of roots, where the fungus can change the quality and quantity of root exudates, but also in the hyphosphere, where the microbes interact directly. Additional support for the antagonistic effects of G. intraradices on certain bacteria was reported by Wamberg et al. [ 58].

Intercellular interactions could be important because they allow rapid exchange of energy and nutrients between plant roots, mycorrhizal fungi and associated bacteria. The mycorrhizosphere may provide a beneficial environment for certain associated bacteria, which may in turn have positive effects on nutrient supply and control of pathogens.

8 Relevance of mycorrhizosphere interactions to sustainable agriculture

8.1 Sustainable nutrient supply

It is frequently suggested that AM may improve P nutrition, enhance N uptake, or improve disease resistance in their host plants. Other microbes, e.g., N fixing bacteria or P solubilising bacteria, may synergistically interact with AM fungi and thereby benefit plant development and growth [ 37]. The mycorrhizal symbiosis becomes even more important in sustainable agricultural systems where nutrient inputs are low. Under these circumstances AM mycelium (possibly in conjunction with bacteria or other fungi) could play an important role in nutrient mobilisation from crop residues. Hodge et al. [ 19] demonstrated that the presence of the AM symbiont Glomus hoi enhanced decomposition of plant litter in soil and resulted in increased N capture from the litter ( ¹⁵N- ¹³C labelled Lolium perenne leaves). Hyphal growth of the fungal symbiont was also increased in the presence of the organic material. Bacteria associated with the AM can also assist in mobilising nutrients from soil. Abundant examples of this are available from bacterial-AM-legume tripartite symbiotic relationships, where diazotrophic bacteria provide fixed N not only for the plant, but also for the fungus. As previously mentioned, nodulation of legumes by N-fixing bacteria and establishment of AM often occur simultaneously and synergistically. The presence of genes for N fixation in endosymbiotic Burkholderia bacteria in AM hyphae has been demonstrated by Minerdi et al. [ 46] and suggests that there may be a potential for improved N supply to mycorrhizal plants through fixation of atmospheric N.

Studies of tripartite symbioses are still in their infancy: more research is also needed on the possible interactions of mycorrhizal fungi with decomposition processes. As inputs of fertilisers are reduced it is increasingly necessary to exploit naturally occurring nutrient resources. These resources are distributed heterogeneously on both temporal and spatial scales, but the possible roles of mycorrhizosphere organisms in recycling these nutrients to plants are still poorly understood. There is now an increasing awareness of functional differences between different AM fungi and as our awareness of their functional capacities increases we may be able to select suitable species to maximise the ability to recycle nutrients.

8.2 Biocontrol

Microbial inoculants can be used as an alternative means for controlling pests and disease in agricultural cropping systems, permitting the reduced use of pesticides that could otherwise pose threats to human health and non-targeted organisms. The biocontrol organisms may affect AM fungi, or be affected themselves by AM fungi, in similar ways to the interactions already described above. Biocontrol agents against pathogenic fungi may in particular have negative effects on "non-target" AM fungi. The mechanisms of antagonistic interactions resulting in biocontrol may involve competition for colonisation sites or nutrients and production of fungistatic compounds. Although the literature concerning biocontrol is extensive, few studies have explicitly considered interactions involving AM fungi. Some positive effects of bacteria on AM fungal colonisation of roots may be due to antagonistic effects on competing pathogens [ 21], but also direct synergistic effects on mycorrhizal colonisation itself [ 59].

Various plant-root colonising or seed-borne Pseudomonas spp. have been shown to be potent microbiological control agents in plant-pathogen systems in vitro [ 60, 61], in greenhouse [ 62], and in the field [ 62, 63]. In one study, a bacterial isolate P. chlororaphis PCL1391 appeared to be an efficient coloniser of tomato roots and efficiently antagonised the root pathogen Fusarium oxysporum[ 64]. The bacterial strain produced a broad spectrum of antifungal substances, including phenazine-1-carboxamide (PCN), hydrogen cyanide, chitinases and proteases [ 64]. By knocking out the phenazine-biosynthetic operon it was shown that the mutants exhibited significantly lower biocontrol activity, indicating that this substance was an important antifungal factor for suppressing disease in tomato roots. For the same fungal and bacterial strains, tagged with green and red fluorescent protein, respectively, it was shown that the presence of the biocontrol bacteria resulted in 70-80% reduction of the density of the hyphal network within tomato roots [ 65]. The effects on AM fungal hyphae were, however, not studied. In addition to producing antifungal compounds, the ability of bacteria to rapidly colonise root surfaces and thereby closely interact with pathogens may further facilitate pathogenic suppression [ 54].

Research on AM fungi as protective agents against pathogens has been going on for about 30 years. Many studies have been published, but the underlying mechanisms are poorly understood. Some basic mechanisms have been suggested: improvement of plant nutrition and competition for photosynthates [ 21], however AM-induced suppression of root pathogens and stimulation of saprotrophs and plant growth promoting microorganisms may also be important [ 66]. Some authors have discussed other mechanisms, which often tend to be inconsistent among studies: these include anatomical or morphological changes in the root system induced by the AM fungus; and local elicitation of plant defence mechanisms by AM fungi [ 67]. Due to difficulties in producing large quantities of pure culture AM inoculum, relatively few studies have explored the practical use of AM fungi as inoculants to increase plant resistance to root-rotting pathogens. Combined inoculation of AM fungi with growth stimulating bacteria may favour the inoculum production [ 68]. Several studies have demonstrated that some AM fungi exhibit biocontrol properties [ 20, 22, 35] against root pathogens. Whether AM fungi could be used as biocontrol agents practically, or possibly function as vectors for associated bacteria with biocontrol properties, remains to be explored.

9 Influence of agricultural management on soil microbial communities

Different management strategies introduce different types of disturbances, which may influence microbial communities in various ways. Tillage causes a physical disruption of fungal mycelia and may change physicochemical properties of the soil. Crop rotation may cause a temporal disturbance in the presence of plant roots of a particular species. The aim of this management strategy is to disturb populations of pathogens, but it can also affect the availability of compatible host species necessary to ensure continued growth of particular mycorrhizal species and their associated mycorrhizosphere microflora. Fertilisation and application of pesticides represent chemical disturbances, and their effects depend upon application rates and involved species and soils.

Reduced tillage has been adopted more often in order to conserve soil water and reduce erosion and soil compaction caused by conventional intensive management. It is generally accepted that reducing tillage of agricultural soils can increase early-season P uptake in crops, especially in low-input farming systems [ 69]. Mixing of soil may negatively affect AM colonisation of plant roots, due to disruption of the extraradical mycelium, however, non-mycorrhizal fungi may also be affected [ 6]. Excessive soil compaction can lead to reduced soil microbial biomass and enzyme activity with adverse implications for long-term soil health [ 70]. Since AM fungi may ameliorate the nutrient status of their hosts and provide protection against pathogens, it is possible that a low degree of tillage could be beneficial to AM colonisation and crop health. Conservation tillage (i.e., no tillage or less frequent tillage) tends to concentrate plant debris and consequently microbial biomass in the topsoil, and thus promotes survival of pathogens [ 5]. The debris itself can provide an energy source available to the pathogen prior to and during host infection. However, since disease-causing microbes constitute only a proportion of the soil microbial population, a high soil microbial activity can lead to competition effects that may ameliorate pathogen activity and survival [ 5].

Fontenla et al. [71] reported that AM colonisation was not inhibited when non-host plants were grown at the same time and in the same pots as host plants. However, when non-host plants were grown in the pots before the host plants, the inoculum potential and in some cases the AM colonisation of the host plants were decreased. The authors concluded that non-host species may produce substances that inhibit the establishment of AM fungi in host roots. These compounds appear to affect the AM fungi before they become established in the root and are apparently non-systemic in nature. Another possibility, however, is that the presence of the non-host plants may have modified the bacterial community in the pots, which in turn adversely influenced the growth and colonisation of the AM fungus.

Using soils from conventional, integrated and organically managed farms, Knudsen et al. [ 72] investigated soil suppressiveness against the root pathogen Fusarium culmorum. They found that soils from integrated and organically managed systems harboured higher microbial biomass, including the pathogen population, and concluded that specific organic amendments, such as mulching with straw and the practice of using legumes as a break-crop in cereal cultivation, may contribute to a build-up of soil-borne pathogens.

Only a few studies have investigated the long-term effects of management history on microbial communities. Mäder et al. [ 73] compared AM colonisation in plots with 7-year identical crop rotation and tillage schemes that differed only in the amount and type of applied fertiliser. Root length colonised by AM fungi was 30-60% higher in plants grown in soils from low-input farming systems than those grown in conventionally fertilised soils. Additionally, soil biological activity and microbial biomass were higher in low-input soils than in conventionally managed soils. Soil aggregate stability was 10-60% higher in the low-input plots and was positively correlated with microbial biomass [ 8]. Thus, the nutrient input regime alone could influence structure and activity of microbial communities.

In a Swedish study, the variation in AM colonisation rates of three plant species found in semi-natural grasslands with different soil management histories was compared [74]. AM colonisation was significantly higher in semi-natural pastures with a long continuous management regime, compared to sites with a short or interrupted management regime (new cultural pastures). Furthermore, there was a significant positive correlation between plant species diversity and colonisation by mycorrhiza, possibly due to the fact that a long continuous management is associated with an increasing likelihood of successful dispersal of both plant and fungal species.

There are also strong indications that AM fungi have the potential to determine plant community structure [ 75] and vice versa [ 76]. AM fungi may affect the nature of weed communities in agro-ecosystems in a variety of ways, including changing the relative abundance of mycotrophic and non-mycotrophic weed species. There is thus a potential role for AM fungi in weed management [ 77].

In conclusion, conservation tillage or low levels of soil disturbance promote AM fungal development. Under these conditions plant pathogen inoculum may build up, but the improved AM fungal development may in turn control the development of pathogens and weeds. In sustainable agricultural systems the resident soil microflora becomes ever more important for ecosystem processes such as nutrient cycling and pest control. The influence of management practices on soil microbial functional groups is an important issue that needs further investigation if the full potential of these organisms is to be appreciated.

10 Outlook

Since the concepts of "rhizosphere" and "mycorrhizosphere" were coined it has been recognised that microbial populations may vary in different fractions of soil and in the various zones of the rhizosphere and the mycorrhizosphere. Many earlier studies relied on dilution plate counts to enumerate and describe microbial populations. Such methods, however, only detect culturable organisms. A large proportion of mycorrhizosphere bacteria remains unculturable, and it is therefore difficult to assess the microbial diversity in the mycorrhizosphere and the relative contribution of unculturable microorganisms to the interactions in the mycorrhizosphere. AM fungi themselves cannot be grown in pure culture, but root organ cultures [ 78] are routinely used to culture AM fungi in vitro and can be used for investigating the interactions of AM fungi with their biotic and abiotic environment [ 32, 33].

The analysis of rRNA genes has lately become an important tool for studying the diversity of soil bacterial [ 79, 80] and mycorrhizal [ 13] communities in different ecosystems. The use of fatty acid patterns of phospholipids and lipopolysaccharides (reviewed by Zelles [ 81]) and the utility of ergosterols as bioindicators of fungi in soil [ 82] have also been useful tools in the characterisation of microbial communities. Genetic markers, e.g., gfp or genes coding for various forms of luciferase [ 83, 84], or viability stains have enabled direct counts of microorganisms using luminometry, flow cytometry or microscopy [ 52, 85].

Recently, Borneman [86] described a method to identify active, but non-culturable cells in environmental samples based on their ability to incorporate the thymidine nucleotide analogue bromodeoxyuridine (BrdU) during DNA synthesis. After incubation with BrdU, the total DNA was extracted and the DNA containing BrdU was isolated by immunocapture, revealing notable differences in the bacterial communities among the different P supplementation treatments and total DNA banding patterns.

An increasing number of studies make use of PCR-based methods like denaturing gradient gel electrophoresis (DGGE) [ 79] or terminal-restriction fragment length polymorphism (T-RFLP) [ 80] for characterising complex soil bacterial communities. The advantage of DGGE is that it recognises very small differences in the nucleotide sequence, allowing a description of the community structure expressed as band patterns on a gel. This method also allows extraction and sequencing of the individual bands in the gel gradient. The advantage of T-RFLP is that it reveals the community structure without requiring culture or cloning. In common with DGGE, it gives a description of the species composition and an estimate of the relative abundance of taxa in the sample, based on the abundance of different restriction fragments detected by laser-induced fluorescence on an automated gene sequencer.

Whilst the above methods enable the in situ study of microbial communities with improved resolution, additional information is still often required about the functional capacities of identified taxa. Stable isotope profiling (SIP) now provides a promising method for describing the fraction of the community that is functionally active in metabolising a particular substrate containing one or several stable isotopes [87].

There is an inherent difficulty in determining whether mycorrhizosphere bacteria are specifically associated with roots or mycorrhizal fungi, or they simply form opportunistic associations with a range of other organisms. Fluorescent antibodies allow specific detection of cells when used in conjunction with flow cytometry or fluorescence microscopy [ 88]. However, these methods are often destructive since samples need to be fixed, and therefore continuous in situ monitoring of cells cannot be performed. New molecular techniques such as tagging of microbes with marker genes in combination with flow cytometry or microscopy have enabled non-destructive, direct visual study of microorganisms in situ [ 57, 83]. It has been recently shown that a gfp-tagged Bacillus cereus isolate from fallow field soil, incorporating BrdU, appears to attach to AM hyphal fragments [ 89]. This work raises the interesting question of the extent to which different bacteria obtain their carbon saprotrophically from dead hyphae or in association with intact mycorrhizal hyphal systems supplying assimilates derived from their plant hosts. Visualisation of microbial cells using fluorescent viability stains and confocal microscopy [ 50, 85], visualisation of fungal structures in naturally autofluorescent AM fungal species [ 90], as well as scanning electron microscopy [ 91] can be used for studying spatial interactions between bacteria and fungi. However, additional methodologies are necessary to elucidate physiological interactions.

Although the composition of microbial communities in the various parts of the mycorrhizosphere in different ecosystems has been described and discussed in many papers, the underlying mechanisms behind the interactions are still poorly known. To a great extent, this has been due to difficulties in culturing and monitoring AM fungi and associated microorganisms. In particular, the spatial complexity and possible temporal variation in the mycorrhizosphere represent formidable obstacles. However, methodological advances have greatly improved the monitoring of the fate and behaviour of microorganisms in both natural and artificial systems. An intriguing field of research that needs to be further explored is the role of cell-to-cell interactions of microorganisms. The ability of organisms to attach to and form biofilms on hyphae, roots and other surfaces could contribute to their successful application in biocontrol. Fungal hyphae may play important roles for the distribution of natural bacterial populations and could therefore act as vectors for bacteria in microbial inocula. Studying the spatiotemporal stability of such bacterial-fungal associations would provide more information on this potential and improve our understanding of microbial interactions, which may be important for the development of sustainable management of soil fertility and crop production.

Acknowledgements

Our sincere thanks go to Malin Elfstrand for critical reading of the manuscript, and Björn Lindahl and Andy Taylor for comments on an earlier version of the manuscript. We also thank Janet Jansson and Veronica Artursson for interesting discussions. We thank the two anonymous reviewers who provided critical constructive comments on the manuscript. Financial support was provided by The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS).

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Mutualism

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In many cases the fungus and the alga which together make the lichen may each be found living in nature without its partner, but many other lichens include a fungus which cannot survive on its own -- it has become dependent on its algal partner for survival.

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