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https://bubbl.us/?h=3301b4/66037c/33s34V.UYcxuM&r=344085058

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-The plant immune system
(Box 1) in particular is thought to have a key role in
determining plant microbiome structure.

-In the phyllosphere of A. thaliana, induction of salicylic-acid mediated
defense reduced the diversity of endophytes,
whereas plants deficient in jasmonate-mediated defense
showed higher epiphytic diversity.(suggest that:

effects of plant defense processes on the microbiome are variable

SAR is responsible for controlling the populationsof some bacteria

-Pseudomonas syringae
produces hormone analogs that interfere with jasmonate
and ethylene signaling, resulting in stomatal opening and pathogen entry.

-Microbial deamination of ACC prevents plant
ethylene signaling, resulting in plants more tolerant to
environmental stress.

-flavonoids trigger diverse
responses in rhizobia, mycorrhiza, root pathogens and other plants.
- Strigolactones induce hyphal branching
in mycorrhizal fungi and promote seed germination of
parasitic plants.
-Some plant genes and pathways have roles in establishment of multiple interactions with
different microbes:

mycorrhizal and rhizobial symbioses

the mycorrhizal symbiosis and infection by oomycetes

rhizobial symbiosis
and infection by nematodes

-Plants produce a wide variety of antimicrobial compounds

both constitutively and in response to pathogens.

-The eukaryotic Amoebozoa and Alveolata were strongly
affected by the lack of avenacins in the mutant, whereas bacterial communities were unaffected.(a small change in plant genotype can have complex and unforeseen effects on the plant microbiome).

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Approaches that have been made to study plant microbiome:

1. PCR amplification of ubiquitous 16S ribosomal RNA gene is commonly used to study prokaryotes – allows precise taxonomic identification.

2. The hypervariable internally transcribed spacer is often used to study eukaryotic microbes. Limited to only identifies the target organisms.

3. Metagenomics – Reveal the functional potential of a microbiome (the abundance of genes involved in particular metabolic processes).

4. Metatranscriptomics
– Provide snapshots of community-wide gene expressions.

– Has revealed kingdom-level changes in the structure of crop-plant rhizosphere microbiomes.

5. Metaproteomics – Provide snapshots of protein abundance.

6. Stable isotope probing allows organisms metabolizing a particular labeled substrates to be identified – used in the studies of rhizosphere microbiomes.

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1. Rhizosphere: region of soil influenced by plant roots through rhizodeposition of exudates,mucilage and sloughed cells.

2. Root exudates determine of rhizosphere microbiome structure.

3. Sloughing of root cells and the release of mucilage deposits cellulose and pectin into the rhizosphere.

4. The decomposition of pectin releases methanol which can b used as a carbon source by
other microbes, and active metabolism of methanol in the rhizosphere.

5. Rhizosphere promote rhizobacteria. Rhizobacteria act antagonistically towards plant pathogens by producing
antimicrobials or by interfering with virulence factors via effectors delivered by type 3 secretion systems.

6.The soil becomes disease suppressive as a result of the establishment of antagonistic microbial communities

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-Endophytic bacteria reside within plant tissues
-Non-pathogenic,but can cause disease by latent pathogen if triggered by environmental factors and the genotype of the plant
-Differs from Rhizospheric bacteria in terms of entry to the plant.
-Entry to the plant roots through natural breaks in roots or plant root tips
-Colonization at apoplast
-Huge diversity of endophyte in crops sugarcane or rice
-Rhizobia is a common endiphyte
-Alters the expression of plant defense-response gene.Eg. R gene and LRR-containing-like-receptor kinases.
-When challenged by phytopathogen,the transcription of the gene will be upregulated(ERFs)
-Mutualistic behaviour(endophytic diazotrophs,protecting agent,growth characteristics.

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1. Also known as aerial surface of a plant.

2. Nutrient poor environment.

3. Microbial colonization of leaves is affected by the leaf structures (veins, hairs & stomata).

4. Phyllosphere is a more dynamic environment than rhizosphere (because the phyllosphere microbes can withstand changes in temperature, moistures and radiation during the day and night).

5. The abiotic factors indirectly cause changes in plant metabolism.

6. Factors that aid in variability of phyllosphere microbes :

o   Precipitation

o   Wind

7. Microbes are more abundant in environment :

o   Warm

o   Humid

8. Dominant bacterial phylum in phyllosphere :

o   Proteobacteria (the most dominant)

o   Bacteroidetes

o   Actinobacteria

9. Phyllosphere microbiomes have little similarity to airborne microbes.

10. Primary nitrogen and carbon sources :

o   Ammonium

o   Amino acids

o   Simple carbohydrates

11. Evidences present that indicate phyllosphere is a nutrient-poor environment :

o   Stress response proteins

o   Porins

o   Components of ATP binding cassette (ABC) transporters

o   TonB-dependent receptors

12. Phyllosphere microbes are not entirely dependent on the plant for their energy metabolism (due to the presence of microbial rhodopsin).

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Roles of plant microbiome :
~key determinant of plant health and productivity
~assists root uptake of mineral nutrients (phosphate)
~key players in global biogeochemical cycles

Manipulation of plant microbiome :
-reduce the incidence of plant disease
-increase agricutural production
-reduce chemical inputs
-reduce emissions of greenhouse gases

Ecology of plant microbiome :

1-Rhizosphere
region of rich,largely soil-derived,microbial diversity,influenced by deposition of plant mucilage and root exudates

2-Phyllosphere
nutrient poor,subject to extreme of temperature,radiation,moisture

3.Endosphere