The Plant Microbiome

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The Plant Microbiome by Mind Map: The Plant Microbiome

1. Introduction

1.1. Plant microbiome is a key determinant of plant health and productivity

1.2. Microbial inhabitants of the rhizosphere and phyllosphere (those near or on plant tissue) are considered epiphyte

1.3. Microbes residing within plant tissues (the endosphere), whether in leaves, roots or stems, are considered endophytes

1.4. Plant-associated microbes are key players in global biogeochemical cycles

1.5. Manipulation of the plant microbiome has the potential to

1.5.1. Reduce the incidence of plant disease

1.5.2. Increase agricultural production

1.5.3. Reduce chemical inputs

1.5.4. Reduce emissions of greenhouse gases

1.6. In agriculture, microbes may contribute to the greenhouse effect

1.6.1. Denitrification (release N2O)

1.6.2. Methanogenesis (release methane)

2. Approches for Studying

2.1. Numerous culture-independent, molecular techniques are used in microbial ecology

2.2. For studying prokaryotes, PCR amplification of the ubiquitous 16S ribosomal RNA (rRNA) gene is commonly used. Sequencing the variable regions of this gene allows precise (species- and strainlevel) taxonomic identification. They are also revealing the abundances of even rare microbial species

2.3. For studying eukaryotic microbes such as fungi, the equivalent rRNA gene (18S) may not provide sufficient taxonomic discrimination so the hypervariable internally transcribed spacer is often used

2.4. Global analyses like Metagenomics can reveal the functional potential of a microbiome (the abundance of genes involved in particular metabolic processes)

2.5. Metatranscriptomics and metaproteomics provide snapshots of community-wide gene expression and protein abundance, respectively. Metatranscriptomics has revealed kingdom-level changes in the structure of crop-plant rhizosphere microbiomes

2.6. Stable isotope probing allows organisms metabolizing a particular labeled substrate to be identified. This has been used in studies of rhizosphere microbiomes where CO2 was fed to plants and fixed by photosynthesis, revealing that a subset of the microbial community actively metabolized plant-derived carbon

3. The Rhizosphere Environment

3.1. Definition

3.1.1. Region of soil influenced by plant roots through rhizode position of exudates , mucilage and sloughed cell .

3.2. Composition

3.2.1. Root exudates

3.2.1.1. Contain organic acids and sugars, amino acids, fatty acids,vitamins , growth factors, hormones and antimicrobial compound

3.2.2. Sloughing of root cells

3.2.2.1. Deposit a large amount of materials into rhizosphere -> plant cell polymers -> cellulose and pectin

3.2.2.2. Carbon source to rhizospheres microbes

3.2.2.3. Provide structure on which microbes can attach

3.3. Distribution

3.3.1. Rhizobacteria

3.3.1.1. Act antagonistically towards plant pathogens by producing antimicrobials or by interfering with virulence factors of pathogens

3.3.2. Actinomyces

3.3.2.1. Provide compound with antibacterial, antifungal , antiviral , nematicidal and insecticidal properties. One of most abundant bacteria in soil and rhizosphere

3.3.3. Proteobacteria, Firmicutes, Actinobacteria

3.3.3.1. Contributes to soils suppressive toward the root-rotting fungus Rhizoctonia

4. The Endosphere Environment

4.1. Endophytic bacteria

4.1.1. Lives in intercellular apoplast and in dead or dying cells

4.1.2. Non pathogenic

4.1.3. Sub population of rhizosphere microbiome

4.1.4. Surface layers of plant tissue was removed using sonification and the remaining tissue used to study the endophyte microbiome

4.1.5. Young plant has higher bacterial concentration than mature one

4.1.6. High concentration of endophytic bacteria trigger host defense response

4.1.7. Example: Azoarcus, Klebsiella and Gluconacetobacter

4.1.8. Culture-independent methods like analyses of 16S rRNA and nifH transcripts and metagenome analyses showed a huge diversity of endophytes in the economically important crops sugarcane and rice

4.1.9. Actinobacteria were consistently enriched in the endosphere

4.1.10. Plant has plant defense-related genes, such as resistance (R) genes and leucine-rich repeat (LRR)-containing-receptor-like kinase, however, the plants react differently towards endophytic bacteria compare with phytopathogens

4.2. Pathway of bacteria enter their host

4.2.1. Enter at lateral root junctions using cell-wall-degrading enzymes

4.2.2. Enter at natural breaks in root tips by vegetative propagation

4.3. Benefits of endophytic bacteria

4.3.1. Nitrogen fixation for their host

4.3.2. Promote growth in plant

4.3.3. Protection against phytopathogenic fungi

5. The Effect of The Host on The Plant Microbiome

5.1. Plant defence process

5.1.1. This effect on microbial community is variable

5.1.2. Example: Induction of salicylic-acid-mediated-defence reduced the diversity of endophytes;whereas the plant deficient in jasmonate-mediated defence showed higher epiphytic diversity

5.2. Plant hormones

5.2.1. Indole-3-acetic acid and Gibberellins

5.2.2. Hormones produced by microbes also affect the microbial community

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

5.3. Chemical signals released by plants

5.3.1. Flavonoids

5.3.1.1. Trigger diverse responses in rhizobia, mycorrhiza, root pathogens and other plants

5.3.2. Strigolactones

5.3.2.1. Induce hyphal branching in mycorrhizal fungi and promote seed germination of parasitic plants

5.4. Antimicrobial compounds released by plants

5.4.1. Phenolics, terpenoids, alkaloids, glusosinolates

5.4.2. Avenacins have large broad-spectrum antifungal activity, but not affected the bacterial community

5.4.3. A small change in plant genotype can have complex and unforeseen effects on the plant microbiome, but the microbial community is not affected between wild-type maize and genetically engineered maize in producing of Bt toxin because Bt toxin being insecticidal rather than antibacterial

6. The Phyllosphere Environment

6.1. Aerial surface of plants

6.2. More dynamic environment than the rhizosphere

6.3. Microbial colonization of leaves

6.3.1. Affected by leaf structures like veins, hairs and stomata, colonized by up to 107 microbes per cm2

6.4. Abiotic factors like temperature, moisture and radiation (day and night) affect phyllosphere microbiome

6.4.1. Changes in plant metabolism

6.5. PCR amplification of rRNA genes

6.5.1. To profile bacterial and fungal communities in the phyllospheres of various plants

6.6. Greater microbial richness in warmer, more humid climates

6.7. Lactic acid bacteria (Firmicutes) are dominant in phyllospheres of several plants (Mediterranean) during summer

6.7.1. Their mode of metabolism allow them to tolerate the hot and dry weather conditions

6.8. Methylobacterium spp. and other methylotrophs

6.8.1. Widely abundant phyllosphere microbes, actively assimilating and metabolizing methanol derived from plant pectin

6.9. Metagenomic analysis of taxonomically diverse plant species

6.9.1. Abundance of various known and novel microbial rhodopsins present in the phyllosphere