Plant–microbiome interactions

1. Presented by:
Mesele
(Integ.3rd year)
Advisor: MoonJae Sun Apr 27, 2022
KRIBB SEMINAR COURSE

2. Contents
1. The plant microbiome
1.1 Composition of plant- associated microbiota
1.2 Core and hub microbiota
1.3 Dynamics of the plant- associated microbiome
2. Plant colonization and community assembly
2.1 Plant sensing and the initiation of colonization
2.2 Uptake of plant metabolites
3. Functions of plant- associated microbiomes
3.1 Nutrient acquisition
3.2 Disease resistance
3.3 Stress tolerance
5. Conclusion

3. 1. The plant microbiome
1.1 Composition of plant- associated microbiota
 Community composition varies significantly between the rhizosphere, endophytes and the phyllo sphere.
 Rhizosphere: The region of soil in the vicinity of plant roots
 Endophytes: microorganisms residing within plant tissues (endosphere)
-Enriched in members of the Proteobacteria and Firmicutes
-Lesser extent in Bacteroidetes (Acidobacteria,Planctomycetes,Chloroflexi & Verrucomicrobia)
 Phyllosphere: All the aboveground organs of plants (leaf, flower, stem and fruit).
-mainly comprises bacteria belonging to phylum
Proteobacteria (constitute ~50%)
Bacteroidetes,
Firmicutes and
Actinomycetes
-The vast diversity of fungi that colonize both above & below ground plant tissues mainly belong to the phyla
Ascomycota and Basidiomycota.
Microbiota =microorganisms that are found within a specific environment. (bacteria, viruses, and fungi)

4. The plant microbiome
 Microbiome composition varies depending on the
plant compartment.
 Pie charts show the averages relative abundances of
major bacterial & fungal phyla that are
 detected in  various plant species (sugarcane, grapes ,
cactus species)
 Abundances were estimated by marker- gene
sequencing (16S rRNA for bacteria, and internal
transcribed spacer (ITS) for fungi).
General structure of the bacterial and fungal communities from various plant-associated niches
Microbial diversity from the soil  endosphere compartments.
The aboveground microbiota is more variable, due open nature
and rapidly fluctuating environmental conditions. (aerosols, insects,
soil, pollen and Migration via other plant tissues).
Composition of plant-associated microbiota
 Determinants factors of community
 host compartment,
 environmental factors and
 Host genotype

5. The plant microbiome
 Core microbiota– the group of MOs commonly found within a microbiota
- persistent & ubiquitous the communities associated with a particular host.
-systematically associated with a given host plant
 Hub microorganisms- Microbial groups that are substantially more connected than other groups
on the basis of centrality measurements (degree, between-ness centrality and closeness centrality).
have a regulatory effect on the network of microbial interactions, as their removal results in the
loss of interactions.
 There abundance functioning: carbohydrate metabolism and stress responses control to Host.
1.2 Core and hub microbiota

6. The plant microbiome
1.3 Dynamics of the plant- associated microbiome
Microbial composition
of microbiomes
Highly dynamic in the early vegetative phase
Begins to converge throughout vegetative growth
Stabilizes during the reproductive phase
These microorganisms possess multiple traits for,
Efficient colonization,
Stress tolerance and
Beneficial effects on the hosts
The assembly of a plant-associated microbiome is a successional, multistep process that is determined by
Dispersal, Species interactions, Environment and Host

7. 2. Plant colonization and community assembly
2.1 Plant sensing and the initiation of colonization
chemotaxis
Sense & respond to plant- derived signals, (organic acids &
sugars present in plant exudates, and to initiate colonization
Once a signal
is perceived
Move towards the plant primarily through the use of flagella
attach to root surface and form a biofilm
After successful
colonization
Diverse host processes, such as the activation of plant signaling
pathways & nutrient-stress-mediated root inhibition alters the host
root architecture.
Chemotaxis (chemo- + taxis) is the movement of an organism or entity in response to a chemical stimulus

8. -The plant interacts with microbiome release of
root exudates
-Quorum sensing/two-component systems- inter &
intramicrobial communications among dt species.
-CRISPR-associated genes-adaptive immunity
against bacteriophages
-Antibiotic-R genes-protection against biological &
chemical warfare (eg.toxins and defense systems)
during the initial stages of community assembly.
-Subsequently, the microbial community moves
towards the plants through chemotaxis, involving
motility proteins and the assembly of flagella.
-Further colonization leading to the formation of a
biofilm on plant
Plant colonization and community assembly
Signaling molecules= organic acids, sugars, phenol,
proteins CHO, and 2nd metabolites
mediated
colonization
Fig2. Plant colonization and microbiome assembly.
Microbial-mediated processes, pathways & proteins that related to colonization ….are shown.
-Gene products from eukaryotic-like plant resembling plant-associated and root-
associated domains (PREPARADOs) are speculated to mimic the host cell signaling,
thus acting as decoys to circumvent plant defenses and gain entry into plant tissues
-Lytic enzymes-facilitate entry into plant
tissue
-MAMPs- recognized by plant immune
response & shape endosphere microbial
assemblages in plant.
-c-di-AMPmediates cell–cell
communication & initiation of
biofilm by influencing express
of genes.
Scopoletin-has antimicrobial activity,
selects for beneficial MOs that ameliorate
stress (altered root exudation)

9. 3. Functions of plant- associated microbiomes
3.1 Nutrient acquisition
 Improving plant nutrition
 Enhance bioavailability of insoluble minerals
 Improve root system architecture of plants, for water and minerals.
 Conservation of nutrients that differentiate exploitative (fast- growing) vs conservative
(slow- growing) plant species
 Effective conversion of organic N2  nitrate and ammonium by the indica- enriched
microbiome may contribute to higher N2 use efficiency in indica rice.

10. Fig.3 Beneficialeffectsoftheplant-associatedmicrobiome
Microbiome-mediated=initiated in any part of a plant (mostly belowground)
and can be transmitted to other parts via plant-mediated transport or signals
(shown as dashed arrows).
N2(atm) NH4+ + NO3-
N2 (soil) NH4+ NO3-
Arg urea + NH4+
Legume plant develop root nodule with N2 fixing bacteria
Mycelium= long distance transport of minerals
Arbuscular = specialized structure cortical cell of PM transport elements
directly to host cytoplasm .
Diazo trophic
bacteria
Amonifying
bacteria
Nitrifying
bacteria
Arbuscular
mycorrhiza fungi
direct effects stimulation of plant growth via stress
alleviation, through the modulation of
- aminocyclopropane-1- carboxylate (ACC)
deaminase expression
- plant hormones,
- detoxification enzymes and
- osmoprotectants.
blue= growth promotion
green= stress control
red= defence against
pathogens and pests
Microbiome

11. Functions of plant- associated microbiomes
3.2 Disease resistance
 plant root exudates stimulate, enrich and support soil MOs as the 1st line of defence
against soil-borne pathogens
 provide extra layer of defense by enriching microbiome members to generate
antimicrobial enzymes & 2nd metabolites against pathogen.
 The abundances of Actinobacteria and Firmicutes used as predictive markers of
disease-suppressive soils against Fusarium oxysporum.

12. Functions of plant- associated microbiomes
3.3 Stress tolerance
 Modify plant evolutionary responses to environmental stress in at least three non-
mutually- exclusive pathways: by
altering the fitness of individual plant genotypes,
the expression of plant traits related to fitness, and
the strength or direction of natural selection occurring within populations.
 Recent studies have shown that naturally occurring and artificial variation in the
microbiome can alter plant flowering time 1–5 days.
early flowering a potential mechanism of drought avoidance.
 fungal endophytes, stress tolerance predicted 26–53% of the endophyte- mediated effects
on plant performance under water stress.

13. Research Gap from this review
Similarly to breeding, the plant microbiota may affect the plant phenotype. BUT
 there is a critical knowledge gap concerning the shape and drivers of other fractions
of the plant microbiome (for example, viruses, archaea, protists and nematodes)
Although bacterial and fungal lineages contribute majority of the plant- associated
microbiome abundance,
Although the optimization of SynComs is rapidly advancing, crop- breeding
programmes have not yet incorporated the selection of beneficial plant–
microorganism interactions in order to breed ‘microorganism- optimized’ plants.

14. 5. Conclusions
 Recently , plant–microbiome research have cross- disciplinary (multi-‘omics’, engineering,
experimental & computational biology and statistics to generate quantitative insights into
plant–microbiome interactions.
GWASs and metagenome- wide association studies have identified key drivers that influence
the
 assembly of plant- associated microbiota and
 linked individual microbial taxa and
 genes to plant colonization,
 plant physiology and
 traits related to plant fitness.
 Plant- associated microbiomes confer fitness advantages to the plant host, including growth
promotion, nutrient uptake, stress tolerance and resistance to pathogens.