Root is the part where plant interact with microbes. Microbes really plays an important role in the overall wellbeing of the crop. Here is some basics regarding root colonization
5. Differentiation of Compartments
1. Rhizosphere soil attached to root is washed of
2. Mechanical disconnection of microbes from roots by,
i. Vigorous shaking with pebbles or glass beads
ii.Ultra-sonic treatment
3. Microbial cells then collected from supernatant
4.But still some microbes can attach to root but we can
conclude with functional diversity of Rhizoplane
1. Chemical treatment with Ethanol or Sodium hypochlorite
2. Verify the surface for the presence of microbes each time
after sterilization
3. Monitoring growth from the imprints of surface sterilized
bacteria on suitable media
4. We can also follow various molecular approaches
8. From soil to roots : gradually changing
communities
Rhizosphere soil have less diversity than Bulk soil
OTU(Operational Taxonomic Unit) richness decrease slightly or not at all in the rhizosphere
Soil
In contrast difference between rhizosphere soil and bulk soil were revealed by
metatranscriptome analysis with evaluation of rRna ,gives idea about the active community
Diversity will depend up on the crops
At genus level we can we can differentiate between bulk and rhizoshpere soil
This suggests that the Microbiome is already enriched for specific bacteria in
rhizosphere soil ,or that some genera are activated in there . In addition, the plant
species had a clear, significant influence on the Microbiome composition in
rhizosphere soil
Bacterial population associated with roots were active than those of bulk soil
(Metagenome studies)
In washed roots of Wheat and cucumber ,the roots were dominated by Proteobacteria(80%)
and in soils , Actinobacteria(40%) were most abundant - phylum level , a major population
9. Shift was reflected in the increase in the relative abundance of gammaproteobacteria
(5.1% in soil to 25.2% in root ) and also Alphaproteobacteria which increased 1.5 fold
Metagenome analysis revealed – root associated communities were enriched in gene
linked to motility, chemotaxis, lipopolysaccharide biosynthesis, plant poly saccharide
degrading enzymes
Endorhizosphere will have less diversity i.e., below 50 OTUs , where in rhizosphere soil
It is 1000 OTUs
Rhizosphere consist of 40% Proteobacteria, 33%Acidobacteria& 10%Verrucomicrobia
Endophytes were composed of 80% Proteobacteria and 40%Acidobacteria.
There was remarkable enrichment of diazotrophs in rice roots, as calculated from
apparent endophyte genome size and abundance of nitrogenase nif genes: More than
50% of endophytes were likely to be diazotropic
10. In to Roots: Ways endophytes get in
TO BECOME AN ENDOPHYTE……
Flagella
Plant polymer degrading enzymes
Type 5 and 6 secretion systems
Quorum sensing
Detoxification of reactive oxygen species
Degradation of compounds
Type 4 pili – twitching motility –Pil T , PilX
mediates –mutants stay up to rhizoplane
11. A 3- Step enrichment model
“Due to this selection pressures
over millions of years, highly
specialized, taxonomically
distinct microbial communities
with very high activities are
likely to occur in roots”
12. Plants shapes their associated microbes
When grow different plants in same soil different
community gathering is observed
Plant exudates
Azocarpus sp. Strain BH72 when provided with exudates
shows elevated gene activities for endophytic colonization
increased – bacterium is primed by exudates for endophytic
lifestyle
Mutation studies are going on
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13. Immune Responses in plants
1. Pathogen Associated Molecular Patterns(PAMPs)
& Damage Associated Molecular Patterns (DAMPs)
2. Carry out by pattern- recognition receptors
3. Beneficial microbes cause
Induced Systemic Resistance (ISR)
4. Host defence stabilized by ISR-Plant hormone
Dependent response(Jasmonate,Ethylene…)
5. Effector Triggered Immunity(ETI) Same hormone
mediated and ROS
How Plant Select their
Endophytic Partners
Verses pathogen is not
known
MUTATION
STUDIES
16. A Quest for Improved Cultivation-Independent Techniques
to Analyze Plant-Associated Microbiomes
Analysis of bacterial populations that are plant associated is challenging, as rRNA genes of plant
organelle genomes belong to the bacterial line of descent and have high sequence similarities to
bacterial rRNAs.
Consequently, PCR products obtained with broad-range 16S rRNA primers from plant samples usually
contain organelle ribosomal sequences.
This is particularly problematic for the cultivation-independent community analysis of
plantassociated bacteria and of bacteria in samples containing plant materials.
23SrRNA Gene targeting primer can be also used
18. Symbiosome
Symbiosomes are a unique structural
entity that performs the role of
biological nitrogen fixation ,an energy-
demanding process that is the primary
entryway of fixed nitrogen into the
biosphere.
Symbiosomes result from the
infection of specific rhizobial strains into
the roots of an appropriate leguminous
host plant forming an organ referred to
as a nodule.
“An appreciable portion of
both the eukaryotic and
prokaryotic proteins in the
symbiosome are also
'moonlighting' proteins, which
are defined as proteins that
perform roles unrelated to
their annotated activities when
found in an unexpected
physiological environment. “
19. Recap…
1. Roots provide a very attractive, nutrient-rich niche that harbors large numbers of active microbes
that are important for plant health and nutrient uptake.
2. Roots provide different microhabitats at the soil-root interface
3. Analysis of bacterial plant-associated populations is challenging
4. Microbial community composition shifts from the bulk soil toward the root
5. A three-step enrichment model
6. To clarify causal relationships for how plants shape their microbiome, the coupling of reductionist
and molecular ecological approaches are required, particularly including specific plant genotypes
and mutants.
