72
S. Ambreetha et al.
better help to understand the undulations in oligotrophic and copiotrophic groups
which may otherwise be missed in conventional culturable methods.
3.2 Holobionts
Plant-associated microbes play inimitable roles in nutrient cycling, stress mitigation,
disease suppression and pest control along with the improvement of soil properties. In
the due course, microbes co-evolved with the associated plants and were mentioned
as plant’s second genome [6]. The plant system along with its associated microbiome can be collectively termed as holobionts. Although the term holobiont (host
and its symbiont) was coined by Lynn Margulis in 1991 and explained as physical
association between living organisms belonging to different species, recently it is
being commonly used to depict plant–microbe and human-microbe symbiosis [86].
More interestingly, the genome of the host and its microbiota are collectively termed
as hologenome. The variations in associated microbial diversity severely influence
the evolution of the holobiont [123]. In the perspective of holobiont theory, plant
and the associated microbes are considered as single entity and thereby thorough
understanding of the functionality of core microbiome of paddy becomes mandatory
to maintain crop sustainability.
3.3 Factors Influencing Paddy Microbiome
Primary factor that makes paddy a predominant hub for diversified microbiota is the
prevalence of oxic-anoxic interface [26]. Universally, paddy ecosystem is classified
as lowland and upland cropping based on the presence or absence of water logging.
Diversified bacterial richness has been documented in the former compared to later
which substantiates the significant influence of flooding over rice microbiota [19].
Next important factor that impacts paddy microbiome is the availability of different
metals and nutrients in cultivated soil. The impact of each individual metal or nutrient
over paddy microbial diversity is discussed elsewhere [80, 87]. Furthermore, fertilization imparts mammoth effects over the diversity and functionality of operational
taxonomic units (OTU) in paddy ecosystem. In comparison with all soil minerals,
nitrogen is hugely dumped into paddy soil due to anthropogenic activity and decoding
its effect on plant associated bacteria and archaea population sounds mandatory.
Inorganic fertilizer amendment does not significantly alter the core microbiota while
addition of N alone hugely modifies their taxonomic diversity [56]. Importantly,
paddy-associated microbes including bacteria and fungi significantly accumulate
the added N inputs despite low availability [77].
However, integrated nutrient management (INM) including inorganic fertilizers
with organic amendments surpasses other fertilization methods by enhancing both
soil organic carbon and microbial biomass carbon [37]. After the harvest, paddy straw
S. Ambreetha et al.
better help to understand the undulations in oligotrophic and copiotrophic groups
which may otherwise be missed in conventional culturable methods.
3.2 Holobionts
Plant-associated microbes play inimitable roles in nutrient cycling, stress mitigation,
disease suppression and pest control along with the improvement of soil properties. In
the due course, microbes co-evolved with the associated plants and were mentioned
as plant’s second genome [6]. The plant system along with its associated microbiome can be collectively termed as holobionts. Although the term holobiont (host
and its symbiont) was coined by Lynn Margulis in 1991 and explained as physical
association between living organisms belonging to different species, recently it is
being commonly used to depict plant–microbe and human-microbe symbiosis [86].
More interestingly, the genome of the host and its microbiota are collectively termed
as hologenome. The variations in associated microbial diversity severely influence
the evolution of the holobiont [123]. In the perspective of holobiont theory, plant
and the associated microbes are considered as single entity and thereby thorough
understanding of the functionality of core microbiome of paddy becomes mandatory
to maintain crop sustainability.
3.3 Factors Influencing Paddy Microbiome
Primary factor that makes paddy a predominant hub for diversified microbiota is the
prevalence of oxic-anoxic interface [26]. Universally, paddy ecosystem is classified
as lowland and upland cropping based on the presence or absence of water logging.
Diversified bacterial richness has been documented in the former compared to later
which substantiates the significant influence of flooding over rice microbiota [19].
Next important factor that impacts paddy microbiome is the availability of different
metals and nutrients in cultivated soil. The impact of each individual metal or nutrient
over paddy microbial diversity is discussed elsewhere [80, 87]. Furthermore, fertilization imparts mammoth effects over the diversity and functionality of operational
taxonomic units (OTU) in paddy ecosystem. In comparison with all soil minerals,
nitrogen is hugely dumped into paddy soil due to anthropogenic activity and decoding
its effect on plant associated bacteria and archaea population sounds mandatory.
Inorganic fertilizer amendment does not significantly alter the core microbiota while
addition of N alone hugely modifies their taxonomic diversity [56]. Importantly,
paddy-associated microbes including bacteria and fungi significantly accumulate
the added N inputs despite low availability [77].
However, integrated nutrient management (INM) including inorganic fertilizers
with organic amendments surpasses other fertilization methods by enhancing both
soil organic carbon and microbial biomass carbon [37]. After the harvest, paddy straw