N Fertilization Dependent Bacterial and Archaeal …
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irrespective of space and time are designated as core microbiome [83]. In crisp, it
includes the population essential for the functioning of that particular ecosystem.
More evidently, scientists have put forth the possibility of positive correlation
between microbial community structure and the functionality of an ecosystem [22].
With the foresaid concept, exploring the core microbiome may ultimately pave
way for better operation of paddy ecosystem wherein the role of microbes remain
inevitable. Undermining the paddy core microbiome is counted as need of the hour
as rice is the staple food for most of Asian countries. Despite the significance, delineating core microbiome is way more lagging due to the daunting efforts required
for thorough understanding of microbial behaviour across distantly located paddy
habitats.
However, a recent continental survey across China has unleased the biogeographic
pattern of microbial distribution in paddy ecosystem. The study has disentangled the
myriad roles of α- and β-diversity of core microbiome in multi-nutrient transformations in paddy field [47]. Paddy ecosystem serves as a hub for N and C biogeochemical
cycles mediated by the associated microbiome. Evidently, nitrite-dependent methane
oxidizing anaerobe Candidatus Methylomirabilis oxyfera has been reported to bridge
both C and N cycling in paddy fields [119]. Paddy ecosystem is generally occupied by
diversified group of ammonia oxidizing archaea and bacteria, nitrifiers, denitrifiers,
methanogens, methanotrophs etc. actively involved in C and N cycling. These active
microbiota associated with paddy undergo spatial variations based on different layers
of soil and distance from the rhizospheric zone of the crop [63]. Differential assemblage of paddy microbiome has documented the occurrence of Xanthomonadales,
Myxococcales, and Methylococcales in oxic surface layer of soil and predominance
of methanogenic archaea and other bacterial anaerobes in anoxic bulk soil [53].
In yet another outlook, an interdisciplinary approach to delineate core microbiota
has demarcated the evidence for the ability of core microbiome to recruit beneficial
native flora while suppressing the plant pathogens [94]. Aforesaid evidence justifies
the need of core microbiome for proper nutrient cycling in paddy ecosystem along
with their significant role in plant health and sustainability.
3.1 K and R Strategic Groups
Microbial community in any ecosystem can be physiologically classified into K
and R strategic groups. K strategic microbes, nutritionally called oligotrophs are
slow growers whose population does not rely on nutritional fluctuations in soil. In
contrary, R strategic or copiotrophic groups have high fecundity and get altered based
on external inputs [30]. For example, N fertilization in paddy field increased the abundance of R strategists belonging to Proteobacteria and Bacteroidetes. Additionally,
it exerted an indirect negative impact on K strategists such as Acidobacteria as the
shoot up of R strategists outcompeted other slow growing bacteria in the soil [31].
While delineating the core microbiome of paddy, metagenomic approaches would
71
irrespective of space and time are designated as core microbiome [83]. In crisp, it
includes the population essential for the functioning of that particular ecosystem.
More evidently, scientists have put forth the possibility of positive correlation
between microbial community structure and the functionality of an ecosystem [22].
With the foresaid concept, exploring the core microbiome may ultimately pave
way for better operation of paddy ecosystem wherein the role of microbes remain
inevitable. Undermining the paddy core microbiome is counted as need of the hour
as rice is the staple food for most of Asian countries. Despite the significance, delineating core microbiome is way more lagging due to the daunting efforts required
for thorough understanding of microbial behaviour across distantly located paddy
habitats.
However, a recent continental survey across China has unleased the biogeographic
pattern of microbial distribution in paddy ecosystem. The study has disentangled the
myriad roles of α- and β-diversity of core microbiome in multi-nutrient transformations in paddy field [47]. Paddy ecosystem serves as a hub for N and C biogeochemical
cycles mediated by the associated microbiome. Evidently, nitrite-dependent methane
oxidizing anaerobe Candidatus Methylomirabilis oxyfera has been reported to bridge
both C and N cycling in paddy fields [119]. Paddy ecosystem is generally occupied by
diversified group of ammonia oxidizing archaea and bacteria, nitrifiers, denitrifiers,
methanogens, methanotrophs etc. actively involved in C and N cycling. These active
microbiota associated with paddy undergo spatial variations based on different layers
of soil and distance from the rhizospheric zone of the crop [63]. Differential assemblage of paddy microbiome has documented the occurrence of Xanthomonadales,
Myxococcales, and Methylococcales in oxic surface layer of soil and predominance
of methanogenic archaea and other bacterial anaerobes in anoxic bulk soil [53].
In yet another outlook, an interdisciplinary approach to delineate core microbiota
has demarcated the evidence for the ability of core microbiome to recruit beneficial
native flora while suppressing the plant pathogens [94]. Aforesaid evidence justifies
the need of core microbiome for proper nutrient cycling in paddy ecosystem along
with their significant role in plant health and sustainability.
3.1 K and R Strategic Groups
Microbial community in any ecosystem can be physiologically classified into K
and R strategic groups. K strategic microbes, nutritionally called oligotrophs are
slow growers whose population does not rely on nutritional fluctuations in soil. In
contrary, R strategic or copiotrophic groups have high fecundity and get altered based
on external inputs [30]. For example, N fertilization in paddy field increased the abundance of R strategists belonging to Proteobacteria and Bacteroidetes. Additionally,
it exerted an indirect negative impact on K strategists such as Acidobacteria as the
shoot up of R strategists outcompeted other slow growing bacteria in the soil [31].
While delineating the core microbiome of paddy, metagenomic approaches would