Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology

The plant rhizosphere interfaces an array of microbiomes related to plant growth
and development. Cultivar-specific soil microbial communities with respect to their taxonomic
structure and specific function have not been investigated explicitly in improving the adaptation
of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the
rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the
diversity of microbial communities and for predicting the function of microbiome genes related to
nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome
sequencing. The metagenome profile of two cultivars detected variable microbiome composition
with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes,
and Thaumarchaeota were abundant phyla in the “Farmer-2” rhizosphere, whereas Actinobacteria,
Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes
of the “Candidatus” category were found to be robustly enriched the rhizosphere of “Moitree”.
Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly
house keeping genes with general metabolism. Additionally, the rhizosphere of “Moitree” had a
high abundance of genes related to denitrification processes. Significant dierence was observed
regarding P cycling genes between the cultivars. “Moitree” with a profuse root system exhibited
better N fixation and translocation ability due to a good “foraging strategy” for improving acquisition
of native P under the nutrient depleted rice-fallow ecology. However, “Farmer-2” revealed a better
“mining strategy” for enhancing P solubilization and further transportation to sinks. This study
warrants comprehensive research for explaining the role of microbiome diversity and cultivar–microbe
interactions towards stimulating