Metagenomic analysis of rice rhizosphere in a uniquely fertile Kole wetland reveals the microbiome contributing to enhanced nutrient availability

Abstract

The Kole wetlands (Kerala state, India) have deeply inundated, clayey and acidic soils rich in humic acids, tannins and mineral ions. High soil fertility coupled with the presence of microflora contributing to the fixation, solubilisation and mobilization of different nutrients is understood to contribute to high rice yields in these fields. However, the rhizosphere microflora of Kole land rice is yet to be profiled. Metagenomic DNA isolated through a manual Modified Improved method was sequenced on Illumina MiSeq platform, targeting the V3-V4 hypervariable region of 16 S rRNA gene. The results have shown a diverse microbial community dominated by bacteria and archaea. Taxonomic annotation highlighted major bacterial phyla Chloroflexota, Acidobacteriota and Pseudomonadota, and archaeal phyla Thermoproteota, Thermoplasmatota, and Halobacteriota. Alpha diversity indices revealed exceptional species richness, yet dominated by a few key species. The analysis has revealed the presence of bacterial and archaeal genera, the members of which are reported to have multifaceted ecological roles including plant growth promotion, nitrogen fixation, carbon-, nitrogen- and phosphorus-cycling, sulphur solubilisation and iron reduction. Bacterial genera accommodating the members with biodegradation, bioremediation and wastewater treatment capabilities, along with methanotrophs and archaeal methanogens were also found. Additionally, microbial phyla including the members having biocontrol, stress adoption, anti-microbial and herbicide degradation potential were identified. This paper provides insights on the microbial diversity and activities contributing to enhanced nutrient availability to rice plants under Kole wetland conditions.