Metagenomic analysis of bacterial diversity in the rice rhizosphere soil microbiome

The rhizosphere is known to provide ecologically favourable niche for most of the beneficial soil microorganisms. The rich microbial activity in the rhizosphere aids in several biological and ecological processes important for plant health. The abundance of nitrogen fixing, phosphate solubilising and plant disease suppressing bacteria in the rhizosphere of crop plants assumes a natural significance from the agronomic point of view. Our knowledge on the diversity of these bacterial communities is limited compared to other components in the rhizosphere. It has been estimated that less than 1% of the total microbial population in the land environment and even less in the marine environment have been successfully isolated in pure culture. The majority of microorganisms on earth resist life in captivity and hence many of them cannot be cultured by current culture-based and traditional methods. Metagenomics is a rapidly developing field that helps in analyzing the complex genomes of microbial niches through culture independent molecular approaches. In this study culture-independent molecular techniques, 16S rRNA clone library generation along with RFLP, sequencing and phylogenetic analysis, were applied to investigate the bacterial diversity associated with the rice rhizosphere bacterial communities from a paddy field ecosystem in Kerala. Clones with close identity with sequences retrieved from database as well as uncultured bacterial sequences were found in the rhizosphere bacterial community. Sequence analysis of 16S rRNA clones indicated a high diversity in the rhizosphere bacterial community with the majority of microbes being closely related to the Proteobacteria. Only a small fraction of the 16S rRNA sequences were highly similar to rRNA sequences from Acidobacteria, Firmicutes, Bacteriodetes groups. Since rhizosphere-associated microbes possess diverse metabolic capabilities and play a crucial role in plant health, knowledge on their community structure is imperative for the proper understanding of their individual roles and metagenomics holds the promise to reveal several important questions regarding the unculturable fraction of the rhizosphere community.