Metagenomics to assess bacterial diversity in the soil as influenced by organic and chemical inputs
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Date
2016
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Center for Plant Biotechnology and Molecular Biology, College of Horticulture, Vellanikkara
Abstract
The rhizosphere region of soil is the dwelling place for many microorganisms.The rich microbial activity supports many biological processes in the soil. The abundance of Plant Growth Promoting Rhizobacteria (PGPR) in rhizosphere assumes natural significance from agronomic point of view. Knowledge about the total diversity of these bacterial communities is less understood as the conventional methods for the study of microbes has their own limitations. It has been estimated that 99 per cent of microbes cannot be cultured easily. Metagenomics is the culture-independent genomic analysis of microbes that has been developed to overcome the drawbacks of culture-based analysis of microbial communities. An attempt was made to analyse the diversity of bacterial community using metagenomic approach in three different rice rhizosphere soils that received organic inputs (ONM), inorganic inputs (I) and soil under integrated management (INM) from permanent manurial trial plots at RARS, Pattambi. Metagenomic DNA was isolated from the soils by direct lysis method and sequencing of V3 region of 16S rRNA gene was carried out by using Illumina MiseqTM platform, at SciGenom, Cochin.The diversity of bacterial taxonomic category was assessed at different Operational Taxonomic Unit (OTU) levels using Ribosomal Database Project (RDP) pipeline and MG-RAST. At phylum level, Actinobacteria was the most dominant in all the three soils, and abundance was highest in INM 57.95%) and lowest in INF (25.80%). Actinomycetes play a major role in organic matter decomposition and their presence is an indicator of soil health. Bacteria under ‘unclassified derived from bacteria’ was highest in INF (33.57%). These bacteria could be novel ones, since no homology was observed with any sequence in database. Acidobacteria was found highest in INF (14.13%) and lowest in ONM (10.31%). Acidobacteria are metabolically and genetically diverse. Members of Proteobacteria increased in response to chemically recalcitrant substances and were dominant in INF (14.55%) and lowest in INM (5.62%). Phylum Firmicutes comprised Bacillus and Clostridium and was found highest in ONM (6.76%) and lowest in INM (4.80%)
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PG
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