Freshwater metagenomics study of Pune City, India
A systematic study of bacterial diversity from different freshwater bodies in Pune was carried out with aim to understand the microbial diversity using metagenomics tool. A total of 209 water samples were collected from 2 rivers, 5 lakes and 6 dams. These samples were subjected to various analytical methods to perform metagenomics-based screening for the identification of bacterial diversity in the mentioned potable water sources.  It involves step-wise protocols for extraction of DNA from the environmental source, T-RFLP-based microbial analysis using GeneMapper, Quantitative and Qualitative analysis of extracted DNA, PCR amplification of 16S rRNA, Cloning of amplicons, BigDye Terminator sequencing, purification, analysis, and identification of sequences.   Metagenomic survey of the total samples collected over various freshwater samples from Pune (Maharshtra) led to a recovery of 3213 sequences representing a myriad of bacterial groups including Enterobacteriaceae, Coxiellaceae, Nocardiceae, Streptomyceteceae, Glycomyceteceae, unculture Proteobacterium, and Bacilliceae. All the freshwater resources had identical populations of bacteria with notable differences in their relative abundance. Furthermore, a seasonal variation in the concentration of bacterial colonies was reported in the various zones of the water column of respective freshwater resource. Out of all groups, approximately 38.46% of sequences were still unassigned to any particular group which satisfies the cause of the study. Identical populations of bacteria with notable differences in their relative abundance were observed season-wise. Furthermore, a seasonal variation in the concentration of bacterial colonies was reported in the various zones of the water column of respective freshwater resources.  An unusual pattern of upper, middle, and bottom zone bacterial biodiversity has been observed. Various pathogenic species and rare species have also been observed in the samples.