Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities

Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.