Metagenomics analysis of sediments of river Ganga, India for bacterial diversity, functional genomics, antibiotic resistant genes and virulence factors

Abstract

The river Ganges in India has faced considerable issues due to water quality degradation caused by various anthropogenic activities. This study employs metagenomic analysis to comprehensively characterize bacterial communities, explore functional genomics, and investigate the prevalence of virulence factors and antibiotic resistant genes (ARGs) within the sediment environment of the river Ganges. Taxonomic profiling revealed that Proteobacteria were the most dominating phyla found in all samples, whereas the abundance of Pseudomonas at the genus level was the highest in all the samples. Functional annotation and pathway analysis uncover the genomic potential of sediment associated bacteria, shedding light on metabolic pathways, biogeochemical processes, human diseases and adaptive mechanisms within the riverine ecosystem. Moreover, identifying the highest number of genes related to virulence factors was observed in K1 samples (3), and the highest number of genes related to ARGs found in K3 (25) samples emphasizes the need to understand potential pathogenicity in these environments. Characterization of ARGs provides crucial insights into the prevalence of resistance determinants, their genetic contexts, and potential sources of antibiotic resistance in this vital aquatic ecosystem. Overall metagenomics analysis in different sampling sites of river Ganga observed nearly the same OTUs at microbial communities at the taxonomic level but not at a functional level. This research can be a critical foundation for assessing the ecological implications of microbial communities, functional genomics, and the resistome in the river Ganges sediments. The findings underscore the importance of metagenomic approaches in elucidating the intricate microbial ecology and the prevalence of genetic elements relevant to environmental health and antimicrobial resistance in aquatic ecosystems. Further investigation would be required to understand the underlying cause behind the restoration of microbial functional profiles, including ARGs and VFs, to unravel the rejuvenation aspects of this unique ecosystem.