Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges

River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy rivers of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India, to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of the microbiome at this confluence and its downstream, remains unexplored. To unveil this, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of a December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firmicutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeota in G15Y and G15DS, indicating Yamuna River's influence. Functional genetic analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may provide the basis of understanding of the impact of Yamuna River, and also the rare event of mass bathing, on the microbiome of River Ganges. Further investigation would be required to understand the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem.