Microbiome divergence across four major Indian riverine water ecosystems impacted by anthropogenic contamination: A comparative metagenomic analysis

Abstract

Background Indian rivers are a major source of livelihood as river water is used for drinking, agriculture, and religious purposes to a large population. In this study, we report comparative microbial structures and functional potential of four major rivers of India, namely Ganga, Narmada, Cauvery, and Gomti. Comparative microbiome study of these geographically distinct rivers was performed using the samples collected from the source to the downstream sites of each river. We employed metagenomic approach to comprehensively determine the taxonomic and functional potential of river microbiome. Results In this study, we report the pollution influences on microbial composition and functional potential of four distantly located rivers. Results revealed significant microbial diversity in contaminated locations as compared to the upstream samples. A total number of 37 bacterial phyla were detected out of which Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia were abundant. Microbial diversity in respect to anthropogenic activities revealed the prevalence of Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes, and Nitrospirae phyla, whereas a decline in Proteobacteria and Bacteroides. Virulent and temperate bacteriophages were found high in Ganga when compared to others. Interestingly, the abundance of bacteriophage decreased with increasing pollution load in the river Ganga, unlike in other rivers. The carbon utilization studies indicated a correlation with functional genes occurred in metal contaminated sites. Ganga water has relatively higher trace elements at pristine-upstream than in the Narmada and Cauvery, indicating its origin from Himalayan rocky mountains and also both Ganga and Cauvery rivers found to harbour a large number of metal resistance genes. Conclusion Our findings indicate a correlation between pollution and the microbiome composition. The insights obtained suggest the role of high abundance of microbial communities with implications for human health and demonstrate the functional capabilities contributed by the microbial communities. Among the four rivers studied, the distinctiveness of Ganga in comparison to others, particularly upstream of Ganga revealed a highly dynamic microbial structure. Bhagirathi and Alaknanda confluence to form Ganga, the microbiome revealed that Alaknanda has the foremost contribution to Ganga with respect to microbial community, bacteriophages, and the type of trace elements and heavy metals detected.

Microbial diversity of river Ganga at Haridwar (Uttarakhand) through metagenomic approaches

“…The total number of reads for the raw data and the trimmed data, i.e., 8522567 and 82429791, respectively, as well as their read orientation (R1 and R2), average GC% of 58, and length of base pair reads for raw data were found to be 159. A similar finding was also reported by the author, in which the GC% was 53 for samples of sediments collected from the Ganga River at Haridwar, and a striking resemblance was also found between the distribution pattern of GC content and the presence of bacterial diversity grouped at the OTU level [18]. After trimming, a read length of 50-156 was further processed for analysis [Table 1].…”

“…Another metagenomic study indicated a correlation between the composition of the microbiome and pollution, revealing a high abundance of microbial communities with implications for human health. The Ganga river, particularly upstream, showed a highly dynamic microbial structure, highlighting the functional capabilities of these communities [18]. To examine the genetic make-up, functional potential, and ecological dynamics of microbial communities in various contexts, modern metagenomic research applies cutting-edge sequencing technology, bioinformatics tools, and analytical methods.…”

Antibiotic Resistance Genes in bacteria from Anthropogenically Impacted Indian River Ecosystems

“…This result showed the heterogeneity of antibiotic resistance gene distribution in distinct water bodies. This comprehensive study probing into the microbial and genetic landscape of the Ganga and Gomti rivers has explored intricate dynamics of antibiotic resistance in these critical water ecosystems (Regar et al, 2020). The comprehensive investigation provided an extensive understanding of the intricate relationship between microbial populations and antibiotic resistance.…”