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Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics

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Abstract

The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

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Data availability

The datasets presented in this study can be found in online repositories of SRA at NCBI (SRS4592195, SRS4592470 and SRS4600533).

Change history

  • 09 July 2022

    1st Author name tagging correction.

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Acknowledgements

We acknowledged Mr. Asim Kumar Jana, Senior Technical Assistant of ICAR-CIFRI, Barrackpore, Kolkata, for sample collection and providing technical support.

Funding

This study was supported by the grant from the CABin program of Session 2020–2025 by the ICAR—Indian Agricultural Statistics Research Institute, New Delhi.

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Author notes

  1. Pranaya Kumar Parida, Bijay Kumar Behera and Budheswar Dehury these authors equally contributed to this work.

Authors and Affiliations

  1. Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India

    Pranaya Kumar Parida, Bijay Kumar Behera, Budheswar Dehury, Ajaya Kumar Rout, Dhruba Jyoti Sarkar & Basanta Kumar Das

  2. Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India

    Anil Rai

  3. Indian Council of Agricultural Research, New Delhi, India

    Trilochan Mohapatra

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  1. Pranaya Kumar Parida
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Contributions

Pranaya Kumar Parida: investigation, data analysis, original draft preparation.

Bijay Kumar Behera: conceptualization, methodology, investigation.

Budheswar Dehury: data interpretation, data analysis, writing the draft.

Ajaya Kumar Rout: writing, data analysis.

Dhruba Jyoti Sarkar: writing and statistical analysis.

Anil Rai: data analysis, critical revision.

Basanta Kumar Das: visualization, investigation.

Trilochan Mohapatra: supervision.

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Correspondence to Bijay Kumar Behera.

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Parida, P.K., Behera, B.K., Dehury, B. et al. Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics. Environ Sci Pollut Res 29, 71311–71325 (2022). https://doi.org/10.1007/s11356-022-20766-1

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