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Metagenomics analysis of water samples collected from the Yamuna River of Agra city, India

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Abstract

Yamuna River water in Agra city of India is contaminated with toxic pollutants, including heavy metals that cause damage to the environment and human health. At present, the direct use of river water for drinking purposes and household activities lead to the direct exposure of society to the contaminants. In this study, Yamuna River water samples were collected from three different sites in Agra city during the monsoon, summer, and winter seasons. The physico-chemical parameters were estimated along with heavy metals. In physico-chemical parameter, the values found were mostly above the permissible limits. The results water samples contain high levels of cadmium, chromium, lead, and nickel above the desirable levels in most cases. The metagenomic analysis revealed that Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctobacteria were the most abundant phyla with a relative abundance of 61%, 9.34%, 5.23%, 4.64%, and 4.3%, respectively. The Comamonadaceae, the most abundant family consists of the genera involved in hydrogen oxidation, iron reduction, degraders of polycyclic aromatic hydrocarbons, and fermentation. The presence of Pseudomonas, Nitrosomonas sp., Thauera humireducens and Dechloromonas denitrificans (decomposition of sewage and organic matter) and Pseudomonas aeruginosa indicates the presence of heavy metal degrading bacteria in water sample. Functional prediction showed the presence of genes responsible for different metabolic pathways that could help developing new bioremediation strategies. The study concludes the status of water contamination, the presence of complex microbial community and suggests the futuristic use and their role in bioremediation.

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Acknowledgements

Dr. Nupur Raghav would like to acknowledge the support of the Late Prof. Janendra Nath Srivastava for providing constant supervision and guidance in this study. All the authors are thankful to Xcelris Labs for extending support, wherever required, and UGC-SAP (India) for financial assistance during the research studies.

Funding

This work was supported by UGC-Botany-SAP Letter No. F.5-8/2018/DRS-I(SAP-II), India.

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Authors and Affiliations

  1. Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India

    Nupur Raghav, Pooja Saraswat & Rajiv Ranjan

  2. Division of Agriculture Bioinformatics, Indian Agricultural Statistical Research Institute, Pusa, New Delhi, 110012, India

    Sunil Kumar

  3. Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, 221305, India

    Anurag Chaurasia

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NR and RR designed the study, NR and PS wrote the manuscript. RR. SK, AC edited the manuscript and made modifications.

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11274_2024_3919_MOESM1_ESM.jpg

Supplementary file1 (JPG 59 KB) The graph shows the relative abundance of water samples at the class level. From the figure, it can be inferred that Betaproteobacteria is the most abundant class followed by Gammaproteobacteria

11274_2024_3919_MOESM2_ESM.jpg

Supplementary file2 (JPG 84 KB) The graph shows the relative abundance of Water samples at the order level. From the figure, it can be inferred that Burkholderiales is the most abundant order followed by Rhodocyclales

11274_2024_3919_MOESM3_ESM.jpg

Supplementary file3 (JPG 66 KB) The graph shows the relative abundance of Water sample at the genus level. From the figure, it can be inferred that Hydrogenophaga is the most abundant genus followed by Thauera

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Raghav, N., Saraswat, P., Kumar, S. et al. Metagenomics analysis of water samples collected from the Yamuna River of Agra city, India. World J Microbiol Biotechnol 40, 113 (2024). https://doi.org/10.1007/s11274-024-03919-x

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