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Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing

Archives of Microbiology volume 203, pages 367–375 (2021)Cite this article

Abstract

A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40′5.53′′ N, 77°15′0.35′′ E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with “omic” studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.

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Acknowledgements

Financial assistance provided by the NASF research grant (project entitled “Bioremediation of chemical contaminants and their complexes present in drainage water with high dynamic flux used for irrigation in urban and peri urban agriculture”), sanction no. NASF/CA-6030/2017-18, is greatly acknowledged. The author Kushneet Kaur Sodhi greatly acknowledge the University Grant Commission (UGC), Government of India, for providing the stipend.MK acknowledges the Hindu College, DU for the research grant for Innovation project (IP-2019-20/SC/06 and 07).

Funding

This study was supported by the funding agency, National Agricultural Science Fund, Indian Council of Agricultural Research, Delhi, India.

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Affiliations

  1. Soil Microbial Ecology, Pesticide Toxicology Laboratory and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India

    Kushneet Kaur Sodhi, Mohit Kumar & Dileep Kumar Singh

  2. Department of Zoology, Hindu College, University of Delhi, Delhi, 110007, India

    Mohit Kumar

Authors
  1. Kushneet Kaur Sodhi
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  2. Mohit Kumar
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  3. Dileep Kumar Singh
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Contributions

KKS: experiment designing, data analysis, and writing. MK: sample processing and editing. DK: supervision.

Corresponding author

Correspondence to Dileep Kumar Singh.

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The study is not related to animals or humans.

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Sodhi, K.K., Kumar, M. & Singh, D.K. Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing. Arch Microbiol 203, 367–375 (2021). https://doi.org/10.1007/s00203-020-02045-0

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  • DOI: https://doi.org/10.1007/s00203-020-02045-0

Keywords

  • Illumina MiSeq
  • V3–V4 sequence
  • Microbial diversity
  • Metagenome