Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing
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ORIGINAL PAPER
Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing Kushneet Kaur Sodhi1 · Mohit Kumar1,2 · Dileep Kumar Singh1 Received: 14 May 2020 / Revised: 11 August 2020 / Accepted: 12 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
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. Keywords Illumina MiSeq · V3–V4 sequence · Microbial diversity · Metagenome
Introduction
Communicated by Erko stackebrandt. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00203-020-02045-0) contains supplementary material, which is available to authorized users. * Dileep Kumar Singh [email protected] Kushneet Kaur Sodhi [email protected] Mohit Kumar [email protected] 1
Soil Microbial Ecology, Pesticide Toxicology Laboratory and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
Department of Zoology, Hindu College, University of Delhi, Delhi 110007, India
2
The River Yamuna is the largest tributary of River Ganga and is the heart of the water supply to Delhi, the National Capital Region. Various studies on the effect of pollutants on the River Yamuna have been carried out due to its immense importance. The Yamuna River originates from the Himalayan
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