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Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes

Environmental Monitoring and Assessment volume 191, Article number: 778 (2019) Cite this article

Abstract

The discharge of solid and liquid waste from domestic, municipal, and hospital premises pollutes the soil and river ecosystems. However, the diversity and functions of the microbial communities present in these polluted environments are not well understood and may contain harmful microbial communities with specialized metabolic potential. In this present study, we adapted the Illumina sequencing technology to analyze microbial communities and their metabolic capabilities in polluted environments. A total of 1113884 sequences of v3–v4 hypervariable region of the 16S rRNA were obtained using Illumina sequencing and assigned to the corresponding taxonomical ranks using Greengenes databases. Proteobacteria and Bacteroidetes were dominantly present in all the four studied sites (solid waste dumping site (SWD); Chite river site (CHR), Turial river site (TUR), and Tuikual river site (TUKR)). It was found that the SWD was dominated by Firmicutes, Actinobacteria; CHR by Acidobacteria, Verrucomicrobia, Planctomycetes; TUR by Verrucomicrobia, Acidobacteria; and TUKR by Verrucomicrobia and Firmicutes, respectively. The dominant bacterial genus present in all samples was Acinetobacter, Flavobacterium, Prevotella, Corynebacterium, Comamonas, Bacteroides, Wautersiella, Cloacibacterium, Stenotrophomonas, Sphingobacterium, and Pseudomonas. Twenty-seven putative bacterial pathogens were identified from the contaminated sites belonging to Salmonella enterica, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. Functional analysis showed a high representation of genes in the KEGG pathway involved in the metabolism of amino acids and carbohydrates and identified several genes associated with antibiotic resistance and xenobiotic degradation in these environments, which can be a serious problem for human health and environment. The results from this research will provide a new understanding of the possible management practices to minimize the spread of pathogenic microorganisms in the environment.

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Funding

This research was supported by the Bioinformatics Infrastructure Facility (BTISNeT) sponsored by Department of Biotechnology, Govt. of India, New Delhi. The grant has enabled us to establish computational facility to work on Metagenomics pipeline, and the Advanced State Biotech Hub grant has helped in sampling and generate NGS data. The DeLCON facility has enabled for study design, analysis, and interpretation of data.

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Authors and Affiliations

  1. Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India

    Surajit De Mandal, Vabeiryureilai Mathipi, Esther Lalnunmawii & Nachimuthu Senthil Kumar

  2. College of Agriculture, South China Agricultural University, Guangzhou, China

    Surajit De Mandal

  3. Department of Chemistry, Mizoram University, Aizawl, Mizoram, 796004, India

    Rajendra Bose Muthukumaran

  4. Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India

    Guruswami Gurusubramanian

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  1. Surajit De Mandal
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  2. Vabeiryureilai Mathipi
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  4. Guruswami Gurusubramanian
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  5. Esther Lalnunmawii
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Correspondence to Nachimuthu Senthil Kumar.

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De Mandal, S., Mathipi, V., Muthukumaran, R. et al. Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes. Environ Monit Assess 191, 778 (2019). https://doi.org/10.1007/s10661-019-7879-0

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Keywords

  • Waste discharge
  • Bacterial community
  • Pathogen
  • Antibiotic-resistant gene
  • Xenobiotic