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Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges

  • Environmental Microbiology
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Abstract

Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878′; E 072°38.478′), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria” and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other “-omic” studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental clean-up projects.

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Abbreviations

MetaSAMS:

Sequence Analysis and Management System for Metagenomic Datasets

EGTs:

Environmental gene tags

LCA:

Lowest common ancestor

GO:

Gene Ontology

COG:

Clusters of Orthologous Groups of proteins

Pfam:

Protein family

KEGG:

Kyoto Encyclopedia of Genes and Genomes

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Acknowledgments

V.S. and D.M. acknowledge the financial support by the German Academic Exchange Service (DAAD) and Department of Biotechnology, New Delhi. M.Z and F.G.E. acknowledge the receipt of a scholarship from the CLIB Graduate Cluster “Industrial Biotechnology” co-financed by the Ministry of Innovation of North Rhine-Westphalia (Germany). The authors thank Dr. Asha Parmar, BRD School of Biosciences, Sardar Patel University, Gujarat, India for discussions and critical suggestions during work plan and manuscript preparation. The bioinformatics and technological support of the Bioinformatics and Genomics Platforms at the Center for Biotechnology (CeBiTec, Bielefeld University, Germany) is gratefully acknowledged.

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Authors and Affiliations

  1. BRD School of Biosciences, Sardar Patel University, Sardar Patel Maidan, Vadtal Road, Satellite Campus, Vallabh Vidyanagar 388 120, Post Box No. 39, Anand, Gujarat, India

    Varun Shah & Datta Madamwar

  2. Center for Biotechnology, Institute for Genome Research and Systems Biology, Genome Research of Industrial Microorganisms, Bielefeld University, P.O. Box 100131, 33501, Bielefeld, Germany

    Martha Zakrzewski, Daniel Wibberg, Felix Eikmeyer & Andreas Schlüter

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  1. Varun Shah
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  2. Martha Zakrzewski
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  6. Datta Madamwar
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Correspondence to Datta Madamwar.

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Shah, V., Zakrzewski, M., Wibberg, D. et al. Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges. Microb Ecol 66, 533–550 (2013). https://doi.org/10.1007/s00248-013-0253-9

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