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

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.

Microbial indicators for soil quality

“…Recent molecular approaches have confirmed most of these old data, and have even shown new important traits of the soil microbiome with respect to the degradation of pollutants. For instance, using metagenomics of microbiomes from industrially-contaminated soil sites in Gujarat (India), Shah et al (2013) identified over 100 different genes for enzymes predicted to be involved in xenobiotic-degradation pathways. Based on these studies, a huge number of potential indicators has become available, however testing of these for robustness regarding the biodegradation potential and activity, and subsequent validation in the context of well-defined soils and metadata, is needed (Shah et al 2013;Sukul et al 2017).…”

The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis

“…For example, it was used for analyzing the microbial communities in uranium tailings and mine water sediment from India [17], revealing the prevalence of biodegradation genes for organic pollutants in activated sludge [18], and assessing the communities of indigenous microorganisms in the contaminated soil with effluents from a variety of industries involved in the manufacturing of various chemicals, dyes, solvents, paints, and other xenobiotic compounds [14]. Kotik et al [19] investigated the bacterial communities in TCE-polluted ground water.…”

“…Many xenobiotic-contaminated areas have undergone a shift in microbial community composition [15]. Some bacteria could evolve to utilize a variety of pollutants, whereas a complete degradation of the pollutants depends on the interaction of diverse microorganisms collectively [14], and any individual microorganism is not able to fulfill the degradation of the pollutants completely. As 99% of the environmental microorganisms cannot be cultivated easily [16], metagenome-based analysis of the entire microbial community becomes imperative for delineating the change of microbial community in the contaminated sites with industrial discharges, and for unveiling which metabolic pathway is responsible for biodegradation [14].…”

“…It is crucial to assess what kind of dechlorinating microorganisms are present to successfully perform a biostimulation or bioaugmentation strategy [13]. Microbial communities play an important role in the catabolism and detoxification of anthropogenic/xenobiotic compounds [14]. Many xenobiotic-contaminated areas have undergone a shift in microbial community composition [15].…”

“…Metagenomics has become the focus of many researches [14] and has provided enormous amounts of biological information that has helped to gain insight into functional aspects in addition to species composition [16]. For example, it was used for analyzing the microbial communities in uranium tailings and mine water sediment from India [17], revealing the prevalence of biodegradation genes for organic pollutants in activated sludge [18], and assessing the communities of indigenous microorganisms in the contaminated soil with effluents from a variety of industries involved in the manufacturing of various chemicals, dyes, solvents, paints, and other xenobiotic compounds [14].…”