A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam

Abstract

Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1) of 89,171 sequences (totaling 125,449,864 base pairs) with an average length of 1406 bps was annotated. About 74,478 sequences containing 101,948 predicted protein coding regions passed the quality control. Taxonomical classification revealed abundance of bacteria that accounted for 98.3% of the microbial population of the metagenome. Eukaryota had an abundance of 1.1% followed by archea that showed 0.4% abundance. In phylum based classification, Proteobacteria was dominant (62.6%) followed by Bacteroidetes (11.7%), Planctomycetes (7.7%), Verrucomicrobia (5.6%), Actinobacteria (3.7%) and Firmicutes (1.9%). The Clusters of Orthologous Groups (COGs) analysis indicated that the protein regulating the metabolic functions constituted a high percentage (18,199 reads; 39.3%) of the whole metagenome followed by the proteins regulating the cellular processes (22.3%). About 0.07% sequences of the whole metagenome were related to genes coding for arsenic resistant mechanisms. Nearly 50% sequences of these coded for the arsenate reductase enzyme (EC. 1.20.4.1), the dominant enzyme of ars operon. Proteins associated with iron acquisition and metabolism were coded by 2% of the metagenome as revealed through SEED analysis. Our study reveals the microbial diversity and provides an insight into the functional aspect of the genes that might play crucial role in arsenic geocycle in contaminated ground water of Assam.

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

“…This method has used for the identification of very rare populations which is present in very low abundance that may necessary for the functional diversity and ecosystem stability (Sogin et al ., 2006; Staley et al ., 2013). Several bacterial communities from different environmental samples like marine waters (Brown et al ., 2009), soils (Jones et al ., 2009), wastewater (Sanapareddy et al ., 2009), contaminated water (Das et al ., 2017) and several human microbiomes were successfully characterized (Staley et al ., 2013; Sanapareddy et al ., 2009).…”

Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling

“…It has also been demonstrated that Burkholderia can enhance arsenic toxicity by reducing methyl-arsenate compounds to toxic methyl-arsenite [46]. Interestingly, Burkholderia was also among the most prominent genus in recent metagenomic surveys from other arsenic-contaminated regions located in India [47] and Bangladesh [48].…”

Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities

“…ABC-type Fe 3+ -siderophore transport system, Ferric hydroxamate ABC transporter (EC 3.A.1.14.3), Isochorismate synthase (EC 5.4.4.2) of siderophore biosynthesis, Siderophore biosynthesis protein, Siderophore synthetase component and TonB-dependent proteins. Different siderophores linked gene sequences that resembled pyoverdine (generally produced by the members of the family Pseudomonaceae, i.e., Azotobacter, Azomonas, Pseudomonas, and Rhizobacter) [75] , achromobactin (siderophore produced by Pseudomonas syringe) [76]; yersiniabactin (siderophore of the pathogenic bacteria Yersinia pestis, Yersinia pseudotuberculosis, and Yersinina enterocolitica) [77]; bacillibactin (siderophore synthesized by the genus Bacillus) [78]; enterobactin and pyochelin (siderophore synthesized by Pseudomonas aeruginosa) [79,80] were traced in the dataset. We speculate that the dominant presence of microbial communities linked with the efficient iron acquisition functions is supposed to make them enable to enhance iron bioavailability in the rhizosphere of kodo plants.…”