Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes

Environmental Microbiome - 2019
Parul Mittal1, Vishnu Prasoodanan Pk1, Darshan B. Dhakan1, Sanjiv Kumar1, Vineet K. Sharma1
1Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh, India

Tóm tắt

Abstract Background Yamuna, a major tributary of Ganga, which flows through the national capital region of Delhi, is among the major polluted rivers in India. The accumulation of various effluents, toxic chemicals, heavy metals, and increased organic load in the Yamuna directly affects the organisms that thrive inside or around this river. It also makes it an ideal site for studying the impact of pollution on the river microflora, which are sentinels of the water quality. Results In this study, the microbial community structure and functional diversity of the Yamuna river water was assessed from the New Delhi region. The community structure of Yamuna during pre-monsoon (June) was found to be significantly different from the post-monsoon (November) time, with Acinetobacter being the most abundant genus during June, and Aeromonas during November. The functional characterization revealed the higher abundance of Methyl-accepting chemotaxis protein in the river water, which could be important for the microbial chemosensory adaptation in the environment. A higher abundance of genes related to nitrogen and sulfur metabolism, metal tolerance, and xenobiotic degradation, and complete degradation pathways of aromatic compounds such as toluene, xylene, benzene and phenol were identified. Further, the results showed the presence of a pool of antibiotic resistance genes in the bacterial microbiome in the Yamuna alongside a large number of broad-spectrum antibiotics, such as carbapenemases and metallo-β-lactamases. Efflux mechanism of resistance was found to dominate among these microbes conferring multi-drug resistance. The Principal Coordinate Analysis of the taxonomic composition of the Yamuna River water with publicly available freshwater and sewage datasets revealed significant differences in the two Yamuna samples and a greater resemblance of pre-monsoon Yamuna sample to sewage sample owing to the higher pollution levels in Yamuna in the pre-monsoon time. Conclusion The metagenomic study of the Yamuna river provides the first insights on the bacterial microbiome composition of this large polluted river, and also helps to understand the dynamics in the community structure and functions due to seasonal variations. The presence of antibiotic resistance genes and functional insights on the metabolic potential of a polluted river microbiome are likely to have several applications in health, biotechnology and bioremediation.

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Tài liệu tham khảo

Singh KP, Malik A, Mohan D, Sinha S. Multivariate statistical techniques for the evaluation of spatial and temporal variations in water quality of Gomti River (India)—a case study. Water Res. 2004;38(18):3980–92.

Jain C. Metal fractionation study on bed sediments of river Yamuna, India. Water Res. 2004;38(3):569–78.

Jain C, Singhal D, Sharma M. Metal pollution assessment of sediment and water in the river Hindon, India. Environ Monit Assess. 2005;105(1–3):193–207.

Khwaja A, Singh R, Tandon S. Monitoring of ganga water and sediments Vis-a-Vis tannery pollution at Kanpur (India): a case study. Environ Monit Assess. 2001;68(1):19–35.

Hamner S, Pyke D, Walker M, Pandey G, Mishra RK, Mishra VB, Porter C, Ford TE. Sewage pollution of the river ganga: an ongoing case study in Varanasi, India. River Sys. 2013;20(3-4):157–67.

Sen I, Shandil A, Shrivastava V. Study for determination of heavy metals in fish species of the River Yamuna (Delhi) by Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES). Adv Appl Sci Res. 2011;2(2):161–66.

Kaur S, Mehra P. Assessment of heavy metals in summer & Winter seasons in river Yamuna segment flowing through Delhi, India. J Environ Ecol. 2012;3(1):149–65.

Singh SS, Singh S, Garg S. Environmental concerns in National Capital Territory of Delhi, India. J Climatol Weather Forecast. 2015;3:147. https://doi.org/10.4172/2332-2594.1000147 .

Upadhyay R, Dasgupta N, Hasan A, Upadhyay S. Managing water quality of river Yamuna in NCR Delhi. Phys Chem Earth, Parts A/B/C. 2011;36(9):372–8.

Azam F, Worden AZ. Oceanography. Microbes, molecules, and marine ecosystems. Science. 2004;303(5664):1622–4.

Reinthaler F, Posch J, Feierl G, Wüst G, Haas D, Ruckenbauer G, Mascher F, Marth E. Antibiotic resistance of E. coli in sewage and sludge. Water Res. 2003;37(8):1685–90.

Xu W, Zhang G, Li X, Zou S, Li P, Hu Z, Li J. Occurrence and elimination of antibiotics at four sewage treatment plants in the Pearl River Delta (PRD), South China. Water Res. 2007;41(19):4526–34.

Gallert C, Fund K, Winter J. Antibiotic resistance of bacteria in raw and biologically treated sewage and in groundwater below leaking sewers. Appl Microbiol Biotechnol. 2005;69(1):106–12.

Linton K, Richmond M, Bevan R, Gillespie W. Antibiotic resistance and R factors in coliform bacilli isolated from hospital and domestic sewage. J Med Microbiol. 1974;7(1):91–103.

Mutiyar PK, Mittal AK. Occurrences and fate of selected human antibiotics in influents and effluents of sewage treatment plant and effluent-receiving river Yamuna in Delhi (India). Environ Monit Assess. 2014;186(1):541–57.

Jha P, Subramanian V, Sitasawad R, Van Grieken R. Heavy metals in sediments of the Yamura River (a tributary of the Ganges), India. Sci Total Environ. 1990;95:7–27.

Vandewalle JL, Goetz GW, Huse SM, Morrison HG, Sogin ML, Hoffmann RG, Yan K, McLellan SL. Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure. Environ Microbiol. 2012;14(9):2538–52.

Jury K, Vancov T, Stuetz R, Khan S. Antibiotic resistance dissemination and sewage treatment plants. Curr Res Technol Educ Topics Appl Microbiol Microb Biotechnol. 2010;2:509–10.

Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(3):R46.

Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017;45(D1):D566–D73.

Miller LP, Crawford JT, Shinnick TM. The rpoB gene of mycobacterium tuberculosis. Antimicrob Agents Chemother. 1994;38(4):805–11.

Friedman L, Alder JD, Silverman JA. Genetic changes that correlate with reduced susceptibility to daptomycin in Staphylococcus aureus. Antimicrob Agents Chemother. 2006;50(6):2137–45.

Weigel LM, Steward CD, Tenover FC. gyrA mutations associated with fluoroquinolone resistance in eight species ofEnterobacteriaceae. Antimicrob Agents Chemother. 1998;42(10):2661–7.

Damier-Piolle L, Magnet S, Bremont S, Lambert T, Courvalin P. AdeIJK, a resistance-nodulation-cell division pump effluxing multiple antibiotics in Acinetobacter baumannii. Antimicrob Agents Chemother. 2008;52(2):557–62.

Rouquette-Loughlin CE, Balthazar JT, Shafer WM. Characterization of the MacA-MacB efflux system in Neisseria gonorrhoeae. J Antimicrob Chemother. 2005;56(5):856–60.

Warner DM, Folster JP, Shafer WM, Jerse AE. Regulation of the MtrC-MtrD-MtrE efflux-pump system modulates the in vivo fitness of Neisseria gonorrhoeae. J Infect Dis. 2007;196(12):1804–12.

Ahammad ZS, Sreekrishnan T, Hands CL, Knapp CW, Graham DW. Increased waterborne Bla NDM-1 resistance gene abundances associated with seasonal human pilgrimages to the upper Ganges River. Environ Sci Technol. 2014;48(5):3014–20.

Sharma AK, Jaiswal SK, Chaudhary N, Sharma VK. A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota. Sci Rep. 2017;7(1):9751.

Valls M, de Lorenzo V. Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution. FEMS Microbiol Rev. 2002;26(4):327–38.

Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DG. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res. 2014;42(Database issue):D737–43.

Mandal P, Upadhyay R, Hasan A. Seasonal and spatial variation of Yamuna River water quality in Delhi, India. Environ Monit Assess. 2010;170(1–4):661–70.

Ravindra K, Kaushik A. Seasonal variations in physico-chemical characteristics of river Yamuna in Haryana and its ecological best-designated use. J Environ Monit. 2003;5(3):419–26.

Rodriguez-Mozaz S, Chamorro S, Marti E, Huerta B, Gros M, Sanchez-Melsio A, Borrego CM, Barcelo D, et al. Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river. Water Res. 2015;69:234–42.

Gibson MK, Crofts TS, Dantas G. Antibiotics and the developing infant gut microbiota and resistome. Curr Opin Microbiol. 2015;27:51–6.

Levy SB. Antibiotic resistance: consequences of inaction. Clin Infect Dis. 2001;33(Suppl 3):S124–9.

Zhang QQ, Ying GG, Pan CG, Liu YS, Zhao JL. Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance. Environ Sci Technol. 2015;49(11):6772–82.

Van Boeckel TP, Gandra S, Ashok A, Caudron Q, Grenfell BT, Levin SA, Laxminarayan R. Global antibiotic consumption 2000 to 2010: an analysis of national pharmaceutical sales data. Lancet Infect Dis. 2014;14(8):742–50.

Zong Z, Zhang X. blaNDM-1-carrying Acinetobacter johnsonii detected in hospital sewage. J Antimicrob Chemother. 2013;68(5):1007–10.

Zhang C, Qiu S, Wang Y, Qi L, Hao R, Liu X, Shi Y, Hu X, et al. Higher isolation of NDM-1 producing Acinetobacter baumannii from the sewage of the hospitals in Beijing. PLoS One. 2014;8(6):e64857.

Ko WC, Yu KW, Liu CY, Huang CT, Leu HS, Chuang YC. Increasing antibiotic resistance in clinical isolates of Aeromonas strains in Taiwan. Antimicrob Agents Chemother. 1996;40(5):1260–2.

Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR. Characterization of a new metallo-beta-lactamase gene, Bla (NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother. 2009;53(12):5046–54.

Zhu YG, Zhao Y, Li B, Huang CL, Zhang SY, Yu S, Chen YS, Zhang T, et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat Microbiol. 2017;2:16270.

McKinney CW, Pruden A. Ultraviolet disinfection of antibiotic resistant bacteria and their antibiotic resistance genes in water and wastewater. Environ Sci Technol. 2012;46(24):13393–400.

Xu J, Xu Y, Wang H, Guo C, Qiu H, He Y, Zhang Y, Li X, et al. Occurrence of antibiotics and antibiotic resistance genes in a sewage treatment plant and its effluent-receiving river. Chemosphere. 2015;119:1379–85.

Pandey G, Jain RK. Bacterial chemotaxis toward environmental pollutants: role in bioremediation. Appl Environ Microbiol. 2002;68(12):5789–95.

Zeyaullah M, Islam B, Ali A. Isolation, identification and PCR amplification of merA gene from highly mercury polluted Yamuna river. Afr J Biotechnol. 2010;9(24):3510–4.

Bhagat N, Vermani M, Bajwa HS. Characterization of heavy metal (cadmium and nickle) tolerant gram negative enteric bacteria from polluted Yamuna River, Delhi. Afr J Microbiol Res. 2016;10(5):127–37.

Singh S, Kumar M. Heavy metal load of soil, water and vegetables in peri-urban Delhi. Environ Monit Assess. 2006;120(1–3):79–91.

Mejáre M, Bülow L. Metal-binding proteins and peptides in bioremediation and phytoremediation of heavy metals. Trends Biotechnol. 2001;19(2):67–73.

Muyzer G, De Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59(3):695–700.

Patel RK, Jain M. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619.

Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957–63.

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10–2.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.

Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, Yamashita H, Lam T-W. MEGAHIT v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.

Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38(12):e132-e.

Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012;28(1):125–6.

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2015;44(D1):D286–93.

Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y, Maciejewski A, Arndt D, et al. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2014;42(D1):D1091–D7.

Poretsky R, Rodriguez RL, Luo C, Tsementzi D, Konstantinidis KT. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One. 2014;9(4):e93827.

Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol. 2009;75(6):1688–96.

Bray JR, Curtis JT. An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr. 1957;27(4):325–49.

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