Abstract
The contamination of drinking water from both arsenic and microbial pathogens occurs in Bangladesh. A general metagenomic survey of well water and surface water provided information on the types of pathogens present and may help elucidate arsenic metabolic pathways and potential assay targets for monitoring surface-to-ground water pathogen transport.
GENOME ANNOUNCEMENT
Bangladesh has two microbial-based public health water resource crises. Diarrheal diseases (1), often attributable to poor sanitary conditions and fecal contamination of drinking water, remain a leading cause of mortality for children younger than 5 years (2, 3). In locations with poor sanitation, groundwater is a cleaner source than surface water; however, shallow wells may still contain waterborne pathogens (4). In parts of Bangladesh, the drinking water situation is further complicated by the presence of geogenic arsenic above drinking water standards (>10 µg/liter), which causes serious and debilitating diseases (5, 6). The goal of this study was to generate metagenomic sequences from arsenic- and pathogen-contaminated ground and surface waters in Bangladesh (7).
Surface and ground water samples were collected 4 times between March 2009 and November 2012 in a 1-km2 area of Bara Haldia, MatLab, Bangladesh (25.467°N 89.517°E) (4) representing both wet and dry seasons (8). In wells, the arsenic concentrations ranged from <1 to 218 parts per billion (ppb), and culturable Escherichia coli concentrations ranged from <1 to 100 most probable number (MPN)/100 ml. DNA was extracted from water filters using the Fast DNA spin kit (MP Biomedicals, CA) (2). DNA from 9 to 12 wells or 3 surface water samples was combined from each date to provide a composite sample. Metagenomic libraries were prepared using the Illumina Nextera DNA library preparation kit (Illumina, Inc., CA), and 2 × 100 bp reads were sequenced on an Illumina HiSeq 2000. The raw sequence reads from 8 metagenomic data sets were annotated using MG-RAST version 3.3.7 (9).
In surface water metagenomes, Bacteria was the dominant domain (94.2%), followed by Eukaryota (3.6%), DNA-based viruses (1.7%), and Archaea (0.4%). The most abundant genera in the surface water samples were Acidovorax (4.8%), Mycobacterium (4.1%), and Burkholderia (2.9%). Sequences matching well-known waterborne bacterial pathogens (10) found in surface water included: Vibrio cholerae and Vibrio parahaemolyticus (0.08%), Salmonella enterica (0.07%), Clostridium difficile (0.03%), Cronobacter sakazakii (0.03%), Shigella flexneri and Shigella dysenteriae (0.03%), Staphylococcus aureus (0.02%), Campylobacter jejuni (0.01%), and Helicobacter pylori (0.01%),
Consistent with the anaerobic conditions in ground water, archaea sequences comprised 20.4% of the sequences, with the genus Methanosarcina representing 4.1% of all well water metagenome sequences. Bacteria comprised 78.1%, eukaryotes 1.2%, and DNA-based viruses <0.1% of the sequences, with Geobacter (3.5%) and Clostridium (2.0%) being the second and third most abundant genera. Sequences matching the surface water pathogens were found in groundwater but generally at lower concentrations, which was expected due to die-off and filtering. Unexpectedly, four pathogens had 3- to 4-fold higher relative sequence abundances in ground than surface water: C. difficile (0.12%), S. aureus (0.04%) C. jejuni (0.03%), and H. pylori (0.03%).
In both surface and well water metagenomes, genes for arsenic metabolism, including arsenate reductase and arsenite oxidation, along with those for arsenic resistance, were present. These genetic pathways may affect arsenic mobility and toxicity (11). In summary, these metagenomic data sets have helped and can continue to further help elucidate the mechanisms of groundwater pathogen and arsenic contamination in Bangladesh.
Nucleotide sequence accession number.
Nucleotide sequences obtained were deposited at the NCBI Sequence Read Archive under the accession no. SRP047074.
ACKNOWLEDGMENTS
Water collection in this research was funded by NIH/Forgarty International Center grant 5R01TW8066-2. Sequencing was supported by the Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN.
Footnotes
Citation Layton AC, Chauhan A, Williams DE, Mailloux B, Knappett PSK, Ferguson AS, McKay LD, Alam MJ, Matin Ahmed K, van Geen A, Sayler GS. 2014. Metagenomes of microbial communities in arsenic- and pathogen-contaminated well and surface water from Bangladesh. Genome Announc. 2(6):e01170-14. doi:10.1128/genomeA.01170-14.
REFERENCES
- 1. Walker CL, Rudan I, Liu L, Nair H, Theodoratou E, Bhutta ZA, O’Brien KL, Campbell H, Black RE. 2013. Global burden of childhood pneumonia and diarrhoea. Lancet 381:1405–1416. 10.1016/S0140-6736(13)60222-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Kosek M, Bern C, Guerrant RL. 2003. The global burden of diarrhoeal disease, as estimated from studies published between 1992 and 2000. Bull. World Health Organ. 81:197–204 http://www.scielosp.org/scielo.php?script=sci_arttext&pid=S0042-96862003000300010&lng=en&nrm=iso&tlng=en. [PMC free article] [PubMed] [Google Scholar]
- 3. Black RE, Cousens S, Johnson HL, Lawn JE, Rudan I, Bassani DG, Jha P, Campbell H, Walker CF, Cibulskis R, Eisele T, Liu L, Mathers C. 2008. Global, regional, and national causes of child mortality in 2008: a systematic analysis. Lancet 375:1969–1987. 10.1016/S0140-6736(10)60549-1. [DOI] [PubMed] [Google Scholar]
- 4. Ferguson AS, Layton AC, Mailloux BJ, Culligan PJ, Williams DE, Smartt AE, Sayler GS, Feighery J, McKay LD, Knappett PS, Alexandrova E, Arbit T, Emch M, Escamilla V, Ahmed KM, Alam MJ, Streatfield PK, Yunus M, van Geen A. 2012. Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater. Sci. Total Environ. 431:314–322. 10.1016/j.scitotenv.2012.05.060. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. van Geen A, Ahmed EB, Pitcher L, Mey JL, Ahsan H, Graziano JH, Ahmed KM. 2014. Comparison of two blanket surveys of arsenic in tubewells conducted 12 years apart in a 25-km2 area of Bangladesh. Sci. Total Environ. 488–489:484–492. 10.1016/j.scitotenv.2013.12.049. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Mailloux BJ, Trembath-Reichert E, Cheung J, Watson M, Stute M, Freyer GA, Ferguson AS, Ahmed KM, Alam MJ, Buchholz BA, Thomas J, Layton AC, Zheng Y, Bostick BC, van Geen A. 2013. Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater. Proc. Natl. Acad. Sci. USA 110:5331–5335. 10.1073/pnas.1213141110. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. van Geen A, Ahmed KM, Akita Y, Alam MJ, Culligan PJ, Emch M, Escamilla V, Feighery J, Ferguson AS, Knappett P, Layton AC, Mailloux BJ, McKay LD, Mey JL, Serre ML, Streatfield PK, Wu J, Yunus M. 2011. Fecal contamination of shallow tubewells in Bangladesh inversely related to arsenic. Environ. Sci. Technol. 45:1199–1205. 10.1021/es103192b. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Leber J, Rahman MM, Ahmed KM, Mailloux B, van Geen A. 2011. Contrasting influence of geology on E. coli and arsenic in aquifers of Bangladesh. Ground Water 49:111–123. 10.1111/j.1745-6584.2010.00689.x. [DOI] [PubMed] [Google Scholar]
- 9. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. 10.1186/1471-2105-9-386. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Cabral JPS. 2010. Water microbiology. Bacterial pathogens and water. Int. J. Environ. Res. Public Health 7:3657–3703. 10.3390/ijerph7103657. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Cai L, Liu G, Rensing C, Wang G. 2009. Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils. BMC Microbiol. 9:4. 10.1186/1471-2180-9-4. [DOI] [PMC free article] [PubMed] [Google Scholar]