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Announcement
20 November 2014

Metagenomes of Microbial Communities in Arsenic- and Pathogen-Contaminated Well and Surface Water from Bangladesh

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.

REFERENCES

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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, and van Geen A. 2012. Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater. Sci. Total Environ. 431:314–322.
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van Geen A, Ahmed EB, Pitcher L, Mey JL, Ahsan H, Graziano JH, and 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.
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Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 2Number 624 December 2014
eLocator: 10.1128/genomea.01170-14

History

Received: 7 October 2014
Accepted: 8 October 2014
Published online: 20 November 2014

Contributors

Authors

Alice C. Layton
Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA
Archana Chauhan
Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
Joint Institute for Biological Sciences, University of Tennessee, Knoxville, and Oak Ridge National Laboratory, Knoxville, Tennessee, USA
Daniel E. Williams
Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
Brian Mailloux
Department of Environmental Science, Barnard College, New York, New York, USA
Peter S. K. Knappett
Department of Geology and Geophysics, Texas A&M University, College Station, Texas, USA
Andrew S. Ferguson
Civil Engineering & Engineering Mechanics, Columbia University, New York, New York, USA
Larry D. McKay
Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA
M. Jahangir Alam
Department of Geology, University of Dhaka, Dhaka, Bangladesh
Kazi Matin Ahmed
Department of Geology, University of Dhaka, Dhaka, Bangladesh
Alexander van Geen
Lamont-Doherty Earth Observatory of Columbia University, Palisades, New York, USA
Gary S. Sayler
Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
Joint Institute for Biological Sciences, University of Tennessee, Knoxville, and Oak Ridge National Laboratory, Knoxville, Tennessee, USA

Notes

Address correspondence to Gary S. Sayler, [email protected].

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