Metagenomes of microbial communities in arsenic- and pathogen-contaminated well and surface water from bangladesh.
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ABSTRACT:
SUBMITTER: Layton AC
PROVIDER: S-EPMC4239352 | biostudies-literature | 2014 Nov
REPOSITORIES: biostudies-literature
Publications
Metagenomes of microbial communities in arsenic- and pathogen-contaminated well and surface water from bangladesh.
Layton Alice C AC Chauhan Archana A Williams Daniel E DE Mailloux Brian B Knappett Peter S K PS Ferguson Andrew S AS McKay Larry D LD Alam M Jahangir MJ Matin Ahmed Kazi K van Geen Alexander A Sayler Gary S GS
Genome announcements 20141120 6
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. ...[more]
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Project description:To identify the causes of salinization and arsenic contamination of surface water on an embanked island (i.e., polder) in the tidal delta plain of SW Bangladesh we collected and analyzed water samples in the dry (May) and wet (October) seasons in 2012-2013. Samples were collected from rice paddies (wet season), saltwater ponds used for brine shrimp aquaculture (dry season), freshwater ponds and tidal channels (both wet and dry season), and rainwater collectors. Continuous measurements of salinity from March 2012 to February 2013 show that tidal channel water increases from ~0.15 ppt in the wet season up to ~20 ppt in the dry season. On the polder, surface water exceeds the World Health Organization drinking water guideline of 10 μg As/L in 78% of shrimp ponds and 27% of rice paddies, raising concerns that produced shrimp and rice could have unsafe levels of As. Drinking water sources also often have unsafe As levels, with 83% of tubewell and 43% of freshwater pond samples having >10 μg As/L. Water compositions and field observations are consistent with shrimp pond water being sourced from tidal channels during the dry season, rather than the locally saline groundwater from tubewells. Irrigation water for rice paddies is also obtained from the tidal channels, but during the wet season when surface waters are fresh. Salts become concentrated in irrigation water through evaporation, with average salinity increasing from 0.43 ppt in the tidal channel source to 0.91 ppt in the rice paddies. Our observations suggest that the practice of seasonally alternating rice and shrimp farming in a field has a negligible effect on rice paddy water salinity. Also, shrimp ponds do not significantly affect the salinity of adjacent surface water bodies or subjacent groundwater because impermeable shallow surface deposits of silt and clay mostly isolate surface water bodies from each other and from the shallow groundwater aquifer. Bivariate plots of conservative element concentrations show that all surface water types lie on mixing lines between dry season tidal channel water and rainwater, i.e., all are related by varying degrees of salinization. High As concentrations in dry season tidal channel water and shrimp ponds likely result from groundwater exfiltration and upstream irrigation in the dry season. Arsenic is transferred from tidal channels to rice paddies through irrigation. Including groundwater samples from the same area (Ayers et al. in Geochem Trans 17:1-22, 2016), principal components analysis and correlation analysis reveal that salinization explains most variation in surface water compositions, whereas progressive reduction of buried surface water by dissolved organic carbon is responsible for the nonconservative behavior of S, Fe, and As and changes in Eh and alkalinity of groundwater.
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Project description:BACKGROUND:Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. RESULTS:We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM. CONCLUSIONS:CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.
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Project description:Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.IMPORTANCE The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.
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Project description: Not available
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Project description:Arsenic contamination of drinking water is a serious public health threat. In Bangladesh, eight major safe water options provide an alternative to contaminated shallow tubewells: piped water supply, deep tubewells, pond sand filters, community arsenic-removal, household arsenic removal, dug wells, well-sharing, and rainwater harvesting. However, it is uncertain how well these options are accepted and used by the at-risk population. Based on the RANAS model (risk, attitudes, norms, ability, and self-regulation) this study aimed to identify the acceptance and use of available safe water options. Cross-sectional face-to-face interviews were used to survey 1,268 households in Bangladesh in November 2009 (n = 872), and December 2010 (n = 396). The questionnaire assessed water consumption, acceptance factors from the RANAS model, and socioeconomic factors. Although all respondents had access to at least one arsenic-safe drinking water option, only 62.1% of participants were currently using these alternatives. The most regularly used options were household arsenic removal filters (92.9%) and piped water supply (85.6%). However, the former result may be positively biased due to high refusal rates of household filter owners. The least used option was household rainwater harvesting (36.6%). Those who reported not using an arsenic-safe source differed in terms of numerous acceptance factors from those who reported using arsenic-safe sources: non-users were characterized by greater vulnerability; showed less preference for the taste and temperature of alternative sources; found collecting safe water quite time-consuming; had lower levels of social norms, self-efficacy, and coping planning; and demonstrated lower levels of commitment to collecting safe water. Acceptance was particularly high for piped water supplies and deep tubewells, whereas dug wells and well-sharing were the least accepted sources. Intervention strategies were derived from the results in order to increase the acceptance and use of each arsenic-safe water option.
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