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USGS2005

Arsenic, microbes and contaminated aquifers

The health of tens of millions of people world-wide is at risk from drinking arsenic-contaminated well water. In most cases this arsenic occurs naturally within the sub-surface aquifers, rather than being derived from identifiable point sources of pollution. The mobilization of arsenic into the aqueous phase is the first crucial step in a process that eventually leads to human arsenicosis. Increasing evidence suggests that this is a microbiological phenomenon.

Trends in Microbiology↗

USGS2009

Microbial disease and the coral holobiont

Tropical coral reefs harbour a reservoir of enormous biodiversity that is increasingly threatened by direct human activities and indirect global climate shifts. Emerging coral diseases are one serious threat implicated in extensive reef deterioration through disruption of the integrity of the coral holobiont – a complex symbiosis between the coral animal, endobiotic alga and an array of microorganisms. In this article, we review our current understanding of the role of microorganisms in coral health and disease, and highlight the pressing interdisciplinary research priorities required to elucidate the mechanisms of disease. We advocate an approach that applies knowledge gained from experiences in human and veterinary medicine, integrated into multidisciplinary studies that investigate the interactions between host, agent and environment of a given coral disease. These approaches include robust and precise disease diagnosis, standardised ecological methods and application of rapidly developing DNA, RNA and protein technologies, alongside established histological, microbial ecology and ecological expertise. Such approaches will allow a better understanding of the causes of coral mortality and coral reef declines and help assess potential management options to mitigate their effects in the longer term.

Trends in Microbiology↗

USGS2000

Microbiological monitoring for the U.S. Geological Survey National Water-Quality Assessment Program

Data to characterize the microbiological quality of the Nation's fresh, marine, and estuarine waters are usually collected for local purposes, most often to judge compliance with standards for protection of public health in swimmable or drinkable waters. Methods and procedures vary with the objectives and practices of the parties collecting data and are continuously being developed or modified. Therefore, it is difficult to provide a nationally consistent picture of the microbial quality of the Nation's waters. Study objectives and guidelines for a national microbiological monitoring program are outlined in this report, using the framework of the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) program. A national program is designed to provide long-term data on the presence of microbiological pathogens and indicators in ground water and surface water to support effective water policy and management. Three major groups of waterborne pathogens affect the public health acceptability of waters in the United States—bacteria, protozoa, and viruses. Microbiological monitoring in NAWQA would be designed to assess the occurrence, distribution, and trends of pathogenic organisms and indicators in surface waters and ground waters; relate the patterns discerned to factors that help explain them; and improve our understanding of the processes that control microbiological water quality.

Water-Resources Investigations Report↗

USGS1973

Characteristics of water quality and streamflow, Passaic River basin above Little Falls, New Jersey

The findings of a problem-oriented river-system investigation of the water-quality and streamflow characteristics of the Passaic River above Little Falls, N.J. (drainage area 762 sq mi) are described. Information on streamflow duration, time-of-travel measurements, and analyses of chemical, biochemical, and physical water quality are summarized. This information is used to define relations between water quality, streamflow, geology, and environmental development in the basin's hydrologic system. The existence, nature, and magnitude of long-term trends in stream quality--as measured by dissolved solids, chloride, dissolved oxygen, biochemical oxygen demand, ammonia, nitrate, and turbidity--and in streamflow toward either improvement or deterioration are appraised at selected sites within the river system. The quality of streams in the upper Passaic River basin in northeastern New Jersey is shown to be deteriorating with time. For example, biochemical oxygen demand, an indirect measure of organic matter in a stream, is increasing at most stream-quality sampling sites. Similarly, the dissolved-solids content, a measure of inorganic matter, also is increasing. These observations suggest that the Passaic River system is being used more and more as a medium for the disposal of industrial and municipal waste waters. Dissolved oxygen, an essential ingredient for the natural purification of streams receiving waste discharges, is undersaturated (that is, below theoretical solubility levels) at all sampling sites and is decreasing with time at most sites. This is another indication of the general deterioration of stream quality in the upper basin. It also indicates that the ability of the river system to receive, transport, and assimilate wastes, although exceeded now only for short periods during the summer months, may be exceeded more continually in the future if present trends hold. Decreasing ratios of ammonia to nitrate in a downstream direction on the main stem Passaic River suggests that nitrification (the biochemical conversion of ammonia to nitrate) as well as microbiological decomposition of organic matter (waste waters) is contributing to the continued and increasing undersaturation of dissolved oxygen in the river system. Passaic River streams are grouped into five general regions of isochemical quality on the basis of predominant constituents and dissolved-solids content during low flows. The predominant cations in all but one region are calcium and magnesium (exceeding 50 percent of total cations) ; in that region, where man's activities probably have altered the natural stream waters, the percentage of sodium and potassium equals that of calcium and magnesium. In two of the five regions, the predominant anion is bicarbonate; a combination of sulfate, chloride, and nitrate is predominant in the other three regions. Dissolved-solids content during low flows generally ranges from 100 to 600 milligrams per liter. Several time-of-travel measurements within the basin are reported. These data provide reasonable estimates of the time required for soluble contaminants to pass through particular parts of the river system. For example, the peak concentration of a contaminant injected into the river system at Chatham during extreme low flow would be expected to travel to Little Falls, about 31 miles, in about 13 days; but at medium flow, in about 5 days.

Water Supply Paper↗

USGS1983

Concentrations and carbon isotopic compositions of CH4 and CO2 in gas from sediments of the Blake Outer Ridge, Deep Sea Drilling Project Leg 76

The principal gaseous carbon-containing components identified in the first 400 m of sediment at Deep Sea Drilling Project Site 533, Leg 76, are methane (CH4 ) and carbon dioxide (CO2 ). Below a sub-bottom depth of about 25 m, sedi ment cores commonly contained pockets caused by the expansion of gas upon core recovery. The carbon isotopic com position (δ13C %0 relative to PDB standard) of CH4 and CO2 in these gas pockets has been measured, resulting in the following observations: (1) δ 1 3CC H 4 values increase with depth from approximately -94% in the uppermost sediment to about -66% in the deepest sediment, reflecting a systematic but nonlinear depletion of 12C with depth. (2) δ 1 3Cc θ 2 values also increase with depth of sediment from about - 25% to about - 4%, snowing a depletion of 12C that closely parallels the trend of the isotopic composition of CH4 . The magnitude and parallel distribution of δ 13C values for both CH4 and CO2 are consistent with the concept that the formation of the CH4 resulted from the microbiological reduction of CO2 from organic substances. These results imply that CH4 and CO2 incorporated in gas hydrates at this site are biogenic.

Initial Reports of the D.S.D.P.↗

USGS1978

Nitrification in four acidic streams in southern New Jersey

Four characteristically acidic streams in southern New Jersey were investigated to determine the effect of secondary effluent on nitrification in the receiving waters. Chemical and microbiological data were obtained at four sites on each stream. From these data seven factors were evaluated to determine the proclivity of each stream to nitrify. pH, water temperature, and dissolved oxygen were used to describe the general condition of the streams, while neutralization of alkalinity, nitrogen species concentration trends, biological and nitrogenous oxygen demand incubations, and nitrifying bacteria densities were used to determine the actual presence of nitrification in each stream. Each stream had a unique distribution of conditions, making it possible to qualitatively rank the streams according to their proclivity to nitrify. Hay StackBrook showes strong evidence for nitrification on the basis of all four nitrification indicators, whereas Landing Creek showed little, if any, evidence of nitrification. Hammonton Creek is apparently nitrifying, but because of the uncertainty in the downstream trends of the nitrogen species and a lower level of alkalinity neutralization, it is nitrifying less than Hay Stack Brook. Squankum Branch also showed some evidence for nitrification, mostly on the basis of the biological and nitrogenous oxygen demand incubations. Although these streams are acidic in character, acidity does not appear to be an exclusive factor in determining whether a stream will undergo nitrification. (Woodard-USGS)

Water-Resources Investigations Report↗

USGS2025

Potential water-quality and hydrology stressors on freshwater mussels with development of environmental DNA assays for selected mussels and macroinvertebrates in Big Darby Creek Basin, Ohio, 2020–22

The richness and abundance of freshwater mussels in the Big Darby Creek Basin has declined in recent decades, according to survey results published by the Ohio Biological Survey. In October 2016, a major mussel die-off of undetermined cause reportedly affected over 50 miles of Big Darby Creek; however, fishes and other wildlife were not noticeably impacted. Pollution, habitat destruction, climate change, and hydrologic modification have all been theorized as potential reasons for the widespread declines in freshwater mussel populations in North America. To better understand potential stressors to mussels and other aquatic organisms in the Big Darby Creek Basin, the U.S. Geological Survey, in cooperation with the Ohio Water Development Authority, evaluated water quality and temporal changes in hydrology at selected locations. In addition, environmental deoxyribonucleic acid (eDNA) quantitative polymerase chain reaction (qPCR) assays were developed to detect the presence of selected mussels and macroinvertebrates using stream water. Time-weighted average concentrations of pesticides, organic wastewater compounds (OWCs), and polycyclic aromatic hydrocarbons (PAHs) were determined for selected locations within the Big Darby Creek Basin. Passive samplers designed to mimic the respiratory exposure of aquatic organisms and the bioconcentration of organic contaminants into their fatty tissues were deployed three times annually at three sites within the Big Darby Creek Basin in 2020 and 2021. Analyses were done for 204 pesticide compounds, 38 OWCs, and 33 PAHs. Of the 204 pesticide compounds, 70 were detected in at least one sample; 30 were detected in all samples. Herbicides and herbicide degradates were the pesticides most frequently detected and also had some of the highest concentrations of the pesticides detected in this study. Three herbicides (atrazine, ametryn, and metribuzin) were detected in at least 88 percent of samples and two fungicides (azoxystrobin and propiconazole) were detected in all samples. Of the 38 OWCs, 24 were detected in at least one sample; however, only one ( N , N -diethyltoluamide [DEET]) was detected in all samples. Of the 33 PAHs, 29 were detected in at least one sample; 12 were detected in all samples. A continuous water-quality monitor was operated seasonally on Big Darby Creek above Georgesville, Ohio, from 2020 to 2022. Dissolved oxygen concentrations generally followed a daily cycle, peaking in early evening and troughing around sunrise. There were occasional 24-hour swings in dissolved oxygen concentration that had a range exceeding 10 milligrams per liter. However, dissolved oxygen concentrations never fell below Ohio’s aquatic life criteria for warmwater habitats (outside of mixing zones) of 4.0 milligrams per liter as an instantaneous minimum and 5.0 milligrams per liter as a minimum 24-hour average. The Ohio water-quality criteria for temperatures are 29.4 degrees Celsius as an instantaneous maximum and 27.8 degrees Celsius as a 24-hour average maximum. In 2020, there were 10 days when the maximum instantaneous value for temperature was exceeded and 3 consecutive days when the maximum 24-hour average temperature was exceeded. Streamflow time-series data from three gaging stations within the Big Darby Creek Basin were evaluated for trends in annual flow statistics and daily nonexceedance probabilities over time. In general, the evaluation of streamflow conditions at the Big Darby Creek gage (with 97 years of record) indicated that streamflow changed between water years 1922 and 2021. During that time span, flows in general increased, the number of high-flow pulses became more frequent, and low-flow pulses and extreme low-flow periods became less frequent. The only strong indication of trends over time in annual flow statistics for the relatively short records for the other two gages (on Little Darby Creek, with 25 years of record, and Hellbranch Run, with 29 years of record) was that as time went on, reversals between rising and falling periods became more frequent. The U.S. Geological Survey Ohio Water Microbiology Laboratory developed eDNA qPCR assays to detect Epioblasma rangiana (northern riffleshell mussels), Chimarra obscura (a species of caddisfly), Maccaffertium pulchellum (a species of mayfly), and optimized a preexisting eDNA qPCR assay to detect for Ptychobranchus fasciolaris (kidneyshell mussels). The assays were validated by using environmental sampling methods. Assay sensitivity was established by determining the limits of detection and quantification. Water samples were collected at 12 sites in the Big Darby Creek Basin between 2020 and 2022 and analyzed for eDNA with the qPCR assays developed for this study.

Ohio↗

USGS2021

Groundwater-quality and select quality-control data from the National Water-Quality Assessment Project, January 2017 through December 2019

Groundwater-quality environmental data were collected from 983 wells as part of the National Water-Quality Assessment Project of the U.S. Geological Survey National Water Quality Program and are included in this report. The data were collected from six types of well networks: principal aquifer study networks, which are used to assess the quality of groundwater used for public water supply; land-use study networks, which are used to assess land-use effects on shallow groundwater quality; major aquifer study networks, which are used to assess the quality of groundwater used for domestic supply; enhanced trends networks, which are used to evaluate the time scales during which groundwater quality changes; vertical flow-path study networks, which are used to evaluate changes in groundwater quality from shallow to deeper depths; and modeling support studies, which are used to provide data to support groundwater modeling. Groundwater samples were analyzed for many water-quality indicators and constituents, including major ions, nutrients, trace elements, volatile organic compounds, pesticides, radionuclides, microbiological indicators, and some constituents of special interest (arsenic speciation, hexavalent chromium [chromium (VI)], and perchlorate). These groundwater-quality data, along with data from quality-control samples, are tabulated in this report and in an associated data release. Data for microbiological indicators for samples collected in 2016 are included in the companion data release.

Data Series↗

USGS2002

USGS leads United States effort in Mallik Well

This winter, in the extremely cold, far reaches of the upper Northwest Territory of Canada, there is an international consortium of researchers participating in a program to study methane hydrates. The researchers are currently drilling a 1200 m-deep production research well through the permafrost. It is one of three wells located in the Mackenzie Delta, on the shore of the Beaufort Sea. Two observation wells were drilled adjacent to the main production test well earlier this year. Research objectives for the program focus on two themes: (1) the assessment of the production and properties of gas hydrates, and (2) an assessment of the stability of continental gas hydrates given warming trends predicted by climate change models. Of particular interest is the physical response of the gas hydrate to depressurization and thermal production stimulation. Cores are being taken from the well, and scientists hope to retrieve at least 200 m of core, including all the gas hydrate-rich intervals. Once cored, the samples are transported 200 kilometers over ice roads to Inuvik. Nearly 60 researchers are examining the cores for everything from geophysical parameters to microbiological analyses.

Fire in the Ice: NETL Methane Hydrate Newsletter↗

USGS2025

Rapid increase in antibodies to influenza A virus H5 and N1 in Lesser Scaup (Aythya affinis) following the introduction of 2.3.4.4B H5N1 into North America

Clade 2.3.4.4b Eurasian-origin H5N1 entered North America in late 2021 and spread across the continent. While studies have characterized the antibody response mounted by dabbling ducks following exposure, little data are available for diving ducks. This study sought to identify influenza A virus (IAV) infection and antibodies in Lesser and Greater Scaup captured in Maryland, Illinois, and Rhode Island. In Maryland, IAV seroprevalence increased from the 2021/2022 to 2022/2023 sampling season, with IAV antibody prevalence increasing for juvenile (38% to 80%) and adult (82% to 90%) Lesser Scaup. While adult Lesser Scaup sampled in Illinois in 2021/2022 had IAV antibody prevalence comparable to those sampled in Maryland (76% and 82%, respectively), they had higher antibody prevalence to both H5 (48% and 18%) and N1 (68% and 35%), potentially due to being sampled in March versus December and January. Our data suggest that Lesser Scaup had limited antibodies to highly pathogenic H5 IAV prior to the introduction of clade 2.3.4.4b H5N1 to North America, but relevant antibodies were widely observed in the months and year following. Our more limited data suggest similar trends may have occurred in Greater Scaup as well.

Canadian Journal of Microbiology↗

USGS2018

Collection methods and quality assessment for Escherichia coli, water quality, and microbial source tracking data within Tumacácori National Historical Park and the upper Santa Cruz River, Arizona, 2015-16

Tumacácori National Historical Park protects the culturally important Mission, San José de Tumacácori, while also managing a portion of the ecologically diverse riparian corridor of the Santa Cruz River. This report describes the methods and quality assurance procedures used in the collection of water samples for the analysis of Escherichia coli ( E. coli ), microbial source tracking markers, suspended sediment, water-quality parameters, turbidity, and the data collection for discharge and stage; the process for data review and approval is also described. Finally, this report provides a quantitative assessment of the quality of the E. coli , microbial source tracking, and suspended sediment data. The data-quality assessment revealed that bias attributed to field and laboratory contamination was minimal, with E. coli detections in only 3 out of 33 field blank samples analyzed. Concentrations in the field blanks were several orders of magnitude lower than environmental concentrations. The microbial source tracking (MST) field blank was below the detection limit for all MST markers analyzed. Laboratory blanks for E. coli at the USGS Arizona Water Science Center and laboratory blanks for MST markers at the USGS Ohio Water Microbiology Laboratory were all below the detection limit. Irreplicate data for E. coli and suspended sediment indicated that bias was not introduced to the data by combining samples collected using discrete sampling methods with samples collected using automatic sampling methods. The split and sequential E. coli replicate data showed consistent analytical variability and a single equation was developed to explain the variability of E. coli concentrations. An additional analysis of analytical variability for E. coli indicated analytical variability around 18 percent relative standard deviation and no trend was observed in the concentration during the processing and analysis of multiple split-replicates. Two replicate samples were collected for MST and individual markers were compared for a base flow and flood sample. For the markers found in common between the two types of samples, the relative standard deviation for the base flow sample was more than 3 times greater than the markers in the flood sample. Sequential suspended sediment replicates had a relative standard deviation of about 1.3 percent, indicating that environmental and analytical variability was minimal. A holding time review and laboratory study analysis supported the extended holding times required for this investigation. Most concentrations for flood and base-flow samples were within the theoretical variability specified in the most probable number approach suggesting that extended hold times did not overly influence the final concentrations reported.

Arizona↗

USGS2013

Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida

The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through permanova, also indicated significant differences in bacterial communities based on the season.

Florida↗

USGS2003

Abundance and characteristics of the recreational water quality indicator bacteria Escherichia coli and enterococci in gull faeces

Aims: To evaluate the numbers and selected phenotypic and genotypic characteristics of the faecal indicator bacteria Escherichia coli and enterococci in gull faeces at representative Great Lakes swimming beaches in the United States. Methods and Results: E. coli and enterococci were enumerated in gull faeces by membrane filtration. E. coli genotypes (rep‐PCR genomic profiles) and E. coli (Vitek ® GNI+) and enterococci (API ® rapid ID 32 Strep and resistance to streptomycin, gentamicin, vancomycin, tetracycline and ampicillin) phenotypes were determined for isolates obtained from gull faeces both early and late in the swimming season. Identical E. coli genotypes were obtained only from single gull faecal samples but most faecal samples yielded more than one genotype (median of eight genotypes for samples with 10 isolates). E. coli isolates from the same site that clustered at ≥85% similarity were from the same sampling date and shared phenotypic characteristics, and at this similarity level there was population overlap between the two geographically isolated beach sites. Enterococcus API ® profiles varied with sampling date. Gull enterococci displayed wide variation in antibiotic resistance patterns, and high‐level resistance to some antibiotics. Conclusions: Gull faeces could be a major contributor of E. coli (10 5 –10 9 CFU g −1 ) and enterococci (10 4 –10 8 CFU g −1 ) to Great Lakes recreational waters. E. coli and enterococci in gull faeces are highly variable with respect to their genotypic and phenotypic characteristics and may exhibit temporal or geographic trends in these features. Significance and Impact of the Study: The high degree of variation in genotypic or phenotypic characteristics of E. coli or enterococci populations within gull hosts will require extensive sampling for adequate characterization, and will influence methods that use these characteristics to determine faecal contamination sources for recreational waters.

Journal of Applied Microbiology↗

USGS2025

The U.S. Geological Survey National Water Quality Network—Groundwater, 2024

The U.S. Geological Survey (USGS) operates a National Water Quality Network (NWQN) to monitor trends in groundwater quality and assess emerging contaminants of concern. It is a “network of networks” with 81 subnetworks being sampled on a decadal time scale. Each year, 8 of the subnetworks are sampled. Subnetworks have 20–30 wells each and include studies of domestic supply wells or shallow groundwater (20–50 feet deep) underlying urban land use or agricultural land use. Currently there are 2,089 wells in the network. All wells are sampled for physical properties, nutrients, major ions, trace elements, per- and polyfluoroalkyl substances (PFAS), and a subset of wells are sampled for pesticides, volatile organic compounds, radionuclides, and microbiological contaminants.

Contiguous United States↗

USGS1994

Spatial variability in biodegradation rates as evidenced by methane production from an aquifer

Accurate predictions of carbon and energy cycling rates in the environment depend on sampling frequencies and on the spatial variability associated with biological activities. We examined the variability associated with anaerobic biodegradation rates at two sites in an alluvial sand aquifer polluted by municipal landfill leachate. In situ rates of methane production were measured for almost a year, using anaerobic wells installed at two sites. Methane production ranged from 0 to 560 μmol · m -2 · day -1 at one site (A), while a range of 0 to 120,000 μmol · m -2 · day -1 was measured at site B. The mean and standard deviations associated with methane production at site A were 17 and 57 μmol · m -2 · day -1 , respectively. The comparable summary statistics for site B were 2,000 and 9,900 μmol · m -2 · day -1 . The coefficients of variation at sites A and B were 340 and 490%, respectively. Despite these differences, the two sites had similar seasonal trends, with the maximal rate of methane production occurring in summer. However, the relative variability associated with the seasonal rates changed very little. Our results suggest that (i) two spatially distinct sites exist in the aquifer, (ii) methanogenesis is a highly variable process, (iii) the coefficient of variation varied little with the rate of methane production, and (iv) in situ anaerobic biodegradation rates are lognormally distributed.

Applied and Environmental Microbiology↗

USGS2006

Dissimilatory arsenate and sulfate reduction in sediments of two hypersaline, arsenic-rich soda lakes: Mono and Searles Lakes, California

A radioisotope method was devised to study bacterial respiratory reduction of arsenate in sediments. The following two arsenic-rich soda lakes in California were chosen for comparison on the basis of their different salinities: Mono Lake (∼90 g/liter) and Searles Lake (∼340 g/liter). Profiles of arsenate reduction and sulfate reduction were constructed for both lakes. Reduction of [ 73 As]arsenate occurred at all depth intervals in the cores from Mono Lake (rate constant [ k ] = 0.103 to 0.04 h −1 ) and Searles Lake ( k = 0.012 to 0.002 h −1 ), and the highest activities occurred in the top sections of each core. In contrast, [ 35 S]sulfate reduction was measurable in Mono Lake ( k = 7.6 ×10 4 to 3.2 × 10 −6 h −1 ) but not in Searles Lake. Sediment DNA was extracted, PCR amplified, and separated by denaturing gradient gel electrophoresis (DGGE) to obtain phylogenetic markers (i.e., 16S rRNA genes) and a partial functional gene for dissimilatory arsenate reduction ( arrA ). The amplified arrA gene product showed a similar trend in both lakes; the signal was strongest in surface sediments and decreased to undetectable levels deeper in the sediments. More arrA gene signal was observed in Mono Lake and was detectable at a greater depth, despite the higher arsenate reduction activity observed in Searles Lake. A partial sequence (about 900 bp) was obtained for a clone (SLAS-3) that matched the dominant DGGE band found in deeper parts of the Searles Lake sample (below 3 cm), and this clone was found to be closely related to SLAS-1, a novel extremophilic arsenate respirer previously cultivated from Searles Lake.

Applied and Environmental Microbiology↗

USGS2020

Repetitive sampling and control threshold improve 16S rRNA results from produced waters associated with hydraulically fractured shales

Sequencing microbial DNA from deep subsurface environments is complicated by a number of issues ranging from contamination to non-reproducible results. Many samples obtained from these environments - which are of great interest due to the potential to stimulate microbial methane generation - contain low biomass. Therefore, samples from these environments are difficult to study as sequencing results can be easily impacted by contamination. In this case, the low amount of sample biomass may be effectively swamped by the contaminating DNA and generate misleading results. Additionally, performing field work in these environments can be difficult, as researchers generally have limited access to and time on site. Therefore, optimizing a sampling plan to produce the best results while collecting the greatest number of samples over a short period of time is ideal. This study aimed to recommend an adequate sampling plan for field researchers obtaining microbial biomass for 16S rRNA gene sequencing, applicable specifically to oil and gas-producing environments. Forty-nine different samples were collected by filtering specific volumes of produced water from a hydraulically fractured well producing from the Niobrara Shale. Water was collected in two different sampling events 24 hours apart. Four to five samples were collected from 11 specific volumes. These samples along with eight different blanks were submitted for analysis. DNA was extracted from each sample, and quantitative polymerase chain reaction (qPCR) and 16S rRNA Illumina MiSeq gene sequencing were performed to determine relative concentrations of biomass and microbial community composition, respectively. The qPCR results varied across sampled volumes, while no discernible trend correlated contamination to volume of water filtered. This suggests that collecting a larger volume of sample may not result in larger biomass concentrations or better representation of a sampled environment. Researchers could prioritize collecting many low volume samples over few high-volume samples. Our results suggest that there also may be variability in the concentration of microbial communities present in produced waters over short (i.e., hours) time scales, which warrants further investigation. Submission of multiple blanks is also vital to determining how contamination or low biomass effects may influence a sample set collected from an unknown environment.

Montana, Wyoming, Colorado, New Mexico, Texas, Okl↗

USGS2015

Total- and methyl-mercury concentrations and methylation rates across the freshwater to hypersaline continuum of the Great Salt Lake, Utah, USA

We examined mercury (Hg) speciation in water and sediment of the Great Salt Lake and surrounding wetlands, a locale spanning fresh to hypersaline and oxic to anoxic conditions, in order to test the hypothesis that spatial and temporal variations in Hg concentration and methylation rates correspond to observed spatial and temporal trends in Hg burdens previously reported in biota. Water column, sediment, and pore water concentrations of methylmercury (MeHg) and total mercury (THg), as well as related aquatic chemical parameters were examined. Inorganic Hg(II)-methylation rates were determined in selected water column and sediment subsamples spiked with inorganic divalent mercury ( 204 Hg(II)). Net production of Me 204 Hg was expressed as apparent first-order rate constants for methylation ( k meth ), which were also expanded to MeHg production potential (MPP) rates via combination with tin reducible ‘reactive’ Hg(II) (Hg(II) R ) as a proxy for bioavailable Hg(II). Notable findings include: 1) elevated Hg concentrations previously reported in birds and brine flies were spatially proximal to the measured highest MeHg concentrations, the latter occurring in the anoxic deep brine layer (DBL) of the Great Salt Lake; 2) timing of reduced Hg(II)-methylation rates in the DBL (according to both k meth and MPP) coincides with reduced Hg burdens among aquatic invertebrates (brine shrimp and brine flies) that act as potential vectors of Hg propagation to the terrestrial ecosystem; 3) values of k meth were found to fall within the range reported by other studies; and 4) MPP rates were on the lower end of the range reported in methodologically comparable studies, suggesting the possibility that elevated MeHg in the anoxic deep brine layer results from its accumulation and persistence in this quasi-isolated environment, due to the absence of light (restricting abiotic photo demethylation) and/or minimal microbiological demethylation.

Utah↗