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Elliott P. Barnhart

Publications and source records attributed to Elliott P. Barnhart.

At least 19 recordsLinked to original sources
USGS2026

Tapwater contaminant mixtures and cumulative risk screening on the Crow (Apsáalooke) Reservation

Introduction: Water insecurity is a challenge for the Apsáalooke (Crow) Tribal Nation in south-central Montana, United States. Both private-well and public-supply tapwater (TW) are vulnerable to a range of contaminants, posing potential risks to community health and well-being. Ongoing community concerns about unrecognized inorganic, organic, and microbial contaminants underscore the need for continued comprehensive monitoring and improved water management strategies. Materials and methods: TW samples were collected from 26 private-well and 12 public-supply participant locations, selected and recruited by the Crow Water Quality Project. A total of 35 inorganic, 450 organic, and three microbial analytes were assessed in these samples. Public-Supply Maximum Contaminant Levels and Health benchmark-based screening levels were used to evaluate contaminant concentrations. Results: Sixty-one organic and 34 inorganic contaminants were detected. Screening levels were frequently exceeded, particularly due to multiple inorganic contaminants in private TW and both chlorine-based disinfection byproducts (DBPs) and inorganics in public TW. These findings highlight gaps in current source-water protection and water treatment practices. Conclusions: After reporting results to participants, anonymized data were shared at community events to inform risk management decisions. The study underscores the importance of broad monitoring and analysis throughout the upper Missouri River basin and across the United States to address Tribal concerns over water insecurity and mitigate potential unrecognized TW contaminant risks, particularly to vulnerable subpopulations.

Montana↗
USGS2026

Deep subsurface organic-rich shale supports abundant, diverse, and novel fungi

As Earth’s principal reservoir of organic carbon and microbial biomass, the deep subsurface hosts microorganisms capable of mobilizing this once-sequestered carbon. Contrary to standard assumptions of eukaryotic scarcity, this study documents abundant fungal communities, ranging from 4.2 × 10 3 to 6.8 × 10 3 fungal cells mL −1 , across a methane-producing organic-rich shale 247–556 meters below the surface. Although fungal:bacterial cell ratios ranged from 1:7028 to 1:713, application of biomass conversion factors developed for oceanic systems yielded a median fungal:bacterial biomass ratio of 1:4.7. 16S rRNA gene amplicons revealed bacterial and archaeal communities mirroring those found in well-characterized extremophilic, carbon-degrading environments, while sequencing of 18S rRNA gene and ITS rRNA spacer amplicons collectively identified a eukaryotic hotspot with 689 fungal OTUs across six phyla. The dominant fungal classes, Agaricomycetes and Dothideomycetes, are well-established degraders of recalcitrant carbon compounds at the surface, suggesting they may similarly contribute to organic matter degradation and ecosystem maintenance in the subsurface. Cultivation and isolation efforts yielded 205 fungal strains, including 13 candidate novel taxa, underscoring the deep subsurface as an underexplored eukaryotic habitat. Stable carbon isotopes indicate methane is predominantly generated via microbial conversion of the fossil carbon, while water isotopes suggest in situ geochemical conditions have been relatively stable since the Late Pleistocene, with subglacial recharge as a plausible mechanism for microbial introduction. Collectively, these findings suggest that fungi are underrecognized contributors to organic matter transformation and functional diversity in the deep biosphere, revealing a critical gap in our understanding of deep subsurface ecosystem processes.

Indiana, Michigan, Ohio↗
USGS2026

Meso-scale pressure reactor demonstrates biostimulation of coal-dependent methanogenesis

Replicating deep subsurface conditions remains a major challenge for advancing subterranean biotechnologies. Microbially enhanced coal bed methane production offers a promising approach to increase biogenic gas recovery from coal seams, yet experimental progress has been limited by the difficulty of simulating in situ conditions. A key question is whether nutrient amendments stimulate coal-dependent methanogenesis or simply convert injected nutrients to methane. Here, we report the use of a large-scale (325 L) reactor to investigate 13 C-labeled microalgae amendments on microbially-enhanced coal bed methane production at in situ pressure. Labeled methane was detected only during the initial stimulation phase, while most of the methane produced over five months originated from the coal. These field-relevant results demonstrate that microalgae can accelerate early methanogenesis and enhance coal-derived methane production over time. This study provides a critical proof-of-concept with broad implications for advancing subsurface biotechnologies toward field-scale deployment.

Communications Earth & Environment↗
USGS2026

Detection of Naegleria fowleri in thermally impacted recreational waters of western United States national parks

Naegleria fowleri is a thermophilic free-living amoeba (FLA) and the causative agent of primary amoebic meningoencephalitis, posing public health risks in warm freshwater environments. This multiyear, multiagency study surveyed 40 thermally impacted recreational waters across five western United States national parks and recreation areas–Yellowstone National Park, Grand Teton National Park, Olympic National Park, Newberry National Volcanic Monument, and Lake Mead National Recreation Area–to assess N. fowleri presence, concentration, and associated environmental conditions. A total of 185 water samples were analyzed by qPCR and Sanger sequencing, revealing widespread detection of N. fowleri in 34% of samples with positive detections from Lake Mead, Yellowstone, and Grand Teton hot springs and thermally impacted waters, with concentrations ranging from 4.9 to 115.7 cells/L. Multiple codetections of N. fowleri with nonpathogenic species including Naegleria australiensis were identified, suggesting they may inhabit similar ecological niches in the natural systems in contrast to engineered systems. These findings indicate that N. fowleri is present in thermally impacted areas across the western United States and underscore the use of enhanced monitoring, public awareness, and risk management strategies in thermally influenced recreational waters.

Arizona, Nevada, Oregon, Washington, Wyoming↗
USGS2026

Per- and polyfluoroalkyl substances in waters associated with oil and gas development in the Denver Basin

Use of per- and polyfluoroalkyl substances (PFAS) in the petroleum industry could be a cause for concern due to the large volumes of produced water (PW) generated during oil and gas extraction, the reuse of these wastes in water-stressed regions, and adverse health outcomes related to PFAS exposures. However, PW PFAS characterization is nearly absent in the literature, and hydraulic fracturing (HF) chemical disclosures often omit the identities of additives as proprietary. Here we evaluate PFAS in PW samples from three petroleum wells in the Denver Basin during their first year of production. Total concentrations of targeted PFAS (Σ 40 PFAS) were < 35 ng/L in PW samples, with short-chain PFAS like perfluorobutanoic acid persisting throughout the sampled duration. Analysis of freshwater inputs for hydraulic fracturing (Σ 40 PFAS ~ 113 ng/L) and mixed fracture fluid (Σ 40 PFAS ~ 69 ng/L) indicated much of the targeted PFAS content was derived from the input water, and not from HF additives, however samples subjected to oxidation indicated the presence of PFAS precursors that would not be detected by targeted analysis. This study highlights that while PFAS content is low in the studied PWs, the potential for redistribution of PFAS in the environment may be a consideration for reuse applications.

Colorado, Nebraska, Wyoming↗
USGS2026

Per- and polyfluoroalkyl substances (PFAS) and other contaminants of concern in tribal waters of Montana

We assessed potential exposures to a broad suite of contaminants (inorganic, organic and microbial) in culturally important surface waters from three watersheds in a northern plains Native American community (Apsáalooke [Crow Tribe of Montana]) in south-central Montana, United States, with water insecurity concerns. Inorganic (37), organic (435) and microbial (3) constituents were assessed in 12 surface water sites from the Pryor Creek ( n = 2), Bighorn River ( n = 2) and Little Bighorn River ( n = 8) valleys. Twenty-six organics, 33 inorganics and Escherichia coli were detected. Despite relatively low concentrations in surface waters within the Crow Reservation, mixture toxicity indicated prevalent chronic ecological effects and human-health secondary contact (recreation) effects at multiple sites. Further, to address Tribal concerns over the prevalence and corresponding risks of per- and polyfluoroalkyl substances (PFAS), we sampled water, sediment, biofilms and fish at a limited number of locations in the Little Bighorn River. Results indicated that PFAS were prevalent in fish tissues, including whole blood and filets, and to a lesser extent in biofilms, despite few detections in water and sediment samples. This is the first attempt to document environmental PFAS contamination within the reservation and the potential human-health concerns for the general population from consumption of recreational/subsistence fish. Overall, this effort provided preliminary information on the contaminant mixtures present and their potential health implications, which can support the protection of community health and culturally meaningful resources across the Crow Reservation.

Montana↗
USGS2025

Metaproteomics and metagenomics reveal microbial pathways of organic matter degradation and methanogenesis in a marginally producing natural gas well

The expansion of natural gas production and utilization worldwide has led to the decline of many once-productive wells, eventually resulting in costly well-plugging and unused infrastructure. However, in areas like the Michigan basin, MI, where the majority of natural gas is biogenically produced, microbial communities could potentially be stimulated to generate additional methane, increasing gas supply and reducing the need to drill new wells. In this study, we performed metaproteomic, metagenomic, and geochemical analyses of Antrim Shale formation water from a marginally producing natural gas well to evaluate resident microbial community functions in the context of potential bioenergy production. Functional proteins involved in methanogenesis, degradation/catabolism (including organic matter degradation), biosynthesis, energy utilization, transmembrane transport, and stress response were among the most commonly identified groups. Three metagenome-assembled genomes (MAGs) were characterized, including Methanomicrobiaceae, Methanothrix , and Smithella . For each, the identified proteins involved in methanogenesis and the degradation of diverse organic compounds, strongly suggest their role in utilizing shale-derived organic matter. These findings provide an increased understanding of the microorganisms and their metabolisms generating natural gas in the Antrim Shale and establish a foundation for future stimulation efforts aimed at enhancing biogenic methane production in marginal gas wells.

Michigan↗
USGS2025

Evaluation of rapid DNA extraction methods to better enable point-of-use environmental DNA detection

Recent developments in molecular testing have created the opportunity for biologists and managers to detect environmental DNA (eDNA) of target species rapidly and without the requirement of a laboratory. These point-of-use protocols may be especially useful for early detection and rapid response for invasive species or surveillance for at-risk native species, where timely management decisions are critical. Point-of-use eDNA protocols also facilitate wider and less expensive implementation of eDNA methods. One of the key components to an effective point-of-use protocol is a rapid DNA extraction method. Several rapid extraction protocols are suitable for implementation in the field, but information regarding their relative effectiveness is lacking. We evaluated extraction efficiency of four DNA rapid extraction protocols using filters spiked with primary cultured grass carp ( Ctenopharyngodon idella ) gill cells. The extraction methods included two syringe-based column extractions, a lysis and extraction solution, and a divalent cation chelation resin (Chelex) extraction protocol alongside a laboratory-based control kit. We estimated DNA yield using a newly designed quantitative polymerase chain reaction (qPCR) assay targeting the grass carp nuclear genome. We evaluated two additional factors, filter type (mixed cellulose ester [MCE] and polyethersulfone [PES]) and background eDNA source (aquaculture or river). The lysis and extraction solution and Chelex extraction both had the highest overall yield, with MCE filters further increasing Chelex yield while the enzyme extraction yield was dependent on interaction with both filter and eDNA source. Our results indicate that rapid extraction protocols, such as solutions with short heating steps, are effective for DNA isolation and help to increase the overall accessibility of eDNA analyses.

Environmental DNA↗
USGS2024

Editorial: Subsurface microbiology within hydrocarbon resources or stored gases

A Research Topic on the microbiology of hydrocarbon and gas storage reservoirs has far reaching industrial applications. In recent decades, there has been a growing interest in understanding microbial communities in subsurface energy reservoirs, such as coal, oil, and shale beds. This area of research has broadened to include gas storage reservoirs for hydrogen and CO 2 . Scientists are beginning to unravel the unexpected impact microorganisms have on these systems, through changing the fluid geochemistry, the gas content, and even the permeability. By recognizing the influence of these tiny organisms on our engineered environments, we can develop better risk assessments, target mitigation strategies, expand energy production, and refine operational guidance, ultimately contributing to a more sustainable energy future.

Frontiers in Ecology and Evolution↗
USGS2024

Autonomous samplers and environmental DNA metabarcoding: Sampling day and primer choice have greatest impact on fish detection probabilities

Unprecedented rates of biodiversity loss and ecosystem function necessitate the use of rapid, efficacious, and cost-effective biomonitoring tools. The combination of autonomous samplers and high throughput sequencing (i.e., “metabarcoding”) of environmental DNA ( eDNA ) samples enables characterization of entire communities at high frequency and can be an important tool for conservation and management, allowing researchers to track fluctuations in biodiversity. We deployed two autonomous samplers at two U.S. Geological Survey streamgage sites in the upper Snake River (Wyoming and Idaho, USA) to collect eDNA samples from July-September 2021 and 2022 to characterize fish diversity. We used a probabilistic approach to evaluate the effects of water temperature, water discharge, filter pore size, water volume filtered, number of samples collected, timing, and primers on the probability of detecting eDNA from fish species known to be present. We detected eDNA from 13/15 species present in these areas of the Snake River. Overall, we did not find evidence that filter pore size, water volume filtered, water discharge, and water temperature affected the probability of detecting fish species’ eDNA . By contrast, primers and sampling day affected fish detection probabilities, indicating that primer choice and sampling day can either over- or under- estimate species diversity. These results indicate that users would ideally consider sampling on non-consecutive days and which primer set will maximize species detections.

Metabarcoding & Metagenomics↗
USGS2024

Naegleria fowleri detected in Grand Teton National Park hot springs

The free-living thermophilic amoeba Naegleria fowleri ( N. fowleri ) causes the highly fatal disease primary amoebic meningoencephalitis. The environmental conditions that are favorable to the growth and proliferation of N. fowleri are not well-defined, especially in northern regions of the United States. In this study, we used culture-based methods and multiple molecular approaches to detect and analyze N. fowleri and other Naegleria spp. in water, sediment, and biofilm samples from five hot spring sites in Grand Teton National Park, Wyoming, U.S.A. These results provide the first detections of N. fowleri in Grand Teton National Park and provide new insights into the distribution of pathogenic N. fowleri and other nonpathogenic Naegleria spp. in natural thermal water systems in northern latitudes.

Wyoming↗
USGS2024

Produced water geochemistry from hydraulically stimulated Niobrara Formation petroleum wells: Origin of salinity and temporal perspectives on treatment and reuse

Produced water (i.e., a mixture of returned injection fluids and geologic formation brines) represents the largest volumetric waste stream associated with petroleum production in the United States. As such, produced water has been the focus of intense study with emphasis on understanding the geologic origin of the fluids, environmental impacts of unintended or intentional release, disposal concerns, and their commodity (e.g., lithium) potential. However, produced water geochemistry from many active petroleum plays remain poorly constrained leading to knowledge gaps associated with the origin of brine salinity and parameters (e.g., radium levels) that can impact treatment, disposal, and possible reuse. Here we evaluate the major ion geochemistry, radium concentrations, and stable water isotope composition of ~120 produced water samples collected from 17 producing unconventional petroleum wells in Weld County, Colorado from the Late Cretaceous Niobrara Formation. This sample set encompasses eight produced water time series from four new wells across production days 0 to ~365 and from four established wells across production days ~1000 to ~1700. Additionally, produced water from nine other established Niobrara Formation wells were sampled at discrete time points ranging from day 458 to day 2256, as well as hydraulic fracturing input fluids. These results expand the available Niobrara Formation produced water geochemical data, previously limited to few wells sampled within the first year of production, allowing for the heterogeneity of major ions and radium to be evaluated. Furthermore, we explore the geochemical relationships between major ion ratios and stable water isotope composition to understand the origin of salinity in Niobrara Formation brines from the Denver-Julesburg Basin. These findings are discussed with perspective toward potential treatment and reuse of Niobrara produced water prior to disposal.

Colorado, Nebraska, Wyoming↗
USGS2024

Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri

Naegleria fowleri has been detected in drinking water distribution systems (DWDS) in Australia, Pakistan and the United States and is the causative agent of the highly fatal disease primary amoebic meningoencephalitis. Previous small scale field studies have shown that Meiothermus may be a potential biomarker for N. fowleri . However, correlations between predictive biomarkers in small sample sizes often breakdown when applied to larger more representative datasets. This study represents one of the largest and most rigorous temporal investigations of Naegleria fowleri colonisation in an operational DWDS in the world and measured the association of Meiothermus and N. fowleri over a significantly larger space and time in the DWDS. A total of 232 samples were collected from five sites over three-years (2016-2018), which contained 29 positive N. fowleri samples. Two specific operational taxonomic units assigned to M. chliarophilus and M. hypogaeus, were significantly associated with N. fowleri presence. Furthermore, inoculation experiments demonstrated that Meiothermus was required to support N. fowleri growth in field-collected biofilms. This validates Meiothermus as prospective biological tool to aid in the identification and surveillance of N. fowleri colonisable sites.

Water Research↗
USGS2024

Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams

Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene ( bcrABCD ). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.

mBio↗
USGS2023

Algal amendment enhances biogenic methane production from coals of different thermal maturity

The addition of small amounts of algal biomass to stimulate methane production in coal seams is a promising low carbon renewable coalbed methane enhancement technique. However, little is known about how the addition of algal biomass amendment affects methane production from coals of different thermal maturity. Here, we show that biogenic methane can be produced from five coals ranging in rank from lignite to low-volatile bituminous using a coal-derived microbial consortium in batch microcosms with and without algal amendment. The addition of 0.1 g/l algal biomass resulted in maximum methane production rates up to 37 days earlier and decreased the time required to reach maximum methane production by 17–19 days when compared to unamended, analogous microcosms. Cumulative methane production and methane production rate were generally highest in low rank, subbituminous coals, but no clear association between increasing vitrinite reflectance and decreasing methane production could be determined. Microbial community analysis revealed that archaeal populations were correlated with methane production rate ( p = 0.01), vitrinite reflectance ( p = 0.03), percent volatile matter ( p = 0.03), and fixed carbon ( p = 0.02), all of which are related to coal rank and composition. Sequences indicative of the acetoclastic methanogenic genus Methanosaeta dominated low rank coal microcosms. Amended treatments that had increased methane production relative to unamended analogs had high relative abundances of the hydrogenotrophic methanogenic genus Methanobacterium and the bacterial family Pseudomonadaceae. These results suggest that algal amendment may shift coal-derived microbial communities towards coal-degrading bacteria and CO 2 -reducing methanogens. These results have broad implications for understanding subsurface carbon cycling in coal beds and the adoption of low carbon renewable microbially enhanced coalbed methane techniques across a diverse range of coal geology.

Frontiers in Microbiology↗
USGS2023

Pressurized upflow reactor system for the bioconversion of coal to methane: Investigation of the coal/sand interface effect

Microbial generation of coal bed methane (CBM) represents a significant source of natural gas on Earth. While biostimulation has been demonstrated in batch cultures, environmental parameters such as overburden pressure and formation water flow need to be tested at the laboratory scale to understand in situ potential. We designed and constructed a high-pressure (HP) flow-through reactor system that simulates in situ conditions of underground coal seams. Two stainless-steel columns contained coal from the Powder River Basin (PRB), USA, or a coal/sand mixture to represent the interface of coal seams with sandstone layers, which are hypothesized to exhibit higher methanogenesis rates in situ . The system was filled with CBM formation water, inoculated with a methanogenic enrichment from PRB coal beds, and stimulated with algal biomass as a nutrient. The reactors were incubated under pressure (5.4 atm) and flow of CBM water (0.01 mL/min), and control batch cultures were incubated at ambient pressure and without flow (± amendment). Dissolved and headspace methane concentrations were analyzed over time by gas chromatography for 75 days. The pressurized reactors exhibited longer latency periods than ambient pressure controls, but methane production did not reach a plateau phase, which might reflect the impact of scale on the inoculum. The coal/sand reactor exhibited higher methane production than the coal-only reactor, a pattern also observed in the corresponding controls, suggesting an interface effect on methanogenesis. This study indicates that the HP flow test system we designed is well suited for the study of methanogenesis and provides a successful demonstration of CBM generation from the PRB in field-relevant laboratory conditions as a precursor to meso‑scale demonstrations.

Cleaner Chemical Engineering↗
USGS2023

Evaluation of portable Raman spectroscopic analysis for source-rock thermal maturity assessments on bulk crushed rock

This study presents a simplified method and empirical relationships for determining organic matter thermal maturity using a portable Raman system equipped with a 785 nm laser, for analysis of crushed, whole-rock samples. Suites of rocks represented by shale and coal samples with various mineralogical composition, thermal maturity, and total organic carbon (TOC) were used to test the method and build correlations between Raman band separation (RBS) values and traditional thermal maturity indicators, organic matter reflectance (Ro), and programmed temperature pyrolysis (Tmax) values. A set of disparate shale samples, where both vitrinite and solid bitumen reflectance values were reported, have Ro values that range from 0.40 to 4.62%. Above 3.35% Ro, the corresponding RBS values plateau at ∼290 cm−1, thus correlations were evaluated with a linear regression (R2 = 0.96) between 0.40 and 3.35% Ro. Shale samples with Ro < 2% and Tmax < 551 were also used to correlate Tmax and RBS, yielding a linear correlation with an R2 of 0.94. For the coal data set, Ro values range from 1.21 to 4.08% and correlated RBS values plateau at ∼250 cm−1 above Ro = 3.0%, suggesting its correlative application below this maturity level. Several sample preparation methods were tested on cuttings material and standard deviation values for RBS were minimized by washing, drying, and hand crushing the material to pass through a 40-mesh sieve, although less preparation can still yield reliable results. The high degrees of correlation between whole-rock RBS data and two thermal maturity indicators demonstrate the utility of this approach for generating source rock thermal maturity data from minimally processed, whole-rock samples which could easily be applied in field or laboratory settings.

International Journal of Coal Geology↗