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USGS1997

Natural attenuation of chlorinated volatile organic compounds in a freshwater tidal wetland, Aberdeen Proving Ground, Maryland

Ground-water contaminant plumes that are flowing toward or currently discharging to wetland areas present unique remediation problems because of the hydrologic connections between ground water and surface water and the sensitive habitats in wetlands. Because wetlands typically have a large diversity of microorganisms and redox conditions that could enhance biodegradation, they are ideal environments for natural attenuation of organic contaminants, which is a treatment method that would leave the ecosystem largely undisturbed and be cost effective. During 1992-97, the U.S. Geological Survey investigated the natural attenuation of chlorinated volatile organic compounds (VOC's) in a contaminant plume that discharges from a sand aquifer to a freshwater tidal wetland along the West Branch Canal Creek at Aberdeen Proving Ground, Maryland. Characterization of the hydrogeology and geochemistry along flowpaths in the wetland area and determination of the occurrence and rates of biodegradation and sorption show that natural attenuation could be a feasible remediation method for the contaminant plume that extends along the West Branch Canal Creek. The aquifer, which received contaminants in the past from sources that were located upgradient of the current eastern boundary of the wetland, is about 40 to 45 feet thick in the study area. The overlying wetland sediments consist of two distinct layers that have a combined thickness of about 6 to 12 feet--an upper unit of peat and a lower unit of silty to sandy clay or clayey sand. Head distributions show strong vertical gradients, and flow directions are predominantly upward through the wetland sediments. Tidal fluctuations, however, cause some reversals in ground-water-flow directions and changes in discharge locations, which affect the distribution and transport of contaminants. The average linear velocity of ground water is estimated to be about 2 to 3 feet per year along vertical flow lines in the wetland area, and the total ground-water discharge along a 1-foot-wide strip of the wetland extending from the eastern wetland boundary to the creek is in the range of 0.13 to 0.25 feet squared per day. The major parent contaminants in the aquifer were trichloroethylene (TCE); 1,1,2,2-tetrachloroethane (PCA); carbon tetrachloride (CT); and chloroform (CF). The aquifer was typically aerobic, but ground water in the wetland sediments became increasingly anaerobic along the upward flow direction. Iron-reducing conditions were predominant in the lower wetland sediment unit composed of clayey sand and silt, and methanogenesis was predominant in an upper unit composed of peat. Total concentrations of VOC's and the relative proportions of parent compounds to anaerobic daughter products changed substantially as the contaminants were transported upward through these changing redox environments. Concentrations of the parent compounds TCE and PCA ranged from about 100 to 2,000 micrograms per liter in the aquifer beneath the wetland, whereas concentrations of daughter products were low or undetectable. In contrast, the parent compounds commonly were not detected in ground water in the wetland sediments, but the daughter compounds 1,2- dichloro-ethylene (12DCE), vinyl chloride (VC), 1,1,2-trichloroethane (112TCA), and 1,2-dichloroethane (12DCA) were observed. 12DCE and VC were the dominant daughter products in the wetland sediments, even where PCA was the primary parent contaminant discharging to the wetland. The presence of these daughter products in water in the wetland sediments indicates that TCE and PCA are degraded by reductive dechlorination reactions in the naturally anaerobic wetland sediments. Although production of daughter products was observed, total concentrations of the VOC's decreased upward through the 6- to 12-feet-thick wetland sediments and were less than 5 micrograms per liter near the surface. The daughter products are apparently further degraded by these anaerobic processes to non-chlorinated, non-toxic endproducts, or are removed by other attenuation processes such as aerobic degradation or volatilization. Several sets of anaerobic microcosms, some amended with TCE concentrations of 400 or 990 micrograms per liter (3.0 or 7.5 micromoles per liter) and one amended with PCA concentration of 480 micrograms per liter (2.9 micromoles per liter), were constructed in the laboratory using wetland sediment and ground water from the study area. These microcosm experiments confirmed field observations that 12DCE and VC are the dominant daughter products from anaerobic biodegradation of both TCE and PCA. Production of 112TCA and 12DCA also was observed in the PCA-amended microcosms, but concentrations were lower than those of 12DCE and VC. These results indicate that degradation of PCA occurs through both hydrogenolysis and dichloroelimination pathways under anaerobic conditions. Daughter products were not observed in sterile controls, except for relatively low concentrations of 12DCE in the PCA-amended controls, suggesting that the reactions were predominantly microbially mediated. Parent and daughter concentrations in the microcosms decreased to less than 5 micrograms per liter in less than 34 days under methanogenic conditions, thus showing extremely rapid biodegradation rates in these organic-rich wetland sediments. Maximum potential rate constants for biodegradation of TCE and PCA, which were calculated from the microcosm exper-iments assuming first-order degradation rates, ranged from 0.10 to 0.31 per day under methanogenic conditions, corresponding to half-lives of 2 to 7 days. The rate constant for TCE biodegradation under sulfate-reducing conditions was 0.045 West Branch, Aberdeen Proving Ground, Maryland 3 per day (half-life of 15 days), which is lower than under methanogenic conditions. These estimated rate constants for the wetland sediments are two to three orders of magnitude higher than those reported in the literature for TCE biodegradation in microcosms constructed with sandy aquifer sediments. Aerobic biodegradation rates for cis-12DCE, trans-12DCE, and VC were in the same range as those measured for TCE and PCA under anaerobic conditions in microcosm experiments. Thus, production of these daughter products by anaerobic biodegradation of TCE and PCA could be balanced by their consumption where oxygen is available in the wetland sediment, such as near roots and land surface. In the aerobic microcosm experiments, biodegradation of cis-12DCE, trans-12DCE, and VC occurred only if methane consumption occurred, indicating that methanotrophs were involved in the process. Aerobic biodegradation was fastest for vinyl chloride and slowest for TCE in the microcosm experiments. These results agree with other laboratory and field studies that have shown faster degradation by methane-utilizing cultures when the compounds are less halogenated. Equilibrium sorption isotherms were measured in 24-hour batch tests and used to estimate distribution coefficients ( K d 's) to describe the ratios of sorbed to aqueous concentrations of PCA and the daughter products cis-12DCE, trans-12DCE, and VC. The estimated K d's for PCA, cis-12DCE, trans-12DCE, and VC were about 2.3, 1.8, 2.4, and 1.3 liters per kilogram of sediment, respectively. Sorbed concentrations of PCA, cis-12DCE, and trans-12DCE in the wetland sediments, therefore, would be expected to be about twice the concentration measured in the water, whereas sorbed concentrations of VC would not be much greater than the aqueous concentrations. Coefficients of retardation, which were calculated using the K d 's and an advective flow velocity of about 2 feet per year, indicate that sorption alone would cause the movement of the contaminants in the wetland sediments to be 6 to 10 times slower than the advective ground-water flow. Biodegradation and sorption, therefore, are significant natural attenuation mechanisms for chlorinated hydrocarbons in these wetland sediments. The relatively thin layers of wetland sediments are critical in reducing contaminant concentrations and toxicity of the ground water before it discharges to the wetland surface and the creek, and natural attenuation in the wetland sediments could be an effective remediation method for the ground-water contaminants.

Maryland↗

USGS1968

Water-mineral relations of Quaternary deposits in the Lower Platte River drainage area in eastern Nebraska

The partial pressure of carbon dioxide (PCO2), the degree of saturation with respect to calcite (IAP/K calcite), the pH, and the concentrations of selected constituents in solution were determined for water from 52 wells and the Platte River. Compared to the PCO2 in the atmosphere, the average PCO2 in the ground water was many times greater and that in .the river water was about twice as great. The high PCO2 in the ground water probably results from the absorption, by infiltrating precipitation, of carbon dioxide produced in the soil by respiration of plant roots ,and microorganisms. The values for IAP/K calcite for the ground water ranged from 0.141 to 1.29 and for the river water the average was 9.6. Water from each of the 10 sampled wells on the terrace plain in southeastern Saunders County was unsaturated with respect to calcite, whereas water from seven of the 42 wells on the Platte River flood plain was nearly saturated or supersaturated. Of the ,seven, two were in the Lincoln city well field where hydrologic relations indicate that a large fraction of the water yielded by the wells is induced seepage from the .river. That more of the city wells did not yield supersaturated water is surprising in view of the high IAP/K calcite values for the river water. Supersaturation of water from five of nine sampled wells downvalley from the well field probably is due to the presence of numerous limestone fragments in the Quaternary deposits in that part of the area. also surprising was the finding that the average pH of the water from the city wells was 1 unit lower than that of the river water. The presence of both dissolved iron and dissolved oxygen in the water from several of the city wells probably reflects derivation of the water from two distinct sources : ground water naturally in the aquifer and induced seepage from the river.

Water Supply Paper↗

USGS2021

Microbial ecology of coral-dominated reefs in the Federated States of Micronesia

Microorganisms are central to the functioning of coral reef ecosystems, but their dynamics are unstudied on most reefs. We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding 7 islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro, and Pohnpei), spanning 875053 km 2 . On the reefs, we found consistently higher coral coverage (mean ± SD = 36.9 ± 22.2%; max 77%) compared to macroalgae coverage (15.2 ± 15.5%; max 58%), and low abundances of fish. Reef waters had low inorganic nutrient concentrations and were dominated by Synechococcus, Prochlorococcus, and SAR11 bacteria. The richness of bacterial and archaeal communities was significantly related to interactions between island/atoll and depth. High coral coverage on reefs was linked to higher relative abundances of Flavobacteriaceae, Leisingera, Owenweeksia, Vibrio, and the OM27 clade, as well as other heterotrophic bacterial groups, consistent with communities residing in waters near corals and within coral mucus. Microbial community structure at reef depth was significantly correlated with geographic distance, suggesting that island biogeography influences reef microbial communities. Reefs at Kosrae Island, which hosted the highest coral abundance and diversity, were unique compared to other locations; seawater from Kosrae reefs had the lowest organic carbon (59.8-67.9 µM), highest organic nitrogen (4.5-5.3 µM), and harbored consistent microbial communities (>85% similar), which were dominated by heterotrophic cells. This study suggests that the reef-water microbial ecology on Micronesian reefs is influenced by the density and diversity of corals as well as other biogeographical features.

Aquatic Microbial Ecology↗

USGS2025

Detection of the Diadema antillarum scuticociliatosis Philaster clade on sympatric metazoa, plankton, and abiotic surfaces and assessment for its potential reemergence

A ciliate belonging to the Diadema antillarum scuticociliatosis (DaSc)-associated Philaster clade (DaScPc) caused catastrophic long-spined urchin mass mortality in spring and summer of 2022. The ciliate can be grown in culture in both the presence and absence of D. antillarum tissues, suggesting that it may persist outside its host by consuming microorganisms or dissolved organic nutrients. We hypothesized that DaScPc was present outside its host during and after mass mortality and absent prior to 2022. We examined DaScPc in DNA extracted from 500 swabs of sym- patric metazoa and abiotic surfaces, and plankton samples, collected at 35 sites in the Caribbean in 2022 and 2023. DaScPc was detected on corals, turf algae, and a sponge, predominantly at sites with active or prior DaSc. We examined whether it was present prior to 2022 by surveying extracted DNA from Caribbean corals and water collected near corals by PCR and by mining publicly available transcriptomes and metagenomes for DaScPc rRNAs. These efforts yielded no DaScPc genes. We further hypothesized that DaScPc may recruit to the specific corals detected in field surveys, and that these may then infect naïve hosts. A mesocosm experiment to test DaScPc recruitment suggested that, while it recruited to corals, it did so inconsistently between coral species. Incubation of corals that recruited DaScPc with naïve urchins yielded inconclusive results since urchins died without characteristic DaSc signs. Overall, our results suggest that DaScPc may occur outside its urchin host, and that it may have been absent in the region prior to 2022.

Florida↗

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↗

USGS2020

Stony coral tissue loss disease in Florida is associated with disruption of host–zooxanthellae physiology

Samples from eight species of corals ( Colpophyllia natans , Dendrogyra cylindrus , Diploria labyrinthiformis , Meandrina meandrites , Montastraea cavernosa , Orbicella faveolata, Pseudodiploria strigosa , and Siderastrea siderea ) that exhibited gross clinical signs of acute, subacute, or chronic tissue loss attributed to stony coral tissue loss disease (SCTLD) were collected from the Florida Reef Tract during 2016–2018 and examined histopathologically. The hallmark microscopic lesion seen in all eight species was focal to multifocal lytic necrosis (LN) originating in the gastrodermis of the basal body wall (BBW) and extending to the calicodermis, with more advanced lesions involving the surface body wall. This was accompanied by other degenerative changes in host cells such as mucocyte hypertrophy, degradation and fragmentation of gastrodermal architecture, and disintegration of the mesoglea. Zooxanthellae manifested various changes including necrosis (cytoplasmic hypereosinophilia, pyknosis); peripheral nuclear chromatin condensation; cytoplasmic vacuolation accompanied by deformation, swelling, or atrophy; swollen accumulation bodies; prominent pyrenoids; and degraded chloroplasts. Polyhedral intracytoplasmic eosinophilic periodic acid–Schiff-positive crystalline inclusion bodies (∼1–10 μm in length) were seen only in M. cavernosa and P. strigosa BBW gastrodermis in or adjacent to active lesions and some unaffected areas (without surface lesions) of diseased colonies. Coccoidlike or coccobacilloidlike structures (Gram-neutral) reminiscent of microorganisms were occasionally associated with LN lesions or seen in apparently healthy tissue of diseased colonies along with various parasites and other bacteria all considered likely secondary colonizers. Of the 82 samples showing gross lesions of SCTLD, 71 (87%) were confirmed histologically to have LN. Collectively, pathology indicates that SCTLD is the result of a disruption of host–symbiont physiology with lesions originating in the BBW leading to detachment and sloughing of tissues from the skeleton. Future investigations could focus on identifying the cause and pathogenesis of this process.

Florida↗

USGS2021

Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes

All animals are host to a multitude of microorganisms that are essential to the animal’s health. Host-associated microbes have been shown to defend against potential pathogens, provide essential nutrients, interact with the host’s immune system, and even regulate mood. However, it can be difficult to preserve and obtain nucleic acids from some host-associated microbiomes, making studying their microbial communities challenging. Corals are an example of this, in part due to their potentially remote, underwater locations, their thick surface mucopolysaccharide layer, and various inherent molecular inhibitors. This study examined three different preservatives (RNAlater, DNA/RNA Shield, and liquid nitrogen) and two extraction methods (the Qiagen PowerBiofilm kit and the Promega Maxwell RBC kit with modifications) to determine if there was an optimum combination for examining the coral microbiome. These methods were employed across taxonomically diverse coral species, including deep-sea/shallow, stony/soft, and zooxanthellate/azooxanthellate: Lophelia pertusa , Paragorgia johnsoni , Montastraea cavernosa , Porites astreoides , and Stephanocoenia intersepta . Although significant differences were found between preservative types and extraction methods, these differences were subtle, and varied in nature from coral species to coral species. Significant differences between coral species were far more profound than those detected between preservative or extraction method. We suggest that the preservative types presented here and extraction methods using a bead-beating step provide enough consistency to compare coral microbiomes across various studies, as long as subtle differences in microbial communities are attributed to dissimilar methodologies. Additionally, the inclusion of internal controls such as a mock community and extraction blanks can help provide context regarding data quality, improving downstream analyses.

Frontiers in Marine Science↗

USGS2016

Municipal solid waste landfills harbor distinct microbiomes

Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH 4 and CO 2 ) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

Frontiers in Microbiology↗

USGS2016

Viral lysis of photosynthesizing microbes as a mechanism for calcium carbonate nucleation in seawater

Removal of carbon through the precipitation and burial of calcium carbonate in marine sediments constitutes over 70% of the total carbon on Earth and is partitioned between coastal and pelagic zones. The precipitation of authigenic calcium carbonate in seawater, however, has been hotly debated because despite being in a supersaturated state, there is an absence of persistent precipitation. One of the explanations for this paradox is the geochemical conditions in seawater cannot overcome the activation energy barrier for the first step in any precipitation reaction; nucleation. Here we show that virally induced rupturing of photosynthetic cyanobacterial cells releases cytoplasmic-associated bicarbonate at concentrations ~23-fold greater than in the surrounding seawater, thereby shifting the carbonate chemistry toward the homogenous nucleation of one or more of the calcium carbonate polymorphs. Using geochemical reaction energetics, we show the saturation states (Ω) in typical seawater for calcite (Ω = 4.3), aragonite (Ω = 3.1), and vaterite (Ω = 1.2) are significantly elevated following the release and diffusion of the cytoplasmic bicarbonate (Ω calcite = 95.7; Ω aragonite = 68.5; Ω vaterite = 25.9). These increases in Ω significantly reduce the activation energy for nuclei formation thresholds for all three polymorphs, but only vaterite nucleation is energetically favored. In the post-lysis seawater, vaterite's nuclei formation activation energy is significantly reduced from 1.85 × 10 −17 J to 3.85 × 10 −20 J, which increases the nuclei formation rate from highly improbable (<<1.0 nuclei cm −3 s −1 ) to instantaneous (8.60 × 10 25 nuclei cm −3 s −1 ). The proposed model for homogenous nucleation of calcium carbonate in seawater describes a mechanism through which the initial step in the production of carbonate sediments may proceed. It also presents an additional role of photosynthesizing microbes and their viruses in marine carbon cycles and reveals these microorganisms are a collective repository for concentrated and reactive dissolved inorganic carbon (DIC) that is currently not accounted for in global carbon budgets and carbonate sediment diagenesis models.

Frontiers in Microbiology↗

USGS2018

Airborne bacteria in Earth’s lower stratosphere resemble taxa detected in the troposphere: results from a new NASA aircraft bioaerosol collector (ABC)

Airborne microorganisms in the upper troposphere and lower stratosphere remain elusive due to a lack of reliable sample collection systems. To address this problem, we designed, installed, and flight-validated a novel Aircraft Bioaerosol Collector (ABC) for NASA's C-20A that can make collections for microbiological research investigations up to altitudes of 13.7 km. Herein we report results from the first set of science flights—four consecutive missions flown over the United States (US) from 30 October to 2 November, 2017. To ascertain how the concentration of airborne bacteria changed across the tropopause, we collected air during aircraft Ascent / Descent (0.3 to 11 km), as well as sustained Cruise altitudes in the lower stratosphere (~12 km). Bioaerosols were captured on DNA-treated gelatinous filters inside a cascade air sampler, then analyzed with molecular and culture-based characterization. Several viable bacterial isolates were recovered from flight altitudes, including Bacillus sp., Micrococcus sp., Arthrobacter sp., and Staphylococcus sp. from Cruise samples and Brachybacterium sp. from Ascent/Descent samples. Using 16S V4 sequencing methods for a culture-independent analysis of bacteria, the average number of total OTUs was 305 for Cruise samples and 276 for Ascent/Descent samples. Some taxa were more abundant in the flight samples than the ground samples, including OTUs from families Lachnospiraceae, Ruminococcaceae and Erysipelotrichaceae as well as the following genera: Clostridium, Mogibacterium, Corynebacterium, Bacteroides, Prevotella, Pseudomonas , and Parabacteroides . Surprisingly, our results revealed a homogeneous distribution of bacteria in the atmosphere up to 12 km. The observation could be due to atmospheric conditions producing similar background aerosols across the western US, as suggested by modeled back trajectories and satellite measurements. However, the influence of aircraft-associated bacterial contaminants could not be fully eliminated and that background signal was reported throughout our dataset. Considering the tremendous engineering challenge of collecting biomass at extreme altitudes where contamination from flight hardware remains an ever-present issue, we note the utility of using the stratosphere as a proving ground for planned life detection missions across the solar system.

Arizona, California, Colorado, Nevada, Utah↗

USGS2021

Resistance, resilience, and recovery of dryland soil bacterial communities across multiple disturbances

Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. In this study, the recovery of surface soil bacterial communities from multiple physical and environmental disturbances is assessed. Samples were collected from three field sites in the vicinity of Moab, UT, United States, 6 to 7 years after physical and climate disturbance manipulations had been terminated, allowing for the assessment of community recovery. Additionally, samples were collected in a transect that included three habitat patches: the canopy zone soils under the dominant shrubs, the interspace soils that are colonized by biological soil crusts, and edge soils at the plot borders. Field site and habitat patch were significant factors structuring the bacterial communities, illustrating that sites and habitats harbored unique soil microbiomes. Across the different sites and disturbance treatments, there was evidence of significant bacterial community recovery, as bacterial biomass and diversity were not significantly different than control plots. There was, however, a small number of 16S rRNA gene amplicon sequence variants that distinguished particular treatments, suggesting that legacy effects of the disturbances still remained. Taken together, these data suggest that dryland bacterial communities may possess a previously unappreciated potential to recover within years of the original disturbance.

Frontiers in Microbiology↗

USGS2014

Adaptations of indigenous bacteria to fuel contamination in karst aquifers in south-central Kentucky

The karst aquifer systems in southern Kentucky can be dynamic and quick to change. Microorganisms that live in these unpredictable aquifers are constantly faced with environmental changes. Their survival depends upon adaptations to changes in water chemistry, taking advantage of positive stimuli and avoiding negative environmental conditions. The U.S. Geological Survey conducted a study in 2001 to determine the capability of bacteria to adapt in two distinct regions of water quality in a karst aquifer, an area of clean, oxygenated groundwater and an area where the groundwater was oxygen depleted and contaminated by jet fuel. Water samples containing bacteria were collected from one clean well and two jet fuel contaminated wells in a conduit-dominated karst aquifer. Bacterial concentrations, enumerated through direct count, ranged from 500,000 to 2.7 million bacteria per mL in the clean portion of the aquifer, and 200,000 to 3.2 million bacteria per mL in the contaminated portion of the aquifer over a twelve month period. Bacteria from the clean well ranged in size from 0.2 to 2.5 mm, whereas bacteria from one fuel-contaminated well were generally larger, ranging in size from 0.2 to 3.9 mm. Also, bacteria collected from the clean well had a higher density and, consequently, were more inclined to sink than bacteria collected from contaminated wells. Bacteria collected from the clean portion of the karst aquifer were predominantly (,95%) Gram-negative and more likely to have flagella present than bacteria collected from the contaminated wells, which included a substantial fraction (,30%) of Gram-positive varieties. The ability of the bacteria from the clean portion of the karst aquifer to biodegrade benzene and toluene was studied under aerobic and anaerobic conditions in laboratory microcosms. The rate of fuel biodegradation in laboratory studies was approximately 50 times faster under aerobic conditions as compared to anaerobic, sulfur-reducing conditions. The optimum pH for fuel biodegradation ranged from 6 to 7. These findings suggest that bacteria have adapted to water-saturated karst systems with a variety of active and passive transport mechanisms.

Kentucky↗

USGS2023

Stimulation of aquatic bacteria from Mammoth Cave, Kentucky, by sublethal concentrations of antibiotics

Many microorganisms secrete secondary metabolites with antibiotic properties; however, there is debate whether the secretions evolved as a means to gain a competitive edge or as a chemical signal to coordinate community growth. The objective of this research was to investigate if select antibiotics acted as a weapon or as a chemical signal by exposing communities of aquatic cave bacteria to increasing concentrations of antibiotics. Water samples were collected from six cave locations where actinobacterial mats appeared to be plentiful. Bacterial growth was measured using colony counts on 10 % tryptic soy agar augmented with increasing concentrations of erythromycin, tetracycline, kanamycin, gentamicin, or quaternary ammonia compounds (QAC). Colony counts generally decreased as the gentamicin, kanamycin and QAC dose increased. In contrast, the colony numbers increased on agar plates supplemented with 0.01 mg L −1 , 0.10 mg L −1 and 1.00 mg L −1 erythromycin or tetracycline. A 10.00 mg L −1 dose of each antibiotic treatment reduced bacteria colonies by 98 % or more. Community-level physiological capabilities were evaluated using Ecolog plates inoculated with cave water dosed with either 0.00 mg L −1 or 0.10 mg L −1 of erythromycin. Incubation with the antibiotic almost doubled the number of food substrates used in the first 24 hours. There was a significant increase in the use of acetyl glucosamine, arginine, and putrescine when bacteria were exposed to 0.10 mg L −1 erythromycin triggered by the antibiotic acting as a chemical messenger. Principal component analysis confirmed a shift in substrate preferences when erythromycin was added. A conceptual ecological model is proposed based on the response of aquatic cave bacteria to sublethal antibiotics.

Kentucky↗

USGS2016

Methane and sulfate dynamics in sediments from mangrove-dominated tropical coastal lagoons, Yucatan, Mexico

Porewater profiles in sediment cores from mangrove-dominated coastal lagoons (Celestún and Chelem) on the Yucatán Peninsula, Mexico, reveal the widespread coexistence of dissolved methane and sulfate. This observation is interesting since dissolved methane in porewaters is typically oxidized anaerobically by sulfate. To explain the observations we used a numerical transport-reaction model that was constrained by the field observations. The model suggests that methane in the upper sediments is produced in the sulfate reduction zone at rates ranging between 0.012 and 31 mmol m −2 d − 1 , concurrent with sulfate reduction rates between 1.1 and 24 mmol SO 4 2− m −2 d −1 . These processes are supported by high organic matter content in the sediment and the use of non-competitive substrates by methanogenic microorganisms. Indeed sediment slurry incubation experiments show that non-competitive substrates such as trimethylamine (TMA) and methanol can be utilized for microbial methanogenesis at the study sites. The model also indicates that a significant fraction of methane is transported to the sulfate reduction zone from deeper zones within the sedimentary column by rising bubbles and gas dissolution. The shallow depths of methane production and the fast rising methane gas bubbles reduce the likelihood for oxidation, thereby allowing a large fraction of the methane formed in the sediments to escape to the overlying water column.

Yucatan↗

USGS2023

Antimony in mine wastes: Geochemistry, mineralogy, microbiology

Antimony (Sb) is a valuable mined commodity, used mostly in fire retardants, and considered a critical element. It is also a potential environment hazard classed as a carcinogen. Antimony is concentrated in tailings and waste rock from Sb mines as well as other locations, such as precious metal deposits, where Sb is present in the ore but not recovered. This review covers the aqueous geochemistry, isotope chemistry, mineralogy, and microbiology of Sb in the context of mine waste. The primary minerals stibnite and sulfosalts may release Sb in surface and groundwaters and result in contamination of soils, plants, and river sediments. In some cases, Sb mobility is limited by its adsorption and incorporation into Fe (oxyhydr)oxides. At higher Sb concentrations, precipitation of Sb secondary hosts such as tripuhyite (FeSbO 4 , relatively insoluble) and brandholzite (Mg[Sb(OH) 6 ] 2 · 6H 2 O, highly soluble) influence Sb concentrations in water associated with mine waste. Although Sb is nonessential to organisms, microorganisms are involved in oxidation, reduction, and methylation processes that can drive biogeochemical transformations. Limited toxicological information about Sb makes it challenging to establish regulations or guidelines limiting the concentration of Sb. Antimony is frequently associated with arsenic in mine waste, and remediation design is often based on the assumption that both metalloids behave in a similar way. However, new research suggests that in some environments, this is not the case, and Sb should be considered based on its unique biogeochemical behavior.

Economic Geology↗

USGS2007

Coral microbiology

In the last 30 years, there has been approximately a 30% loss of corals worldwide, largely due to emerging diseases (Harvell et al., 2002, 2007; Hughes et al., 2003). Coral microbiology is a new field, driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms and to use this knowledge to eventually prevent the spread of coral diseases.

Oceanography↗

USGS1994

Relationship between resistance of salmonids to furunculosis and recovery of Aeromonas salmonicida from external mucus

Fish were sampled at the Ed Weed State Fish Hatchery (South Hero, Vermont, USA) in September 1992. Aeromonas salmonicida was common, with concentrations as high as 10 5 to 10 7 colony-forming units per gram of mucus, and readily recovered from most mucus samples obtained from furunculosis-sensitive populations of brook trout ( Salvelinus fontinalis ), lake trout ( Salvelinus namaycush ), and Atlantic salmon (Salmo salar) . The pathogen was the predominant microorganism and accounted for greater than 85% of the total number of bacteria isolated from the mucus of these fish. By comparison, A. salmonicida was recovered only from two rainbow trout ( Oncorhynchus mykiss ), and bacterial frequencies did not exceed 10 3 colony-forming units per gram of mucus. The pathogen was not recovered from the mucus of steelhead ( O. mykiss ) or Rome brown trout ( Salmo trutta ) selectively bred for resistance to furunculosis, even though there was widespread contagion throughout the hatchery and fish were cultured on a common, unprotected water supply.

Journal of Wildlife Diseases↗

USGS2023

Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)

Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy “receiver” coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the presence of numerous previously identified SCTLD bioindicators within our mesocosms. The identification in our mesocosms of specific bacterial amplicon sequence variants that also appear across prior studies spanning different collection years, geographic regions, source material, and coral species, suggests that bacteria may play some role in the disease.

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