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USGS2006

Effects of altered temperature and precipitation on desert protozoa associated with biological soil crusts

Biological soil crusts are diverse assemblages of bacteria, cyanobacteria, algae, fungi, lichens, and mosses that cover much of arid land soils. The objective of this study was to quantify protozoa associated with biological soil crusts and test the response of protozoa to increased temperature and precipitation as is predicted by some global climate models. Protozoa were more abundant when associated with cyanobacteria/lichen crusts than with cyanobacteria crusts alone. Amoebae, flagellates, and ciliates originating from the Colorado Plateau desert (cool desert, primarily winter precipitation) declined 50-, 10-, and 100-fold, respectively, when moved in field mesocosms to the Chihuahuan Desert (hot desert, primarily summer rain). However, this was not observed in protozoa collected from the Chihuahuan Desert and moved to the Sonoran desert (hot desert, also summer rain, but warmer than Chihuahuan Desert). Protozoa in culture began to encyst at 37??C. Cysts survived the upper end of daily temperatures (37-55??C), and could be stimulated to excyst if temperatures were reduced to 15??C or lower. Results from this study suggest that cool desert protozoa are influenced negatively by increased summer precipitation during excessive summer temperatures, and that desert protozoa may be adapted to a specific desert's temperature and precipitation regime. ?? 2006 by the International Society of Protistologists.

Journal of Eukaryotic Microbiology↗

USGS2008

Methanogenic pathways of coal-bed gas in the Powder River Basin, United States: The geologic factor

Coal-bed gas of the Tertiary Fort Union and Wasatch Formations in the Powder River Basin in Wyoming and Montana, U.S. was interpreted as microbial in origin by previous studies based on limited data on the gas and water composition and isotopes associated with the coal beds. To fully evaluate the microbial origin of the gas and mechanisms of methane generation, additional data for 165 gas and water samples from 7 different coal-bed methane-bearing coal-bed reservoirs were collected basinwide and correlated to the coal geology and stratigraphy. The C1/(C2 + C3) ratio and vitrinite reflectance of coal and organic shale permitted differentiation between microbial gas and transitional thermogenic gas in the central part of the basin. Analyses of methane ??13C and ??D, carbon dioxide ??13C, and water ??D values indicate gas was generated primarily from microbial CO2 reduction, but with significant gas generated by microbial methyl-type fermentation (aceticlastic) in some areas of the basin. Microbial CO2 reduction occurs basinwide, but is generally dominant in Paleocene Fort Union Formation coals in the central part of the basin, whereas microbial methyl-type fermentation is common along the northwest and east margins. Isotopically light methane ??13C is distributed along the basin margins where ??D is also depleted, indicating that both CO2-reduction and methyl-type fermentation pathways played major roles in gas generation, but gas from the latter pathway overprinted gas from the former pathway. More specifically, along the northwest basin margin gas generation by methyl-type fermentation may have been stimulated by late-stage infiltration of groundwater recharge from clinker areas, which flowed through highly fractured and faulted coal aquifers. Also, groundwater recharge controlled a change in gas composition in the shallow Eocene Wasatch Formation with the increase of nitrogen and decrease of methane composition of the coal-bed gas. Other geologic factors, such as burial, thermal and maturation history, lateral and vertical continuity, and coalification of the coal beds, also played a significant role in controlling methanogenic pathways and provided new perspectives on gas evolution and emplacement. The early-stage gas produced by CO2 reduction has mixed with transitional thermogenic gas in the deeper, central parts of the Powder River Basin to form 'old' gas, whereas along the basin margins the overprint of gas from methyl-type fermentation represents 'new' gas. Thus, a clear understanding of these geologic factors is necessary to relate the microbiological, biogeochemical, and hydrological processes involved in the generation of coal-bed gas.

International Journal of Coal Geology↗

USGS2007

U.S. Geological Survey scientific activities in the exploration of Antarctica: 1946-2006 record of personnel in Antarctica and their postal cachets: U.S. Navy (1946-48, 1954-60), International Geophysical Year (1957-58), and USGS (1960-2006)

Antarctica, a vast region encompassing 13.2 million km2 (5.1 million mi2), is considered to be one of the most important scientific laboratories on Earth. During the past 60 years, the USGS, in collaboration and with logistical support from the National Science Foundation's Office of Polar Programs, has sent 325 USGS scientists to Antarctica to work on a wide range of projects: 169 personnel from the NMD (mostly aerial photography, surveying, and geodesy, primarily used for the modern mapping of Antarctica), 138 personnel from the GD (mostly geophysical and geological studies onshore and offshore), 15 personnel from the WRD (mostly hydrological/glaciological studies in the McMurdo Dry Valleys), 2 personnel from the BRD (microbiological studies in the McMurdo Dry Valleys), and 1 person from the Director's Office (P. Patrick Leahy, Acting Director, 2005–06 austral field season). Three GD scientists and three NMD scientists have carried out field work in Antarctica 9 or more times: John C. Behrendt (15), who started in 1956–57 and published two memoirs (Behrendt, 1998, 2005), Arthur B. Ford (10), who started in 1960–61, and Gary D. Clow (9), who started in 1985–86; Larry D. Hothem (12), who began as a winter-over geodesist at Mawson Station in 1968–69, and Jerry L. Mullins (12), who started in 1982–83 and followed in the legendary footsteps of his NMD predecessor, William R. MacDonald (9), who started in 1960–61 and supervised the acquisition of more than 1,000,000 square miles of aerial photography of Antarctica. This report provides a record as complete as possible, of USGS and non-USGS collaborating personnel in Antarctica from 1946–2006, the geographic locations of their work, and their scientific/engineering disciplines represented. Postal cachets for each year follow the table of personnel and scientific activities in the exploration of Antarctica during those 60 years. To commemorate special events and projects in Antarctica, it became an international practice to create postal cachets. A cachet is defined as a seal, emblem, or commemorative design printed or stamped on an envelope to mark a philatelic or special event. All stamp collectors are familiar with engraved cachets on envelopes of "First-Day-of-Issue" stamps. For Antarctica, a stamped (inked) impression informs the scientist, historian, stamp collector, and general public about the multidisciplinary science projects staffed by USGS scientists and other specialists during a specific austral summer field season. Because philatelic cachets were created by team members for each USGS field season, in most cases depicting the specific areas and scientific objectives, the cachets have become a convenient documentation of the people, projects, and geographic places for that year. Because the cachets are representative of USGS activities, each year's cachet is included in that year's Open-File Report (1960–61 to 2005–06). Starting with the 1983–84 season, however, two USGS cachets were prepared for the next seven years, one for the winter team at Amundsen-Scott South Pole Station, until 1992–93, and the other for all other field sites. Multiple cachets were created by USGS divisional programs during the 1962–63, 1963–64, 1970–71, 1972–73, 1975–76, 1978–79, 1979–80, 1983–84, 1984–85, 1986–87, 1995–96, 2003–04, and the 2005–06 years. This report includes facsimiles of each annual postal cachet (or postal cachets) designed by USGS graphic specialists and provides a record of USGS personnel (and non-USGS collaborating scientists) and their science division affiliation for each austral field season. In addition, cachets used by USGS personnel for U.S. Navy Operation Highjump (1946–47), U.S. Navy Operation Windmill (1947–48), U.S. Navy U.S.S. Atka reconnaissance cruise (1954–55), U.S. Navy Operation Deep Freeze (DF) (I, 1955–56; II, 1956–57; III, 1957–58; IV, 1958–59; and DF 60, 1959–60), and the International Geophysical Year (1957–58) are included, because USGS scientists made use of these cachets when involved in each of the field activities during these austral field seasons.

Open-File Report↗

USGS2007

Formation of tellurium nanocrystals during anaerobic growth of bacteria that use Te oxyanions as respiratory electron acceptors

Certain toxic elements support the metabolism of diverse prokaryotes by serving as respiratory electron acceptors for growth. Here, we demonstrate that two anaerobes previously shown to be capable of respiring oxyanions of selenium also achieve growth by reduction of either tellurate [Te(VI)] or tellurite [Te(IV)] to elemental tellurium [Te(0)]. This reduction achieves a sizeable stable-Te-isotopic fractionation (isotopic enrichment factor [ε] = −0.4 to −1.0 per ml per atomic mass unit) and results in the formation of unique crystalline Te(0) nanoarchitectures as end products. The Te(0) crystals occur internally within but mainly externally from the cells, and each microorganism forms a distinctly different structure. Those formed by Bacillus selenitireducens initially are nanorods (∼10-nm diameter by 200-nm length), which cluster together, forming larger (∼1,000-nm) rosettes composed of numerous individual shards (∼100-nm width by 1,000-nm length). In contrast, Sulfurospirillum barnesii forms extremely small, irregularly shaped nanospheres (diameter < 50 nm) that coalesce into larger composite aggregates. Energy-dispersive X-ray spectroscopy and selected area electron diffraction indicate that both biominerals are composed entirely of Te and are crystalline, while Raman spectroscopy confirms that they are in the elemental state. These Te biominerals have specific spectral signatures (UV-visible light, Raman) that also provide clues to their internal structures. The use of microorganisms to generate Te nanomaterials may be an alternative for bench-scale syntheses. Additionally, they may also generate products with unique properties unattainable by conventional physical/chemical methods.

Applied and Environmental Microbiology↗

USGS2010

Advances in the hydrogeochemistry and microbiology of acid mine waters

The last decade has witnessed a plethora of research related to the hydrogeochemistry and microbiology of acid mine waters and associated tailings and waste-rock waters. Numerous books, reviews, technical papers, and proceedings have been published that examine the complex bio-geochemical process of sulfide mineral oxidation, develop and apply geochemical models to site characterization, and characterize the microbial ecology of these environments. This review summarizes many of these recent works, and provides references for those investigating this field. Comparisons of measured versus calculated Eh and measured versus calculated pH for water samples from several field sites demonstrate the reliability of some current geochemical models for aqueous speciation and mass balances. Geochemical models are not, however, used to predict accurately time-dependent processes but to improve our understanding of these systems and to constrain possible processes that contribute to actual or potential water quality issues. Microbiological studies are demonstrating that there is much we have yet to learn about the types of different microorganisms and their function and ecology in mine-waste environments. A broad diversity of green algae, bacteria, archaea, yeasts, and fungi are encountered in acid mine waters, and a better understanding of their ecology and function may potentially enhance remediation possibilities as well as our understanding of the evolution of life.

International Geology Review↗

USGS2006

Wildlife tuberculosis in South African conservation areas: Implications and challenges

Tuberculosis, caused by Mycobacterium bovis, was first diagnosed in African buffalo in South Africa's Kruger National Park in 1990. Over the past 15 years the disease has spread northwards leaving only the most northern buffalo herds unaffected. Evidence suggests that 10 other small and large mammalian species, including large predators, are spillover hosts. Wildlife tuberculosis has also been diagnosed in several adjacent private game reserves and in the Hluhluwe-iMfolozi Park, the third largest game reserve in South Africa. The tuberculosis epidemic has a number of implications, for which the full effect of some might only be seen in the long-term. Potential negative long-term effects on the population dynamics of certain social animal species and the direct threat for the survival of endangered species pose particular problems for wildlife conservationists. On the other hand, the risk of spillover infection to neighboring communal cattle raises concerns about human health at the wildlife-livestock-human interface, not only along the western boundary of Kruger National Park, but also with regards to the joint development of the Greater Limpopo Transfrontier Conservation Area with Zimbabwe and Mozambique. From an economic point of view, wildlife tuberculosis has resulted in national and international trade restrictions for affected species. The lack of diagnostic tools for most species and the absence of an effective vaccine make it currently impossible to contain and control this disease within an infected free-ranging ecosystem. Veterinary researchers and policy-makers have recognized the need to intensify research on this disease and the need to develop tools for control, initially targeting buffalo and lion. ?? 2005 Elsevier B.V. All rights reserved.

Kruger National Park↗

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↗

USGS2004

Use of PRD1 bacteriophage in groundwater viral transport, inactivation, and attachment studies

PRD1, an icosahedra-shaped, 62 nm (diameter), double-stranded DNA bacteriophage with an internal membrane, has emerged as an important model virus for studying the manner in which microorganisms are transported through a variety of groundwater environments. The popularity of this phage for use in transport studies involving geologic media is due, in part, to its relative stability over a range of temperatures and low degree of attachment in aquifer sediments. Laboratory and field investigations employing PRD1 are leading to a better understanding of viral attachment and transport behaviors in saturated geologic media and to improved methods for describing mathematically subsurface microbial transport at environmentally significant field scales. Radioisotopic labeling of PRD1 is facilitating additional information about the nature of viral interactions with solid surfaces in geologic media, the importance of iron oxide surfaces, and allowing differentiation between inactivation and attachment in field-scale tracer tests.

FEMS Microbiology Ecology↗

USGS2023

Paranannizziopsis spp. infections in wild snakes and a qPCR assay for detection of the fungus

The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential effects of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola , little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive collections, and P. australasiensis was recently identified as the cause of skin infections in non-native wild panther chameleons ( Furcifer pardalis ) in Florida, USA. Here we describe five cases of Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and one additional case from a captive snake from Connecticut, USA. In addition to demonstrating that wild Nearctic snakes can serve as a host for these fungi, we also provide evidence that the genus Paranannizziopsis is widespread in wild snakes, with cases being identified in Louisiana (USA), Minnesota (USA), Virginia (USA), and British Columbia (Canada). Phylogenetic analyses conducted on multiple loci of the fungal strains we isolated identified P. australasiensis in Louisiana and Virginia; the remaining strains from Minnesota and British Columbia did not cluster with any of the described species of Paranannizziopsis , although the strains from British Columbia appear to represent a single lineage. Finally, we designed a pan- Paranannizziopsis real-time PCR assay targeting the internal transcribed spacer region 2. This assay successfully detected DNA of all described species of Paranannizziopsis and the two potentially novel taxa isolated in this study and did not cross-react with closely related fungi or other fungi commonly found on the skin of snakes. The assay was 100% sensitive and specific when screening clinical (skin tissue or skin swab) samples, although full determination of the assay’s performance will require additional follow up due to the small number of clinical samples ( n = 14 from 11 snakes) available for testing in our study. Nonetheless, the PCR assay can provide an important tool in further investigating the prevalence, distribution, and host range of Paranannizziopsis spp. and facilitate more rapid diagnosis of Paranannizziopsis spp. infections that are otherwise difficult to differentiate from other dermatomycoses.

Frontiers in Microbiology↗

USGS2009

Deep drilling in the Chesapeake Bay impact structure - An overview

The late Eocene Chesapeake Bay impact structure lies buried at moderate depths below Chesapeake Bay and surrounding landmasses in southeastern Virginia, USA. Numerous characteristics made this impact structure an inviting target for scientific drilling, including the location of the impact on the Eocene continental shelf, its threelayer target structure, its large size (??85 km diameter), its status as the source of the North American tektite strewn field, its temporal association with other late Eocene terrestrial impacts, its documented effects on the regional groundwater system, and its previously unstudied effects on the deep microbial biosphere. The Chesapeake Bay Impact Structure Deep Drilling Project was designed to drill a deep, continuously cored test hole into the central part of the structure. A project workshop, funding proposals, and the acceptance of those proposals occurred during 2003-2005. Initial drilling funds were provided by the International Continental Scientific Drilling Program (ICDP) and the U.S. Geological Survey (USGS). Supplementary funds were provided by the National Aeronautics and Space Administration (NASA) Science Mission Directorate, ICDP, and USGS. Field operations were conducted at Eyreville Farm, Northampton County, Virginia, by Drilling, Observation, and Sampling of the Earth's Continental Crust (DOSECC) and the project staff during September-December 2005, resulting in two continuously cored, deep holes. The USGS and Rutgers University cored a shallow hole to 140 m in April-May 2006 to complete the recovered section from land surface to 1766 m depth. The recovered section consists of 1322 m of crater materials and 444 m of overlying postimpact Eocene to Pleistocene sediments. The crater section consists of, from base to top: basement-derived blocks of crystalline rocks (215 m); a section of suevite, impact melt rock, lithic impact breccia, and cataclasites (154 m); a thin interval of quartz sand and lithic blocks (26 m); a granite megablock (275 m); and sediment blocks and boulders, polymict, sediment-clast-dominated sedimentary breccias, and a thin upper section of stratified sediments (652 m). The cored postimpact sediments provide insight into the effects of a large continental-margin impact on subsequent coastal-plain sedimentation. This volume contains the first results of multidisciplinary studies of the Eyreville cores and related topics. The volume is divided into these sections: geologic column; borehole geophysical studies; regional geophysical studies; crystalline rocks, impactites, and impact models; sedimentary breccias; postimpact sediments; hydrologic and geothermal studies; and microbiologic studies. ?? 2009 The Geological Society of America.

Special Paper of the Geological Society of America↗

USGS2015

Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska

In August 2008, Kasatochi volcano erupted and buried a small island in pyroclastic deposits and fine ash; since then, microbes, plants and birds have begun to re-colonize the initially sterile surface. Five years post-eruption, bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) copy numbers and extracellular enzyme activity (EEA) potentials were one to two orders of magnitude greater in pyroclastic materials with organic matter (OM) inputs relative to those without, despite minimal accumulation of OM (< 0.2%C). When normalized by OM levels, post-eruptive surfaces with OM inputs had the highest β-glucosidase, phosphatase, NAGase and cellobiohydrolase activities, and had microbial population sizes approaching those in reference soils. In contrast, the strongest factor determining bacterial community composition was the dominance of plants versus birds as OM input vectors. Although soil pH ranged from 3.9 to 7.0, and %C ranged 100×, differentiation between plant- and bird-associated microbial communities suggested that cell dispersal or nutrient availability are more likely drivers of assembly than pH or OM content. This study exemplifies the complex relationship between microbial cell dispersal, soil geochemistry, and microbial structure and function; and illustrates the potential for soil microbiota to be resilient to disturbance.

Alaska↗

USGS1994

Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer

A PCR primer set and an internal probe that are specific for Pseudomonas sp. strain B13, a 3-chlorobenzoate-metabolizing strain, were developed. Using this primer set and probe, we were able to detect Pseudomonas sp. strain B13 DNA sequences in DNA extracted from aquifer samples 14.5 months after Pseudomonas sp. strain B13 had been injected into a sand and gravel aquifer. This primer set and probe were also used to analyze isolates from 3-chlorobenzoate enrichments of the aquifer samples by Southern blot analysis. Hybridization of Southern blots with the Pseudomonas sp. strain B13-specific probe and a catabolic probe in conjunction with restriction fragment length polymorphism (RFLP) analysis of ribosome genes was used to determine that viable Pseudomonas sp. strain B13 persisted in this environment. We isolated a new 3-chlorobenzoate-degrading strain from one of these enrichment cultures. The B13-specific probe does not hybridize to DNA from this isolate. The new strain could be the result of gene exchange between Pseudomonas sp. strain B13 and an indigenous bacterium. This speculation is based on an RFLP pattern of ribosome genes that differs from that of Pseudomonas sp. strain B13, the fact that identically sized restriction fragments hybridized to the catabolic gene probe, and the absence of any enrichable 3-chlorobenzoate-degrading strains in the aquifer prior to inoculation.

Massachusetts↗

USGS2016

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulic conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112 to 120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ 13 C values (−67&permil; average), high alkalinity values (22 meq/kg average), relatively positive δ 13 C-DIC values (4&permil; average), and no detectable higher chain hydrocarbons, NO 3 − , or SO 4 2− . Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situ bacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down hydrocarbons. Identifying microorganisms involved in coal degradation and the hydrogeochemical conditions that promote their activity is crucial to understanding and improving in situ CBM production.

Montana, Wyoming↗

USGS2021

Pilot-scale expanded assessment of inorganic and organic tapwater exposures and predicted effects in Puerto Rico, USA

A pilot-scale expanded target assessment of mixtures of inorganic and organic contaminants in point-of-consumption drinking water (tapwater, TW) was conducted in Puerto Rico (PR) to continue to inform TW exposures and corresponding estimations of cumulative human-health risks across the US. In August 2018, a spatial synoptic pilot assessment of than 524 organic, 37 inorganic, and select microbiological contaminant indicators was conducted in 14 locations (7 home; 7 commercial) across PR. A follow-up 3-day temporal assessment of TW variability was conducted in December 2018 at two of the synoptic locations (1 home, 1 commercial) and included daily pre- and post-flush samples. Concentrations of regulated and unregulated TW contaminants were used to calculate cumulative in vitro bioactivity ratios and Hazard Indices (HI) based on existing human-health benchmarks. Synoptic results confirmed that human exposures to inorganic and organic contaminant mixtures, which are rarely monitored together in drinking water at the point of consumption, occurred across PR and consisted of elevated concentrations of inorganic contaminants (e.g., lead, copper), disinfection byproducts (DBP), and to a lesser extent per/polyfluoroalkyl substances (PFAS) and phthalates. Exceedances of human-health benchmarks in every synoptic TW sample support further investigation of the potential cumulative risk to vulnerable populations in PR and emphasize the importance of continued broad characterization of drinking-water exposures at the tap with analytical capabilities that better represent the complexity of both inorganic and organic contaminant mixtures known to occur in ambient source waters. Such health-based monitoring data are essential to support public engagement in source water sustainability and treatment and to inform consumer point-of-use treatment decision making in PR and throughout the US.

Puerto Rico↗