SEARCH · Search USGS

Results for “International Microbiology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

26 records · Page 2Linked to original sources

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↗