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Acetylene fermentation assays, nitrogen fixation assays, and growth studies were performed with Pelobacter sp. strain SFB93 and Pelobacter acetylenicus DSM3246. Data includes concentrations of acetylene and ethylene over time, and growth measured with OD680 and cell counts.
This dataset provides results of a targeted bacterial community metagenomic analysis of surface water, groundwater, and sand samples at Jeorse Park on Lake Michigan in East Chicago, Indiana. Seventy-two samples were collected from 6 sites in 2017. Samples were analyzed for the 16S ribosomal RNA (16S rRNA) gene (the S in 16S refers to the rate of sedimentation, in Svedberg units, of the RNA molecule in a centrifugal field), and one sample was excluded because it produced too few reads. The 16S rRNA gene is the most conserved of three rRNA genes (16S, 23S, and 5S) and is considered the most reliable for identification and taxonomic classification of bacterial species (Bouchet and others, 2008). Taxonomic analysis...
The data document the results of several microbe bioassays performed by the USGS on Phragmites australis plants, including those performed on mature leaves, seedlings, and dead leaf tissues exploration of the literature to find accounts of microbes associated with Phragmites worldwide. For the bioassays, we prepared 162 pure cultures isolated from Phragmites plants in North America along the east coast, Florida, the Gulf of Mexico, and the Great Lakes area, 125 of which were from a previous study, and 38 represent new collections. The DNA sequences used to identify the 37 new collections are included. Microbes were isolated from plants collected from 2015-2018. We performed assays using both North American plant...
Site-specific multiple linear regression models were developed for one beach in Ohio (three discrete sampling sites) and one beach in Pennsylvania to estimate concentrations of Escherichia coli (E. coli) or the probability of exceeding the bathing-water standard for E. coli in recreational waters used by the public. Traditional culture-based methods are commonly used to estimate concentrations of fecal indicator bacteria, such as E. coli; however, results are obtained 18 to 24 hours post sampling and do not accurately reflect current water-quality conditions. Beach-specific mathematical models use environmental and water-quality variables that are easily and quickly measured as surrogates to estimate concentrations...
Three regression models were developed for describing variability of host-specific flux data in eight Great Lakes tributaries. Models include one for Lachnospiraceae flux, one for human bacteroides flux, and one for ruminant bacteroides flux. Models were developed using the R project for statistical computing with core functionality and the survival, smwrBase, and smwrQW packages. Predictor variables for these models are included in the data file and input files provided. These include sampling dates and times, rainfall depth, percent of watershed underlain by tile drainage, cattle population (for the ruminant marker model) and human population (for the human marker models). Sample collection and laboratory analyses...
Categories: Data;
Tags: Bacteria,
Great Lakes Region,
Regression analysis,
Surface water quality,
USGS Science Data Catalog (SDC)
Soil organic matter (SOM) biomarker methods were utilized in this study to investigate the responses of fungi and bacteria to freeze–thaw cycles (FTCs) and to examine freeze–thaw-induced changes in SOM composition and substrate availability. Unamended, grass-amended, and lignin-amended soil samples were subject to 10 laboratory FTCs. Three SOM fractions (free lipids, bound lipids, and lignin-derived phenols) with distinct composition, stability and source were examined with chemolysis and biomarker Gas Chromatography/Mass Spectrometry methods and the soil microbial community composition was monitored by phospholipid fatty acid (PLFA) analysis. Soil microbial respiration was also measured before and during freezing...
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: Soil Biology and Biochemistry,
bacteria,
biomarkers,
bound lipids,
co2 flush,
At the Naturita site in Colorado, USA, groundwaters were sampled and analyzed for chemical composition and by culture and culture-independent microbiological techniques. In addition, sediments were extracted with a dilute sodium carbonate solution to determine quantities of labile uranium within the sediments. Samples from the upgradient portion of the contaminated aquifer, where very little dissolved Fe(II) is found in the groundwater, have uranium content that is controlled by U(VI) adsorption and few metal-reducing bacteria are observed. In the extreme downgradient portion of the aquifer, where dissolved Fe(II) is observed, uranium content of the sediments includes significant quantities of reduced U(IV) and...
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: Physics and Chemistry of the Earth,
bacteria,
iron,
reduction,
sediments,
At the Naturita site in Colorado, USA, groundwaters were sampled and analyzed for chemical composition and by culture and culture-independent microbiological techniques. In addition, sediments were extracted with a dilute sodium carbonate solution to determine quantities of labile uranium within the sediments. Samples from the upgradient portion of the contaminated aquifer, where very little dissolved Fe(II) is found in the groundwater, have uranium content that is controlled by U(VI) adsorption and few metal-reducing bacteria are observed. In the extreme downgradient portion of the aquifer, where dissolved Fe(II) is observed, uranium content of the sediments includes significant quantities of reduced U(IV) and...
We characterized, at millimeter resolution, bacterial biomass, diversity, and vertical stratification of biological soil crusts in arid lands from the Colorado Plateau. Microscopic counts, extractable DNA, and plate counts of viable aerobic copiotrophs (VAC) revealed that the top centimeter of crusted soils contained atypically large bacterial populations, tenfold larger than those in uncrusted, deeper soils. The plate counts were not always consistent with more direct estimates of microbial biomass. Bacterial populations peaked at the immediate subsurface (1-2 mm) in light-appearing, young crusts, and at the surface (0-1 mm) in well-developed, dark crusts, which corresponds to the location of cyanobacterial populations....
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: DNA,
Microbial Ecology,
RNA,
bacteria,
biomass,
Controlled waterborne exposures of Pacific herring (Clupea pallasii) to Vibrio anguillarum and V. ordalii failed to result in overt signs of disease or mortality from vibriosis. Cumulative mortalities among Vibrio - exposed Pacific herring (3.3 - 5.0%) were similar to those of saline-exposed negative controls (10%) and significantly less (P < 0.001) than those of Vibrio - exposed Chinook salmon (60 - 97%), a known susceptible species. Gross signs of disease did not occur on any dead or surviving Pacific herring; however, exposed Chinook salmon demonstrated classic gross signs of vibriosis. The results indicate that early reports of presumed vibriosis in Pacific herring during the 1950’s were likely misdiagnosed...
Categories: Data;
Tags: Ecology,
USGS Science Data Catalog (SDC),
Wildlife Disease,
bacteria,
biota,
The diagnosis of bacterial disease in freshwater unionid mussels has been hindered by a lack of baseline information regarding the microbial communities associated with these animals. In this study, we cultured and identified bacteria from the hemolymph of stable mussel populations from the upper Mississippi River basin and compared results to mussel populations associated with a mortality event in the Clinch River, VA and TN. Several bacterial genera were consistently identified across mussel species and locations, appearing to be part of the natural bacterial flora. One noteworthy isolate was identified from the Clinch River. Yokenella regensbergei was found with relatively high prevalence during the mortality...
Categories: Data;
Tags: Bacteria,
Clinch River, Virginia, USA,
Clinch River,Tennessee, USA,
Hemolymph,
USGS Science Data Catalog (SDC),
Water-quality data were collected by the Providence Water Supply Board (PWSB) from tributaries in the Scituate Reservoir drainage area, October 1, 2017 through September 30, 2022 (water years 2018 through 2022). Water-quality samples were collected by the PWSB either monthly or quarterly at fixed stations on 38 tributaries in the Scituate Reservoir drainage area, Rhode Island. These data were used to calculate instantaneous loads and yields of constituents in reports by the U.S. Geological Survey. Water-quality samples were collected following a strict sampling schedule so that water-quality samples would be representative of various weather conditions. Samples were analyzed at the PWSB water-quality laboratory...
The mobility and bioavailability of Se depend on its redox state, and reduction of Se oxyanions to less mobile, reduced species controls transport of this potentially toxic element in the environment. Stable isotope fractionation of Se is currently being developed as an indicator of Se immobilization through reduction. In this study, Se isotope fractionation resulting from reduction of Se(VI) and Se(IV) oxyanions by natural microbial consortia was measured in sediment slurry experiments under nearly natural conditions, with no substrate added. Experiments were conducted with a wide range of initial Se concentrations and with sediment and water from three locations with contrasting environmental settings. The products...
Categories: Publication;
Types: Citation;
Tags: Bacteria,
Selenium,
Stable isotopes,
Water contaminat
Soil organic matter (SOM) biomarker methods were utilized in this study to investigate the responses of fungi and bacteria to freeze?thaw cycles (FTCs) and to examine freeze?thaw-induced changes in SOM composition and substrate availability. Unamended, grass-amended, and lignin-amended soil samples were subject to 10 laboratory FTCs. Three SOM fractions (free lipids, bound lipids, and lignin-derived phenols) with distinct composition, stability and source were examined with chemolysis and biomarker Gas Chromatography/Mass Spectrometry methods and the soil microbial community composition was monitored by phospholipid fatty acid (PLFA) analysis. Soil microbial respiration was also measured before and during freezing...
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: Soil Biology and Biochemistry,
bacteria,
biomarkers,
bound lipids,
co2 flush,
Manure deep-pits are commonly used to store manure at confined animal feeding operations. However, previous to this study little information had been collected on the impacts of deep-pits on groundwater quality to provide science-based guidance in formulating regulations and waste management strategies that address risks to human health and the environment. Groundwater quality has been monitored since January 1999 at two hog finishing facilities in Illinois that use deep-pit systems for manure storage. Groundwater samples were collected on a monthly basis and analyzed for inorganic and bacteriological constituent concentrations. The two sites are located in areas with geologic environments representing different...
Categories: Publication;
Types: Citation;
Tags: Bacteria,
Data Visualization & Tools,
Groundwater,
Isotopes,
Landscapes,
These data show grass crop and model species response to toxic chemicals (Arsenic (As)) and humic acids. Experiments were performed by collaboration between the U.S. Geological Survey, Rutgers University, and Rey Juan Carlos University. A series of individual experiments investigated beneficial effects of endophytic bacteria on grass crop growth and resilience to known plant toxicity.
Categories: Data;
Tags: Ecology,
Genetics,
North America,
USGS Science Data Catalog (SDC),
bacteria,
Molecular methodologies were used to characterize fungal communities associated with lichen-dominated biological soil crusts (BSCs) at two sites on the Colorado Plateau (USA) in order to investigate their diversity and abundance, in relation to that of bacteria, as well as how these parameters corresponded to overall soil crust cover and the presence of anthropogenic disturbance. Fungal community diversity and composition were assessed with denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR amplified ribosomal genes and by sequencing. Quantitative PCR, specific for fungi as well as bacteria, was used to evaluate relative microbial densities. Two sites with similar soil characteristics, both of...
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: Journal of Arid Environments,
bacteria,
biological soil crust,
colorado plateau,
dgge,
Warming-induced release of CO2 from the large carbon (C) stores in arctic soils could accelerate climate change. However, declines in the response of soil respiration to warming in long-term experiments suggest that microbial activity acclimates to temperature, greatly reducing the potential for enhanced C losses. As reduced respiration rates with time could be equally caused by substrate depletion, evidence for thermal acclimation remains controversial. To overcome this problem, we carried out a cooling experiment with soils from arctic Sweden. If acclimation causes the reduction in soil respiration observed after experimental warming, then it should subsequently lead to an increase in respiration rates after cooling....
Categories: Publication;
Types: Citation,
Journal Citation;
Tags: Acclimatization,
Acclimatization: physiology,
Analysis of Variance,
Arctic Regions,
Bacteria,
Data supporting the establishment of Syntrophotalea acetylenivorans SFB93 as a new microbial species. Data release includes growth curve and preferred growth conditions for the species.
Categories: Data;
Tags: Aquatic Biology,
Environmental Health,
USGS Science Data Catalog (SDC),
Water Quality,
Water Resources,
Groundwater and surface-water samples were collected and analyzed for microbial source tracking markers to identify the primary sources of fecal bacteria at a Lake Michigan beach in Northwestern Indiana.
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