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Avian botulism toxicity is a common cause of death to water and shore birds that live near or migrate through Lake Michigan. The botulism neuro-toxin type E (bontE) gene is responsible for the production of botulinum neurotoxin type E. Quantitative Polymerase Chain Reaction (qPCR) was performed using a Step One Plus Thermocycler (Applied Biosystems) and protocol described in Getchell and others, 2011, Journal of Aquatic Animal Health. The assay was used to assess microbial community DNA obtained from environmental samples that were collected by Great Lakes Science Center and by National Park Service from 2011 to 2014 for the bontE gene. Samples were obtained by ponar grab or by divers and matrices collected...
These data were collected as part of a voluntary initiative to create a White-Nose Syndrome Diagnostic Laboratory Network among laboratories participating in research and surveillance for Pseudogymonascus destructans (Pd) - the fungal pathogen causing White-Nose Syndrome in bats. Pd_qPCR_InterlaboratoryLODdata.xlsx is raw qPCR data from multiple laboratories running serial dilutions of Pd gBlock in known concentrations for the collectively used Muller (2013) Pd qPCR assay. Pd_qPCR_InterlaboratoryResults_LOD.xlsx contains the data output for each laboratory from running a generic LOD/LOQ calculator script. the generic LOD/LOQ calculator script is available at:https://github.com/cmerkes/qPCR_LOD_Calc. Pd_qPCR_InterlaboratoryPTResults_PanelData.xlsx...
Categories: Data;
Tags: USGS Science Data Catalog (SDC),
Wildlife Disease,
biota,
health,
microbiology,
Water resources around the world are contaminated with per- and polyfluoroalkyl substances (PFAS) due to releases from point sources on military installations, fire training centers, and chemical manufacturing sites. Non-point sources have also been identified including wastewater effluent, landfills, and biosolids application. PFAS are a major concern to myriad stakeholders as some are known to bioaccumulate, they have eco-toxicity effects, and they are highly recalcitrant. PFAS are often called “forever chemicals” due to their environmental persistence but many precursor PFAS are transformed in the environment by microbes. Recent work has shown that PFAS can be biologically degraded in laboratory studies, but...
Categories: Data;
Tags: Barnstable County,
Cape Cod,
DNA sequencing,
Environmental Health,
Hydrology,
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,
Mono Lake is a hypersaline soda lake rich in dissolved inorganic arsenic with its primary production currently dominated by Picocystis str. ML. We set out to determine if this picoplankter could metabolize inorganic arsenic, and in doing so form unusual arsenolipids (e.g., methylated arsinoyl ribosides) as reported in other saline ecosystems and by halophilic algae. We cultivated Picocystis str. ML on an inorganic seawater-based medium with either low (37 µM) or high (1,000 µM) phosphate in the presence of arsenite (~0.4 mM), arsenate (~0.8 mM), or without arsenic additions.
Categories: Data;
Tags: Environmental Health,
Geochemistry,
Mono Lake,
Picocystis,
USGS Science Data Catalog (SDC),
This dataset contains data tables of laboratory quality-control data associated with environmental samples analyzed for microbiological constituents at the Ohio Water Microbiology Laboratory of the U.S. Geological Survey (USGS). The environmental samples were collected across the United States by USGS National Projects and projects in Water Science Centers. These quality-control data can be used to assess the quality of microbiological data for the associated environmental samples.
Acetylene (C2H2) is a molecule rarely found in nature, with few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs, however we hypothesized that there may be yet unrecognized diversity of acetylenotrophs in nature. In this study, we expanded this diversity by isolating an aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethene (TCE)-contaminated soils undergoing bioremediation. TCE-contaminated soils from the NASA Ames Research Center in California were used to establish soil microcosms with acetylene as the primary carbon substrate and acetylene...
This U.S. Geological Survey (USGS) data release provides a comprehensive dataset of water-quality results, physical-parameter measurements, hydrologic measurements, and site information collected to study the nature and extent of water quality along groundwater flow paths adjacent to glacial-kettle lakes on Cape Cod, Massachusetts. Water-quality samples were collected in 2003, 2005, and 2012 through 2018 in and near seven kettle lakes located on western Cape Cod, with most of the data collected in 2015-2017 from Ashumet Pond, which is located in the towns of Falmouth and Mashpee. Data were also collected at other lakes to compare the lake-specific influences of geochemistry and hydrology on the downgradient groundwater...
This study aimed to (1) enrich microbial acetylenotrophs from trichloroethylene (TCE) contaminated groundwater and (2) evaluate whether these enrichments could degrade TCE coupled to acetylene degradation. Acetylenotrophs are microorganisms that use acetylene as their carbon and energy source. TCE contaminated groundwater was collected from wells at the Naval Air Warfare Center (NAWC) in West Trenton, New Jersey. Microbial acetylene uptake in groundwater samples was established by mixing the groundwater with a defined mineral medium to supply nutrients and providing acetylene as the sole electron donor and carbon source. The structure of the microbial community in those enrichments was characterized as shown by...
Categories: Data;
Tags: Environmental Health,
Trenton West,
USGS Science Data Catalog (SDC),
Water Resources,
aquatic biology,
Oil and gas (OG) wastewaters are commonly disposed of by underground injection and previous research showed that activities at a disposal facility in West Virginia affected stream biogeochemistry and sediment microbial communities downstream from the facility. Microorganisms can control the fate and transport of organic and inorganic components of OG wastewater highlighting the need to characterize the effects of OG wastewater components on microbial activity. We conducted a series of aerobic microcosm experiments to assess the influence of high total dissolved solids (TDS) and hydraulic fracturing fluid additives (2,2-dibromo-3-nitrilopropionamide (DBNPA), a biocide, and ethylene glycol, an anti-scaling additive),...
Categories: Data;
Tags: Biochemistry,
DNA sequencing,
Energy Resources,
Environmental Health,
Fayette County,
The Permian Basin, straddling New Mexico and Texas, is one of the most productive oil and gas (OG) provinces in the United States. OG production yields large volumes of wastewater that contain elevated concentrations of major ions including salts (also referred to as brines), and trace organic and inorganic constituents. These OG wastewaters pose unknown environmental health risks, particularly in the case of accidental or intentional releases. Releases of OG wastewaters have resulted in water-quality and environmental health effects at sites in West Virginia (Akob, et al., 2016, Orem et al. 2017, Kassotis et al. 2016) and in the Williston Basin region in Montana and North Dakota (Cozzarelli et al. 2017, Cozzarelli...
This environmental dataset consists of 56 sediment, 24 Cladophora and 22 water samples collected from beaches at Glen Haven, Good Harbor, Platte Bay and Esch road beach, located within The Sleeping Bear Dunes National Lakeshore, Leelanau and Benzie counties, Michigan. The dataset includes matrix type, location, data, time and the qPCR reported value for each sample collected.
The data being released were part of a project funded by the United States Environmental Protection Agency (USEPA). This study sought to identify the planktonic communities (cyanobacteria, eukaryotic algae) potentially contributing to eutrophication within the Grand Calumet River Area of Concern (AOC) in northern Indiana along the southern shore of Lake Michigan. In 2021, triplicate water samples were collected from five locations during three events, 4/19/21 and 4/20/21, 7/7/21, and 9/15/21. Water samples were processed and planktonic communities were determined by a DNA-based technology (algal metabarcoding). Sampling locations: 1. Columbia Avenue, Hammond, IN 2. Lake George drainage ditch, Hammond, IN 3. Indiana...
Categories: Data;
Tags: Aquatic Biology,
DNA sequencing,
East Chicago, Indiana,
Ecology,
Gary, Indiana,
The U.S. Geological Survey (USGS), in cooperation with the Great Lakes Restoration Initiative, collected data in 2017 to study the sources and occurrences of continual detections of high Escherichia coli (E. coli) detections at urban beaches along the Lake Michigan shoreline in northwest Indiana and northeastern Illinois. High E. coli detections cause the beaches to be closed for recreational use until additional samples verify that E. coli levels have fallen below the threshold of 235 counts per 100 ml. The project used microbial source tracking (MST) and metagenomics analyses to evaluate the sources of E. coli. This data release provides the phytoplankton, mictobial source tracking, and metagenomics components...
The data being released were part of a project funded by the Great Lakes Restoration Initiative (GLRI). This study sought to examine the influence of filter pore size (5.0 µm pre and 0.22 µm final filtration) on microbial communities and source-specific microbial source tracking (MST) markers at three locations along southern Lake Michigan: Racine, WI; Chicago, IL; and East Chicago, IN; between 2015 and 2017. In 2015, triplicate water samples were collected during three events, in 2016 individual water samples were collected during three events, and in 2017, individual water samples were collected one day a week for ten weeks between June and August. Samples were collected from twelve locations, two river, two river...
Categories: Data;
Tags: Aquatic Biology,
Chicago,
DNA sequencing,
East Chicago,
Environmental Health,
This dataset contains data tables of laboratory quality-control data associated with environmental samples analyzed for microbiological constituents at the Ohio Water Microbiology Laboratory of the U.S. Geological Survey (USGS) during federal fiscal years 2012-2017 (October 1, 2011 through September 30, 2017). The environmental samples were collected across the United States by the USGS National Water Quality Assessment Project and other projects in Water Science Centers. The microbiological constituents include total coliforms, Escherichia coli (E. coli), enterococci, coliphage (F-specific and somatic), aerobic endospores, and actinomycetes. These quality-control data can be used to assess the quality of microbiological...
Categories: Data;
Tags: USGS Science Data Catalog (SDC),
United States of America,
bacteria,
laboratory methods,
microbiology
The U.S. Geological Survey, in cooperation with the Tennessee Department of Transportation, conducted an investigation of acid-rock drainage from road cuts in Tennessee during 2014-2015. The Devonian Chattanooga Shale contains disseminated pyrite and is a primary producer of acid-rock drainage (ARD) in Tennessee. One objective of the overall investigation was to attenuate ARD by manipulating the indigenous microbial community through different treatment injections. The scope of the study included establishing flow-through microcosms constructed with shale from the Chattanooga Shale formation rich in pyrite collected from an ARD site in Middle Tennessee. The microcosms were subjected to various treatments and evaluations...
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Hickman County,
USGS Science Data Catalog (SDC),
Williamson County,
acid-rock drainage,
geochemical processes,
The data associated with the following data release were collected between 2016 and 2017 at three locations on Lake Michigan: Racine, WI; Chicago, IL; and East Chicago, IN. Individual water samples were collected one day a week for ten weeks between June and August. Samples were collected from eight specific sites made up of two river and six shoreline type environments. Sampling was completed at sites where various morphology (embayment, sand and sediment characteristics, size and shape) and hydrologic conditions (currents and waves) were present. Then samples were analyzed using microbial communities (metagenomic analysis), markers of contamination (microbial source tracking), and fecal indicator bacteria (E....
Data were collected as part of a study to identify sources of E. coli contamination at several beaches located in the Grand Calumet River Areas of Concern, located in northern Indiana on Lake Michigan. The study was funded by the Great Lakes Restoration Initiative. Water samples were collected at each site (Jeorse Park 1, Jeorse Park 2, Hammond East, Hammond West, Whihala West, Whihala East, Whihala west breakwater, Hammond Marina, Whihala offshore locations, and the Grand Calumet River) one day a week or three times a week between 2015 and 2018. While the 2015 data were included in analysis, these data were previously publicly released https://doi.org/10.5066/F7H70F3D. Samples (water, sand, sediment) were analyzed...
A large spill of wastewater from oil and gas operations was discovered adjacent to Blacktail Creek near Williston, North Dakota in January 2015. To determine the effects of this spill on streambed microbial communities over time, bed sediment samples were taken from Blacktail Creek upstream, adjacent to, and at several locations downstream from the spill site. Blacktail Creek is a tributary of the Little Muddy River, and additional samples were taken upstream and downstream from the confluence of Blacktail Creek and the Little Muddy River. Samples were collected in February 2015, June 2015, June 2016, and June 2017. DNA was extracted from these sediments, and sequencing of the 16S ribosomal RNA gene was performed...
Categories: Data;
Tags: Aquatic Biology,
Blacktail Creek,
DNA sequencing,
Ecology,
Little Muddy River,
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