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At least 1,225 records · Page 68Linked to original sources
USGS2020

Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)

Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental, etc.). Relatively little work, however, has explored the feasibility of utilizing historical samples (e.g., museum archived samples) of varying age, quality, and preservation type. Because natural history collections span multiple decades, these biorepositories have the potential to provide fundamental historical baselines to measure and better understand biodiversity on a changing planet. Utilizing even a small proportion of museum specimens could provide a means of sampling past microbial communities, allowing for direct comparison to contemporary communities and more complete understanding of dynamic shifts through time. We examined the feasibility of obtaining 16S rRNA amplicon microbiome data from whole gastrointestinal tracts (GIs) of shrews of varying age and preservation method, including 5 freshly collected shrew GIs immediately fixed in liquid nitrogen (LN2), 10 ten-year old shrew GIs frozen at −20°C (whole animal), and 10 shrews of varying ages (4 from 1968, 1 from 1980, 1 from 2001, 1 from 2004, 1 from 2007, 1 from 2011 and 2 from 2013) fixed and stored whole in 70% ethanol. Not surprisingly, results of 16S rDNA amplicon sequencing reveal significantly different bacterial communities between different preservation techniques and age of samples. Ten-year old frozen samples had bacterial communities most similar to freshly collected (LN2) samples, while the bacterial communities of both were significantly different from the 70% ethanol preserved samples of various ages. Amongst those preserved in 70% ethanol, age of samples also influenced bacterial community composition. Additionally, we compare results of OTU based and ASV based analyses. Looking ahead, field collectors and museums should develop and adopt best practices related to frozen preservation to ensure adequate material for future microbiome investigations.

Frontiers in Ecology and Evolution↗
USGS2007

Invasive species management and research using GIS

Geographical Information Systems (GIS) are powerful tools in the field of invasive species management. GIS can be used to create potential distribution maps for all manner of taxa, including plants, animals, and diseases. GIS also performs well in the early detection and rapid assessment of invasive species. Here, we used GIS applications to investigate species richness and invasion patterns in fish in the United States (US) at the 6-digit Hydrologic Unit Code (HUC) level. We also created maps of potential spread of the cane toad (Bufo marinus) in the southeastern US at the 8-digit HUC level using regression and environmental envelope techniques. Equipped with this potential map, resource managers can target their field surveys to areas most vulnerable to invasion. Advances in GIS technology, maps, data, and many of these techniques can be found on websites such as the National Institute of Invasive Species Science (www.NIISS.org). Such websites provide a forum for data sharing and analysis that is an invaluable service to the invasive species community.

Conference Paper↗
USGS2005

A method adapting microarray technology for signature tagged mutagenesis of Dusulfovibrio dusulfuricans G20 and Shewanella oneidensis MR-1 in anaerobic sediment survival experiments

Signature-tagged mutagenesis (STM) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. To date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. We used a mini-Tn 10 transposon-bearing plasmid, pBSL180, that efficiently and randomly mutagenized Desulfovibrio desulfuricans G20 in addition to Shewanella oneidensis MR-1. Using these organisms as model sediment-dwelling anaerobic bacteria, we developed a new screening system, modified from former STM procedures, to identify genes that are critical for sediment survival. The screening system uses microarray technology to visualize tags from input and output pools, allowing us to identify those lost during sediment incubations. While the majority of data on survival genes identified will be presented in future papers, we report here on chemotaxis-related genes identified by our STM method in both bacteria in order to validate our method. This system may be applicable to the study of numerous environmental bacteria, allowing us to identify functions and roles of survival genes in various habitats.

Applied and Environmental Microbiology↗
USGS2025

Scaling from microsite to landscape to resolve litter decomposition dynamics in globally extensive drylands

1. Decomposition controls the release of carbon and nutrients from decaying plant litter into soils or the atmosphere. In most biomes decomposition rates can be accurately predicted with simple mathematical models, but these models have long under-predicted decomposition in globally- extensive drylands. 2. We posit that the exposed surface conditions characteristic of drylands makes litter decomposition uniquely subject to microsite-specific environmental controls and spatially-variable microbial communities. As such, decomposition in dryland ecosystems – which are characterized by extremes in temporal heterogeneity of climate conditions and spatial heterogeneity of vegetation cover with corresponding microclimate variability – is a prime example of a macrosystems process that can be addressed by merging field data with new predictive models operating across a hierarchical continuum of spatial scales and process resolutions. 3. A macrosystems approach offers promise to reconcile model-measurement discrepancies by integrating observations and experiments across multiple scales, from microsites (e.g., shrub sub-canopy or intercanopy) to regions (e.g., across a 100s of km2 study site with complex topography, precipitation, and temperature) and ultimately to a continental perspective (e.g., North American drylands). 4. Recent developments in technology and data availability position the scientific community to integrate lab, field, modeling, and remote sensing approaches across a hierarchical range of scales to capture the spatiotemporal distribution of litter and environmental conditions needed to predict decay dynamics at the micro-to-macroscale. This multi-scale approach promises a path forward to resolving a longstanding disconnect between measured and modeled data in dryland litter decomposition. 5. Dryland litter decomposition presents an excellent case study for resolving spatially and temporally complex biogeochemical dynamics through a hierarchical, multidisciplinary macrosystems approach. 6. We focus on dryland litter decomposition, but the hierarchical, multidisciplinary macrosystems approach we outline shows great potential for resolving other spatially and temporally complex biogeochemical processes across a wide range of ecosystems.

Functional Ecology↗
USGS2024

Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind. To that end, EEB is developing new tools to analyze the massive, complex, transdisciplinary datasets that result from such studies. The American Society for Microbiology’s Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the trajectory of EEB both within the Society and microbiology at large. Retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The retreat repeatedly emphasized that the future of science is through transdisciplinary collaborations that promote integration of diverse datasets and advanced technologies, while also genuinely fostering inclusivity, global collaborations, and public engagement. The American Society for Microbiology and EEB stand poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.

mSphere↗
USGS1976

ERTS-1, a new window on our planet

The launch, on July 23, 1972, of the first Earth Resources Technology Satellite (ERTS-1) by the National Aeronautics and Space Administration was a major step forward in extending man 's ability to inventory the Earth 's resources and to evaluate objectively his impact upon the environment. ERTS spacecraft represent the first step in merging space and remote-sensing technologies into a system for inventorying and managing the Earth 's resources. Examples presented in this book demonstrate ERTS ' vast potential for inventorying resources, monitoring environmental conditions, and measuring changes. Such information is essential for the full evaluation of the Federal lands and determining their future use, as well as for improved planning of overall land use throughout the United States and the world. Ten bureaus of the U.S. Department of Interior have roles in the ERTS project. Nearly all of these participating bureaus are represented in almost 100 papers included in this book. Chapter 3 is entitled ' Applications to Water Resources ' and contains 23 separate sections. (Woodard-USGS)

Professional Paper↗
USGS1999

Specimen collection and preservation

Specimens are used to provide supporting information leading to the diagnosis of a cause of disease or death. A specimen may be an intact carcass, tissues removed from carcasses, parasites, ingested food, feces, or environmental samples. The specimen should be as fresh and undamaged as possible.

Information and Technology Report↗
USGS2012

Competing risks and the development of adaptive management plans for water resources: Field reconnaissance investigation of risks to fishes and other aquatic biota exposed to endocrine disrupting chemicals (edcs) in lake mead, Nevada USA

The analysis and characterization of competing risks for water resources rely on a wide spectrum of tools to evaluate hazards and risks associated with their management. For example, waters of the lower Colorado River stored in reservoirs such as Lake Mead present a wide range of competing risks related to water quantity and water quality. These risks are often interdependent and complicated by competing uses of source waters for sustaining biological resources and for supporting a range of agricultural, municipal, recreational, and industrial uses. USGS is currently conducting a series of interdisciplinary case-studies on water quality of Lake Mead and its source waters. In this case-study we examine selected constituents potentially entering the Lake Mead system, particularly endocrine disrupting chemicals (EDCs). Worldwide, a number of environmental EDCs have been identified that affect reproduction, development, and adaptive behaviors in a wide range of organisms. Many EDCs are minimally affected by current treatment technologies and occur in treated sewage effluents. Several EDCs have been detected in Lake Mead, and several substances have been identified that are of concern because of potential impacts to the aquatic biota, including the sport fishery of Lake Mead and endangered razorback suckers (Xyrauchen texanus) that occur in the Colorado River system. For example, altered biomarkers relevant to reproduction and thyroid function in fishes have been observed and may be predictive of impaired metabolism and development. Few studies, however, have addressed whether such EDC-induced responses observed in the field have an ecologically significant effect on the reproductive success of fishes. To identify potential linkages between EDCs and species of management concern, the risk analysis and characterization in this reconnaissance study focused on effects (and attendant uncertainties) that might be expressed by exposed populations. In addition, risk reduction measures that may be of interest to resource managers are considered relative to emerging contaminants in treated effluents, interdependencies among biological resources at risk, and uses of reservoir waters derived from multiple inflows of widely varying qualities. ??2009 ASCE.

Nevada↗
USGS2020

Surficial geochemistry and bioaccessibility of tellurium in semi-arid mine tailings

Tellurium (Te) is a critical element due to its use in solar technology. However, some forms are highly toxic. Few studies have examined Te behavior in the surficial environment, thus little is known about its potential human and environmental health impacts. This study characterizes two physicochemically distinct Te-enriched mine tailings piles (big and flat tailings) deposited by historic gold (Au) mining in the semi-arid Delamar mining district, Nevada. The big tailings are characterized by smaller particle size and higher concentrations of potentially toxic elements (up to 290 mg Te kg-1), which are enriched at the tailings surface. In contrast, the flat tailings have larger particle size and properties that are relatively invariant with depth. Based on the sulfate to sulfide ratio, the tailings were determined to be sulfate dominated suggesting a high degree of weathering, although the flat tailings did contain significant amounts of sulfides (~40%). Tellurium x-ray absorption spectroscopy of the big tailings indicates that tellurate, the less toxic Te species, is the principal form of Te. Electron microscopy indicates that most of the Te present at the site is associated with iron (oxy)hydroxides, sometimes with other potentially toxic elements, especially lead and antimony. Physiologically-based extraction tests indicate that substantially more Te is solubilized in synthetic stomach fluids than in lung fluids, with gastric bioaccessibility ranging from 13-31% of total Te. This points to low to medium bioaccessibility, which is common for iron (oxy)hydroxide associated elements. Together, these results represent a preliminary assessment of Te surficial behavior in a semi-arid environment and indicate that Te in these tailings represent a moderate health concern.

Environmental Chemistry↗
USGS2011

A model for estimating passive integrated transponder (PIT) tag antenna efficiencies for interval-specific emigration rates

Our goal was to understand movement and its interaction with survival for populations of stream salmonids at long-term study sites in the northeastern United States by employing passive integrated transponder (PIT) tags and associated technology. Although our PIT tag antenna arrays spanned the stream channel (at most flows) and were continuously operated, we are aware that aspects of fish behavior, environmental characteristics, and electronic limitations influenced our ability to detect 100% of the emigration from our stream site. Therefore, we required antenna efficiency estimates to adjust observed emigration rates. We obtained such estimates by testing a full-scale physical model of our PIT tag antenna array in a laboratory setting. From the physical model, we developed a statistical model that we used to predict efficiency in the field. The factors most important for predicting efficiency were external radio frequency signal and tag type. For most sampling intervals, there was concordance between the predicted and observed efficiencies, which allowed us to estimate the true emigration rate for our field populations of tagged salmonids. One caveat is that the model's utility may depend on its ability to characterize external radio frequency signals accurately. Another important consideration is the trade-off between the volume of data necessary to model efficiency accurately and the difficulty of storing and manipulating large amounts of data.

Transactions of the American Fisheries Society↗
USGS2025

Environmental DNA monitoring of invasive Central American boas in St. Croix at Salt River Bay National Historical Park and Ecological Preserve (SARI)

Invasive Central American boas ( Boa imperator ) have established a reproducing population on the western side of St. Croix, U.S. Virgin Islands but prevalence throughout the island is largely unknown. The large snakes threaten endemic and endangered species through competition and predation, jeopardizing island biodiversity. Environmental DNA (eDNA) methods were used to investigate occurrence and focal areas for management efforts in the Salt River Bay National Historical Park and Ecological Preserve (SARI). To validate a previously developed assay, we collected tissue samples and 13 × 60 mL water samples from a captive boa enclosure in St. Croix. We implemented this assay for both a pilot and main field sampling effort. The pilot in December 2023 resulted in analysis of 7 × 60 mL water samples per site from SARI (3 sites) and from the western forests where boas are established (1 site). The main sampling event in July 2024 collected 15 × 60 mL water samples per site within SARI (11 sites) and western forests (4 sites). Pilot sample replicates were filtered individually, while main samples were consolidated into groups, resulting in seven replicates for pilot sites and five replicates for main event sites, totaling 103 environmental samples. eDNA was isolated using a modified phenol-chloroform isolation method to remove PCR inhibitors, and target eDNA was amplified using droplet digital PCR technology. Water samples from the captive boa amplified target eDNA in 12 of 13 samples, indicating assay effectiveness ex-situ. Low concentrations of eDNA (below the 95% limit of detection) were amplified in 4 of 5 sites in the western forest and in 8 of 14 sites within the National Historic Park. Overall, boa eDNA concentrations were consistently low, as expected in water samples targeting a semi-arboreal snake species with a low rate of eDNA shedding. Further optimization of methods could enable recovery of greater eDNA concentrations in future studies. Additional eDNA method testing and ground-truthing may help to improve the assessment of invasive Boa imperator in St. Croix.

Science Report↗
USGS2011

U.S. Department of Energy's regional carbon sequestration partnership initiative: Update on validation and development phases

The U.S. Department of Energy (DOE) is the lead federal agency for the development and deployment of carbon sequestration technologies. The Regional Carbon Sequestration Partnerships (RCSPs) are the mechanism DOE utilizes to prove the technology and to develop human capital, stakeholder networks, information for regulatory policy, best practices documents and training to work toward the commercialization of carbon capture and storage (CCS). The RCSPs are tasked with determining the most suitable technologies, regulations, and infrastructure for carbon capture, transport, and storage in their respective geographic areas of responsibility. The seven partnerships include more than 400 state agencies, universities, national laboratories, private companies, and environmental organizations, spanning 43 states and four Canadian provinces. The Regional Partnerships Initiative is being implemented in three phases: Characterization, Validation, and Development. The initial Characterization Phase began in 2003 and was completed in 2005 and focused on characterization of CO2 storage potential within each region. It was followed by the Validation Phase, which began in 2005 and is nearing completion in 2011. The focus of the Validation Phase has been on small-scale field tests throughout the seven partnerships in various formation types such as saline, oil-bearing, and coal seams. The Validation Phase has characterized suitable CO2 storage reservoirs and identified the need for comprehensive legal and regulatory frameworks to enable commercial-scale CCS deployment. Finally, the Development Phase will consist of a series of large-scale, one-million-ton, injection tests throughout the United States and Canada. The objective of these large-scale tests is to identify the regulatory path or challenges in permitting CCS projects, to demonstrate the technology can inject CO2 safely, and to verify its permanence in geologic formations in preparation for the commercialization of geologic sequestration. ?? 2010 Elsevier Ltd. All rights reserved. ?? 2011 Published by Elsevier Ltd.

Conference Paper↗
USGS2025

Sapsucker wells as a keystone nutritional resource: Evaluating methods for detection of secondary sap consumers

North American sapsuckers are considered double keystone species because they (1) excavate nest cavities that are used by other birds, small mammals, and invertebrates, and (2) create and maintain sap wells, a temporary nutritional resource available to a variety of secondary consumers. Most previous reports of secondary sap consumption relied on human observers and were based on either brief or incidental observations. However, modern technology can greatly enhance observational techniques and provide additional insights into the functional, community-level importance of sap wells. We used visual surveys, camera traps, and environmental DNA (eDNA) to identify secondary consumers of sap from wells created by red-naped ( Sphyrapicus nuchalis ) and Williamson's ( S. thyroideus ) sapsuckers among three functional groups of shrubs and trees in south-central Colorado: shrub willows ( Salix spp.), Rocky Mountain maple ( Acer glabrum ), and conifer trees (Pinopsida). Camera traps and eDNA revealed additional sap-well visitors not identified from direct observations. Camera traps were effective for detecting nocturnal sap-well visitors such as small rodents as well as occasional diurnal visitors. Environmental DNA analyses corroborated findings from other methods and identified four additional taxa as possible sap consumers. The physiology of sap-well visitors, such as the ability to taste and assimilate compounds within sap, may aid in determining consumption versus contact when evaluating the results of eDNA analyses. Total vertebrate taxa detected using all 3 methods included 17 bird taxa in 10 families within 3 orders and 8 mammal taxa in 6 families within 4 orders. Shrub-willow sap wells attracted the most diverse vertebrate taxa (23), followed by Rocky Mountain maple (13) and conifer trees (10). Invertebrates in 13 families within 3 orders were observed feeding from sap wells during visual surveys. Because many secondary sap consumers perform ecological services such as pollination, seed dispersal, and pest control, the methods described here may aid in elucidating the importance of sap-well creators in supporting biodiversity and ecosystem functioning.

Colorado↗
USGS2004

Uranium mill tailings: Nuclear waste and natural laboratory for geochemical and radioecological investigations

Uranium mill tailings (UMT) are a high volume, low specific activity radioactive waste typically disposed in surface impoundments. This review focuses on research on UMT and related earth materials during the past decade relevant to the assessment of: (1) mineral hosts of radionuclides; (2) the use of soil analogs in predicting long-term fate of radionuclides; (3) microbial and diagenetic processes that may alter radionuclide mobility in the surficial environment; (4) waste-management technologies to limit radionuclide migration; and (5) the impact of UMT on biota.

Journal of Environmental Radioactivity↗
USGS2025

A critical perspective on the Society of Environmental Toxicology and Chemistry’s adherence to founding principles—Opportunities for the future

The Society of Environmental Toxicology and Chemistry (SETAC) is a global organization whose mission is the advancement of environmental science and the promotion of science-informed decision making. On SETAC’s 45th anniversary, the following question was raised: Are the 1979 founding principles of SETAC, multidisciplinary approaches to solving environmental problems, multisector engagement and scientific objectivity, still relevant to the fulfillment of its mission? In a special session held at the 45th Annual Meeting in Fort Worth, Texas, U.S., a critical evaluation of the founding principles was initiated by reviewing SETAC’s history and ongoing activities, and recommendations were made for the future. With few exceptions, participants appreciated SETAC’s purposeful efforts to approach challenging environmental issues through multisector balance, an approach that is unique amongst scientific societies. We recognized that scientists have biases and views of what they find important, regardless of employing organization, and that objectivity is best served by being aware of these biases and views. SETAC’s founding principles have stood the test of time and continue to provide a strong foundation for the Society’s mission, and with a few suggested improvements, will continue to be instrumental in guiding environmental science, stewardship and policy into the future. The significance of SETAC’s contribution of robust science grounded in reliable evidence and data was recognized as being especially crucial at this time of triple planetary crisis (climate change, pollution and biodiversity loss), compounded by rapid technological developments and geopolitical issues.

Environmental Toxicology and Chemistry↗
USGS2009

U.S. Department of Energy's Regional Carbon Sequestration Partnership Program: Overview

The U.S. Department of Energy (DOE) has formed a nationwide network of seven regional partnerships to help determine the best approaches for capturing and permanently storing gases that can contribute to global climate change. The Regional Carbon Sequestration Partnerships (RCSPs) are tasked with determining the most suitable technologies, regulations, and infrastructure for carbon capture, transport, and storage in their areas of the country and parts of Canada. The seven partnerships include more than 350 state agencies, universities, national laboratories, private companies, and environmental organizations, spanning 42 states, two Indian nations, and four Canadian provinces. The Regional Partnerships initiative is being implemented in three phases: ???Characterization Phase (2003-2005): The objective was to collect data on CO 2 sources and sinks and develop the human capital to support and enable future carbon sequestration field tests and deployments. The completion of this Phase was marked by release of the Carbon Sequestration Atlas of the United States and Canada-Version 1 which included a common methodology for capacity assessment and reported over 3,000GT of storage capacity in saline formations, depleted oil and gas fields, and coal seams.???Validation Phase (2005-2009): The objective is to plan and implement small-scale (<1??million tons CO 2 ) field testing of storage technologies in areas determined to be favorable for carbon storage. The partnerships are currently conducting over 20 small-scale geologic field tests and 11 terrestrial field tests.???Development Phase (2008-2018): The primary objective is the development of large-scale (>1??million tons of CO 2 ) Carbon Capture and Storage (CCS) projects, which will demonstrate that large volumes of CO 2 can be injected safely, permanently, and economically into geologic formations representative of large storage capacity. Even though the RCSP Program is being implemented in three phases, it should be viewed as an integrated whole, with many of the goals and objectives transitioning from one phase to the next. Accomplishments and results from the Characterization Phase have helped to refine goals and activities in the Validation and Deployment Phases. The RCSP Program encourages and requires open information sharing among its members by sponsoring both general workshops and meetings to facilitate information exchange. Although each RCSP has its own objectives and field tests, mutual cooperation has been an important part of the Program thus far. The primary goal of the RCSP initiative is to promote the development of a regional framework and the infrastructure necessary to validate and deploy carbon sequestration technologies within each Partnership's region. ?? 2009 Elsevier Ltd. All rights reserved.

Conference Paper↗
USGS1979

Geochemical surveys in the United States in relation to health.

Geochemical surveys in relation to health may be classified as having one, two or three dimensions. One-dimensional surveys examine relations between concentrations of elements such as Pb in soils and other media and burdens of the same elements in humans, at a given time. The spatial distributions of element concentrations are not investigated. The primary objective of two-dimensional surveys is to map the distributions of element concentrations, commonly according to stratified random sampling designs based on either conceptual landscape units or artificial sampling strata, but systematic sampling intervals have also been used. Political units have defined sample areas that coincide with the units used to accumulate epidemiological data. Element concentrations affected by point sources have also been mapped. Background values, location of natural or technological anomalies and the geographic scale of variation for several elements often are determined. Three-dimensional surveys result when two-dimensional surveys are repeated to detect environmental changes. -Author

Philosophical Transactions of the Royal Society B:↗
USGS2016

Water data to answer urgent water policy questions: Monitoring design, available data, and filling data gaps for determining whether shale gas development activities contaminate surface water or groundwater in the Susquehanna River Basin

Throughout its history, the United States has made major investments in assessing natural resources, such as soils, timber, oil and gas, and water. These investments allow policy makers, the private sector and the American public to make informed decisions about cultivating, harvesting or conserving these resources to maximize their value for public welfare, environmental conservation and the economy. As policy issues evolve, new priorities and challenges arise for natural resource assessment, and new approaches to monitoring are needed. For example, new technologies for oil and gas development or alternative energy sources may present new risks for water resources both above and below ground. There is a need to evaluate whether today’s water monitoring programs are generating the information needed to answer questions surrounding these new policy priorities. The Northeast-Midwest Institute (NEMWI), in cooperation with the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program, initiated this project to explore the types and amounts of water data needed to address water-quality related policy questions of critical concern to today’s policy makers and whether those data are currently available. The collaborating entities identified two urgent water policy questions and conducted case studies in the Northeast-Midwest region to determine the water data needed, water data available, and the best ways to fill the data gaps relative to those questions. This report details the output from one case study and focuses on the Susquehanna River Basin, a data-rich area expected to be a best-case scenario in terms of water data availability.

Maryland, New York, Pennsylvania↗