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USGS2023

Isothermal recombinant polymerase amplification and CRIPSR (CAS12A) assay detection of Renibacterium salmoninarum as an example for wildlife pathogen detection in environmental DNA samples

Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon ( Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum , is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20–40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.

Journal of Wildlife Diseases↗

USGS2012

A standard operating procedure for the surgical implantation of transmitters in juvenile salmonids

Biotelemetry is a useful tool to monitor the movements of animals and is widely applied in fisheries research. Radio or acoustic technology can be used, depending on the study design and the environmental conditions in the study area. A broad definition of telemetry also includes the use of Passive Integrated Transponder (PIT) tags, either separately or with a radio or acoustic transmitter. To use telemetry, fish must be equipped with a transmitter. Although there are several attachment procedures available, surgical implantation of transmitters in the abdominal cavity is recognized as the best technique for long-term telemetry studies in general (Stasko and Pincock, 1977; Winter, 1996; Jepsen, 2003), and specifically for juvenile salmonids, Oncorhynchus spp. (Adams and others, 1998a, 1998b; Martinelli and others, 1998; Hall and others, 2009). Studies that use telemetry assume that the processes by which the animals are captured, handled, and tagged, as well as the act of carrying the transmitter, will have minimal effect on their behavior and performance. This assumption, commonly stated as a lack of transmitter effects, must be valid if telemetry studies are to describe accurately the movements and behavior of an entire population of interest, rather than the subset of that population that carries transmitters. This document describes a standard operating procedure (SOP) for surgical implantation of radio or acoustic transmitters in juvenile salmonids. The procedures were developed from a broad base of published information, laboratory experiments, and practical experience in tagging thousands of fish for numerous studies of juvenile salmon movements near Columbia River and Snake River hydroelectric dams. Staff from the Western Fisheries Research Center's Columbia River Research Laboratory (CRRL) frequently have used telemetry studies to evaluate new structures or operations at hydroelectric dams in the Columbia River Basin, and these evaluations typically require large numbers of tagged fish. For example, a study conducted at the dams on the Columbia River and funded by the U.S. Army Corps of Engineers required tagging and monitoring of 40,000 juvenile salmon during a 3-month migration period (Counihan and others, 2006a, 2006b; Perry and others, 2006). To meet the demands of such a large study, the authors and CRRL staff refined the SOP to increase efficiency in the tagging process while maintaining high standards of fish care. The SOP has been used in laboratory and field settings for more than 15 years, and consistently has produced low mortality rates (<1 percent) and transmitter loss rates (<0.01 percent) in the 24-36 hours after tagging. In addition to describing the detailed surgical procedures required for transmitter implantation, this document provides guidance on fish collection, handling and holding, and the release of tagged fish. Although often overlooked, or at least underemphasized, these processes can have a large impact on the outcome of the tagging procedure. Stress associated with the individual steps in handling and tagging can be cumulative and lethal (Maule and others, 1988; Wedemeyer and others, 1990; Portz and others, 2006), so the goal is to provide the best possible fish care at every step in order to manage the overall effect on study fish.

Open-File Report↗

USGS2007

Natural bitumen and extra-heavy oil

Since 2005, oil price increases have greatly increased investment in the production of extra- heavy oil and natural bitumen (tar sands or oil sands) to supplement conventional oil supplies. These oils are characterised by their high viscosity, high density (low API gravity), and high concentrations of nitrogen, oxygen, sulphur, and heavy metals. Extra-heavy oil and natural bitumen are the remnants of very large volumes of conventional oils that have been generated and subsequently degraded, principally by bacterial action. Chemically and texturally, they resemble the residuum produced by refinery distillation of light oil. Although these viscous oils are much more costly to extract, transport and refine than conventional oils, production levels have increased to more than 1.6 million barrels per day, or just under 2% of world crude oil production. The resource base of extra-heavy oil and natural bitumen is immense and can easily support a substantial expansion in production. This resource base can make a major contribution to oil supply, if it can be extracted and transformed into useable refinery feedstock at sufficiently high rates and at costs that are competitive with alternative resources. Technology must continue to be developed to address emerging challenges (both environmental and economic) in the market supply chain.

Book chapter↗

USGS1988

Environmental impacts and regulatory policy. Implications of spray disposal of dredged material in Louisiana wetlands

The capabilities of a new wetland dredging technology were assessed along with associated newly developed state and federal regulatory policies to determine if policy expectations realistically match the technological achievement. Current regulatory practices require amelioration of spoil bank impacts upon abandonment of an oil/gas well, but this may not occur for many years or decades, if at all. Recently, a dreding method (high-pressure spray spoil disposal) was developed that does not create a spoil bank in the traditional sense. Its potential for reducing environmental impacts was recognized immediately by regulatory agencies for whom minimizing spoil bank impacts is a major concern. The use of high-pressure spray disposal as a suitable alternative to traditional dreding technology has been adopted as policy even though its value as a management tool has never been tested or verified. A qualitative evaluation at two spoil disposal sites in saline marsh indicates that high-pressure spray disposal may indeed have great potential to minimize impacts, but most of this potential remains unverified. Also, some aspects of current regulatory policy may be based on unrealistic expectations as to the ability of this new technology to minimize or eliminate spoil bank impacts.

Louisiana↗

USGS2013

The environmental-data automated track annotation (Env-DATA) system: linking animal tracks with environmental data

The movement of animals is strongly influenced by external factors in their surrounding environment such as weather, habitat types, and human land use. With advances in positioning and sensor technologies, it is now possible to capture animal locations at high spatial and temporal granularities. Likewise, scientists have an increasing access to large volumes of environmental data. Environmental data are heterogeneous in source and format, and are usually obtained at different spatiotemporal scales than movement data. Indeed, there remain scientific and technical challenges in developing linkages between the growing collections of animal movement data and the large repositories of heterogeneous remote sensing observations, as well as in the developments of new statistical and computational methods for the analysis of movement in its environmental context. These challenges include retrieval, indexing, efficient storage, data integration, and analytical techniques.

Movement Ecology↗

USGS2006

The Amphibian Research and Monitoring Initiative (ARMI): 5-year report

The Amphibian Research and Monitoring Initiative (ARMI) is an innovative, multidisciplinary program that began in 2000 in response to a congressional directive for the Department of the Interior to address the issue of amphibian declines in the United States. ARMI’s formulation was cross-disciplinary, integrating U.S. Geological Survey scientists from Biology, Water, and Geography to develop a course of action (Corn and others, 2005a). The result has been an effective program with diverse, yet complementary, expertise. ARMI’s approach to research and monitoring is multiscale. Detailed investigations focus on a few species at selected local sites throughout the country; monitoring addresses a larger number of species over broader areas (typically, National Parks and National Wildlife Refuges); and inventories to document species occurrence are conducted more extensively across the landscape. Where monitoring is conducted, the emphasis is on an ability to draw statistically defensible conclusions about the status of amphibians. To achieve this objective, ARMI has instituted a monitoring response variable that has nationwide applicability. At research sites, ARMI focuses on studying species/environment interactions, determining causes of observed declines, and developing new techniques to sample populations and analyze data. Results from activities at all scales are provided to scientists, land managers, and policymakers, as appropriate. The ARMI program and the scientists involved contribute significantly to understanding amphibian declines at local, regional, national, and international levels. Within National Parks and National Wildlife Refuges, findings help land managers make decisions applicable to amphibian conservation. For example, the National Park Service (NPS) selected amphibians as a vital sign for several of their monitoring networks, and ARMI scientists provide information and assistance in developing monitoring methods for this NPS effort. At the national level, ARMI has had major exposure at a variety of meetings, including a dedicated symposium at the 2004 joint meetings of the Herpetologists’ League, the American Society of Ichthyologists and Herpetologists, and the Society for the Study of Amphibians and Reptiles. Several principal investigators have brought international exposure to ARMI through venues such as the World Congress of Herpetology in South Africa in 2005 (invited presentation by Dr. Gary Fellers), the Global Amphibian Summit, sponsored by the International Union for Conservation of Nature (IUCN) and Wildlife Conservation International, in Washington, D.C., 2005 (invited participation by Dr. P.S. Corn), and a special issue of the international herpetological journal Alytes focused on ARMI in 2004 (edited by Dr. C.K. Dodd, Jr.). ARMI research and monitoring efforts have addressed at least 7 of the 21 Threatened and Endangered Species listed by the U.S. Fish and Wildlife Service (California red-legged frog [Rana draytonii], Chiricahua leopard frog [R. chiricahuensis], arroyo toad [Bufo californicus], dusky gopher frog [Rana sevosa], mountain yellow-legged frog [R. muscosa], flatwoods salamander [Ambystoma cingulatum], and the golden coqui [Eleutherodactylus jasperi]), and 9 additional species of concern recognized by the IUCN. ARMI investigations have addressed time-sensitive research, such as emerging infectious diseases and effects on amphibians related to natural disasters like wildfire, hurricanes, and debris flows, and the effects of more constant, environmental change, like urban expansion, road development, and the use of pesticides. Over the last 5 years, ARMI has partnered with an extensive list of government, academic, and private entities. These partnerships have been fruitful and have assisted ARMI in developing new field protocols and analytic tools, in using and refining emerging technologies to improve accuracy and efficiency of data handling, in conducting amphibian disease, malformation, and environmental effects research, and in implementing a network of monitoring and research sites. Accomplishments from these endeavors include more than 40 publications on amphibian status and trends, nearly 100 publications on amphibian ecology and causes of declines, and over 30 methodological publications. Several databases have emerged as a result of ARMI and its partnerships; one, a digital atlas of ranges for all U.S. amphibian species, was used by the IUCN to display amphibian distribution maps in the Global Amphibian Assessment Project. Given the scope of ARMI and the panoply of projects, findings have had implications for policy. Investigations that demonstrate amphibian declines or illuminate causes of declines provide valuable information about habitat management, environmental effects, mechanisms for the spread of disease, and human/amphibian interfaces. This information has been made available to land managers, scientists, educators, Congress and other policymakers, and the public. The support afforded ARMI by Congress has been influential in the program’s development and success. The value of ARMI’s efforts will continue to increase as we are able to extend our studies spatially and temporally to answer critical questions with more confidence. We are using ARMI’s resources efficiently and continuing to develop innovative mechanisms for leveraging resources for maximum effectiveness during challenging financial times. This report is a 5-year retrospective of the structure, methodology, progress, and contributions to the broader scientific community that have resulted from this national USGS program. We evaluate ARMI’s success to date, with regard to the challenges faced by the program and the strengths that have emerged. We chart objectives for the next 5 years that build on current accomplishments, highlight areas meriting further research, and direct efforts to overcome existing weaknesses.

Scientific Investigations Report↗

USGS2024

Integrated science for the study of microplastics in the environment—A strategic science vision for the U.S. Geological Survey

Executive Summary Evidence of the widespread occurrence of microplastics throughout our environment and exposure to humans and other organisms over the past decade has led to questions about the possibility of health hazards and mitigation of exposures. This document discusses nanoplastics as well as microplastics (referred to solely as microplastics); the microplastics have a range from 1 micrometer to 5 millimeters (1 μm–5 mm) in length, whereas the nanoplastics are less than 1 μm in length (sidebar ES1). A myriad of environmental exposure pathways with microplastics to humans and wildlife, including ingestion, inhalation, and bodily absorption, are likely to exist. A growing body of evidence has documented bioaccumulation of microplastics in tissues and organs of humans and wildlife, benthic community effects, and potential nutritional and reproductive effects in some wildlife species. Understanding if or when environmental exposures pose a health risk is complicated by the diversity of microplastic sizes, morphologies, polymer types, and chemicals added during manufacturing or sorbed from the environment; ongoing challenges in analytical methods used to detect, quantify, and characterize microplastics and associated chemicals in our ecosystems; and the fact that ecotoxicological studies regarding microplastics are still in their infancy. Therefore, the study of environmental exposures and potential related health hazards of microplastics to the public and wildlife is a One Health (sidebar ES2) research topic that necessitates integrated science approaches. A better understanding of the sources, pathways, fate, and biological effects of microplastics has become a priority of the Federal Government, State governments, Tribes, stakeholders, and the public. Examples of Federal and State microplasticfocused legislation and programs to prioritize microplastic research and reduction include the Federal Microbead-Free Waters Act of 2015, California Senate Bills 1422 and 1263 (2018), the U.S. Environmental Protection Agency (EPA) Trash Free Waters Program, the National Institute of Standards and Technology’s Microplastic and Nanoplastic Metrology project, and Minnesota’s microplastic project. With its unique expertise and capabilities, the U.S. Geological Survey (USGS) is well positioned to help fill some of the most important microplastic science gaps. This strategic science vision document for microplastics identifies current (2023) microplastic science gaps and prioritizes research relevant to the mission, expertise, and capabilities of the USGS. It is intended for USGS scientists and stakeholders to use as a starting point for planning, prioritizing, and designing collaborative environmental microplastic science. Many of the microplastic science gaps and priorities are scalable, from local to national, and thus, can be made commensurate with available funding and evolving analytical and field tools, laboratory capacity, and stakeholder needs. Current (2023) or future research by academia and other Federal or State agencies, and Tribes may be aimed at some of the same microplastic science gaps identified in this document. Therefore, this document can be used as an information resource to maximize strengths and capabilities and minimize redundancy in communication and collaboration.

Circular↗

USGS1998

North American landscape characterization project: The production of a continental scale three-decade Landsat data set

The North American Landscape Characterization (NALC) project is a component of the National Aeronautics and Space Administration (NASA) Landsat Pathfinder program. Pathfinder projects are focused on the investigation of global change utilizing current remote sensing technologies. The NALC project is a cooperative effort between the U. S. Environmental Protection Agency (EPA), the U.S. Geological Survey (USGS), and NASA to make Landsat data available to the widest possible user community for scientific research and general public interest. The NALC project is principally funded by the EPA Office of Research and Development and the USGS's Earth Resources Observation Systems (EROS) Data Center (EDC). The objectives of the NALC project are to produce standardized remote sensing data sets, develop standardized analysis methods, and derive standardized land cover change products for a large portion of the North American continent (the conterminous United States and Mexico) (Lunetta and Sturdevant, 1993). The standard product is the NALC “triplicate”;, consisting of co‐registered Landsat multispectral scanner data for the years 1973, 1986, and 1991 (plus or minus one year), plus co‐registered 3 arcsecond digital terrain elevation data. Processing began with the 1986 scene, which was precision corrected (with full terrain correction) to a 60 meter Universal Transverse Mercator base. Automated cross‐correlation procedures were used to co‐register the 1970's and 1990's data to the 1980's base, and independent verifications of registration quality were performed on all triplicate components. The pertinent metadata were compiled in a relational database, which includes WRS2 path/rows, scene ID's, image dates, solar azimuth and elevation, verification RMSE's, and the number of verification control points. NALC triplicate data sets are being used for a number of applications, including the analysis of urbanization patterns, dynamics of climatic fluctuations, deforestation studies, and vegetation classification and mapping. These data are being distributed through the Earth Observing System Data and Information System (EOSDIS) Information Management System (IMS) at a cost of $15(U.S.) for each triplicate.

Geocarto International↗

USGS2017

Cobalt

Cobalt is a silvery gray metal that has diverse uses based on certain key properties, including ferromagnetism, hardness and wear-resistance when alloyed with other metals, low thermal and electrical conductivity, high melting point, multiple valences, and production of intense blue colors when combined with silica. Cobalt is used mostly in cathodes in rechargeable batteries and in superalloys for turbine engines in jet aircraft. Annual global cobalt consumption was approximately 75,000 metric tons in 2011; China, Japan, and the United States (in order of consumption amount) were the top three cobalt-consuming countries. In 2011, approximately 109,000 metric tons of recoverable cobalt was produced in ores, concentrates, and intermediate products from cobalt, copper, nickel, platinum-group-element (PGE), and zinc operations. The Democratic Republic of the Congo (Congo [Kinshasa]) was the principal source of mined cobalt globally (55 percent). The United States produced a negligible amount of byproduct cobalt as an intermediate product from a PGE mining and refining operation in southeastern Montana; no U.S. production was from mines in which cobalt was the principal commodity. China was the leading refiner of cobalt, and much of its production came from cobalt ores, concentrates, and partially refined materials imported from Congo (Kinshasa). The mineralogy of cobalt deposits is diverse and includes both primary (hypogene) and secondary (supergene) phases. Principal terrestrial (land-based) deposit types, which represent most of world’s cobalt mine production, include primary magmatic Ni-Cu(-Co-PGE) sulfides, primary and secondary stratiform sediment-hosted Cu-Co sulfides and oxides, and secondary Ni-Co laterites. Seven additional terrestrial deposit types are described in this chapter. The total terrestrial cobalt resource (reserves plus other resources) plus past production, where available, is calculated to be 25.5 million metric tons. Additional resources of cobalt are known to occur on the modern sea floor in aerially extensive deposits of Fe-Mn(-Ni-Cu-Co-Mo) nodules and Fe-Mn(-Co-Mo-rare-earth-element) crusts. Legal, economic, and technological barriers have prevented exploitation of these cobalt resources, which lie at water depths of as great as 6,000 meters, although advances in technology may soon allow production of these resources to be economically viable. Environmental issues related to cobalt mining concern mainly the elevated cobalt contents in soils and waters. Although at low levels cobalt is essential to human health (it is the central atom in the critical nutrient vitamin B12), overexposure to high levels of cobalt may cause lung and heart dysfunction, as well as dermatitis. The ecological impacts of cobalt vary widely and can be severe for some species of fish and plants, depending on various environmental factors.

Professional Paper↗

USGS2023

Environmental factors influencing detection efficiency of an acoustic telemetry array and consequences for data interpretation

Background Acoustic telemetry is a commonly used technology to monitor animal occupancy and infer movement in aquatic environments. The information that acoustic telemetry provides is vital for spatial planning and management decisions concerning aquatic and coastal environments by characterizing behaviors and habitats such as spawning aggregations, migrations, corridors, and nurseries, among others. However, performance of acoustic telemetry equipment and resulting detection ranges and efficiencies can vary as a function of environmental conditions, leading to potentially biased interpretations of telemetry data. Here, we characterize variation in detection performance using an acoustic telemetry receiver array deployed in Wellfleet Harbor, Massachusetts, USA from 2015 to 2017. The array was designed to study benthic invertebrate movements and provided an in situ opportunity to identify factors driving variation in detection probability. Results The near-shore location proximate to environmental monitoring allowed for a detailed examination of factors influencing detection efficiency in a range-testing experiment. Detection ranges varied from < 50 to 1,500 m and efficiencies varied from 0 to 100% within those detection ranges. Detection efficiency was affected by distance, wind speed and direction, wave height and direction, water temperature, water depth, and water quality. Conclusions Performance of acoustic telemetry systems is strongly contingent on environmental conditions. Our study found that wind, waves, water temperature, water quality, and depth all affected performance to an extent that could seriously compromise a study if these effects were not taken into consideration. Other unmeasured factors may also be important, depending on the characteristics of each site. This information can help guide future telemetry study designs by helping researchers anticipate the density of receivers required to achieve study objectives. Researchers can further refine and document the reliability of their data by incorporating continuously deployed range-testing tags and prior knowledge on varying detection efficiency into movement and occupancy models.

Massachusetts↗

USGS2016

Managing nutrients, water, and energy for producing more food with low pollution (MoFoLoPo); What would success look like?

Synthetic nitrogen (N) fertilizer has enabled modern agriculture to greatly improve human nutrition during the 20th century, but it has also created unintended human health and environmental pollution challenges for the 21st century. Averaged globally, about half of the fertilizer N applied to farms is removed with the crops, while the other half remains in the soil or is lost from farmers’ fields, resulting in water and air pollution. As human population continues to grow and food security improves in the developing world, the dual development goals of producing more nutritious food with low pollution will require both technological and socio-economic innovations in agriculture.

Environmental Development↗

USGS2015

Using motion-sensor camera technology to infer seasonal activity and thermal niche of the desert tortoise ( Gopherus agassizii )

Understanding the relationships between environmental variables and wildlife activity is an important part of effective management. The desert tortoise ( Gopherus agassizii ), an imperiled species of arid environments in the southwest US, may have increasingly restricted windows for activity due to current warming trends. In summer 2013, we deployed 48 motion sensor cameras at the entrances of tortoise burrows to investigate the effects of temperature, sex, and day of the year on the activity of desert tortoises. Using generalized estimating equations, we found that the relative probability of activity was associated with temperature (linear and quadratic), sex, and day of the year. Sex effects showed that male tortoises are generally more active than female tortoises. Temperature had a quadratic effect, indicating that tortoise activity was heightened at a range of temperatures. In addition, we found significant support for interactions between sex and day of the year, and sex and temperature as predictors of the probability of activity. Using our models, we were able to estimate air temperatures and times (days and hours) that were associated with maximum activity during the study. Because tortoise activity is constrained by environmental conditions such as temperature, it is increasingly vital to conduct studies on how tortoises vary their activity throughout the Sonoran Desert to better understand the effects of a changing climate.

California↗

USGS1974

Oil shale development and its environmental considerations

The petroleum shortage recently experienced by many nations throughout the world has created an intense interest in obtaining new and supplemental energy sources. In the United States, this interest has been centered on oil shale. Any major action by the federal government having significant environmental effects requires compliance with the National Environmental Policy Act of 1969 (NEPA). Since most oil shale is found on federal lands, and since its development involves significant environmental impacts, leasing oil shale lands to private interests must be in compliance with NEPA. For oil shale, program planning began at approximately the same time that NEPA was signed into law. By structuring the program to permit a resource and technological inventory by industry and the federal agencies, the Department of the Interior was able simultaneously to conduct the environmental assessments required by the act. This required: 1. Clearly defined program objections; 2. An organization which could integrate public policy with diverse scientific disciplines and environmental concerns; and 3. Flexible decisionmaking to adjust to policy changes as well as to evolving interpretations on EPA as clarified by court decisions. This paper outlines the program, the organization structure that was created for this specific task, and the environmental concerns which were investigated. The success of the program has been demonstrated by meeting the requirements of NEPA, without court challenge, and by industry's acceptance of a leasing program that included the most stringent environmental protection provisions ever required. The need for energy development has spurred the acceptance of the program. However, by its awareness and willingness to meet the environmental challenges of the future, industry has shown a reasonable understanding of its commitments. The pros and cons of development were publicly considered in hearings and analyzed in the final environmental statement. This action aided greatly in preventing legal challenges. The prototype oil shale program is now under way and this new energy source, developed with strict environmental safeguards, may soon be available to our nation.

Conference Paper↗

USGS2015

Trends in pesticide use on soybean, corn and cotton since the introduction of major genetically modified crops in the United States

BACKGROUND Genetically modified (GM) varieties of soybean, corn and cotton have largely replaced conventional varieties in the United States. The most widely used applications of GM technology have been the development of crops that are resistant to a specific broad-spectrum herbicide (primarily glyphosate) or that produce insecticidal compounds within the plant itself. With the widespread adoption of GM crops, a decline in the use of conventional pesticides was expected. RESULTS There has been a reduction in the annual herbicide application rate to corn since the advent of GM crops, but the herbicide application rate is mostly unchanged for cotton. Herbicide use on soybean has increased. There has been a substantial reduction in the amount of insecticides used on both corn and cotton since the introduction of GM crops. CONCLUSIONS The observed changes in pesticide use are likely to be the result of many factors, including the introduction of GM crops, regulatory restrictions on some conventional pesticides, introduction of new pesticide technologies and changes in farming practices. In order to help protect human and environmental health and to help agriculture plan for the future, more detailed and complete documentation on pesticide use is needed on a frequent and ongoing basis.

Pest Management Science↗

USGS2021

Terrestrial ecological risk analysis via dietary exposure at uranium mine sites in the Grand Canyon watershed (Arizona, USA)

The U.S. Department of the Interior recently included uranium (U) on a list of mineral commodities that are considered critical to economic and national security. The uses of U for commercial and residential energy production, defense applications, medical device technologies, and energy generation for space vehicles and satellites are known, but the environmental impacts of uranium extraction are not always well quantified. We conducted a screening-level ecological risk analysis based on exposure to mining-related elements via diets and incidental soil ingestion for terrestrial biota to provide context to chemical characterization and exposures at breccia pipe U mines in northern Arizona. Relative risks, calculated as hazard quotients (HQs), were generally low for all biological receptor models. Our models screened for risk to omnivores and insectivores (HQs>1) but not herbivores and carnivores. Uranium was not the driver of ecological risk; arsenic, cadmium, copper, and zinc were of concern for biota consuming ground-dwelling invertebrates. Invertebrate species composition should be considered when applying these models to other mining locations or future sampling at the breccia pipe mine sites. Dietary concentration thresholds (DCTs) were also calculated to understand food concentrations that may lead to ecological risk. The DCTs indicated that critical concentrations were not approached in our model scenarios, as evident in the very low HQs for most models. The DCTs may be used by natural resource and land managers as well as mine operators to screen or monitor for potential risk to terrestrial receptors as mine sites are developed and remediated in the future.

Arizona↗

USGS2021

Acoustic tag retention and tagging mortality of juvenile cisco Coregonus artedi

Release of hatchery-reared juvenile cisco ( Coregonus artedi ) is an important tool for recovering Great Lakes populations, but post-release survival is unknown. Telemetry using small acoustic tags provides opportunities to assess the efficacy of hatchery-reared fish releases. However, better understanding of the tolerance of juvenile cisco to acoustic tags is needed. Juvenile cisco mortality and tag retention as a function of tag size:body size (Relative Tag Weight, RTW) was observed for 30 d post tag implantation in the laboratory. Tag loss and mortality increased with RTW. A single mortality occurred for RTW ≤ 3% and tag retention and survival was <50% for RTW > 7.0%. Logistic regression predicted >95% survival and tag retention to 30 d for RTW < 2.5%, with full survival of study fish for RTW of ≤2%. Sedation and surgery times did not affect survival of tagged fish, but results of anesthesia-only and sham surgeries highlight the need to minimize handling effects for effective acoustic telemetry studies. Our findings clarify thresholds of RTW and indicate that juvenile cisco can receive acoustic tag implants. Observing these limitations can improve the effectiveness of acoustic telemetry to assess success of cultured juvenile fish releases for conservation or restoration of native forage fish populations. Evaluation of the effects of acoustic tags over longer time periods and under environmental conditions, like those at release sites, are needed to further validate this technology.

Journal of Great Lakes Research↗

USGS2025

Evapotranspiration terminology and definitions

Evapotranspiration (ET), the combined process of evaporation from soil and plant surfaces and transpiration from plant tissue, plays a pivotal role in the global water and energy balance. Accurately quantifying ET at various spatial scales is important for diverse applications, including irrigation and natural resource management. While efforts to standardize ET methodology have progressed over the last few decades, some confusion and disagreements in terminology persist among communities of researchers and practitioners involved in the measurement, estimation, and simulation of ET. This technical note addresses the historical evolution and standardization of ET terminology, aiming to reduce and mitigate disparities in definitions and usage by advocating for standardized definitions and emphasizing the adoption of reference ET ( ET ref ) terminology to promote consistency and accuracy and to avoid ambiguity. This document provides comprehensive definitions of key terms, including crop (i.e., vegetation cover) coefficients, consumptive use (CU), actual crop evapotranspiration ( ET a ), and ET ref variants for short (grass, ET o ) and tall (alfalfa, ET r ) reference crops. Practical discussion on several relevant topics is given: (1) single and dual crop coefficient approaches, (2) applications to nonagricultural vegetation, (3) recommended subscripts for terms, (4) practical guidelines and considerations for ET ref calculation, (5) encouragement to replace “potential ET” terminology with better terms, (6) clarification on maximum ET ( ET max ) and maximum crop coefficient ( K c max ) terms, (7) ET products derived from remote sensing, (8) a brief description of the role of ET in water rights, and (9) a figure illustrating the use of the terms defined herein. The conclusion emphasizes the importance of consistent terminology for effective communication among researchers and end-users, which will facilitate the adoption of standardized ET methods and technologies. This technical note was created by the American Society of Civil Engineers, Environmental and Water Resources Institute (ASCE-EWRI), Evapotranspiration in Irrigation and Hydrology Committee, with input and endorsement from other relevant organizations in the United States and internationally. This note serves as a comprehensive reference guide for ET practitioners and researchers.

Irrigation and Drainage Engineering↗

USGS2013

Transcriptome resources for the frogs Lithobates clamitans and Pseudacris regilla , emphasizing antimicrobial peptides and conserved loci for phylogenetics

We developed genetic resources for two North American frogs, Lithobates clamitans and Pseudacris regilla , widespread native amphibians that are potential indicator species of environmental health. For both species, mRNA from multiple tissues was sequenced using 454 technology. De novo assemblies with Mira3 resulted in 50 238 contigs (N50 = 687 bp) and 48 213 contigs (N50 = 686 bp) for L. clamitans and P. regilla , respectively, after clustering with CD-Hit-EST and purging contigs below 200 bp. We performed BLASTX similarity searches against the Xenopus tropicalis proteome and, for predicted ORFs, HMMER similarity searches against the Pfam-A database. Because there is broad interest in amphibian immune factors, we manually annotated putative antimicrobial peptides. To identify conserved regions suitable for amplicon resequencing across a broad taxonomic range, we performed an additional assembly of public short-read transcriptome data derived from two species of the genus Rana and identified reciprocal best TBLASTX matches among all assemblies. Although P. regilla , a hylid frog, is substantially more diverged from the ranid species, we identified 56 genes that were sufficiently conserved to allow nondegenerate primer design with Primer3. In addition to providing a foundation for comparative genomics and quantitative gene expression analysis, our results enable quick development of nuclear sequence-based markers for phylogenetics or population genetics.

Molecular Ecology Resources↗