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At least 667 records · Page 37Linked to original sources
USGS2022

Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Estuaries and Coasts↗
USGS2023

Forecasting sea level rise-driven inundation in diked and tidally restricted coastal lowlands

Diked and drained coastal lowlands rely on hydraulic and protective infrastructure that may not function as designed in areas with relative sea-level rise. The slow and incremental loss of the hydraulic conditions required for a well-drained system make it difficult to identify if and when the flow structures no longer discharge enough water, especially in tidal settings where two-way flows occur through the dike. We developed and applied a hydraulic mass-balance model to quantify how water levels in the diked and tidally restricted coastal wetlands and water bodies dynamically respond to sea-level rise, specifically applied to the Herring River Estuary in MA, USA, from 2020 to 2100. Sensitivity testing of the model parameters indicated that primary outcomes were not sensitive to many of the chosen input values, though the terrestrial water input rate to the estuary and the flow coefficient for the hydraulic infrastructure were important. The relative importance of parameters, however, is expected to be site specific. We introduced a drainability metric that quantifies the net water volume drained over every tidal cycle to monitor and forecast how rising water levels on either side of the dike affected the net draining or impounding conditions of the system. Ensembles of model results across parameter and sea-level scenario uncertainties indicated that substantial impoundment of the Herring River Estuary was expected within ~ 20 years with the existing flow structures, a sluice and two flap gates. Simulations with up to three additional gates did not dampen this trend toward impoundment, suggesting that rising impounded water levels are likely even with major construction upgrades. Increasingly impounded diked coastal waterbodies present a hydrologic challenge with socioecological implications due to projected flooding and ecosystem impacts. Solutions to this challenge may be to allow coastal wetland restoration pathways or require substantial and recurring infrastructure improvement projects.

Massachusetts↗
USGS2026

Co-producing coastal bird research on the Gulf Coast through structured decision making (SDM) and constructed value of information (CVoI)

Conservation practitioners face the complex challenge of addressing global biodiversity threats within social-ecological systems with multiple jurisdictions, numerous interest groups, and changing environmental conditions. Bridging the research-to-implementation gap between scientists and managers, which integrates diverse perspectives that represent the variety of considerations impacting management outcomes can help to inform efficient and effective conservation. Avian conservation programs along the U.S. Gulf Coast exemplify these challenges, as management decisions must address diverse threats to declining coastal bird populations across large breeding, wintering, and migratory ranges while facing uncertainty surrounding the efficacy of large-scale strategies. This provides opportunities for improving management through co-produced research with structured decision making (SDM). We present a case study that demonstrates the application of co-production principles and SDM to collaboratively develop high-priority research questions informing effective avian conservation and management. Additionally, we applied a constructed value of information (CVoI) framework to identify and prioritize which uncertainties to reduce and better understand how research questions impact management actions. The integration of SDM’s five-step decision making framework ensured key principles of co-production were met, while co-production enhanced SDM outcomes by incorporating diverse perspectives and knowledge bases. CVoI further allowed participants to collectively determine final high-priority research questions in the face of complexity and uncertainty. Together, these approaches supported co-produced knowledge-generation, strategic hypothesis prioritization, and identification of research questions most likely to improve conservation decisions. This case study from the U.S. Gulf Coast demonstrates how co-produced research through SDM offers a broadly applicable approach for navigating ecological complexity and bridging the research-to-implementation gap in avian conservation.

Gulf Coast↗
USGS2025

Development of species-specific primers for the identification of Atlantic and shortnose sturgeons

Atlantic ( Acipenser oxyrinchus oxyrinchus ) and shortnose sturgeon ( Acipenser brevirostrum ) are broadly distributed along the Atlantic Coast of North America, where they use rivers, estuaries, and coastal habitats. In order to support management under the U.S. Endangered Species Act, it is important to understand when and where these fish occur. However, this presents a challenge as the two taxa are sometimes misidentified and some life stages (e.g., eggs) are challenging to identify with confidence. In this study, we used cytochrome b sequences to develop molecular primers to confirm the identity of shortnose and Atlantic sturgeon samples. We tested these primers using reference DNA samples for these two species. The results suggested that the primers were able to positively identify and distinguish Atlantic and shortnose sturgeon. The accuracy of the Atlantic sturgeon primers was 95.34%, whereas the accuracy of the shortnose sturgeon primers was 90.7%. Even though there were some individuals that were not positively identified as their corresponding species (false negatives), we did not observe any false positives. Our paper does not aim to develop eDNA markers; rather, the objective of our study was to create species-specific, unlabeled, and cost-effective primers which can be amplified using conventional PCR. The amplification product can be observed in a 2% agarose gel run through electrophoresis. This entire procedure is relatively inexpensive and involves basic instruments found in most conservation genetics laboratories.

Conservation Genetics Resources↗
USGS2026

Nonstationary demographic state-space models using unreplicated counts for species undergoing environmental stressors

A fundamental task in ecological statistics is to estimate abundance and growth rate distributions from wildlife monitoring data to inform conservation management. Modeling time series of wildlife populations presents a number of challenges from both statistical and ecological perspectives, including discreteness; lack of replication; nonstationarity; and observation, demographic, and other phenomenological processes. Nonstationary dynamics are often exhibited by populations undergoing environmental stressors. Models must account for these characteristics to produce reliable estimates of abundance and trends, yet estimation can be challenging with unreplicated data. We propose nonstationary demographic state-space models using unreplicated counts for populations undergoing environmental stressors. A reduced growth rate model matches the complexity of the unreplicated count data, and a fecundity bound on growth rate distributions allows the separation of processes affecting growth rates like environmental stressors from those affecting abundance external to growth rates like migration. NDSSMs allow for the embedding of nonstationary model components, and we explore the use of changepoints, volatility clustering, and migration processes. We apply the proposed nonstationary models in case studies of herons affected by predator/competitor reestablishment and three bat species affected by a fungal pathogen causing white-nose syndrome. Nonstationary models outperform stationary models and generalized linear mixed effects models according to model scoring and visual inspection of predictions, and provide estimates more consistent with published values. Incorporating migration improves model fit universally, even with approximate one-way immigration, most likely because populations are extirpated, recolonized, and increase multiple-fold over the upper bound set by species fecundity. In addition, estimates of the timing and severity of the environmental stressor differed for models with migration. Including nonstationary and demographic components in a fecundity-bounded growth rate model improves inference and benefits interpretability of hyperparameters. In turn, this adjusts uncertainties in predictions of abundance and growth rates over time, providing the ingredients needed for informed conservation analysis and for directing future monitoring of at-risk species.

Journal of Agricultural, Biological and Environmen↗
USGS2021

NABat: A top-down, bottom-up solution to collaborative continental-scale monitoring

Collaborative monitoring over broad scales and levels of ecological organization can inform conservation efforts necessary to address the contemporary biodiversity crisis. An important challenge to collaborative monitoring is motivating local engagement with enough buy-in from stakeholders while providing adequate top-down direction for scientific rigor, quality control, and coordination. Collaborative monitoring must reconcile this inherent tension between top-down control and bottom-up engagement. Highly mobile and cryptic taxa, such as bats, present a particularly acute challenge. Given their scale of movement, complex life histories, and rapidly expanding threats, understanding population trends of bats requires coordinated broad-scale collaborative monitoring. The North American Bat Monitoring Program (NABat) reconciles top-down, bottom-up tension with a hierarchical master sample survey design, integrated data analysis, dynamic data curation, regional monitoring hubs, and knowledge delivery through web-based infrastructure. NABat supports collaborative monitoring across spatial and organizational scales and the full annual lifecycle of bats.

Ambio↗
USGS2026

Wicked problems in practice: Responding to ecological transformation in wilderness

Congressionally designated wilderness offers the highest level of land protection in the USA, comparable to category 1b wilderness as defined by the International Union for Conservation of Nature, yet wilderness areas face impacts of climate change. Researchers and managers increasingly recognize the immense challenge of stewarding wilderness in a changing climate. Although responding to climate change is considered a wicked problem, this framing has not been applied to wilderness contexts. We move theory into practice by using wicked problem framing and four illustrative cases to explore how the resist–accept–direct (RAD) framework can help untangle the wicked problem of addressing unprecedented ecological transformation in wilderness. The RAD framework clarifies a range of response options including resisting transformation, accepting it, or directing it toward preferred new conditions. As climate change continues to challenge wilderness managers, the RAD framework can help assess trade-offs and preserve wilderness character into the twenty-first century.

Ambio↗
USGS2015

Volcano warning systems: Chapter 67

Messages conveying volcano alert level such as Watches and Warnings are designed to provide people with risk information before, during, and after eruptions. Information is communicated to people from volcano observatories and emergency management agencies and from informal sources and social and environmental cues. Any individual or agency can be both a message sender and a recipient and multiple messages received from multiple sources is the norm in a volcanic crisis. Significant challenges to developing effective warning systems for volcanic hazards stem from the great diversity in unrest, eruption, and post-eruption processes and the rapidly advancing digital technologies that people use to seek real-time risk information. Challenges also involve the need to invest resources before unrest to help people develop shared mental models of important risk factors. Two populations of people are the target of volcano notifications–ground- and aviation-based populations, and volcano warning systems must address both distinctly different populations.

Book chapter↗
USGS2019

Reproductive failure in the Eastern Migratory Population: The interaction of research and management

The reintroduction of the Eastern Migratory Population of Whooping Cranes ( Grus americana ) has shown the most promise of any effort to date toward the establishment of a self-sustaining population. However, reproduction – including both nest success and chick survival – has been a major challenge. Here, we review the research and management efforts deployed to identify and address this challenge. While there is evidence that a proximal cause of nest failure is harassment by blood-feeding black flies ( Simulium spp. ), this is not likely to be the only contributing factor, and we present alternative hypotheses. There is less understanding of the causes of poor chick survival, and we present hypotheses for factors that may be contributing to chick mortality, including environmental, genetic, and behavioral factors. For both nest success and chick survival, we carried out a value of information analysis, using expert judgment, which allowed us to prioritize the alternative hypotheses for evaluation based on the expected management benefit of addressing each hypothesis. On the horizon are multiple opportunities to explore hypotheses about environmental factors as well as genetic and behavioral characteristics of the birds themselves that may contribute to poor reproduction. If bird-specific characteristics, such as genetics or rearing methods, are hindering reproduction, this has important implications for all efforts to restore Whooping Crane populations.

Book chapter↗
USGS2019

Health and disease treatment in captive and reintroduced Whooping Cranes

The principles and applications of medicine in Whooping Cranes ( Grus americana ) are similar to that for other crane species, though the necessity of managing Whooping Crane health across the captive, reintroduced, and remnant populations poses particular challenges. In this chapter, we review the important aspects of crane medicine relevant to managing Whooping Cranes in captive and reintroduced environments. We pay special attention to viral, parasitic, fungal, and bacterial diseases that are important to manage for reintroduction efforts to be successful. We also introduce some common aspects of treatment and surgery. Anesthesia is important for successful surgery and is discussed. Radio transmitter implant surgery, as it applies to studying causes of mortality in wild Whooping Crane chicks, is included as a subject of special interest to recovery efforts. Orthopedic problems, which pose a major challenge to the healthy development of young, captive-reared cranes, are discussed. Treatment and vaccination recommendations are made to aid in producing healthy Whooping Cranes for reintroduction to the wild. The literature about crane medicine is reviewed along with the personal insights of the three authors, and an overview of the development of crane medicine programs is included.

Book chapter↗
USGS2017

Turtles: Freshwater

With their iconic shells, turtles are morphologically distinct in being the only extant or extinct vertebrate animals to have their shoulders and hips inside their rib cages. By the time an asteroid hit the earth 65.5 million years ago, causing the extinction of dinosaurs, turtles were already an ancient lineage that was 70% through their evolutionary history to date. The remarkable evolutionary success of turtles over 220 million years is due to a combination of both conservative and effective life history traits and an essentially unchanging morphology that withstood the test of time. However, the life history traits of many species make them particularly susceptible to overharvest and habitat destruction in the modern world, and a majority of the world’s species face serious conservation challenges with several extinctions documented in modern times. The global plight of turtles is underscored by the fact that the percentage of imperiled species exceeds that of even the critically endangered primates. Freshwater turtles, with over 260 recognized species, have become a focus on a worldwide scale for many conservation issues. This article is a synthesis of a diverse body of information on the general biology of freshwater turtles, with particular emphasis on the extensive research on ecology, life history, and behavior that has been accomplished in the last half century. Much of the research has been applicable to the aforementioned conservation challenges. The studies presented include a combination of laboratory and field experiments and observational studies on this intriguing group of animals.

Book chapter↗
USGS2009

Coastline degradation as an indicator of global change

Finding a climate change signal on coasts is more problematic than often assumed. Coasts undergo natural dynamics at many scales, with erosion and recovery in response to climate variability such as El Niño, or extreme events such as storms and infrequent tsunamis. Additionally, humans have had enormous impacts on most coasts, overshadowing most changes that one can presently attribute directly to climate change. Each area of coast is experiencing its own pattern of relative sea-level change and climate change, making discrimination of the component of degradation that results from climate change problems. The best examples of a climate influence are related to temperature rise at low and high latitudes, as seen by the impacts on coral reefs and polar coasts, respectively. Observations through the twentieth century demonstrate the importance of understanding the impacts of sea-level rise and climate change in the context of multiple drivers of change; this will remain a challenge under a more rapidly changing climate. Nevertheless, there are emerging signs that climate change provides a global threat—sea ice is retreating, permafrost in coastal areas is widely melting. Reefs are bleaching more often, and the sea is rising—amplifying widespread trends of subsidence and threatening low-lying areas. To enhance the sustainability of coastal systems, management strategies will also need to address this challenge, focusing on the drivers that are dominant at each section of coast. Global warming through the twentieth century has caused a series of changes with important implications for coastal areas. These include rising temperatures, rising sea level, increasing CO2 concentrations with an associated reduction in seawater pH, and more intense precipitation on average.

Book chapter↗
USGS2013

Water quality status and trends in the United States

Information about water quality is vital to ensure long-term availability and sustainability of water that is safe for drinking and recreation and suitable for industry, irrigation, fish, and wildlife. Protecting and enhancing water quality is a national priority, requiring information on water-quality status and trends, progress toward clean water standards, continuing problems, and emerging challenges. In this brief review, we discuss U.S. Geological Survey assessments of nutrient pollution, pesticides, mixtures of organic wastewater compounds (known as emerging contaminants), sediment-bound contaminants (like lead and DDT), and mercury, among other contaminants. Additionally, aspects of land use and current and emerging challenges associated with climate change are presented. Climate change must be considered, as water managers continue their efforts to maintain sufficient water of good quality for humans and for the ecosystem.

Book chapter↗
USGS2019

Rapid pre-concentration of mercury in solids and water for isotopic analysis

The precise quantification of mercury (Hg) stable isotope compositions in low concentration or dilute samples poses analytical challenges due to Hg mass limitations. Common Hg pre-concentration procedures require extended processing times, making rapid Hg stable isotope measurements challenging. Here we present a modified pre-concentration method that combines commonly used Hg reduction and gold trap amalgamation followed by semi-rapid thermal desorption (less than 1 h) and chemical trapping. This custom designed system was demonstrated to perform adequately on multiple trapping matrices including a new bromine monochloride (BrCl) wet oxidant trap (40% 3HNO 3 :BrCl), capable of trapping consistently in 2 mL volume over a wide range of Hg masses (5–200 ng). The procedure was also shown to work effectively on natural matrices, waters and sediments, producing comparable isotope results to the direct digestion analyses. Here, we present a method that can effectively triple sample throughput in comparison to traditional procedures, and also access lower concentration matrices without compromising the accuracy or precision of Hg isotope measurements.

Analytica Chimica Acta↗
USGS2025

Extracting data from maps: Lessons learned from the artificial intelligence for critical mineral assessment competition

The U.S. Geological Survey (USGS), Defense Advanced Projects Research Agency (DARPA), NASA Jet Propulsion Laboratory (JPL), and MITRE ran a 12-week machine learning competition aimed at accelerating development of AI tools for critical mineral assessments. The Artificial Intelligence for Critical Mineral Assessment Competition solicited innovative solutions for two challenges: 1) automated georeferencing of historical maps, and 2) automated feature extraction from historical maps. Competitors used a new dataset of historical map images to train, validate, and evaluate their models. Automated georeferencing pipelines attained a median root-mean square error of 1.1 km. Prompt-based extraction (i.e., with user input) of polygons, polylines, and points from geologic maps yielded median F1-scores of 0.77, 0.56, 0.35, respectively. Geologic maps pose numerous challenges for AI workflows because they vary significantly. However, despite its short duration, the competition yielded promising results that have since spurred further innovation in this area and led to the development of new AI tools to semi-automate key, time-consuming parts of the assessment workflow.

Applied Computing and Geosciences↗
USGS2015

Using biotic ligand models to predict metal toxicity in mineralized systems

The biotic ligand model (BLM) is a numerical approach that couples chemical speciation calculations with toxicological information to predict the toxicity of aquatic metals. This approach was proposed as an alternative to expensive toxicological testing, and the U.S. Environmental Protection Agency incorporated the BLM into the 2007 revised aquatic life ambient freshwater quality criteria for Cu. Research BLMs for Ag, Ni, Pb, and Zn are also available, and many other BLMs are under development. Current BLMs are limited to ‘one metal, one organism’ considerations. Although the BLM generally is an improvement over previous approaches to determining water quality criteria, there are several challenges in implementing the BLM, particularly at mined and mineralized sites. These challenges include: (1) historically incomplete datasets for BLM input parameters, especially dissolved organic carbon (DOC), (2) several concerns about DOC, such as DOC fractionation in Fe- and Al-rich systems and differences in DOC quality that result in variations in metal-binding affinities, (3) water-quality parameters and resulting metal-toxicity predictions that are temporally and spatially dependent, (4) additional influences on metal bioavailability, such as multiple metal toxicity, dietary metal toxicity, and competition among organisms or metals, (5) potential importance of metal interactions with solid or gas phases and/or kinetically controlled reactions, and (6) tolerance to metal toxicity observed for aquatic organisms living in areas with elevated metal concentrations.

Applied Geochemistry↗
USGS2020

Pulsed flow-through auto-feeding beaker systems for the laboratory culture of juvenile freshwater mussels

Newly metamorphosed freshwater mussels are small and delicate, so that captive laboratory culture presents challenges for handling; for maintenance of suitable microhabitat, water quality, and food; and for avoidance of competitors and predators. To address these challenges, a new pulsed flow-through auto-feeding beaker system was developed for culturing juvenile mussels. In this system, groups of mussels were maintained in 300- to 1000-mL beakers with a thin layer of sand substrate. The water in the beakers was static except for pulses that were delivered every 1 or 2 h and that displaced about half of the water in each beaker per water cycle. A peristaltic pump delivered food to multiple mixing cells where the water was automatically mixed with food just before the water delivery. In testing this approach, newly metamorphosed mussels of 4 species were cultured in the system for 84 to 357 d. The sand and beakers were replaced weekly. Survival was high (>85% at day 84) for Lampsilis siliquoidea and Villosa iris , but relatively lower for Anodonta californiensis (29% at day 155) and Margaritifera falcata (23% at day 357). Growth rate ranged among the 4 species from 27 to 60 μm/d, with the slowest rate for M. falcata and fastest for A. californiensis. Overall, the new pulsed flow-through auto-feeding beaker system improved survival and growth of juvenile mussels versus other methods previously tested. Additionally, a simplified system for the water and food delivery was developed with a single mixing cell. The use of both systems indicate that they are suitable for laboratory experiments and for captive culture of juvenile mussels.

Aquaculture↗
USGS2005

Contaminants as viral cofactors: assessing indirect population effects

Current toxicological methods often miss contaminant effects, particularly when immune suppression is involved. The failure to recognize and evaluate indirect and sublethal effects severely limits the applicability of those methods at the population level. In this study, the Vitality model is used to evaluate the population level effects of a contaminant exerting only indirect, sublethal effects at the individual level. Juvenile rainbow trout ( Oncorhynchus mykiss ) were injected with 2.5 or 10.0 mg/kg doses of the model CYP1A inducer, β-naphthoflavone (BNF) as a pre-stressor, then exposed to a challenge dose of 10 2 or 10 4 pfu/fish of infectious hematopoietic necrosis virus (IHNV), an important viral pathogen of salmonids in North America. At the end of the 28-d challenge, the mortality data were processed according to the Vitality model which indicated that the correlation between the average rate of vitality loss and the pre-stressor dose was strong: R 2 = 0.9944. Average time to death and cumulative mortality were dependent on the BNF dose, while no significant difference between the two viral dosages was shown, implying that the history of the organism at the time of stressor exposure is an important factor in determining the virulence or toxicity of the stressor. The conceptual framework of this model permits a smoother transfer of results to a more complex stratum, namely the population level, which allows the immunosuppressive results generated by doses of a CYP1A inducer that more accurately represent the effects elicited by environmentally-relevant contaminant concentrations to be extrapolated to target populations. The indirect effects of other environmental contaminants with similar biotransformation pathways, such as polycyclic aromatic hydrocarbons (PAH), could be assessed and quantified with this model and the results applied to a more complex biological hierarchy.

Aquatic Toxicology↗