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USGS2001

Disease emergence in birds: Challenges for the twenty-first century

The paper by Hartup et al. (2001) on House Finch ( Carpodacus mexicanus ) conjunctivitis is an example of the rapid geographic spread that can result from disease emergence in naïve populations. That event was neither novel nor transient relative to its occurrence or effects. Disease emergence and reemergence are hallmarks of the latter part of the twentieth century (Center for Disease Control 1994, Levins et al. 1994, DaSilva and Laccarino 1999, Gratz 1999). Current examples involving domestic animals include the problems in Europe with bovine spongiform encephalopathy (BSE, or “mad cow disease”) (Brown 2001) and foot-and-mouth disease (FMD) (Kitching 1999). Human health has been affected by diseases caused by an array of viruses (Morse 1993, Nichol et al. 1993, Murphy and Nathanson 1994), bacteria (Dennis 1998, DaSilva and Laccarino 1999), rickettsia (Walker and Dumier 1996, Azad et al. 1997), protozoans (Tuerrant 1997, Saini et al. 2000), and metazoan parasites (Hildreth et al. 1991, Gubler 1998), as well as other causes. Acquired immune deficiency syndrome (AIDS) has received the most notoriety of those diseases (Hahn et al. 2000, Schwartlander et al. 2000). A similar pattern exists on a global scale for free-ranging wildlife populations (Table 1) (Friend 1994, 1995; Epstein et al. 1998, Daszak et al. 2000). However, in comparison to disease emergence affecting humans and domestic animals, response to emerging diseases of wildlife is generally superficial. We present concepts and data to support our contention that failure to adequately address disease emergence in free-ranging wildlife is resulting in a diminished capability to achieve and sustain desired geographic distributions and population abundance for species of wild birds, including some threatened and endangered avifauna. For clarity, we define disease and disease emergence in the context of our use of those terms because they are the focus of our comments. Disease is any departure from health (Guralnik 1982); that is, dysfunction contributing to physiological, physical, reproductive, behavioral, or other impairment that reduces the probability of survival of individuals. If enough individuals are affected, the collective effects can reduce the sustainability of the population. Although disease can result from exposure to a wide variety of physical, chemical, and biological agents and other conditions, we focus this paper on microbes and parasites and to overt mortality caused by them. Thus, disease effects presented only represent the proverbial “tip of the iceberg” relative to the challenges wild avifauna face from disease. Our perspective of disease emergence expands the earlier definitions of emerging diseases by others (Centers for Disease Control and Prevention 1994, Morse 1995) to include all species. Our comments are defined by the context of disease occurrences that have increased within the past three decades, or threaten to increase in the near future relative to populations affected, geographic distribution, or magnitude of effects.

The Auk↗

USGS1994

Hydrologic data collection at Crowders Creek and Steele Creek, York County, South Carolina, 1991-92

Rapid industrial and urban growth is anticipated in the vicinity of Crowders Creek near Clover, S.C., and Steele Creek near Fort Mill, S.C. These subbasins are in the Catawba River Basin in York County, S.C. To obtain baseline information on these basins prior to urbanization, gaging stations 02145642 (Crowders Creek near Clover, S.C.) and 021467801 (Steele Creek near Fort Mill, S.C.) were established to collect streamflow and water-quality data. Continuous stream-stage and streamflow data were collected during the periods of March 23, 1991 to September 30, 1992, and May 29, 1991 to September 30, 1992, for stations 02145642 and 021467801, respectively. Average streamflows for stations 02145642 and 021467801 for the study period were 80.5 cubic feet per second and 28.6 cubic feet per second, respectively. Water-quality data were collected on four separate occasions at each gage site; two samplings during low-flow events and two samplings during high-flow events. Fecal coliform concentrations exceeded minimum standards for freshwater with other physical and chemical constituents meeting South Carolina Department of Health and Environmental Control standards.

South Carolina↗

USGS2016

Anticipating environmental and environmental-health implications of extreme storms: ARkStorm scenario

The ARkStorm Scenario predicts that a prolonged winter storm event across California would cause extreme precipitation, flooding, winds, physical damages, and economic impacts. This study uses a literature review and geographic information system-based analysis of national and state databases to infer how and where ARkStorm could cause environmental damages, release contamination from diverse natural and anthropogenic sources, affect ecosystem and human health, and cause economic impacts from environmental-remediation, liability, and health-care costs. Examples of plausible ARkStorm environmental and health concerns include complex mixtures of contaminants such as petroleum, mercury, asbestos, persistent organic pollutants, molds, and pathogens; adverse physical and contamination impacts on riverine and coastal marine ecosystems; and increased incidences of mold-related health concerns, some vector-borne diseases, and valley fever. Coastal cities, the San Francisco Bay area, the Sacramento-San Joaquin River Delta, parts of the Central Valley, and some mountainous areas would likely be most affected. This type of screening analysis, coupled with follow-up local assessments, can help stakeholders in California and disaster-prone areas elsewhere better plan for, mitigate, and respond to future environmental disasters.

Natural Hazards Review↗

USGS1999

Health evaluation of Columbian white-tailed deer on Julia Butler Hansen Refuge for the Columbian white-tailed deer

The Columbian white-tailed deer ( Odocoileus virginianus leucurus) was designated an endangered species in 1968. At that time the estimated population along the lower Columbia River of Washington and Oregon was 300 to 400 deer (Gavin, 1984). The Julia Butler Hansen Refuge for the Columbian White-tailed Deer was established in 1972 to protect Columbian white-tailed deer and associated habitat Currently, an estimated 600 deer are present in several separate populations. The total refuge population is estimated at 200 animals. Of those, the mainland population consists of approximately 60 animals while the largest refuge island (Tenasillahe.Island) supports about 120 animals. The remaining 420 deer are present on private lands near the refuge (AI Clark, pers. com.). Higher than expected deer mortality on Tenasillahe Island in the spring of 1996 prompted refuge personnel to request assistance from the National Wildlife Health Center (NWHC) for diagnostic evaluation to determine the cause of the mortalities. The mortality event occurred in the wake of extraordinary .flooding that reduced the availability and quality of forage on the island. It is estimated that 50% of the deer population on the refuge died during this time period. The basic finding of emaciation attributable to probable starvation raised concerns regarding the health status of the deer herd, available food resources, and current population levels. A health evaluation was conducted on free-ranging deer from the refuge in February, 1998. This evaluation was an analysis of physiologic parameters obtained from live deer in an attempt to determine the health of individual animals and, with adequate sampling, the health of the population. This study was conducted during February to examine individual animal health during the seasonal period when the deer are in their poorest physical condition. The late winter period prior to spring green-up is a time when the effects ofbreeding and winter stress are most evident (Venne and Ozoga, 1971). The objectives of this study were to: (1) gather baseline physiologic data on a subset of the population, (2) evaluate the data to determine the health of the animals sampled, (3) if possible, identify causes of poor health and, ( 4) provide refuge personnel with information that will aid them in managing the population.

Oregon, Washington↗

USGS2023

Observations of coastal circulation, waves, and sediment transport along West Maui, Hawaiʻi (November 2017– March 2018), and modeling effects of potential watershed restoration on decreasing sediment loads to adjacent coral reefs

Terrestrial sediment discharging from watersheds off West Maui, Hawaiʻi, has been documented as a primary stressor to local coral reefs, causing coral reef health to decline. The U.S. Geological Survey acquired and analyzed physical oceanographic and sedimentologic field data off the coast of West Maui to calibrate and validate physics-based, numerical hydrodynamic and sediment transport models of the study area developed by Deltares. These models simulated terrestrial sediment transport and dispersal from West Maui watersheds into coastal waters and how terrestrial sediment affects nearby coral reefs under different oceanographic forcing and watershed restoration scenarios. Wave energy and near-bed turbidity are positively correlated in the field observations, illustrating a process not captured by the model simulations in which sediment already deposited on the seabed is resuspended by wave action and subsequently transported by prevailing currents. In the model simulations, large waves during flood events led to a decrease in suspended-sediment concentrations. Notably, however, the model results only consider sediment entering coastal waters from five stream sources and do not simulate sediment already present on the seabed. The model simulations project that the Honokeana and Māhinahina coral reefs would experience the greatest reduction in sediment impacts from theoretical watershed restoration. Additionally, when large waves coincide with flood events, post-storm sedimentation generally decreases in the nearshore region, but increases in the region offshore of the reefs. The measured and modeled sediment dynamics demonstrate a demarcation between the coral reefs sheltered within embayments (Honolua reef) or behind points (Wahikuli reef) and those along the relatively open coastline between Kapalua and Kāʻanapali (Kapalua, Honokeana, Māhinahina, and Honokōwai reefs). The sheltered sites are affected by terrestrial sediment from single stream mouths, where most sediment is delivered within hours of a flood (rain) event. Once this sediment enters the nearshore, it settles out and remains within the reef area for a prolonged period owing to a lack of wave or current-driven bed shear stress. Thus, the primary effect of sediment on the reefs within these sheltered areas is sedimentation. In contrast, coral reefs along the unsheltered (or “open”) section of coastline (between Kapalua and Kāʻanapali) are more exposed to waves and terrestrial sediment from multiple stream sources. At these reefs, fine-grained terrestrial sediment can rarely settle but instead remains in suspension. Thus, even long after a flood event has occurred, these sites chronically experience light attenuation from suspended sediment. These analyses underscore the importance of understanding how coastal ocean waves and circulation can lead to different sediment dynamics and stressors for coral reefs along the same region of the West Maui coastline. These differing factors indicate that the most effective watershed restoration and mitigation strategies may vary among the different coral reefs and streams. An important next step is to determine how the science of this study can support management goals for these coral reefs: what are target reductions of sedimentation, suspended-sediment concentrations, or the resulting light attenuation? Then, using the coupled hydrodynamic-sediment model, we can examine which watershed restoration scenarios in each stream will best achieve those targets.

Hawaii↗

USGS2022

Human and ecosystem health in coastal systems

U.S. coastal economies and communities are facing an unprecedented and growing number of impacts to coastal ecosystems including beach and fishery closures, harmful algal blooms, loss of critical habitat, as well as shoreline damage. This paper synthesizes our present understanding of the dynamics of human and ecosystem health in coastal systems with a focus on the need to better understand nearshore physical process interactions with coastal pollutants and ecosystems (e.g. fate and transport, circulation, depositional environment, climate change). It is organized around two major topical areas and six subtopic areas: 1) Identifying and mitigating coastal pollutants, including fecal pollution, nutrients and harmful algal blooms, and microplastics; and 2) Resilient coastal ecosystems, which focuses on coastal fisheries, shellfish and natural and nature-based features (NNBF). Societal needs and the tools and technologies needed to address them are discussed for each subtopic. Recommendations for scientific research, observations, community engagement, and policies aim to help prioritize future research and investments. A better understanding of coastal physical processes and interactions with coastal pollutants and resilient ecosystems (e.g. fate and transport, circulation, depositional environment, climate change) is a critical need. Other research recommendations include the need to quantify potential threats to human and ecosystem health through accurate risk assessments and to quantify the resulting hazard risk reduction of natural and nature-based features; improve pollutant and ecosystem impacts forecasting by integrating frequent and new data points into existing and novel models; collect environmental data to calibrate and validate models to predict future impacts on coastal ecosystems and their evolution due to anthropogenic stressors (land-based pollution, overfishing, coastal development), climate change, and sea level rise; and develop lower cost and rapid response tools to help coastal managers better respond to pollutant and ecosystem threats.

Shore and Beach↗

USGS2011

Differences in macroinvertebrate community structure in streams and rivers with different hydrologic regimes in the semi-arid Colorado Plateau

Aquatic macroinvertebrates are sensitive to changes in their chemical and physical environment, and as such, serve as excellent indicators of overall ecosystem health. Moreover, temporal and spatial differences in macroinvertebrate community structure can be used to investigate broad issues in aquatic science, such as the hypothesis that changes in climate are likely to have disproportionately large effects on small, intermittent stream ecosystems. We quantified macroinvertebrate community structure and abiotic conditions at ten stream sites with different dominant hydrologic regimes in the Colorado Plateau, ranging from small, intermittent desert streams to large perennial mountain rivers. Considerable differences were observed in community structure between sites with differing hydrologic regimes. Quantitative results of non-metric multidimensional scaling (NMDS) ordination and Spearman rank correlations between physical habitat and macroinvertebrate resemblance matrices indicate that discharge, geomorphic channel unit type (% pools vs. % riffles), percent of substrate composed of sand, and velocity were the subset of measured habitat variables that best explained the differences in macroinvertebrate community structure among sites. Of the 134 taxa identified, nine taxa explained 95 % of the variability in community structure between sites. These results add to a growing base of knowledge regarding the functioning of lotic ecosystems in the Colorado Plateau, and provide timely information on anticipated changes in the structure and function of aquatic ecosystems in response to predicted future environmental conditions.

Colorado Plateau↗

USGS2024

Spatio-temporal ecological models via physics-informed neural networks for studying chronic wasting disease

To mitigate the negative effects of emerging wildlife diseases in biodiversity and public health it is critical to accurately forecast pathogen dissemination while incorporating relevant spatio-temporal covariates. Forecasting spatio-temporal processes can often be improved by incorporating scientific knowledge about the dynamics of the process using physical models. Ecological diffusion equations are often used to model epidemiological processes of wildlife diseases where environmental factors play a role in disease spread. Physics-informed neural networks (PINN) are deep learning algorithms that constrain neural network predictions based on physical laws and therefore are powerful forecasting models useful even in cases of limited and imperfect training data. In this paper, we develop a novel ecological modeling tool using PINNs, which fits a feedforward neural network and simultaneously performs parameter identification in a partial differential equation (PDE) with varying coefficients. We demonstrate the applicability of our model by comparing it with the commonly used Bayesian stochastic partial differential equation method and traditional machine learning approaches, showing that our proposed model exhibits superior prediction and forecasting performance when modeling chronic wasting disease in deer in Wisconsin. Furthermore, our model provides the opportunity to obtain scientific insights into spatiotemporal covariates affecting spread and growth of diseases. This work contributes to future machine learning and statistical methodology development by studying spatio-temporal processes enhanced by prior physical knowledge.

Spatial Statistics↗

USGS2012

Biotic, water-quality, and hydrologic metrics calculated for the analysis of temporal trends in National Water Quality Assessment Program Data in the Western United States

The U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program was established by Congress in 1991 to collect long-term, nationally consistent information on the quality of the Nation's streams and groundwater. The NAWQA Program utilizes interdisciplinary and dynamic studies that link the chemical and physical conditions of streams (such as flow and habitat) with ecosystem health and the biologic condition of algae, aquatic invertebrates, and fish communities. This report presents metrics derived from NAWQA data and the U.S. Geological Survey streamgaging network for sampling sites in the Western United States, as well as associated chemical, habitat, and streamflow properties. The metrics characterize the conditions of algae, aquatic invertebrates, and fish. In addition, we have compiled climate records and basin characteristics related to the NAWQA sampling sites. The calculated metrics and compiled data can be used to analyze ecohydrologic trends over time.

Open-File Report↗

USGS2019

Physicochemical controls on zones of higher coral stress where Black Band Disease occurs at Mākua Reef, Kauaʻi, Hawaiʻi

Pervasive and sustained coral diseases contribute to the systemic degradation of reef ecosystems, however, to date an understanding of the physicochemical controls on a coral disease event is still largely lacking. Water circulation and residence times and submarine groundwater discharge all determine the degree to which reef organisms are exposed to the variable chemistry of overlying waters; understanding these physical controls is thus necessary to interpret spatial patterns in coral health. The recent discovery of coral Black Band Disease at Mākua Reef on Kauaʻi, Hawaiʻi prompted an investigation into the physicochemical drivers and geomorphic controls of reef water circulation, and the temporally variable nutrient fluxes derived from submarine groundwater discharge. Results reveal localized stagnant water parcels at Mākua Reef where groundwater-derived high nutrient loading and low salinities act in concert as stressors to coralline health – and where Black Band Disease was uniquely identified. The observed high nutrient levels during low tide conditions are likely associated with nearby upstream cesspools and drain fields. Information obtained using such a multidisciplinary approach has direct value for successful management of coastal aquifers and the health and sustainability of adjacent nearshore coral reef ecosystems.

Hawaii↗

USGS2003

Applying indicators of hydrologic alteration to Texas streams: overview of methods with examples from the Trinity River basin

Streamflow is a component of aquatic ecosystem health, and long-term alteration of streamflow characteristics can produce large changes in aquatic ecosystem structure and function. The physical, chemical, and biological properties of aquatic ecosystems are all affected by the magnitude and frequency of streamflow. For example, the physical structure (hydrogeomorphology) of aquatic habitats is a property of the interaction between streamflow magnitude and frequency and the physical landscape (Leopold and others, 1992). Chemical processes are affected by changes in water residence time, which is a function of streamflow. Similarly, the structure and function of biological communities associated with stream ecosystems depend in large part on the hydrologic regime (Poff and Ward, 1989, 1990; Sparks, 1992). Within-year variation in streamflow is essential to the survival, growth, and reproduction of aquatic species. Altering streamflow magnitude and frequency and within-year variability has the potential to modify critical aspects of the physical habitat (Bain and others, 1988). Documenting the degree to which streamflow has been modified by the cumulative effects of water development is critical to assessing aquatic ecosystem health. The U.S. Geological Survey (USGS), in cooperation with the Texas Commission on Environmental Quality, conducted a study of the application of the Indicators of Hydrologic Alteration (IHA) methods developed by Richter and others (1996, 1997) to identify streams at risk for biological impairment from the loss of streamflow-dependent habitat. This report provides a brief overview of selected IHA methods for assessing hydrologic alteration; presents examples that illustrate the application of the methods using streamflow data from a subset of USGS stations in the Trinity River Basin, Texas, analyzed in the study; and addresses applicability of the methods statewide.

Texas↗

USGS2005

Risk analysis for biological hazards: What we need to know about invasive species

Risk analysis for biological invasions is similar to other types of natural and human hazards. For example, risk analysis for chemical spills requires the evaluation of basic information on where a spill occurs; exposure level and toxicity of the chemical agent; knowledge of the physical processes involved in its rate and direction of spread; and potential impacts to the environment, economy, and human health relative to containment costs. Unlike typical chemical spills, biological invasions can have long lag times from introduction and establishment to successful invasion, they reproduce, and they can spread rapidly by physical and biological processes. We use a risk analysis framework to suggest a general strategy for risk analysis for invasive species and invaded habitats. It requires: (1) problem formation (scoping the problem, defining assessment endpoints); (2) analysis (information on species traits, matching species traits to suitable habitats, estimating exposure, surveys of current distribution and abundance); (3) risk characterization (understanding of data completeness, estimates of the “potential” distribution and abundance; estimates of the potential rate of spread; and probable risks, impacts, and costs); and (4) risk management (containment potential, costs, and opportunity costs; legal mandates and social considerations and information science and technology needs).

Risk Analysis↗

USGS2010

Climate change and wildlife health: direct and indirect effects

Climate change will have significant effects on the health of wildlife, domestic animals, and humans, according to scientists. The Intergovernmental Panel on Climate Change projects that unprecedented rates of climate change will result in increasing average global temperatures; rising sea levels; changing global precipitation patterns, including increasing amounts and variability; and increasing midcontinental summer drought (Intergovernmental Panel on Climate Change, 2007). Increasing temperatures, combined with changes in rainfall and humidity, may have significant impacts on wildlife, domestic animal, and human health and diseases. When combined with expanding human populations, these changes could increase demand on limited water resources, lead to more habitat destruction, and provide yet more opportunities for infectious diseases to cross from one species to another. Awareness has been growing in recent years about zoonotic diseases— that is, diseases that are transmissible between animals and humans, such as Lyme disease and West Nile virus. The rise of such diseases results from closer relationships among wildlife, domestic animals, and people, allowing more contact with diseased animals, organisms that carry and transmit a disease from one animal to another (vectors), and people. Disease vectors include insects, such as mosquitoes, and arachnids, such as ticks. Thus, it is impossible to separate the effects of global warming on wildlife from its effects on the health of domestic animals or people. Climate change, habitat destruction and urbanization, the introduction of exotic and invasive species, and pollution—all affect ecosystem and human health. Climate change can also be viewed within the context of other physical and climate cycles, such as the El Niño Southern Oscillation (El Niño), the North Atlantic Oscillation, and cycles in solar radiation that have profound effects on the Earth’s climate. The effects of climate change on wildlife disease are summarized in several areas of scientific study discussed briefly below: geographic range and distribution of wildlife diseases, plant and animal phenology (Walther and others, 2002), and patterns of wildlife disease, community and ecosystem composition, and habitat degradation.

Fact Sheet↗

USGS2004

The effects of urbanization on the biological, physical, and chemical characteristics of coastal New England streams

During August 2000, responses of biological communities (invertebrates, fish, and algae), physical habitat, and water chemistry to urban intensity were compared among 30 streams within 80 miles of Boston, Massachusetts. Sites chosen for sampling represented a gradient of the intensity of urban development (urban intensity) among drainage basins that had minimal natural variability. In this study, spatial differences were used as surrogates for temporal changes to represent the effects of urbanization over time. The degree of urban intensity for each drainage basin was characterized with a standardized urban index (0-100, lowest to highest) derived from land cover, infrastructure, and socioeconomic variables. Multivariate and multimetric analyses were used to compare urban index values with biological, physical, and chemical data to determine how the data indicated responses to urbanization. Multivariate ordinations were derived for the invertebrate-, fish-, and algae-community data by use of correspondence analysis, and ordinations were derived for the chemical and physical data by use of principal-component analysis. Site scores from each of the ordinations were plotted in relation to the urban index to test for a response. In all cases, the primary axis scores showed the strongest response to the urban index, indicating that urbanization was a primary factor affecting the data ordination. For the multimetric analyses, each of the biological data sets was used to calculate a series of community metrics. For the sets of chemical and physical data, the individual variables and various combinations of individual variables were used as measured and derived metrics, respectively. Metrics that were generally most responsive to the urban index for each data set included: EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa for invertebrates; cyprinid taxa for fish; diatom taxa for algae; bicarbonate, conductivity, and nitrogen for chemistry; and water depth and temperature for physical habitat. The slopes of the responses generally were higher between the urban index values of 0 to 35, indicating that the greatest change in aquatic health may occur between low and moderate levels of urban intensity. Additionally, many of the responses showed that at urban index values greater than 35, there was a threshold effect where the response variable no longer changed with respect to urban intensity. Recognizing and understanding this type of response is important in management and monitoring programs that rely on decisive interpretations of variable responses. Any biological, physical, or chemical variable that is used to characterize stream health over a gradient of disturbance would not be a reliable indicator when a level of disturbance is reached where the variable does not respond in a predictable manner.

Maine, Massachusetts, New Hampshire↗

USGS1985

Wildlife health implications of sewage disposal in wetlands

Wildlife health concerns associated with disposal of sewage effluent in wetlands are of three primary types: (1) introduction of pathogens, (2) introduction of pollutants that adversely impact on host body defense mechanisms, and (3) changes in the physical and chemical properties of wetlands that favor the development and maintenance of disease problems. Unlike the situation with human health concerns, introduction of pathogens is not the major concern regarding wildlife health. Instead, the focus of attention needs to be directed at environmental changes likely to take place as a result of effluent discharges into different types of wetlands. Unless these changes are adequately addressed from a disease perspective, marshes utilized for sewage disposal could become disease incubators and wildlife death traps. This result would be unfortunate because the backlash would likely negate the potentially beneficial aspects of the use of sewage wastewater for the creation of new wetlands and have a severe impact on progress being made towards evaluation of the compatibility of wildlife and sewage effluents.

Book chapter↗

USGS2014

The environmental and medical geochemistry of potentially hazardous materials produced by disasters

Many natural or human-caused disasters release potentially hazardous materials (HM) that may pose threats to the environment and health of exposed humans, wildlife, and livestock. This chapter summarizes the environmentally and toxicologically significant physical, mineralogical, and geochemical characteristics of materials produced by a wide variety of recent disasters, such as volcanic eruptions, hurricanes and extreme storms, spills of mining/mineral-processing wastes or coal extraction by-products, and the 2001 attacks on and collapse of the World Trade Center towers. In describing these characteristics, this chapter also illustrates the important roles that geochemists and other earth scientists can play in environmental disaster response and preparedness. In addition to characterizing in detail the physical, chemical, and microbial makeup of HM generated by the disasters, these roles also include (1) identifying and discriminating potential multiple sources of the materials; (2) monitoring, mapping, and modeling dispersal and evolution of the materials in the environment; (3) understanding how the materials are modified by environmental processes; (4) identifying key characteristics and processes that influence the materials' toxicity to exposed humans and ecosystems; (5) estimating shifts away from predisaster environmental baseline conditions; and (6) using geochemical insights learned from past disasters to help estimate, prepare for, and increase societal resilience to the environmental and related health impacts of future disasters.

Book chapter↗

USGS2023

Ecology and ecosystem impacts of submerged and floating aquatic vegetation in the Sacramento-San Joaquin Delta

Substantial increases in non-native aquatic vegetation have occurred in the upper San Francisco Estuary over the last 2 decades, largely from the explosive growth of a few submerged and floating aquatic plant species. Some of these species act as ecosystem engineers by creating conditions that favor their further growth and expansion as well as by modifying habitat for other organisms. Over the last decade, numerous studies have investigated patterns of expansion and turn-over of aquatic vegetation species; effects of vegetation on ecosystem health, water quality, and habitat; and effects of particular species or communities on physical processes such as carbon and sediment dynamics. Taking a synthetic approach to evaluate what has been learned over the last few years has shed light on just how significant aquatic plant species and communities are to ecosystems in the Sacramento-San Joaquin Delta. Aquatic vegetation affects every aspect of the physical and biotic environment, acting as ecosystem engineers on the landscape. Furthermore, their effects are constantly changing across space and time, leaving many unanswered questions about the full effects of aquatic vegetation on Delta ecosystems and what future effects may result, as species shift in distribution and new species are introduced. Remaining knowledge gaps underlie our understanding of aquatic macrophyte effects on Delta ecosystems, including their roles and relationships with respect to nutrients and nutrient cycling, evapotranspiration and water budgets, carbon and sediment, and emerging effects on fish species and their habitats. This paper explores our current understanding of submerged and floating aquatic vegetation (SAV and FAV) ecology with respect to major aquatic plant communities, observed patterns of change, interactions between aquatic vegetation and the physical environment, and how these factors affect ecosystem services and disservices within the upper San Francisco Estuary.

California↗

USGS2025

Learning complex spatial dynamics of wildlife diseases with machine learning-guided partial differential equations

Emerging wildlife pathogens often display geographic variability due to landscape heterogeneity. Modeling approaches capable of learning complex, non-linear spatial dynamics of diseases are needed to rigorously assess and mitigate the effects of pathogens on wildlife health and biodiversity. We propose a novel machine learning (ML)-guided approach that leverages prior physical knowledge of ecological systems, using partial differential equations. We present our approach, taking advantage of the universal function approximation property of neural networks for flexible representation of the underlying dynamics of the geographic spread and growth of wildlife diseases. We demonstrate the benefits of our approach by comparing its forecasting power with commonly used methods and highlighting the obtained insights on disease dynamics. Additionally, we show the theoretical guarantees for the approximation error of our model. We illustrate the implementation of our ML-guided approach using data from white-nose syndrome (WNS) outbreaks in bat populations across the US. WNS is an infectious fungal disease responsible for significant declines in bat populations. Our results on WNS are useful for disease surveillance and bat conservation efforts. Our methods can be broadly used to assess the effects of environmental and anthropogenic drivers impacting wildlife health and biodiversity.

Environmental Data Science↗