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USGS2007

Biological effects of anthropogenic contaminants in the San Francisco Estuary

Concentrations of many anthropogenic contaminants in the San Francisco Estuary exist at levels that have been associated with biological effects elsewhere, so there is a potential for them to cause biological effects in the Estuary. The purpose of this paper is to summarize information about biological effects on the Estuary's plankton, benthos, fish, birds, and mammals, gathered since the early 1990s, focusing on key accomplishments. These studies have been conducted at all levels of biological organization (sub-cellular through communities), but have included only a small fraction of the organisms and contaminants of concern in the region. The studies summarized provide a body of evidence that some contaminants are causing biological impacts in some biological resources in the Estuary. However, no general patterns of effects were apparent in space and time, and no single contaminant was consistently related to effects among the biota considered. These conclusions reflect the difficulty in demonstrating biological effects due specifically to contamination because there is a wide range of sensitivity to contaminants among the Estuary's many organisms. Additionally, the spatial and temporal distribution of contamination in the Estuary is highly variable, and levels of contamination covary with other environmental factors, such as freshwater inflow or sediment-type. Federal and State regulatory agencies desire to develop biological criteria to protect the Estuary's biological resources. Future studies of biological effects in San Francisco Estuary should focus on the development of meaningful indicators of biological effects, and on key organism and contaminants of concern in long-term, multifaceted studies that include laboratory and field experiments to determine cause and effect to adequately inform management and regulatory decisions.

California↗

USGS2003

Irrigation-induced contamination of water, sediment, and biota in the western United States-synthesis of data from the National Irrigation Water Quality Program

In October 1985 the U.S. Department of the Interior (DOI), through the National Irrigation Water Quality Program (NIWQP), began a series of field investigations at 26 areas in the Western United States to determine whether irrigation drainage has had harmful effects on fish, wildlife, and humans or has reduced beneficial uses of water. In 1992 NIWQP initiated the Data Synthesis Project to evaluate data collected during the field investigations. Geologic, climatologic, and hydrologic data were evaluated and water, sediment, and biota from the 26 areas were analyzed to identify commonalities and dominant factors that result in irrigation-induced contamination of water and biota. Data collected for the 26 area investigations have been compiled and merged into a common data base. The structure of the data base is designed to enable assessment of relations between contaminant concentrations in water, sediment, and biota. The data base is available to the scientific community through the World Wide Web at URL http://www.usbr.gov/niwqp . Analysis of the data base for the Data Synthesis included use of summary statistics, factor analysis, and logistic regression. A Geographic Information System was used to store and analyze spatially oriented digital data such as land use, geology and evaporation rates. In the U.S. Department of the Interior (DOI) study areas, samples of water, bottom sediment, and biota were collected for trace-element and pesticide analysis. Contaminants most commonly associated with irrigation drainage were identified by comparing concentrations in water with established criteria. For surface water, the criteria used were typically chronic criteria for the protection of freshwater aquatic life. Because ground water can discharge to the surface where wildlife can be exposed to it, the criteria used for ground water were both the maximum contaminant levels (MCL's) for drinking water and the chronic criteria for the protection of freshwater aquatic life. Data collected by the NIWQP studies indicated that, in surface water, filtered and unfiltered samples had nearly the same concentrations of arsenic, boron, molybdenum, and selenium for concentrations greater than about 10 micrograms per liter. Therefore, in this concentration range, filtered concentrations can be directly compared to biological-effect levels developed for unfiltered samples. In the range of 1 to 10 micrograms per liter there may be a tendency for unfiltered arsenic concentrations to be greater than filtered concentrations. For selenium, however, the data suggest differences from equality in that range result from analytical imprecision and not a general tendency for unfiltered concentrations to be greater than filtered concentrations. This relation may not be true in lentic, nutrient-rich waters because in such settings algae can bioaccumulate large amounts of selenium and other trace elements. Selenium was the trace element in surface water that most commonly exceeded chronic criteria for the protection of freshwater aquatic life; more than 40 percent of the selenium concentrations in surface-water samples exceeded the U.S. Environmental Protection Agency (USEPA) aquatic-life chronic criterion (5 micrograms per liter). In 12 of the 26 areas at least 25 percent of the surface water-samples had selenium concentrations that either equaled or exceeded the chronic criterion (5 micrograms per liter). More than 28 percent of boron concentrations and almost 17 percent of the molybdenum concentrations exceeded the aquatic life criteria established by the State of California (550 and 19 micrograms per liter, respectively). In ground water, more than 22 percent of the arsenic concentrations and more than 35 percent of the selenium concentrations exceeded the MCL (10 and 50 micrograms per liter, respectively). Few samples of uranium in surface water exceeded a criterion for the protection of aquatic life (300 micrograms per liter), but 44 percent of the uranium concentrations in ground water exceeded the MCL (30 micrograms per liter). Molybdenum, selenium and uranium were the trace elements most commonly found in bottom-sediment samples that exceeded the upper limit of the 95th percentile expected range in soils of the Western United States. Selenium is the only trace element for which ecological sediment guidelines are used in this report. Selenium concentrations commonly exceeded the ecological sediment guideline of two micrograms per gram. DDT and its degradation products DDD and DDE were the most common pesticide residues found in surface water at concentrations exceeding criteria. However, almost all the samples exceeding the criteria were from a single study area, the Owyhee-Vale Reclamation Project areas in Oregon and Idaho. The organochlorine pesticide chlordane was detected in 30 percent of the bottom-sediment samples, and undegraded DDT was detected in 21 percent. DDT or its degradation products were detected in all 21 study areas where bottom-sediment samples were analyzed for organochlorine pesticides. A principal-components analysis indicated that elevated selenium concentrations in surface water are not associated with elevated boron, molybdenum, or arsenic concentrations. The occurrence of selenium is associated with sulfate and uranium. The association of boron and molybdenum with chloride suggests that evaporative processes control their concentrations. Arsenic is not associated with any other measured trace element and is associated negatively with selenium. This report focuses on selenium because it was the trace element most frequently found at concentrations exceeding criteria for the protection of aquatic life. Selenium concentrations in water are dynamic, and, at a given site, the selenium concentration can change by an order of magnitude during a year and from one year to another. In some areas, selenium contamination may not occur during normal or wet periods. However, during a drought, reduced water deliveries may result in selenium contamination by evaporative concentration. Marine sedimentary rocks, especially those of Late Cretaceous age, are likely to be seleniferous. Irrigation of soils derived from them can contribute large amounts of selenium to drainwater; shallow wells in and near irrigated areas contained hundreds to thousands of micrograms per liter of selenium. The median selenium concentration in surface-water samples from NIWQP sites associated with Upper Cretaceous marine sedimentary rocks is 7 micrograms per liter (range less than 1 to 8,300 micrograms per liter) and from sites not associated with such rocks is 0.4 micrograms per liter (range less than 1 to 390 micrograms per liter). Irrigation-induced selenium contamination has been observed only in arid or semiarid areas. In those NIWQP study areas having local geologic sources of selenium, typically more than 25 percent of the surface-water samples exceed the chronic criterion for selenium if the evaporation rate is 3.0 times greater than the annual precipitation. In terminal water bodies, selenium accumulates and is not flushed out. In both terminal and flow-through lakes and ponds, the median selenium concentrations in surface water for samples collected from June through August are nearly the same (1.0 and 0.8 micrograms per liter, respectively). However, the 75th-percentile selenium concentration for terminal water bodies (24 µg/L) is significantly higher than for flow-through systems (4 µg/L). Selenium concentrations in biota were compared with concentrations that have been demonstrated to have adverse effects on similar species (the effect level) or to have adverse effects on another species if consumed (the dietary effect level). Twenty-five percent of the plant samples had selenium concentrations exceeding the dietary effect level (3 micrograms per gram dry weight) whereas more than 57 percent of the invertebrate samples and 61 percent of the fish samples exceeded the dietary effect level. Of the more than 2,000 bird eggs collected, 44 percent had selenium concentrations exceeding 6 micrograms per gram, a threshold value for reduced hatchability. In 14 areas, selenium concentrations in eggs from some populations of birds exceeded 6 micrograms per gram. Selenium-caused deformities of bird embryos were found in four of the NIWQP study areas; however, most study areas were not systematically surveyed for such deformities. Eggs were sampled from 34 species of birds belonging to 10 orders. Nearly all the eggs collected come from aquatic species of birds, with American coots, mallards, and American avocets being the three species most frequently collected. Of the 34 species, at least one set of eggs from 16 species had a geometric-mean selenium concentration of at least 12.5 micrograms per gram, a high-risk threshold. All three species of grebes yielded at least one set of high risk eggs, as did four of five species of shorebirds and five of eleven species of waterfowl. Egg-set data were examined to determine if some feeding guilds are more at risk to selenium poisoning than others. Analysis of data for waterbird eggs from the study areas where the 75th percentile selenium concentration in surface water exceeded 5 µg/L suggests that herbivorous birds may bioaccumulate less selenium than insect- and fish-eating birds. For birds from these study areas, selenium concentrations for 39 percent of the egg sets from herbivorous birds fell in the normal range (less than 3 µg/g) while only 7 and 0 percent, respectively, of egg sets from insect- and fish-eating birds fall in the normal range. Although herbivorous birds may bioaccumulate less selenium, it does not appear that any waterbird feeding guilds are particularly well buffered from exposure to selenium contamination. Predictive tools were developed to aid managers in identifying specific land areas at risk for irrigation-induced selenium contamination. The tools range from identifying broad geographic regions where selenium contamination is likely, to assessing the probability that selenium concentrations in a specific stream or lake exceed the chronic criterion for selenium. A geographic information system was used to prepare a map that identifies land areas in the Western United States that are susceptible to selenium contamination if irrigated. On the basis of the 75th percentile, selenium concentration in surface water, 12 of the 26 NIWQP study areas were classified as contaminated, two as seleniferous, and 12 as uncontaminated. The map correctly identified both seleniferous areas and 10 of 12 selenium-contaminated areas as susceptible; 10 of 12 uncontaminated areas were correctly identified as not being susceptible. About 160,000 square miles are identified as being susceptible; of that area, about 4,100 square miles have been identified by satellite imagery as actively being irrigated. Principal-components analysis and pattern-recognition techniques indicate that major-ion chemistry of water samples alone can be used to identify selenium- and nonselenium-producing areas in the Western United States. Water samples composed of simple salts of sulfate typically have concentrations of selenium that exceed 3 µg/g, whereas samples composed of simple salts of chloride or carbonate typically have low selenium concentrations. Weathering of soils that contain reduced-sulfur minerals, such as pyrite, mobilizes sulfur and selenium because selenium commonly substitutes for sulfur in these minerals. In areas where the bedrock is composed of Upper Cretaceous marine sedimentary rocks, logistic regression of data from the NIWQP sites indicates that if the dissolved-solids concentration equals 1,000 milligrams per liter, the probability is about 69 percent that the selenium concentration will exceed 5 micrograms per liter, the U.S. Environmental Protection Agency chronic criterion. In areas where the bedrock is not composed of such rocks, the probability is only about 10 percent. The avian-egg data within the biotic data base were used to make a quantitative toxicological risk assessment. Of the 23 study areas where avian eggs were sampled, 14 areas yielded at least one egg containing 6 µg/g selenium, the threshold for embryotoxicity. However, only 6 of the study areas yielded eggs containing enough selenium to expect selenium-induced teratogenesis of duck embryos. Predicted probabilities of discovering embryo teratogenesis matched field observations in 13 of the 14 study areas reporting results of embryo assessments. Bird eggs were collected from 161 individual sampling sites and at 79 of those sites selenium concentrations in one or more eggs exceeded 6 µg/g. At the 79 sites where biological effects are expected on the basis of selenium concentrations in the eggs, the median rate was 3.9 percent of the hens losing at least one egg to selenium-induced embryotoxicity. This corresponds to about 1.2 percent selenium-induced egg inviability among otherwise viable eggs. Across all NIWQP study areas, the overall rate of hens projected to lose at least one egg to selenium-induced embryotoxicity is estimated to be 1.9 percent, which corresponds to about 0.3 percent selenium-induced egg inviability among otherwise viable eggs. After accounting for increased mortality of selenium poisoned-hatchlings due to other factors such as weather and predators, it was estimated that that increases of 0.3 and 1.2 percent in inviable eggs would cause approximately a 1.4 and 5.4 percent depression in nesting success. Regional surveys of nesting success among ducks revealed that duck populations commonly exist near their demographic break-even point. The vulnerable demographic condition of North American duck populations during the mid-1960's to mid-1980's was primarily due to noncontaminant factors, such as poor-quality nesting habitat and dry climatic cycles. Under such conditions, rates of 1.4- to 5.4-percent depression in nesting success caused by exposure to selenium from irrigation projects can be crucial for avian populations already close to their demographic break-even point. Even the worst-case levels of contaminant effects, however, could be tolerated by populations of ducks existing just modestly above demographic break-even points. This suggests the biotic risk to ducks could be addressed by reducing irrigation-induced water pollution but more effectively by restoring high-quality (more predator-safe) nesting habitat. An analysis at the nesting-site level was made of the relation between selenium content of water and bird eggs. Eggs from 93 bird populations were collected from nesting sites where the water sample collected during April-July contained less than 5 µg/L selenium. The average selenium concentration in egg sets was embryotoxic in 19 of the 93 populations. Of the populations collected at sites where the selenium in the water was less than 1 microgram per liter, only four of 54 populations contained embryotoxic concentrations. Eggs from 65 populations of birds were collected from nesting sites where selenium concentrations in water samples collected during April-July equaled or exceeded 5 µg/L, and 55 of those 65 populations contained embryotoxic concentrations of selenium in the eggs. An analysis at the study-area level was made of the relation between selenium contamination of water and selenium contamination of the food chain and egg loss due to selenium poisoning. Most food organisms, particularly aquatic invertebrates and fish, contained potentially harmful amounts of selenium in study areas where selenium concentrations in more than 25 percent of the water samples exceed 5 µg/L. The analysis also indicates that some hens are predicted to lose eggs to selenium poisoning in all study areas where selenium concentrations in more than 25 percent of the water samples exceed 5 µg/L. These results suggest that areas where selenium contamination of the food chain and loss of eggs to selenium poisoning is occurring may be identified using the same methods developed to identify areas where selenium contamination of water is likely to occur.

western United States↗

USGS1989

Acid rain publications by the U.S. Fish and Wildlife Service, 1979-1989

Pollution of aquatic and terrestrial ecosystems has been a concern to society since the burning of fossil fuels began in the industrial revolution. In the past decade or so, this concern has been heightened by evidence that chemical transformation in the atmosphere of combustion by-products and subsequent long-range transport can cause environmental damage in remote areas. The extent of this damage and the rates of ecological recovery were largely unknown. "Acid rain" became the environmental issue of the 1980's. To address the increasing concerns of the public, in 1980 the Federal government initiated a 10-year interagency research program to develop information that could be used by the President and the Congress in making decisions for emission controls. The U.S. Fish and Wildlife Service has been an active participant in acid precipitation research. The Service provided support to a number of scientific conferences and forums, including the Action Seminar on Acid Precipitation held in Toronto, Canada, in 1979, an international symposium on Acidic Precipitation and Fishery Impacts in Northeastern North America in 1981, and a symposium on Acidic Precipitation and Atmospheric Deposition: A Western Perspective in 1982. These meetings as well as the growing involvement with the government's National Acidic Precipitation Assessment Program placed the Service in the lead in research on the biological effects of acidic deposition. Research projects have encompassed water chemistry, aquatic invertebrates, amphibians, fish, and waterfowl. Water quality surveys have been conducted to help determine the extent of acid precipitation effects in the northeast, Middle Atlantic, and Rocky Mountain regions. In addition to lake and stream studies, research in wetland and some terrestrial habitats has also been conducted. Specific projects have addressed important sport species such as brook trout (Salvelinus fontinalis), Atlantic salmon (Salmo salar), and striped bass (Morone saxatilis). Trace metal accumulation in fish has been investigated and a symposium sponsored on related work. U.S> Fish and Wildlife Service scientists serve as advisors and participants in research being conducted by industry, nonprofit groups, State and other Federal agencies. Researcher have worked closely with colleagues in Canada, England, Norway, Scotland, the Soviet Union, and Sweden to gain additional understanding of the problem. In 1982, the Service implemented a mitigation research program to provide resource managers with information to help them protect sensitive ecosystems, and rehabilitation methods for resources already affected by acidification. An international workshop was convened to outline the research needs. Several conferences were organized to develop appropriate field and laboratory procedures. Scientists with the mitigation research program are evaluating the ecological effects of liming (addition of base material) surface waters and surrounding watershed to provide buffering against acidic inputs. Through long-term cooperative project with States and other organizations, investigations are studying possible abatement methods for regions most affected by acidic deposition. To date, more than 200 reports the describe these studies have been published. These products include conference proceedings, journal articles, and in-house scientific publications. An education poster describing the effects of acid rain on aquatic ecosystems was developed and distributed to individuals, conservations and State organizations, and the public education system. This annotated bibliography lists current publications by Service authors, cooperators, or contractors on acid rain and related quality. Entire are arranged alphabetically by author surname. For further information about the research program, contact the U.S. Fish and Wildlife Service, Acid Precipitation Section, National Fishery Research Center -- Leetown, Box 700, Kearneysville, WV 25430.

Biological Report↗

USGS2018

Food‐web structure and ecosystem function in the Laurentian Great Lakes—Toward a conceptual model

The relationship between food‐web structure (i.e., trophic connections, including diet, trophic position, and habitat use, and the strength of these connections) and ecosystem functions (i.e., biological, geochemical, and physical processes in an ecosystem, including decomposition, production, nutrient cycling, and nutrient and energy flows among community members) determines how an ecosystem responds to perturbations, and thus is key to understanding the adaptive capacity of a system (i.e., ability to respond to perturbation without loss of essential functions). Given nearly ubiquitous changing environmental conditions and anthropogenic impacts on global lake ecosystems, understanding the adaptive capacity of food webs supporting important resources, such as commercial, recreational, and subsistence fisheries, is vital to ecological and economic stability. Herein, we describe a conceptual framework that can be used to explore food‐web structure and associated ecosystem functions in large lakes. We define three previously recognised broad habitat compartments that constitute large lake food webs (nearshore, pelagic, and profundal). We then consider, at three levels, how energy and nutrients flow: (a) into each basal resource compartment; (b) within each compartment; and (c) among multiple compartments (coupling). Flexible shifts in food‐web structures (e.g., via consumers altering their diet or habitat) that sustain these flows in the face of perturbations provide evidence for adaptive capacity. We demonstrate the conceptual framework through a synthesis of food‐web structure and ecosystem function in the Laurentian Great Lakes, with emphasis on the upper trophic levels (i.e., fishes). Our synthesis showed evidence of notable adaptive capacity. For example, fishes increased benthic coupling in response to invasion by mussels and round gobies. However, we also found evidence of loss of adaptive capacity through species extirpations (e.g., widespread collapse in the abundance and diversity of ciscoes, Coregonus spp., except in Lake Superior). In large freshwater lakes, fishery managers have traditionally taken a top‐down approach, focusing on stocking and harvest policy. By contrast, water quality managers have focused on nutrient effects on chemical composition and lower trophic levels of the ecosystem. The synthesised conceptual model provides resource managers a tool to more systematically interpret how lower food‐web dynamics influence harvestable fish populations, and vice versa, and to act accordingly such that sustainable resource practices can be achieved. We identify key gaps in knowledge that impede a fuller understanding of the adaptive capacities of large lakes. In general, we found a greater uncertainty in our understanding of processes influencing energy and nutrient flow within and among habitats than flows into the system.

Great Lakes↗

USGS2006

Reproductive condition and occurrence of intersex in bighead carp and silver carp in the Missouri River

Little is known about the reproductive biology of the exotic bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix in the Missouri River. In order to fill this gap in understanding, herein is described the reproductive condition of these Asian carps. Evidence is presented which indicates that bighead and silver carp in the Missouri River have a protracted spawning period that extends from early spring through fall and some individual bighead and silver carp are spawning multiple times during a reproductive season. Although bighead and silver carps are successfully maturing and spawning in the Missouri River some reproductive abnormalities such as intersex, atresia, and sterility were observed. Knowledge of the reproductive activity of these invasive carps may be useful to resource managers tasked with their control. Furthermore, the reproductive abnormalities observed should be considered when evaluating the environmental condition of the Missouri River relative to supporting a healthy fish fauna. ?? Springer 2006.

Hydrobiologia↗

USGS2003

Simulation of Temperature, Nutrients, Biochemical Oxygen Demand, and Dissolved Oxygen in the Catawba River, South Carolina, 1996-97

Time-series plots of dissolved-oxygen concentrations were determined for various simulated hydrologic and point-source loading conditions along a free-flowing section of the Catawba River from Lake Wylie Dam to the headwaters of Fishing Creek Reservoir in South Carolina. The U.S. Geological Survey one-dimensional dynamic-flow model, BRANCH, was used to simulate hydrodynamic data for the Branched Lagrangian Transport Model. Waterquality data were used to calibrate the Branched Lagrangian Transport Model and included concentrations of nutrients, chlorophyll a, and biochemical oxygen demand in water samples collected during two synoptic sampling surveys at 10 sites along the main stem of the Catawba River and at 3 tributaries; and continuous water temperature and dissolved-oxygen concentrations measured at 5 locations along the main stem of the Catawba River. A sensitivity analysis of the simulated dissolved-oxygen concentrations to model coefficients and data inputs indicated that the simulated dissolved-oxygen concentrations were most sensitive to watertemperature boundary data due to the effect of temperature on reaction kinetics and the solubility of dissolved oxygen. Of the model coefficients, the simulated dissolved-oxygen concentration was most sensitive to the biological oxidation rate of nitrite to nitrate. To demonstrate the utility of the Branched Lagrangian Transport Model for the Catawba River, the model was used to simulate several water-quality scenarios to evaluate the effect on the 24-hour mean dissolved-oxygen concentrations at selected sites for August 24, 1996, as simulated during the model calibration period of August 23 27, 1996. The first scenario included three loading conditions of the major effluent discharges along the main stem of the Catawba River (1) current load (as sampled in August 1996); (2) no load (all point-source loads were removed from the main stem of the Catawba River; loads from the main tributaries were not removed); and (3) fully loaded (in accordance with South Carolina Department of Health and Environmental Control National Discharge Elimination System permits). Results indicate that the 24-hour mean and minimum dissolved-oxygen concentrations for August 24, 1996, changed from the no-load condition within a range of - 0.33 to 0.02 milligram per liter and - 0.48 to 0.00 milligram per liter, respectively. Fully permitted loading conditions changed the 24-hour mean and minimum dissolved-oxygen concentrations from - 0.88 to 0.04 milligram per liter and - 1.04 to 0.00 milligram per liter, respectively. A second scenario included the addition of a point-source discharge of 25 million gallons per day to the August 1996 calibration conditions. The discharge was added at S.C. Highway 5 or at a location near Culp Island (about 4 miles downstream from S.C. Highway 5) and had no significant effect on the daily mean and minimum dissolved-oxygen concentration. A third scenario evaluated the phosphorus loading into Fishing Creek Reservoir; four loading conditions of phosphorus into Catawba River were simulated. The four conditions included fully permitted and actual loading conditions, removal of all point sources from the Catawba River, and removal of all point and nonpoint sources from Sugar Creek. Removing the point-source inputs on the Catawba River and the point and nonpoint sources in Sugar Creek reduced the organic phosphorus and orthophosphate loadings to Fishing Creek Reservoir by 78 and 85 percent, respectively.

South Carolina↗

USGS1995

Kodiak brown bears

Brown bears ( Ursus arctos middendorffi ) on the Kodiak Archipelago are famous for their large size and seasonal concentrations at salmon streams. Sport hunting of Kodiak bears has been popular since World War II. Their value as captivating subjects to observe or photograph is a more recent development that is increasing rapidly; visitors from around the world come to experience brown bears on Kodiak, adding substantially to Alaska's economy. An equally important contribution of brown bears is their value as an indicator of ecosystem vitality. Despite high population numbers, Kodiak bears are vulnerable to the environmental effects that have seriously depleted brown bear populations in Europe and parts of North America (Cowan 1972; Servheen 1990). They are long-lived mammals that require large expanses of land to meet biological needs, and their low reproductive rate limits population recovery. Energy development, depletion of salmon resources, and recreational growth are factors that can adversely affect bears and, in doing so, signal a loss of environmental quality affecting many species. Management of Kodiak brown bears is directed at maintaining current density, distribution, and habitat-use patterns. This goal is challenged by growing levels of commercial and private use throughout the region. An immediate concern is cabin and lodge development on 121,500 ha (300,000 acres), formerly part of the Kodiak National Wildlife Refuge, that were deeded to Alaska Natives via the Alaska Native Claims Settlement Act. Much of that Native-conveyed land is coastal or riparian habitat especially important to brown bears during summer and fall. Concurrently, recreational use of the Kodiak refuge is increasing about 10% annually (USFWS 1987). Sport fishing, bear photography, and deer and elk hunting often put bears and humans in direct conflict (Smith et al. 1989). Timber harvest on Afognak Island, uncertain trends of salmon populations due to natural or human-caused events (e.g., Exxon Valdez oil spill), and hydroelectric development (Smith and Van Daele 1990) could impose additional long-term effects on localized bear populations.

Alaska↗

USGS2013

Selenium in ecosystems within the mountaintop coal mining and valley-fill region of southern West Virginia-assessment and ecosystem-scale modeling

Coal and associated waste rock are among environmental selenium (Se) sources that have the potential to affect reproduction in fish and aquatic birds. Ecosystems of southern West Virginia that are affected by drainage from mountaintop coal mines and valleys filled with waste rock in the Coal, Gauley, and Lower Guyandotte watersheds were assessed during 2010 and 2011. Sampling data from earlier studies in these watersheds (for example, Upper Mud River Reservoir) and other mining-affected watersheds also are included to assess additional hydrologic settings and food webs for comparison. Basin schematics give a comprehensive view of sampled species and Se concentration data specific to location and date. Food-web diagrams document the progression of Se trophic transfer across suspended particulate material, invertebrates, and fish for each site to serve as the basis for developing an ecosystem-scale model to predict Se exposure within the hydrologic conditions and food webs of southern West Virginia. This approach integrates a site-specific predator’s dietary exposure pathway into modeling to ensure an adequate link to Se toxicity and, thus, to species vulnerability. Site-specific fish abundance and richness data in streams documented various species of chub, shiner, dace, darters, bass, minnow, sunfish, sucker, catfish, and central stoneroller (Campostoma anomalum), mottled sculpin (Cottus bairdii), and least brook lamprey (Lampetra aepyptera). However, Se assessment species for streams, and hence, model species for streams, were limited to creek chub (Semotilus atromaculatus) and central stoneroller. Both of these species of fish are generally considered to have a high tolerance for environmental stress based on traditional comparative fish community assessment, with creek chub being present at all sites. Aquatic insects (mayfly, caddisfly, stonefly, dobsonfly, chironomid) were the main invertebrates sampled in streams. Collection of suspended particulate material acted as an integrator of organic-rich, fine-grained biomass present in streams. The base-case food web modeled for streams was suspended particulate material to aquatic insect to creek chub, with comparative modeling of a direct particulate-to-stoneroller food web. Model species for a reservoir setting were based on an earlier study of bluegill sunfish (Lepomis macrochirus), green sunfish (Lepomis cyanellus), and largemouth bass (Micropterus salmoides). Several reservoir food webs were considered based on a variety of invertebrates (insect, snail, clam). For stream and reservoir settings, predicted Se concentrations in exposure scenarios showed a high degree of correlation (r 2 = 0.91 for invertebrates and 0.75 for fish) with field observations of Se concentrations when modeling was initiated from suspended-particulate-material Se concentrations and model transfer parameters defined previously in the literature were used. These strong correlations validate the derived site-specific model and establish sufficient confidence that the predictions from the developed model can be quantitatively applied to the ecosystems in southern West Virginia. An application of modeling used a metric describing the partitioning of Se between particulate material and dissolved phases (K d ) to allow determination of a dissolved Se concentration that would be necessary to attain a site-specific Se fish body burden. The operationally defined K d quantifies the complex process of transformation at the base of a food web on a site-specific basis. The magnitude of this metric is known to vary with such factors as Se speciation, particulate-material type, and hydrology. This application (1) ties dissolved Se concentrations to fish tissue concentrations; (2) allows consideration of different choices for intervening site-specific exposure steps that set Se bioaccumulation, partitioning, and bioavailability; and (3) generates implications for management decisions that define protection through different regulatory pathways and guidelines. The range of model outcomes accounts for critical sources of variability and establishes whether site and food-web characterization were adequate to represent the dynamics of the system with certainty. This is especially true in terms of particulate-material phases at the base of the food web and utilization of K d in different hydrologic settings. For streams, a range of field-derived K d ds were applied to food-web exposure scenarios within a framework of locational and hydrologic variables (area of stream basin; stream gradient and discharge) that may affect the magnitude of K d . Overlaying even a coarse temporal scale that acknowledges variability in stream dissolved Se and Se speciation, such as through seasonal derivation of K d , can substantially narrow model uncertainty. Modeling that constrains the place and time of greatest ecosystem Se sensitivity within a specified food web gives insight into Se risk and identifies controlling management alternatives within a watershed or stream basin. If there is a range of hydrologic settings, specificity is needed to establish a hierarchy of in-stream and off-stream habitats for a watershed approach that takes into account Se-enriched water moving through different K d and food web environments. If there is a range of predator vulnerabilities (measured as a combination of food-web Se biodynamics and response in Se toxicity tests) within the site-specific community of fish species to be protected, then choice of fish species is critical to protection because it determines the food web and, hence, the magnitude of biotransfer through which Se is modeled. Whether creek chub is representative of the vulnerability to Se of all fish species encountered within the study-site ecosystems will require additional species-specific data and analysis. A range of site-specific scenarios illustrated here set model outcomes, but the final quantitative evaluation of alternatives and their implications will be those generated through choices and guidance formulated by state and other agencies in their decisionmaking processes. Proposed additions and refinements to the ecosystem-scale site-specific approach developed here include consideration of: measurement of temporally matched pairs of dissolved and suspended-particulate-material Se concentrations across a broader range of stream sites to expand the stream K d database and to test the representativeness of a suspended-particulate-material sample within a stream; characterization of different phases of particulate material across seasons to better define the base of the food web and connect to invertebrate feeding; refinement of model assumptions concerning dietary preferences and composition for fish to develop additional trophic transfer factors (TTFs) (for example, calculation of TTFinvertebrate composite for mixed diets); expansion of modeling of fish species and their food webs to include Se-vulnerable species; temporal characterization of a predator’s life cycle and habitat use as additional model layers to integrate with Se biodynamics in streams; investigation of the effect of stream gradient on K d based on a finer scale than presented here in terms of such variables as residence time, watershed dilution, and physical habitat attributes (for example, amount of ponding versus run or riffle within a stream); and linkage to discharge through use of stream gaging to record variability and enable model organization within water-year types and discharge seasons. Investigating the presence and variability of prey and predator species in demographically open systems such as streams also is key to model outcomes given the overall environmental stressors (for example, general landscape change, food-web disruption, recolonization potential) imposed on the composition of biological communities in coal mining and valley-fill affected watersheds

West Virginia↗

USGS2020

Fisheries research and monitoring activities of the Lake Erie Biological Station, 2019

A comprehensive understanding of fish populations and their interactions is the cornerstone of modern fishery management and the basis for Fish Community Goals and Objectives for Lake Erie (Ryan et al. 2003). This report is responsive to U.S. Geological Survey (USGS) obligations via Memorandum of Understanding (MOU) with the Great Lakes Council of Lake Committees (CLC) to provide scientific information in support of fishery management. Goals for the USGS Great Lakes Deepwater Fish Assessment and Ecological Studies in 2019 were to monitor long-term changes in the fish community and population dynamics of key fishes of interest to management agencies. Specific to Lake Erie, expectations of this agreement were sustained investigations of native percids, forage (prey) fish populations, and Lake Trout. Our 2019 deepwater program operations began in April and concluded in December, and utilized trawl, gillnet, hydroacoustic, lower trophic sampling, and telemetry methods. This work resulted in 88 bottom trawls covering 65 ha of lake-bottom and catching 24,140 fish totaling 3,622 kg during three separate trawl surveys in the West and Central basins of Lake Erie. Overnight gillnet sets (n=44) for cold water species were performed at 42 unique locations in the West and East basins of Lake Erie. A total of 8.0 km of gillnet was deployed during these surveys, which caught 286 fish, 114 of which were native coldwater species: Lake Trout, Burbot, and Lake Whitefish. USGS hydroacoustic surveys in 2019 produced 240 km of transects, and lower trophic sampling provided data from zooplankton samples (n=21) and water quality profiles (n=21) to populate a database maintained by the Ontario Ministry of Natural Resources and Forestry (OMNRF), Ohio Division of Natural Resources (ODNR), Michigan Division of Natural Resources (MDNR), Pennsylvania Fish and Boat Commission (PFBC), and New York State Department of Environmental Conservation (NYSDEC). USGS also assisted CLC member agencies with deployment and maintenance of the Great Lakes Acoustic Telemetry Observation System (GLATOS) throughout all three Lake Erie sub-basins, supporting multiple coordinated telemetry investigations. In 2019, Lake Trout investigations included annual gill net surveys and acoustic telemetry of spawning migration and habitat use in coordination with OMNRF, NYSDEC, and PFBC. Results from Lake Trout investigations were reported in the Coldwater Task Group annual report to the Great Lakes Fishery Commission (GLFC) and the CLC (Coldwater Task Group 2020). Likewise, interagency forage fish assessments conducted with hydroacoustics were summarized and reported in the Forage Task Group annual report (Forage Task Group 2020). This report presents biomass-based summaries of fish communities in western Lake Erie derived from USGS bottom trawl surveys conducted from 2013 to 2019 during June and September. The survey design provided temporal and spatial coverage that did not exist in the historic interagency trawl database, and thus complemented the August ODNR-OMNRF effort to reinforce stock assessments with more robust data. Analyses herein evaluated trends in: total biomass, abundance of dominant predator and forage species, non-native species composition, biodiversity and community structure. Data from this effort can be explored interactively online (https://lebs.shinyapps.io/western-basin/), and are accessible for download (https://doi.org/10.5066/P9LL6YOR, Keretz et al. 2020). Annual survey data are added to these sources as the data become available.

Lake Erie↗

USGS1997

Comparison of three qualitative habitat indices and their applicability to prairie streams

Qualitative stream habitat indices are important tools in classifying, interpreting, and assessing the conditions of stream ecosystems. Habitat indices are numerical values produced from scoring various features of a stream. Three commonly used habitat indices are the qualitative habitat evaluation index (QHEI), the rapid bioassessment protocols (RBP), and the riparian, channel, and environmental inventory (RCE). All three indices were used to assess the habitat conditions of 18 prairie streams of different sizes and environmental settings in the Red River of the North basin. Correlations suggest that these three indices provide similar results (r ranged from 0.83 to 0.85, P ≤ 0.003); however, the indices emphasize different aspects of the stream environment. Metrics from each index were classified as one of the following: channel geomorphology, riparian zone, substrate related, and instream cover and biota. The QHEI and RBP indices emphasize channel geomorphology metrics (41% of total score for the QHEI and 42% of the total score for the RBP). The RCE had a more balanced emphasis among the four classes but emphasized riparianzone metrics (32% of total score). There is redundancy within indices. Several metrics showed high correlations (e.g., r = 0.74 for land use and riparian-zone width in QHEI; r = 0.86 for bank vegetative protection and bank condition in RBP; r = 0.83 for macrobenthos and fish in RCE). To evaluate biological applicability, index scores were correlated to scores of the index of biotic integrity and fish community statistics of species richness, evenness, diversity, and percent of individuals in four trophic groups. No significant correlations were identified. We concluded that the metrics making up the habitat indices were either not applicable or not weighted appropriately for northern prairie streams.

North American Journal of Fisheries Management↗

USGS2014

A multi-scaled approach to evaluating the fish assemblage structure within southern Appalachian streams USA.

There is considerable uncertainty about the relative roles of stream habitat and landscape characteristics in structuring stream-fish assemblages. We evaluated the relative importance of environmental characteristics on fish occupancy at the local and landscape scales within the upper Little Tennessee River basin of Georgia and North Carolina. Fishes were sampled using a quadrat sample design at 525 channel units within 48 study reaches during two consecutive years. We evaluated species–habitat relationships (local and landscape factors) by developing hierarchical, multispecies occupancy models. Modeling results suggested that fish occupancy within the Little Tennessee River basin was primarily influenced by stream topology and topography, urban land coverage, and channel unit types. Landscape scale factors (e.g., urban land coverage and elevation) largely controlled the fish assemblage structure at a stream-reach level, and local-scale factors (i.e., channel unit types) influenced fish distribution within stream reaches. Our study demonstrates the utility of a multi-scaled approach and the need to account for hierarchy and the interscale interactions of factors influencing assemblage structure prior to monitoring fish assemblages, developing biological management plans, or allocating management resources throughout a stream system.

Georgia, North Carolina, Tennessee↗

USGS2021

Interaction between sex and contaminant type attributable to males eliminating mercury at a faster rate

The observed interaction between sex and contaminant type (polychlorinated biphenyls (PCBs) or mercury (Hg)) in adult teleost fishes is most likely due to adult males having a substantially higher Hg-elimination rate than adult females. In contrast, long-term elimination of PCBs by teleost fishes has been characterized as negligible for both sexes. In addition, the variation in the differences between the PCB ratio (ratio of whole-fish PCB concentration in males to whole-fish PCB concentration in females) and Hg ratio (ratio of whole-fish Hg concentration in males to whole-fish Hg concentration in females) across species appears to be attributable, at least in part, to variation in Hg-elimination rates of adult males across species. According to this proposed relationship, the difference between the two ratios increases with increasing Hg-elimination rate of adult males. Further, the variation in Hg-elimination rates of adult males across species appears to be partly explained by levels of certain androgens in the males. In mammals, the key androgen enhancing Hg-elimination rate in males is testosterone. Hg-elimination rate increases with increasing testosterone level. In teleost fishes, testosterone and 11-ketotestosterone are the agents likely responsible for enhanced Hg-elimination rate in adult males. I uncovered new evidence to indicate that the variability in Hg-elimination rates of adult males across strains of laboratory mice (Mus musculus) is explained, at least in part, by variability in testosterone levels in adult males across strains. Specifically, Hg-elimination rate of the adult males tends to increase with increasing testosterone level. This new evidence supported the abovementioned hypotheses.

Great Lakes, New Jersey coast↗

USGS2018

Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales

Developing fast, cost-effective assessments of wild animal abundance is an important goal for many researchers, and environmental DNA (eDNA) holds much promise for this purpose. However, the quantitative relationship between species abundance and the amount of DNA present in the environment is likely to vary substantially among taxa and with ecological context. Here, we report a strong quantitative relationship between eDNA concentration and the abundance of spawning sockeye salmon in a small stream in Alaska, USA, where we took temporally- and spatially-replicated samples during the spawning period. This high-resolution dataset suggests that (1) eDNA concentrations vary significantly day-to-day, and likely within hours, in the context of the dynamic biological event of a salmon spawning season; (2) eDNA, as detected by species-specific quantitative PCR probes, seems to be conserved over short distances (tens of meters) in running water, but degrade quickly over larger scales (ca. 1.5 km); and (3) factors other than the mere presence of live, individual fish — such as location within the stream, live/dead ratio, and water temperature — can affect the eDNA-biomass correlation in space or time. A multivariate model incorporating both biotic and abiotic variables accounted for over 75% of the eDNA variance observed, suggesting that where a system is well-characterized, it may be possible to predict species' abundance from eDNA surveys, although we underscore that species- and system-specific variables are likely to limit the generality of any given quantitative model. Nevertheless, these findings provide an important step toward quantitative applications of eDNA in conservation and management.

Alaska↗

USGS2005

Visitor and community survey results for Kilauea Point National Wildlife Refuge and Lighthouse: Completion report

The U.S. Fish and Wildlife Service (USFWS) and the Central Federal Lands Highway Division of the Federal Highway Administration, U.S. Department of Transportation are currently pursuing the planning and potential design of an alternative transportation system (ATS) for Kilauea Point National Wildlife Refuge (Refuge or Kilauea Point NWR). The USFWS and CFLHD seek an alternative transportation solution that provides the highest quality visitor experience and is sensitive to biological and cultural resources and the needs of the local community. In planning the alternative transportation system, managers need to consider how an ATS would change factors such as visitor access, visitor experience, visitor willingness to pay, and visitor net economic benefits. The Policy Analysis and Science Assistance branch (PASA) at the U.S. Geological Survey Fort Collins Science Center is dedicated to studying relations between humans and the environment. The objective of PASA is to conduct studies to understand how humans are affected by environmental management decisions and how human activities impact use and conservation of natural resources.

Hawaii↗

USGS2023

Climate change and pulse migration: Intermittent Chugach Inuit occupation of glacial fiords on the Kenai Coast, Alaska

For millennia, Inuit peoples of the Arctic and Subarctic have been challenged by the impacts of climate change on the abundance of key subsistence species. Responses to climate-induced declines in animal populations included switching to alternative food sources and/or migrating to regions of greater availability. We examine these dynamics for the Chugach Inuit (Sugpiat) people of southern coastal Alaska by synthesizing a large body of evidence from archeological sites, including radiocarbon dates and archaeofaunal assemblages, and by applying contemporary knowledge of glaciomarine ecosystems, spatial patterns of resource richness, and ocean-climate induced regime shifts in the Gulf of Alaska. We hypothesize that Chugach groups migrated from Cook Inlet and Prince William Sound to the Kenai Peninsula during periods of low sea surface temperatures (SSTs) to harvest harbor seals, which were seasonally aggregated near tidewater glaciers during pupping season, as well as piscivorous seabirds, Pacific cod, and other species that thrive under cool ocean conditions. During warming phases, the Chugach returned to Cook Inlet and Prince William Sound to fish for salmon and other species that abound during higher SSTs. Drivers of this coupled human-natural system of repeated (pulse) migration include the Pacific Decadal Oscillation (PDO), the dominant pattern of sea surface temperatures in the North Pacific that has been shown to generate step-like regime shifts in the marine food web; and coastal glaciers that structure the functioning of fiord ecosystems and support high levels of biological productivity. The culturally-constructed Chugach niche in the glaciomarine habitat of the Gulf of Alaska was based on intergenerationally transmitted ecological knowledge that enabled a resilient, mobile response to climate and resource variation.

Alaska↗

USGS2018

Habitat mosaics and path analysis can improve biological conservation of aquatic biodiversity in ecosystems with low-head dams

Conserving native biodiversity depends on restoring functional habitats in the face of human-induced disturbances. Low-head dams are a ubiquitous human impact that degrades aquatic ecosystems worldwide. To improve our understanding of how low-head dams impact habitat and associated biodiversity, our research examined complex interactions among three spheres of the total environment. i.e., how low-head dams ( anthroposphere ) affect aquatic habitat ( hydrosphere ), and native biodiversity ( biosphere ) in streams and rivers. Creation of lake-like habitats upstream of low-head dams is a well-documented major impact of dams. Alterations downstream of low head dams also have important consequences, but these downstream dam effects are more challenging to detect. In a multidisciplinary field study at five dammed and five undammed sites within the Neosho River basin, KS, we tested hypotheses about two types of habitat sampling (transect and mosaic) and two types of statistical analyses (analysis of covariance and path analysis). We used fish as our example of biodiversity alteration. Our research provided three insights that can aid environmental professionals who seek to conserve and restore fish biodiversity in aquatic ecosystems threatened by human modifications. First, a mosaic approach identified habitat alterations below low-head dams (e.g. increased proportion of riffles) that were not detected using the more commonly-used transect sampling approach. Second, the habitat mosaic approach illustrated how low-head dams reduced natural variation in stream habitat. Third, path analysis, a statistical approach that tests indirect effects, showed how dams, habitat, and fish biodiversity interact. Specifically, path analysis revealed that low-head dams increased the proportion of riffle habitat below dams, and, as a result, indirectly increased fish species richness . Furthermore, the pool habitat that was created above low-head dams dramatically decreased fish species richness. As we show here, mosaic habitat sampling and path analysis can help conservation practitioners improve science-based management plans for disturbed aquatic systems worldwide.

Kansas↗

USGS2020

Resilience management for conservation of inland recreational fisheries

Resilience thinking has generated much interest among scientific communities, yet most resilience concepts have not materialized into management applications. We believe that using resilience concepts to characterize systems and the social and ecological processes affecting them is a way to integrate resilience into better management decisions. This situation is exemplified by inland recreational fisheries, which represent complex socioecological systems that face unpredictable and unavoidable change. Making management decisions in the context of resilience is increasingly important given mounting environmental and anthropogenic perturbations to inland systems. Herein, we propose a framework that allows resilience concepts to be better incorporated into management by (i) recognizing how current constraints and management objectives focus on desired or undesired systems (specific fish and anglers), (ii) evaluating the state of a system in terms of how both social and ecological forces enforce or erode the desired or undesired system, (iii) identifying the resilience-stage cycles a system state may undergo, and (iv) determining the broad management strategies that may be viable given the system state and resilience stage. We use examples from inland recreational fisheries to illustrate different system state and resilience stages and synthesize several key results. Across all combinations of socioecological forces, five common types of viable management strategies emerge: (i) adopt a different management preference or focus, (ii) change stakeholder attitudes or behaviors via stakeholder outreach, (iii) engage in (sometimes extreme) biological intervention, (iv) engage in fishery intervention, and (v) adopt landscape-level management approaches focusing on achieving different systems in different waters. We then discuss the challenges and weaknesses of our approach, including specifically the cases in which there are multiple strong social forces (i.e., stakeholders holding competing objectives or values) and situations where waters are not readily divisible, such as rivers or great lakes, and in which spatial separation of competing objectives will be difficult. We end with our vision of how we believe these types of operationalized resilience approaches could improve or transform inland recreational fisheries management.

Frontiers in Ecology and Evolution↗

USGS2023

A science and management partnership to restore coregonine diversity to the Laurentian Great Lakes

Similar to many freshwater ecosystems, the Laurentian Great Lakes of North America have undergone numerous anthropogenic stressors resulting in considerable loss of biodiversity and habitat. Among Great Lakes fishes, the coregonine sub-family has endured the most extensive declines, including extinction of several species ( Coregonus johannae, C. alpenae , and C. kiyi orientalis ) and at least 10 instances of local extirpations of other species ( C. nigripinnis, C. reighardi, C. zenithicus, C. hoyi , and C. artedi ) across all 5 lakes, much of which occurred prior to the 1960s owing to overfishing, interactions with non-indigenous species, and habitat loss. Despite these declines, no federal-, provincial-, or state-mandated actions were ever implemented to conserve coregonine diversity, potentially because so much of the coregonine declines occurred prior to the enactment of federal conservation legislation. Possible explanations for inaction since enactment of that legislation include insufficient data on biological vulnerability or threats, unresolved taxonomy, and limited support from the fishery management agencies and their stakeholders prior to the 2000s. In recent decades, however, several fishery management agencies have undertaken efforts to re-introduce coregonine diversity. These efforts helped lead to development of a science-based framework to restore coregonines that was universally endorsed by fishery managers representing eight U.S. states, four U.S. tribal organizations, and the province of ON, Canada, in May 2018. The basin-wide framework is based on principles of conservation biology and adaptive management. We describe details of its key steps, including planning, restoring, and evaluating, while also describing recent implementation efforts to develop methods, improve available resources, and enhance coordination across the basin. Although our paper describes a regional effort to restore native coregonines, our adaptive-management approach could be used by other multi-agency stakeholders seeking to conserve or restore native fishes.

Laurentian Great Lakes↗