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USGS2006

Sedimentation and Occurrence and Trends of Selected Chemical Constituents in Bottom Sediment, Empire Lake, Cherokee County, Kansas, 1905-2005

For about 100 years (1850-1950), the Tri-State Mining District in parts of southeast Kansas, southwest Missouri, and northeast Oklahoma was one of the primary sources of lead and zinc ore in the world. The mining activity in the Tri-State District has resulted in substantial historical and ongoing input of cadmium, lead, and zinc to the environment including Empire Lake in Cherokee County, southeast Kansas. The environmental contamination caused by the decades of mining activity resulted in southeast Cherokee County being listed on the U.S. Environmental Protection Agency's National Priority List as a superfund hazardous waste site in 1983. To provide some of the information needed to support efforts to restore the ecological health of Empire Lake, a 2-year study was begun by the U.S. Geological Survey in cooperation with the U.S. Fish and Wildlife Service and the Kansas Department of Health and Environment. A combination of sediment-thickness mapping and bottom-sediment coring was used to investigate sediment deposition and the occurrence of cadmium, lead, zinc, and other selected constituents in the bottom sediment of Empire Lake. The total estimated volume and mass of bottom sediment in Empire Lake were 44 million cubic feet and 2,400 million pounds, respectively. Most of the bottom sediment was located in the main body and the Shoal Creek arm of the reservoir. Minimal sedimentation was evident in the Spring River arm of the reservoir. The total mass of cadmium, lead, and zinc in the bottom sediment of Empire Lake was estimated to be 78,000 pounds, 650,000 pounds, and 12 million pounds, respectively. In the bottom sediment of Empire Lake, cadmium concentrations ranged from 7.3 to 76 mg/kg (milligrams per kilogram) with an overall median concentration of 29 mg/kg. Compared to an estimated background concentration of 0.4 mg/kg, the historical mining activity increased the median cadmium concentration by about 7,200 percent. Lead concentrations ranged from 100 to 950 mg/kg with an overall median concentration of 270 mg/kg. Compared to an estimated background concentration of 33 mg/kg, the median lead concentration was increased by about 720 percent as a result of mining activities. The range in zinc concentrations was 1,300 to 13,000 mg/kg with an overall median concentration of 4,900 mg/kg. Compared to an estimated background concentration of 92 mg/kg, the median zinc concentration was increased by about 5,200 percent. Within Empire Lake, the largest sediment concentrations of cadmium, lead, and zinc were measured in the main body of the reservoir. Within the Spring River arm of the reservoir, increased concentrations in the downstream direction likely were the result of tributary inflow from Short Creek, which drains an area that has been substantially affected by historical lead and zinc mining. Compared to nonenforceable sediment-quality guidelines, all Empire Lake sediment samples (representing 21 coring sites) had cadmium concentrations that exceeded the probable-effects guideline (4.98 mg/kg), which represents the concentration above which toxic biological effects usually or frequently occur. With one exception, cadmium concentrations exceeded the probable-effects guideline by about 180 to about 1,400 percent. With one exception, all sediment samples had lead concentrations that exceeded the probable-effects guideline (128 mg/kg) by about 10 to about 640 percent. All sediment samples had zinc concentrations that exceeded the probable-effects guideline (459 mg/kg) by about 180 to about 2,700 percent. Overall, cadmium, lead, and zinc concentrations in the bottom sediment of Empire Lake have decreased over time following the end of lead and zinc mining in the area. However, the concentrations in the most recently deposited bottom sediment (determined for 4 of 21 coring sites) still exceeded the probable-effects guideline by about 440 to 640 percent for cadmium, about 40 to 80 percent for lead, and about 580

Scientific Investigations Report↗
USGS2001

Gore Creek watershed, Colorado — Assessment of historical and current water quantity, water quality, and aquatic ecology, 1968–98

The historical and current (1998) water-quantity, water-quality, and aquatic-ecology conditions in the Gore Creek watershed are described as part of a study by the U.S. Geological Survey, done in cooperation with the Town of Vail, the Eagle River Water and Sanitation District, and the Upper Eagle Regional Water Authority. Interpretation of the available water-quantity, water-quality, and aquatic-ecology data collected by various agencies since 1968 showed that background geology and land use in the watershed influence the water quality and stream biota. Surface-water nutrient concentrations generally increased as water moved downstream through the Town of Vail, but concentrations at the mouth of Gore Creek were typical when compared with national data for urban/undeveloped sites. Nitrate concentrations in Gore Creek were highest just downstream from a wastewater-treatment plant discharge, but concentrations decreased at sites farther downstream because of dilution and nitrogen uptake by algae. Recent total phosphorus concentrations were somewhat elevated when compared to the U.S. Environmental Protection Agency recommended level of 0.10 milligram per liter for control of eutrophication in flowing water. However, total phosphorus concentrations at the mouth of Gore Creek were relatively low when compared to a national study of phosphorus in urban land-use areas. Historically, suspended sediment associated with construction of Interstate 70 in the early 1970's has been of primary concern; however, recent data indicate that streambed aggradation of sediment originating from Interstate 70 traction sanding currently is a greater concern. About 4,000 tons of coarse sand and fine gravel is washed into Black Gore Creek each year following application of traction materials to Interstate 70 during adverse winter driving conditions. Suspended-sediment concentrations were low in Black Gore Creek; however, bedload-transport rates of as much as 4 tons per day have been measured. Water samples were collected during spring and fall of 1997 from five alluvial monitoring wells located throughout the Town of Vail. Nutrient concentrations generally were low in the alluvial monitoring wells. Specific-conductance values ranged from 265 to 557 microsiemens per centimeter at 25 degrees Celsius. Concentrations of radon in monitoring-well samples exceeded the 300-picocuries-per-liter U.S. Environmental Protection Agency proposed maximum contaminant level (which has been suspended pending further review). Low levels of bacteria and methylene blue active substances indicate there is little or no wastewater contamination of shallow ground water in the vicinity of the monitoring wells and one of the municipal water-supply wells. Ground-water ages in the alluvial aquifer ranged from about 2 to about 50 years old. These ages indicate that changes in land-management practices may not have an effect on ground-water quality for many years. Differences in macroinvertebrate-community structure were found among sites in Gore Creek by evaluating changes in relative abundance, total abundance, and dominant functional feeding groups of the major macroinvertebrate groups. Ephemeroptera (mayflies), Plecoptera (stoneflies), Trichoptera (caddisflies), and Coleoptera (beetles) exhibited relatively low tolerance to water-quality degradation when compared with Diptera (midges) and non-insects (sludge worms). More than 80 percent of the macroinvertebrate community at sites located farthest upstream was composed of mayflies, stoneflies, and caddisflies, indicating favorable water-quality and habitat conditions. The relative percentages of midges and sludge worms greatly increased in the downstream reaches of Gore Creek, which drain relatively larger areas of urban and recreation land uses, indicating the occurrence of nutrient and organic enrichment in Gore Creek. The macroinvertebrate community in Black Gore Creek indicated adverse effects from sediment deposition. Macroinvertebrate abundance was considerably reduced at the two sites where streambed sediment was more prevalent; however, differences in abundance also may have been related to differences in habitat and availability of food resources. The lower 4 miles of Gore Creek, downstream from Red Sandstone Creek, have been designated a Gold Medal fishery in recognition of the high recreational value of the abundant brown trout community. Gore Creek contained twice as many trout as a reference site with similar habitat characteristics in Rocky Mountain National Park. Moderate increases in nutrient concentrations above background conditions have increased the growth and abundance potential for aquatic life in Gore Creek, while at the same time, esthetic and water-quality conditions have remained favorable. The spatial distribution of nitrate concentrations was consistent with the observed spatial distribution of algal biomass and macroinvertebrate-community characteristics. Algal biomass was limited by available resources (sunlight and nutrients) in the upstream reaches of Gore Creek and limited by macroinvertebrate grazing and water-quality conditions in the downstream reaches. The fish community has benefited from enhanced biological production in the downstream reach of Gore Creek. Increases in algal biomass and macroinvertebrate abundance, in response to higher nutrient concentrations, provide ample food resources necessary to support the abundant fish community. Trace-element data for surface water, ground water, streambed sediment, fish tissue, and macroinvertebrate tissue indicate that concentrations are generally low in the Gore Creek watershed. In streambed-sediment samples, cadmium, copper, and zinc concentrations were below background levels reported for the Upper Colorado River Basin in Colorado. Concentrations of cadmium, copper, iron, and silver in surface water have occasionally exceeded stream standards in the past, but recent surface-water data indicate these trace elements currently are not of concern. Manganese concentrations commonly exceeded the 50-microgram-per-liter stream standard in Black Gore Creek. Elevated manganese concentrations were primarily attributable to the sedimentary geology of the area. Concentrations of organic constituents are low in the Gore Creek watershed. Pesticides were detected infrequently and at low concentrations in surface-water, ground-water, bed-sediment, and whole-body fish-tissue samples. Volatile organic compounds also were detected at low concentrations in surface- and ground-water samples.

Colorado↗
USGS2016

A global review of freshwater crayfish temperature tolerance, preference, and optimal growth

Conservation efforts, environmental planning, and management must account for ongoing ecosystem alteration due to a changing climate, introduced species, and shifting land use. This type of management can be facilitated by an understanding of the thermal ecology of aquatic organisms. However, information on thermal ecology for entire taxonomic groups is rarely compiled or summarized, and reviews of the science can facilitate its advancement. Crayfish are one of the most globally threatened taxa, and ongoing declines and extirpation could have serious consequences on aquatic ecosystem function due to their significant biomass and ecosystem roles. Our goal was to review the literature on thermal ecology for freshwater crayfish worldwide, with emphasis on studies that estimated temperature tolerance, temperature preference, or optimal growth. We also explored relationships between temperature metrics and species distributions. We located 56 studies containing information for at least one of those three metrics, which covered approximately 6 % of extant crayfish species worldwide. Information on one or more metrics existed for all 3 genera of Astacidae, 4 of the 12 genera of Cambaridae, and 3 of the 15 genera of Parastacidae. Investigations employed numerous methodological approaches for estimating these parameters, which restricts comparisons among and within species. The only statistically significant relationship we observed between a temperature metric and species range was a negative linear relationship between absolute latitude and optimal growth temperature. We recommend expansion of studies examining the thermal ecology of freshwater crayfish and identify and discuss methodological approaches that can improve standardization and comparability among studies.

Reviews in Fish Biology and Fisheries↗
USGS2006

Cadmium risks to freshwater life: derivation and validation of low-effect criteria values using laboratory and field studies

In 2001, the U.S. Environmental Protection Agency (EPA) released updated aquatic life criteria for cadmium. Since then, additional data on the effects of cadmium to aquatic life have become available from studies supported by the EPA, Idaho Department of Environmental Quality (IDEQ), and the U.S. Geological Survey, among other sources. Updated data on the effects of cadmium to aquatic life were compiled and reviewed and low-effect concentrations were estimated. Low-effect values were calculated using EPA's guidelines for deriving numerical national water-quality criteria for the protection of aquatic organisms and their uses. Data on the short-term (acute) effects of cadmium on North American freshwater species that were suitable for criteria derivation were located for 69 species representing 57 genera and 33 families. For longer-term (chronic) effects of cadmium on North American freshwater species, suitable data were located for 28 species representing 21 genera and 17 families. Both the acute and chronic toxicity of cadmium were dependent on the hardness of the test water. Hardness-toxicity regressions were developed for both acute and chronic datasets so that effects data from different tests could be adjusted to a common water hardness. Hardness-adjusted effects values were pooled to obtain species and genus mean acute and chronic values, which then were ranked by their sensitivity to cadmium. The four most sensitive genera to acute exposures were, in order of increasing cadmium resistance, Oncorhynchus (Pacific trout and salmon), Salvelinus ('char' trout), Salmo (Atlantic trout and salmon), and Cottus (sculpin). The four most sensitive genera to chronic exposures were Hyalella (amphipod), Cottus, Gammarus (amphipod), and Salvelinus. Using the updated datasets, hardness dependent criteria equations were calculated for acute and chronic exposures to cadmium. At a hardness of 50 mg/L as calcium carbonate, the criterion maximum concentration (CMC, or 'acute' criterion) was calculated as 0.75 mug/L cadmium using the hardness-dependent equation CMC = e(0.8403 ? ln(hardness)-3.572) where the 'ln hardness' is the natural logarithm of the water hardness. Likewise, the criterion continuous concentration (CCC, or 'chronic' criterion) was calculated as 0.37 mug/L cadmium using the hardness-dependent equation CCC = (e(0.6247 ? ln(hardness)-3.384)) ? (1.101672 - ((ln hardness) ? 0.041838))). Using data that were independent of those used to derive the criteria, the criteria concentrations were evaluated to estimate whether adverse effects were expected to the biological integrity of natural waters or to selected species listed as threatened or endangered. One species was identified that would not be fully protected by the derived CCC, the amphipod Hyalella azteca. Exposure to CCC conditions likely would lead to population decreases in Hyalella azteca, the food web consequences of which probably would be slight if macroinvertebrate communities were otherwise diverse. Some data also suggested adverse behavioral changes are possible in fish following long-term exposures to low levels of cadmium, particularly in char (genus Salvelinus). Although ambiguous, these data indicate a need to periodically review the literature on behavioral changes in fish following metals exposure as more information becomes available. Most data reviewed indicated that criteria conditions were unlikely to contribute to overt adverse effects to either biological integrity or listed species. If elevated cadmium concentrations that approach the chronic criterion values occur in ambient waters, careful biological monitoring of invertebrate and fish assemblages would be prudent to validate the prediction that the assemblages would not be adversely affected by cadmium at criterion concentrations.

Scientific Investigations Report↗
USGS2017

Contaminants of emerging concern in the Great Lakes Basin: A report on sediment, water, and fish tissue chemistry collected in 2010-2012

Despite being detected at low levels in surface waters and sediments across the United States, contaminants of emerging concern (CECs) in the Great Lakes Basin are not well characterized in terms of spatial and temporal occurrence. Additionally, although the detrimental effects of exposure to CECs on fish and wildlife have been documented for many CECs in laboratory studies, we do not adequately understand the implications of the presence of CECs in the environment. Based on limited studies using current environmentally relevant concentrations of chemicals, however, risks to fish and wildlife are evident. As a result, there is an increasing urgency to address data gaps that are vital to resource management decisions. The U.S. Fish and Wildlife Service, in collaboration with the U.S. Geological Survey, is leading a Great Lakes Basin-wide evaluation of CECs (CEC Project) with the objectives to (a) characterize the spatial and temporal distribution of CECs; (b) evaluate risks to fish and wildlife resources; and (c) develop tools to aid resource managers in detecting, averting, or minimizing the ecological consequences to fish and wildlife that are exposed to CECs. This report addresses objective (a) of the CEC Project, summarizing sediment and water chemistry data collected from 2010 to 2012 and fish liver tissue chemistry data collected in 2012; characterizes the sampling locations with respect to potential sources of CECs in the landscape; and provides an initial interpretation of the variation in CEC concentrations relative to the identified sources. Data collected during the first three years of our study, which included 12 sampling locations and analysis of 134 chemicals, indicate that contaminants were more frequently detected in sediment compared to water. Chemicals classified as alkyphenols, flavors/ fragrances, hormones, PAHs, and sterols had higher average detection frequencies in sediment compared to water, while the opposite was observed for pesticides, pharmaceuticals, and plasticizers/flame retardants. The St. Louis River and Maumee River sampling locations had the most CEC detections in water and sediment, relative to other sites, as well as the largest number of maximum detected concentrations across all sites in the Basin. No consistent temporal CEC occurrence patterns were observed at locations sampled multiple times each day. Most appearances and increases in chemical concentrations in sediments occurred at sites immediately downstream from wastewater treatment plants and at sites with predominantly developed land use. The location with the most observed appearances and increases was the St. Louis River. Perfluorinated compounds were commonly detected in fish liver tissues with detections in 100% of both benthic and pelagic species. The occurrence of these chemicals in liver tissue of benthic and pelagic species was generally similar. Abstract

Great Lakes Basin↗
USGS2012

Physical habitat, water quality, and riverine biological assemblages of selected reaches of the Sheyenne River, North Dakota, 2010

In 2010, data on physical habitat, water quality, and riverine biological assemblages were collected at selected reaches in four locations (Kleven, Sheyenne, Cooperstown, and West Fargo) on the Sheyenne River in east-central North Dakota. Three of the locations (Kleven, Sheyenne, and Cooperstown) are above Baldhill Dam and one location (West Fargo) is below Baldhill Dam on the Sheyenne River. The 2010 data provide information to establish a better understanding of the water-quality and ecological conditions of the Sheyenne River. Concerns were raised about the water-quality and ecological conditions of the Sheyenne River because of the interbasin transfer of water from nearby Devils Lake. The transfer of water from Devils Lake to the Sheyenne River occurs through the Devils Lake State Outlet near Peterson Coulee or, if lake elevations exceed 1,459 feet above National Geodetic Vertical Datum of 1929 (NGVD 29), through a natural outlet, Tolna Coulee. The field measurements of water-quality characteristics and results of chemical analyses generally are comparable to summary statistics calculated for Sheyenne River for 1980 through 2006. Overall, water-quality results show differences between the Kleven, Sheyenne, Cooperstown, and West Fargo reaches. Sulfate concentrations were less than the State of North Dakota criterion of 750 milligrams per liter for the upper Sheyenne River above Baldhill Dam and less than the criterion of 450 milligrams per liter for the lower Sheyenne River below Baldhill Dam. Arsenic concentrations at most reaches exceeded the U.S. Environmental Protection Agency drinking-water standard of 10 micrograms per liter. Nutrient concentrations (nitrogen, phosphorus) were higher in the upper Sheyenne River above Baldhill Dam than below Baldhill Dam where concentrations decreased by about half. In 2010, 35 families and 44 genera of benthic macroinvertebrates were collected and identified. On the basis of the index of biotic intergrity scores for benthic macroinvertebrate communities present in the Sheyenne River, all the reaches were determined to have condition classes of moderately disturbed to most disturbed. The benthic macroinvertebrate communities at the Cooperstown reaches were classed as moderately disturbed, whereas benthic macroinvertebrate communities at the Kleven, Sheyenne, West and Fargo reaches were most disturbed. During data collection, 37 genera and 165 species of periphyton (diatoms and soft-bodied algae) were collected and identified. In periphyton communities, similar taxa species were dominant in the Kleven, Sheyenne, and Cooperstown reaches, and different taxa species were dominant in the West Fargo reaches. For diatoms, the Kleven 3 reach had the lowest species richness value of 33.0, whereas the Cooperstown 8 reach had the highest species richness value of 57.0. For soft-bodied algae, the species richness values ranged from 8.0 at the Sheyenne 4 reach to 20.0 at the West Fargo 10 reach. During the fish collection, 32 species, representing 10 families, were collected in the Sheyenne River. All but two species are native to the Sheyenne River system. Common carp and white crappie are the two introduced species. Of the 32 species, 29 are tolerant to moderately tolerant to changes in water quality and habitat degradation, 16 species are tolerant to moderately tolerant to turbidity, and 16 species are tolerant to moderately tolerant to sensitivity to total dissolved solids, sulfate, and chloride. All fish species were categorized into four trophic groups. The largest group of 19 species was the insectivores (both benthic and general). The predator group consisted of seven species, and the omnivores consisted of six species. More fish were found in the lower Sheyenne River below Baldhill Dam than in the upper Sheyenne River above Baldhill Dam.

North Dakota↗
USGS2015

Coastal landforms and processes at the Cape Cod National Seashore, Massachusetts—A primer

Anyone who spends more than a few days on Cape Cod (the Cape) quickly becomes a coastal geologist, quickly learning the rhythms of daily tides and the seasonal cycles of beaches growing and being swept away by storms; swimmers and surfers track how the breakers appear, and dog-walkers notice the hard-packed sand blanketed overnight by an airy layer that leaves deep labored tracks. Careful observers whose paths wander to the ocean’s edge will observe many of the landforms and coastal processes described in this book and if we have done our job well, the stories told here will seem familiar. Watchful experience brings insights; indeed, this is how scientists and perhaps how artists work, describing patterns that explain and predict. When is the next high tide? What will the winter bring? Where do we build, fish, swim? How do wind and waves offshore in the North Atlantic help arrange the plants and dunes and hollows on the beach? And most of all, as human animals drawn to live and play on the edge of the ocean, how do we get the benefits of this complex natural system of geology and biology? How do we affect coastal processes; how is the coast changing now and how is the coast likely to change in years ahead with climate warming and climate change? This book is about the highly dynamic coastal landforms of Cape Cod—the beaches, bluffs, spits, dunes, barrier beaches, estuaries, and salt marshes. What they are, why they are where they are, how they behave with respect to the greater Cape Cod coastal system—how the landforms respond to day-to-day and long-term geologic processes, such as waves and currents, change in sediment transport, relative sea-level rise, and meteorological processes such as hurricanes, nor’easters, and cold front passages. It is also about how the landforms got to be where they are and the way they are and where they are headed in the near future with the predicted effects of global climate warming and change. Our objective is to provide a single source of understandable and readable scientific information for those who live, play, and work on outer Cape Cod and at the Cape Cod National Seashore, as well as to provide an introduction to Cape Cod’s coastal landforms for anyone with an interest in Earth science and nature who wants a better understanding of coastal systems and processes. Basic to an understanding of coastal landforms is the fact that they work together—they interact—as elements of many systems, and therefore our ultimate concern is not the individual landform itself but rather the geologic systems that make up Cape Cod and the Cape Cod National Seashore. Much of this discussion can be applied as well to Nantucket, Martha’s Vineyard, and other coastal regions. The coast of outer Cape Cod, about 15,000 years old and about 30 miles (mi; 50 kilometers [km]) long, is but a tiny piece of the global Earth system that operates within a much larger realm of space and time. Cape Cod’s coastal landforms are temporary holding patterns within a continual interplay of land, sea, atmosphere, climate, ice, and life, including a variety of human activities that both affect and are affected by these processes. These interactions produce the landforms, and the landforms alter the interactions. The resulting landforms provide habitats for a wide variety of coastal plants and animals. The habitats along with their inhabitants and the interacting environmental factors controlling them constitute the Cape’s complex and varied ecosystems. But for now, we are here to enjoy it. We welcome you to delight and wonder at the perpetually changing handshake between the ocean and shore at New England’s Great Beach.

Massachusetts↗
USGS2016

Conservation status of the American horseshoe crab, (Limulus polyphemus): A regional assessment

Horseshoe crabs have persisted for more than 200 million years, and fossil forms date to 450 million years ago. The American horseshoe crab ( Limulus polyphemus ), one of four extant horseshoe crab species, is found along the Atlantic coastline of North America ranging from Alabama to Maine, USA with another distinct population on the coasts of Campeche, Yucatán and Quintana Roo in the Yucatán Peninsula, México. Although the American horseshoe crab tolerates broad environmental conditions, exploitation and habitat loss threaten the species. We assessed the conservation status of the American horseshoe crab by comprehensively reviewing available scientific information on its range, life history, genetic structure, population trends and analyses, major threats, and conservation. We structured the status assessment by six genetically-informed regions and accounted for sub-regional differences in environmental conditions, threats, and management. The transnational regions are Gulf of Maine (USA), Mid-Atlantic (USA), Southeast (USA), Florida Atlantic (USA), Northeast Gulf of México (USA), and Yucatán Peninsula (México). Our conclusion is that the American horseshoe crab species is vulnerable to local extirpation and that the degree and extent of risk vary among and within the regions. The risk is elevated in the Gulf of Maine region due to limited and fragmented habitat. The populations of horseshoe crabs in the Mid-Atlantic region are stable in the Delaware Bay area, and regulatory controls are in place, but the risk is elevated in the New England area as evidenced by continuing declines understood to be caused by over-harvest. The populations of horseshoe crabs in the Southeast region are stable or increasing. The populations of horseshoe crabs in the Florida Atlantic region show mixed trends among areas, and continuing population reductions at the embayment level have poorly understood causes. Within the Northeast Gulf of Mexico, causes of population trends are poorly understood and currently there is no active management of horseshoe crabs. Horseshoe crabs within México have conservation protection based on limited and fragmented habitat and geographic isolation from other regions, but elevated risk applies to the horseshoe crabs in the Yucatán Peninsula region until sufficient data can confirm population stability. Future species status throughout its range will depend on the effectiveness of conservation to mitigate habitat loss and manage for sustainable harvest among and within regions.

Reviews in Fish Biology and Fisheries↗
USGS2006

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

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

Scientific Investigations Report↗
USGS2010

Southeast Regional Assessment Project for the National Climate Change and Wildlife Science Center, U.S. Geological Survey

The Southeastern United States spans a broad range of physiographic settings and maintains exceptionally high levels of faunal diversity. Unfortunately, many of these ecosystems are increasingly under threat due to rapid human development, and management agencies are increasingly aware of the potential effects that climate change will have on these ecosystems. Natural resource managers and conservation planners can be effective at preserving ecosystems in the face of these stressors only if they can adapt current conservation efforts to increase the overall resilience of the system. Climate change, in particular, challenges many of the basic assumptions used by conservation planners and managers. Previous conservation planning efforts identified and prioritized areas for conservation based on the current environmental conditions, such as habitat quality, and assumed that conditions in conservation lands would be largely controlled by management actions (including no action). Climate change, however, will likely alter important system drivers (temperature, precipitation, and sea-level rise) and make it difficult, if not impossible, to maintain recent historic conditions in conservation lands into the future. Climate change will also influence the future conservation potential of non-conservation lands, further complicating conservation planning. Therefore, there is a need to develop and adapt effective conservation strategies to cope with the effects of climate and landscape change on future environmental conditions. Congress recognized this important issue and authorized the U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center (NCCWSC; http://nccw.usgs.gov/) in the Fiscal Year 2008. The NCCWSC will produce science that will help resource management agencies anticipate and adapt to climate change impacts to fish, wildlife, and their habitats. With the release of Secretarial Order 3289 on September 14, 2009, the mandate of the NCCWSC was expanded to address climate change-related impacts on all Department of the Interior (DOI) resources. The NCCWSC will establish a network of eight DOI Regional Climate Science Centers (RCSCs) that will work with a variety of partners to provide natural resource managers with tools and information that will help them anticipate and adapt conservation planning and design for projected climate change. The forecasting products produced by the RCSCs will aid fish, wildlife, and land managers in designing suitable adaptive management approaches for their programs. The DOI also is developing Landscape Conservation Cooperatives (LCCs) as science and conservation action partnerships at subregional scales. The USGS is working with the Southeast Region of the U.S. Fish and Wildlife Service (FWS) to develop science collaboration between the future Southeast RCSC and future LCCs. The NCCWSC Southeast Regional Assessment Project (SERAP) will begin to develop regional downscaled climate models, land cover change models, regional ecological models, regional watershed models, and other science tools. Models and data produced by SERAP will be used in a collaborative process between the USGS, the FWS (LCCs), State and federal partners, nongovernmental organizations, and academia to produce science at appropriate scales to answer resource management questions. The SERAP will produce an assessment of climate change, and impacts on land cover, ecosystems, and priority species in the region. The predictive tools developed by the SERAP project team will allow end users to better understand potential impacts of climate change and sea level rise on terrestrial and aquatic populations in the Southeastern United States. The SERAP capitalizes on the integration of five existing projects: (1) the Multi-State Conservation Grants Program project "Designing Sustainable Landscapes," (2) the USGS multidisciplinary Science Thrust project "Water Availability for Ecological Needs," (3) the USGS Southeast Pilot Project "Climate Change in the Southeastern U.S. and its Impacts on Bird Distributions and Habitats," (4) a sea-level rise impacts study envisioned jointly with the National Oceanic and Atmospheric Administration (NOAA), and (5) two USGS sea-level rise impact assessment projects that address inundation hazards and provide probabilistic forecasts of coastal geomorphic change. The SERAP will expand on these existing projects and include the following tasks, which were initiated in summer 2009: * Regionally downscaled probabilistic climate-change projections * Integrated coastal assessment * Integrated terrestrial assessment * Multi-resolution assessment of potential climate change effects on biological resources: aquatic and hydrologic dynamics * Optimal conservation strategies to cope with climate change The SERAP seeks to formally integrate these tasks to aid conservation planning and design so that ecosystem management decisions can be optimized for providing desirable outcomes across a range of species and environments. The following chapters detail SERAP's efforts in providing a suite of regional climate, watershed, and landscape-change analyses and develop the interdisciplinary framework required for the biological planning phases of adaptive management and strategic conservation. The planning phase will include the identification of conservation alternatives, development of predictive models and decision support tools, and development of a template to address similar challenges and goals in other regions. The project teams will explore and develop ways to link the various ecological models arising from each component. The SERAP project team also will work closely with members of the LCCs and other partnerships throughout the life of the project to ensure that the objectives of the project meet resources mangers needs in the Southeast.

Open-File Report↗
USGS2016

Physical, chemical, and biological characteristics of selected headwater streams along the Allegheny Front, Blair County, Pennsylvania, July 2011–September 2013

The Altoona Water Authority (AWA) obtains all of its water supply from headwater streams that drain western Blair County, an area underlain in part by black shale of the Marcellus Formation. Development of the shale-gas reservoirs will require new access roads, stream crossing, drill-pad construction, and pipeline installation, activities that have the potential to alter existing stream channel morphology, increase runoff and sediment supply, alter streamwater chemistry, and affect aquatic habitat. The U.S. Geological Survey, in cooperation with Altoona Water Authority and Blair County Conservation District, investigated the water quality of 12 headwater streams and biotic health of 10 headwater streams. Channel morphology was characterized at 10 of 12 stream sites using 500-foot (minimum) longitudinal profiles, four cross-sections each, and pebble counts. Channel slopes ranged from 0.008 in Poplar Run near Newry to 0.045 in Mill Run. In general, streams draining watersheds of 5 square miles or less and at higher elevation had the steepest slopes. On the basis of the median particle size, determined during pebble counts, the streambed substrate can be characterized as cobble (Mill Run, Bells Gap Run, Tipton Run, and Sink Run), a mix of gravel and cobble (South Poplar Run, Dry Gap Run, Glenwhite Run, Sugar Run, Blair Gap Run), and gravel (Poplar Run, Newry). Daily mean values of gage height were determined, and continuous (30-minute interval) data consisting of specific conductance and water temperature were collected, at four sites; each site showed typical seasonal fluctuations and the effects of precipitation. Streamflow affected discrete water-quality. Dissolved oxygen always increased with increased streamflow. Most cations (including barium and strontium), along with pH, specific conductance, and total dissolved solids, decreased with greater streamflow, reflecting the dilution effect of moderately acidic surface runoff and precipitation on groundwater discharge (base flow) into the stream channels. Concentrations of trace elements varied by constituent and streamflow. On the basis of the results of water-quality analyses for the selected constituents, the water quality in 9 of the 12 streams can be considered fair or attaining with no measured constituent exceeding a U.S. Environmental Protection Agency maximum or secondary contaminant level. Abandoned mine drainage (AMD) affects Glenwhite Run, Blair Gap Run, and Sugar Run. For Sugar Run, the AMD is reflected in the elevated iron concentration (greater than 300 micrograms per liter). Manganese concentrations greater than 50 micrograms per liter were measured in Glenwhite Run, Sugar Run, and Blair Gap Run. A mixing curve based upon chloride/bromide ratios for two end points—precipitation and deicing salts—indicate that deicing salt is migrating to the streams. A similar curve representative of late-emerging flowback water from Marcellus gas wells indicated that the surface-water samples had not been influenced by such brines. On the basis of the concentration of major ions, the streams in the study area generally had mixed cation and anion compositions. Calcium is the dominant cation in one stream. Carbonate and bicarbonate are the dominant anions for two streams, and sulfate is dominant in three streams. The remaining six streams do not have a dominant ion. Biotic health was characterized at 10 of 12 stream sites; the two sites excluded were established late in the study period (May 2013) for refinement of water quality in the headwaters of Poplar Run and the location of Marcellus Formation gas wells. On the basis of the Maryland Index of Biotic Integrity (MdIBI) for fish assemblages, 8 of 10 streams can be considered in fair health. Tipton Run had the highest MdIBI score (3.75) and the greatest number of native species. South Poplar Run had the lowest MdIBI score (1.75); pollution tolerant blacknose dace was dominant. On the basis of the Pennsylvania Department of Environmental Protection macroinvertebrate index of biotic integrity, 9 of 10 streams were characterized as attaining, with scores as high as 88.9 at Tipton Run. Only Sugar Run was characterized as impaired, with a score of 40.4.

Pennsylvania↗
USGS2010

Long-term increases in young-of-the-year growth of Arctic cisco Coregonus autumnalis and environmental influences

Arctic cisco Coregonus autumnalis young-of-year (YOY) growth was used as a proxy to examine the long-term response of a high-latitude fish population to changing climate from 1978 to 2004. YOY growth increased over time (r2 = 0·29) and was correlated with monthly averages of the Arctic oscillation index, air temperature, east wind speed, sea-ice concentration and river discharge with and without time lags. Overall, the most prevalent correlates to YOY growth were sea-ice concentration lagged 1 year (significant correlations in 7 months; r 2 = 0·14-0·31) and Mackenzie River discharge lagged 2 years (significant correlations in 8 months; r 2 = 0·13-0·50). The results suggest that decreased sea-ice concentrations and increased river discharge fuel primary production and that life cycles of prey species linking increased primary production to fish growth are responsible for the time lag. Oceanographic studies also suggest that sea ice concentration and fluvial inputs from the Mackenzie River are key factors influencing productivity in the Beaufort Sea. Future research should assess the possible mechanism relating sea ice concentration and river discharge to productivity at upper trophic levels.

Journal of Fish Biology↗
USGS2021

A characterization of deep-sea coral and sponge communities along the California and Oregon coast using a remotely operated vehicle on the EXPRESS 2018 expedition

Deep-sea coral and sponge (DSCS) communities serve as essential fish habitats (EFH) by providing shelter and nursery habitat, increasing diversity, and increasing prey availability (Freese and Wing, 2003; Bright, 2007; Baillon et al., 2012; Henderson et al., 2020). Threats to these long-lived, fragile organisms from bottom contact fishing gear, potential offshore renewable energy development, and ocean warming and acidification have increased the need for DSCS research along the U.S. West Coast (Gomez et al., 2018; Salgado et al., 2018; Yoklavich, et al., 2018; Gugliotti et al., 2019). The focus of these studies has varied from species distribution and abundance (Yoklavich and Love, 2005; Tissot et al., 2006) to developing and validating predictive distribution models (Huff et al., 2013; Rooper et al., 2017; Kreidler, 2020) to finding medicinal uses for corals and sponges (Essack et al., 2011; Shrestha et al., 2018). Due to the vast area of unexplored seafloor within the U.S. exclusive economic zone (EEZ; 200 nautical miles off the coast) and the technological requirements and expanse of deep-sea research, there is still much to learn about the distributions and biology of DSCS. This information is critical to resource managers for effective conservation and management of DSCS habitats. Protections are provided by the Pacific Fishery Management Council (PFMC) designation of groundfish EFH conservation areas (EFHCA) and the National Marine Sanctuaries Act (NMSA). Areas designated as EFHCA are closed to bottom trawl fishing to protect and preserve seafloor habitats. Recently the PFMC adopted Amendment 28 to the Groundfish Fishery Management Plan (GFMP; Pacific Fishery Management Council, 2019) which modified EFHCAs by closing new areas identified as vulnerable and reopening areas deemed not vulnerable. The NMSA prohibits bottom disturbance from certain activities within areas designated as national marine sanctuaries, such as oil and gas exploration or extraction, cable laying, and other forms of seabed alteration or construction that disturb benthic communities. NOAA’s Deep-Sea Coral and Research Technology Program (DSCRTP) began a 4-yr funding initiative for the U.S. West Coast in 2017. The goals of the West Coast Deep-Sea Coral Initiative (WCDSCI) were to: 1) gather baseline information on areas subject to fishing regulation changes prior to the implementation of Amendment 28; 2) improve our understanding of known DSCS bycatch “hot spots”; and 3) explore and assess DSCS resources within NOAA National Marine Sanctuaries with emphasis on areas of sanctuary resource protection and management concerns. During the first year of the program, a research cruise was developed to survey the West Coast from Oregon to California studying the DSCS ecosystems in priority areas. The 31-day expedition (9 Oct – 8 Nov, 2018) was launched from the NOAA Ship Bell M. Shimada, beginning in Newport, OR and ending in San Diego, CA. The science team assembled for this cruise were members of the EXpanding Pacific Research and Exploration of Submerged Systems (EXPRESS) campaign, which brings together researchers from federal and nonfederal institutions to collaborate on scientific expeditions targeting the deepwater areas off California, Oregon, and Washington. EXPRESS supports researchers leveraging funding, resources, personnel, and expertise to accomplish more science than would have been possible by a single entity alone. The 2018 coastwide expedition included research partners from National Marine Fisheries Service (NMFS) Southwest Fisheries Science Center (SWFSC) and Northwest Fisheries Science Center (NWFSC), National Ocean Service (Channel Islands, Cordell Bank, Greater Farallones, and Monterey Bay National Marine Sanctuaries), Bureau of Ocean Energy Management (BOEM), U.S. Geological Survey (USGS), and Monterey Bay Aquarium Research Institute (MBARI). Research objectives for the cruise were to: 1) Collect DSCS baseline information at 10 of the EFHCA sites undergoing protection modifications by the Pacific Fishery Management Council. 2) Collect DSCS and fish data at previously unexplored sites within West Coast National Marine Sanctuaries. 3) Revisit a subset of previously surveyed sites to document if changes in DCSC have occurred over time. 4) Collect information to validate BOEM supported cross-shelf habitat suitability models for DSCS. 5) Collect samples to help in identifying (and understanding) West Coast DSCS and expand use of new technologies (ROV, AUV, and environmental DNA [eDNA]). 6) Collect water samples for coastwide eDNA, nutrient, and carbon chemistry studies.

California, Oregon↗
USGS2004

Mercury in the Walker River Basin, Nevada and California: Sources, distribution, and potential effects on the ecosystem

Mercury is one of the most serious contaminants of water, sediment, and biota in Nevada because of its use during 19th century mining activities to recover gold and silver from ores. In 1998, mercury problems were discovered in the Walker River Basin of California and Nevada when blood drawn from three common loons from Walker Lake was analyzed and found to have severely elevated mercury levels. From 1999 to 2001, the U.S. Geological Survey and the U.S. Fish and Wildlife Service collected water, sediment, and biological samples to determine mercury sources, distribution, and potential effects on the Walker River Basin ecosystem. Total-mercury concentrations ranged from 0.62 to 57.11 ng/L in streams from the Walker River system and ranged from 1.02 to 26.8 ng/L in lakes and reservoirs. Total-mercury concentrations in streambed sediment ranged from 1 to 13,600 ng/g, and methylmercury concentrations ranged from 0.07 to 32.1 ng/g. The sediment-effects threshold for mercury for fresh-water invertebrates is 200 ng/g, which was exceeded at nine stream sites in the Walker River Basin. The highest mercury concentrations were in streams with historic mines and milling operations in the watershed. The highest mercury concentration in sediment, 13,600 ng/g, was found in Bodie Creek near Bodie, Calif., a site of extensive gold mining and milling activities during the 19th century. Sediment cores taken from Walker Lake show total-mercury concentrations exceeding 1,000 ng/g at depths greater than 15 cm below lake bottom. The presence of 137Cs above 8 cm in one core indicates that the upper 8 cm was deposited sometime after 1963. The mercury peak at 46 cm in that core, 2,660 ng/g, likely represents the peak of mining and gold extraction in the Bodie and Aurora mining districts between 1870 and 1880. Mercury concentrations in aquatic invertebrates at all sites downstream from mining activities in the Rough Creek watershed, which drains the Bodie and Aurora mining districts, were elevated (range 0.263 to 0.863 ?g/g, dry weight). Mercury concentrations in the Walker Lake tui chub, the most abundant and likely prey for common loons, ranged from approximately 0.09 ?g/g to approximately 0.9 ?g/g (wet weight). Larger tui chub in the lake, which are most likely older, had the highest mercury concentrations. Blood samples from 94 common loons collected at Walker Lake between 1998 and 2001 contained a mean mercury concentration of 2.96 ?g/g (standard deviation 1.72 ?g/g). These levels were substantially higher than those found in more than 1,600 common loons tested across North America. Among the 1,600 common loons, the greatest blood mercury concentration, 9.46 ?g/g, was from a loon at Walker Lake. According to risk assessments for northeastern North America, blood mercury concentrations exceeding 3.0 ?g/g cause behavioral, reproductive, and physiological effects. At least 52 percent of the loons at Walker Lake are at risk for adverse effects from mercury on the basis of their blood-mercury concentrations. The larger loons staging in the spring are the most at risk group. The elevated mercury levels found in tui chub and common loons indicate that there is a potential threat to the well being and reproduction of fish and wildlife that use Walker Lake. Wildlife that use Weber Reservoir may also be at risk because it is the first reservoir downstream from mining activities in the Bodie and Aurora areas and mercury concentrations in sediment were elevated. Additional data on mercury concentrations in top level predators, such as piscivorous fish and birds, are needed to assess public health and other environmental risks.

California, Nevada↗
USGS1996

Organic geochemistry applied to environmental assessments of Prince William Sound, Alaska, after the Exxon Valdez oil spill—a review

Organic geochemistry played a major role in the environmental assessments conducted following the Exxon Valdez oil spill, which occurred on March 24, 1989, and released about 258,000 bbls (41 million liters) of Alaska North Slope crude oil into Prince William Sound. Geochemical analyses of more than 15,000 sediment, tar, and biological samples and about 5000 water samples provide the largest database yet collected on oil-spill chemistry, and we review the results here. The marine environment of the Sound has a complex background of petrogenic, pyrogenic, and biogenic hydrocarbons from natural and anthropogenic sources. Geochemical evaluation of the fate and effects of the spilled oil required that this oil and its residues be distinguished from the background. A variety of molecular and isotopic techniques were employed to identify various hydrocarbon sources and to distinguish quantitatively among mixed sources in the samples. Although the specific criteria used to distinguish multiple sources in the region affected by the Exxon Valdez spill are not necessarily applicable to all spill situations, the principles that governed their selection are. Distributions of polycyclic aromatic hydrocarbons (PAH) and dibenzothiophenes distinguish Exxon Valdez oil and its weathered residues from background hydrocarbons in benthic sediments. Ratios of C 2 -dibenzothiophene C 2 -phenanthrene "> C 2 -dibenzothiopheneC 2 -phenanthrene and C 3 -dibenzothiophene C 3 -phenanthrene "> C 3 -dibenzothiopheneC 3 -phenanthrene were particularly useful. Carbon isotopes and terpane distributions distinguished Exxon Valdez residues found on shorelines from tars from other sources. Diesel and diesel soot were identified by the absence of alkylated chrysenes and a narrow distribution of n -alkanes, whereas pyrogenic products were distinguished by the dominance of 4- to 6-ring PAH over 2- to 3-ring PAH and by the dominance of non-alkylated over alkylated homologues of each PAH series. The presence of 18α(H)-oleanane in benthic sediments, coupled with its absence in Exxon Valdez oil and its residues, confirm another petrogenic source. Results of geochemical studies suggest that the petrogenic component in the background of benthic sediments is derived from oil seeps in the eastern Gulf of Alaska. In 1990 and 1991, Exxon Valdez residues, generally forming a small increment to the pre-spill background, were found to be only sporadically distributed in some shallow, near shore sediments adjacent to shorelines that had been heavily oiled in 1989. In 1994, occurrences of Exxon Valdez tars on shoreline surfaces were rare, although residues could be found buried in shoreline sediments at some isolated locations along the spill path where they were protected from wave action. Spilled oil residues collected 16 months after the spill were degraded, on average, by nearly 50%. Shoreline residues from sources other than the spill were also identified and are widespread throughout the Sound. These residues include (1) geochemically distinct tars and oils imported from California oil fields to Alaska for fuel and construction purposes prior to the discovery of the Cook Inlet and North Slope oil fields, (2) diesel and diesel soot, and (3) more highly refined products. Of the more than 2700 chemical analyses of biological samples of higher life forms (fish, birds, and mammals) about 150 (6%) indicate recognizable residues of Exxon Valdez oil, which were identified by their distribution of polycyclic aromatic hydrocarbons (PAH). Most of these samples (138) were collected in 1989 and most were associated with external surfaces or the gastrointestinal tract. Rarely do internal tissues or fluids contain recognizable fingerprints of spilled oil. This observation includes samples from marine mammals that were visibly oiled externally. Other hydrocarbon sources, including diesel and a non-petroleum artifact that occurs when concentrations of individual PAH are at or near their method detection limit, are also identified in biological samples.

Alaska↗
USGS1999

Fishes of Missouri River, chute, and flood plain habitats: Chapter 4 in Initial biotic survey of Lisbon Bottom, Big Muddy National Fish and Wildlife Refuge

The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge (Refuge) is approximately 2,200 acres and is the first complete unit of the Refuge. Primary objectives of the Refuge are to create and restore diverse riverine aquatic habitats and reconnect the Missouri River to its flood plain where feasible. Management seeks to accomplish these objectives by encouraging natural processes of erosion, deposition, and succession to the greatest extent possible. One of the most salient aquatic features of the Lisbon Bottom Unit is a newly created 2-mile-long free-flowing chute, or side channel (Fig. 1). This chute began forming as a levee breech scour hole during the Great Flood of 1993. The chute continued to develop during the 1995 flood and finally cut through to a flowing side channel during the 1996 flood. Extensive erosion and bank sluffing continued during 1997 due to sustained high flows that occurred throughout most of the year. The chute has progressively become wider and deeper with a developing meander pattern and channel bars have begun to form. Lisbon Bottom also contains several seasonal and permanent wetlands and is subject to periodic flooding at high Missouri River stages. Eight studies have been completed or are ongoing to evaluate Missouri River fishes associated with various habitat components of Lisbon Bottom and adjacent Missouri River reaches (Table 1). Several are part of much larger investigations to evaluate fish use of flood-created habitat features, basinwide fish assessment, and endangered or candidate species concerns. At the Lisbon Bottom Unit or in the Missouri River adjacent to the unit 54 fish species were collected (Table 2). Eight of these species have either a protected status under State or Federal laws or biologists consider them to potentially qualify for protected status. The status of the following fish is listed in Table 2: pallid sturgeon x shovelnose sturgeon hybrid, paddlefish, northern pike, sturgeon chub, sicklefin chub, ghost shiner, western silvery minnow, plains minnow, and blue sucker. Equally important to note are fish species that were not collected. The flathead chub, currently listed as State endangered and proposed for Federal listing, were not collected in any of the studies. Common fish species, collected in all seven sampling studies, included gizzard shad, common carp, river carpsucker, and freshwater drum. Paddlefish, skipjack herring, silver carp, white sucker, redfin shiner, western silvery minnow, bullhead minnow, and black bullhead were each collected in only one of the seven studies. Pflieger (1971) developed a guild system for the fishes of Missouri based on distribution patterns and centers of abundance. Fish were assigned to one of four primary faunal groups: Ozark, Big River, Lowland, and Prairie. Two secondary groups (Ozark-prairie and Ozark-lowland) were defined for species equally abundant and distributed in two of the primary areas. Two Ozark-prairie species, shorthead redhorse and white sucker, were collected on or near the Lisbon Bottom Unit. Big River species are found primarily in the Missouri and Mississippi Rivers. The environmental factors controlling fish distribution in these rivers appear to be substrate, current velocity, and turbidity. On or near the Lisbon Bottom Unit 18 Big River species were collected (Table 2). Lowland species are intolerant of siltation and high turbidity. They inhabit standing or slow-moving water with sand, fine gravel, and organic debris substrates. Two Lowland species, bullhead minnow and mosquitofish, were collected in connected scours on the Lisbon Bottom Unit. Prairie species have broader ecological tolerances than the Ozark and Lowland species. They are largely absent in high gradient streams and cool, clear waters. Prairie species make up a significant proportion of Missouri and Mississippi River fishes. Seven Prairie species were collected on or near the Lisbon Bottom Unit (Table 2). The last group, Wide-ranging, was defined as the species more widespread than the other faunal groups with broader environmental tolerances. Most Wide-ranging species occur at least occasionally in all sections of the state. Nineteen Wide-ranging species were collected on or near the Lisbon Bottom Unit (Table 2). Kubisiak (1997) found that isolated scours in the Lower Missouri River were dominated by Wide-ranging species. Connected scours also held Wideranging species but they contained Prairie species and were dominated by Big River species. Faunal group diversity and species richness were compared between isolated (Study l) and connected (Studies 4, 5, 7, and 8) scours of the Lisbon Bottom Unit. Species richness was similar with 22 species collected in isolated scours and an average of 24.8 species collected in connected scours. Isolated scour fish catches were dominated by Wide-ranging fish (59%) with 14% Big River fishes and 14% Prairie fishes. Connected scours had a larger percentage of Big River fish (32%) and fewer Wide-ranging (36%) and Prairie (13%) species than the isolated scours. In the combined studies, Wide-ranging fish dominated the connected scours. A similar comparison was made of fish from chute habitats and the Missouri River. Chute habitats include the Lisbon Bottom Chute, the chute between the right bank and island located at river mile 219, and a shallow channel running between a large sandbar complex and the channel border adjacent to Lisbon Bottom. Species richness in the chutes (35 species) was greater than that of the adjacent river (23 species). Big River species (40%) dominated the chute samples, followed by Wide-ranging at 31% Cand Prairie Cut 14%. The river samples contained equal numbers of Wide-ranging species (35%) and Big River species (35%) with 17% Prairie species. Differences in fish guild diversity and species richness may be due to numerous factors including sampling effort and sampling season. River samples were collected only in Study 3 in October; chute samples were collected in July, August, and October. Fish may have been using the chute in July and August to spawn, feed, or escape high river levels. The Lisbon Bottom Chute is a truly unique feature of the Lower Missouri River. It is the first naturally created side channel to develop since the U.S. Army Corps of Engineers tamed the river. The Corps eliminated 89% of the islands in the Missouri River between 1879 and 1954 (Funk and Robinson 1974). The chutes between the islands and the shore were shallower with less current than the main channel. These areas provided diversity to the Missouri River fish habitat, serving as nursery and feeding areas. The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge will continue to be studied in an effort to understand the complex role these areas play in river systems.

Missouri↗
USGS2024

Anthropogenic and environmental risk factors of salmonid predation in a tidal freshwater delta

Water diversions that support agricultural and municipal use result in fish mortality through entrainment and impingement. Additionally, this infrastructure may attract both predators and prey fishes, thereby increasing predation rates and prey mortality near these anthropogenic contact points. The Sacramento–San Joaquin Delta (the Delta) in California's Central Valley is a tidal freshwater ecosystem that exports large volumes of water for municipal and agricultural use while at the same time providing valuable migratory and rearing habitat for imperilled fishes. Emigrating juvenile salmonids experience high mortality in the Delta, with predation by non-native fishes contributing substantially. Therefore, this study had three main objectives. First, we determined if small water diversions aggregated piscivorous fishes like other similar structures in freshwater ecosystems. Second, we determined how small diversions may influence juvenile salmon predation risk in conjunction with other known predation risk factors (e.g. predator abundance, temperature and depth). Third, we assessed the predator assemblage, abundance and distribution to determine the likely predator composition in objectives one and two. Throughout the spring of 2021, we used ARIS (adaptive resolution imaging sonar; Sound Metrics) sonars to compare piscivore abundance at 30 water diversions in the north Delta to shorelines adjacent to diversions that did not contain these structures. We used predation event recorders (PERs) to assess the predation risk juvenile salmonids were exposed to, with linear distance (m) from diversions, and other predation risk factors in the north Delta. Finally, we used a boat electrofishing survey to determine the piscivore assemblage and compare spatial trends in black bass ( Micropterus spp.) CPUE and relative abundance throughout these waterways. Piscivore abundance was greater near small water diversions than at adjacent shorelines and the predation risk of juvenile salmonids increased with diversion proximity. Additionally, predation risk increased with increasing piscivore abundance and decreasing water depth. The north Delta predator assemblage was dominated by black basses ( Micropterus spp.), which likely drove the negative relationship of predation risk with water depth, given habitat requirements of these species. Furthermore, increasing smallmouth ( Micropterus dolomieu ) and spotted bass ( Micropterus punctulatus ) abundance in our northern study sites may have weakened temperature effects on predation, given metabolic requirements of these species. Our work demonstrated that small water diversions are likely to increase mortality of endangered salmonids, and that the north Delta predator assemblage was different than recorded by previous work in this system, changing predation risk factors. Although more work is needed to determine the population level impacts of diversions, the ubiquitous distribution of these structures warrants management solutions to reduce mortality from this source. These results indicate that in addition to entrainment and impingement, water diversions may increase mortality of small-bodied fishes by attracting predators and elevating predation risk. Given the continual human demand for freshwater, predator–prey interactions should be considered along with entrainment and impingement when assessing intake infrastructure mitigation, especially when diversions co-occur along migratory routes and essential habitat of imperilled fishes.

California↗
USGS2002

Biomonitoring of Environmental Status and Trends (BEST) Program: Environmental contaminants and their effects on fish in the Mississippi River Basin

We collected, examined, and analyzed 1378 fish of 22 species from 47 sites in the Mississippi River basin (MRB) during 1995 and from a reference site in 1996. The sampling sites in the MRB represented National Contaminant Biomonitoring Program (NCBP) stations situated at key points on major rivers and National Water- Quality Assessment Program (NAWQA) stations located on lower-order rivers and streams in the Eastern Iowa Basins (EIB) and Mississippi Embayment (MSE) Study Units. The reference site was the water supply system of the USGS-Leetown Science Center in rural Jefferson County, WV. Common carp (Cyprinus carpio; carp) and black basses (Micropterus spp.; bass), the targeted species, together represented 82% of the fish collected. Each fish was examined in the field for externally and internally visible gross lesions, selected organs were weighed to compute various ponderal and organo-somatic indices, and selected tissues and fluids were obtained and preserved for analysis of biomarkers. Fish health indicators included splenic macrophage aggregates, lysozyme activity, and hispathological analysis of liver, kidney, and other tissues. Reproductive biomarkers included analysis of plasma concentrations of vitellogenin (vtg) and the sex steroid hormones 17-estradiol (E2) and 11-ketotestosterone (11- kt); and the histological determination of percent oocyte atresia (in female fish) and gonadal stage. Hepatic ethoxyresorufin O-deethylase (EROD) activity was also measured. Composite samples of whole fish from each station were grouped by species and gender and analyzed for persistent organochlorine and elemental contaminants and for dioxin-like activity (TCDD-EQ) using the H4IIE rat hepatoma cell bioassay. Organochlorine and inorganic contaminant concentrations in fish were generally low relative to historical levels at most sites, but remained present at concentrations representing threats to piscivorous wildlife in some locations. Toxaphene and DDT (mostly as p,p?-DDE) concentrations remained elevated in fish from the cottongrowing regions of the lower Mississippi valley, and were generally greater in the smaller streams draining agricultural areas (that is, in the MSE Study Unit) than at large river sites. Cyclodiene pesticide concentrations were also greatest in the EIB Study Unit and elsewhere in the corn-growing regions of the mid-MRB. Former point-sources of organochlorine pesticides also remained evident, especially in the Mississippi River near Memphis, TN. Consistent with previous findings, total PCB concentrations tended to be greatest (1-3 g/g) in the industrialized and urbanized Ohio River and Upper Mississippi sub-basins and at Memphis, TN, and were generally correlated with TCDD-EQ and EROD activity. Conversely, PCB concentrations were low (<0.1 g/g) in the more agricultural parts of the MRB. Concentrations of inorganic contaminants were also relatively low and stable or declining relative to past levels at most sites. Exceptions were Hg and Se; Hg concentrations were slightly elevated (>0.3 g/g) in bass from the Mississippi River at Memphis and several other sites and in carp from one MSE site. Concentrations of Se were also great enough to constitute a hazard to piscivorous wildlife (>0.6 g/g) at several MRB sites in the western parts of the MRB and were especially high (4-5 g/g) in fish from John Martin Reservoir, CO, where elevated concentrations were reported previously. Biomarker results indicated that fish from many stations had been exposed to contaminants, but at no sites did findings indicate exposure to high concentrations of toxic chemicals. Noteworthy among biomarker findings was that 73% of the male smallmouth bass (Micropterus dolomieui) from the Mississippi River at Lake City, MN (Lake Pepin) were intersex as indicated by the histological detection of ovotestes; and the combined EROD and H4IIE results indicated that fish from several rural sites in the

Mississippi River basin↗