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USGS2026

Wind River subbasin restoration: Annual report of U.S. Geological Survey activities January 2024 through December 2024

We sampled juvenile wild Oncorhynchus mykiss (Steelhead Trout) in headwater streams of the Wind River, Washington, to characterize population attributes and investigate life-history metrics, particularly migratory patterns, and early life-stage survival. Additionally, this sampling provides an index of abundance of non-native Brook Trout Salvelinus confluentus . We used passive integrated transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTISs) to track juveniles and adults. The Wind River subbasin is considered a wild Steelhead refuge by Washington Department of Fish and Wildlife (WDFW). No hatchery Steelhead Trout have been released in the Wind River subbasin since 1997, and hatchery adults are estimated at less than one percent of spawners in most years. Over 25 years of Steelhead Trout status and trend monitoring and research in the subbasin is contributing to understanding of population response to numerous restoration actions in the subbasin, including removal of Hemlock Dam from Trout Creek in 2009, which had an inadequate adult ladder and contributed to increased water temperatures, to near lethal levels for salmonids. Data from our study, and companion work by WDFW, are contributing to the Columbia Basin Fish and Wildlife Program (2009) Research, Monitoring, and Evaluation (RM&E) Strategy of Fish Population Status Monitoring. Specifically, this work addresses the sub-strategies of 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and Uncertainties Research regarding differing life histories of a wild Steelhead Trout population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer and fall 2024, we PIT-tagged 2,075 Steelhead Trout parr (age-0 and age-1), in the Trout Creek and upper Wind River watersheds. Age-0 and age-1 parr were at high abundance due to strong spawner numbers in 2023 and 2024 (Estimate of 932 in 2023; and a moderate number of spawners in 2024 though an estimate is not available at this time; 24-year median = 619; Charlie Cochran, WDFW Fish Biologist, personal commun., 2025). An additional 100 parr (age-0 and age-2 or older) were tagged to provide fish for estimating detection efficiencies at PTISs. Steelhead Trout parr were recaptured and detected through repeat headwater sampling, smolt trapping, instream PTISs and Columbia River mainstem PIT-tag detection. We maintained and upgraded six instream PTISs to detect PIT-tagged Steelhead Trout parr, smolts, and adults, providing data for population assessments, and life-cycle research. Detection data from PIT-tagged adult Steelhead Trout at our four primary PTISs allow assessment of adult escapement to tributary watersheds within the Wind River subbasin. Most adult Steelhead detected were tagged by WDFW at an adult trap in the lower Wind River and some as smolts at screw traps. Adult Steelhead Trout detection efficiency estimates at our primary PTIS in Trout Creek have been greater than 99 percent during eight of the past ten years and have exceeded 97% at our primary PTIS in the Wind River during nine of the past ten years. Adult escapement estimates to tributary watersheds are helping evaluate the efficacy of the 2009 removal of Hemlock Dam from rkm 2.0 of Trout Creek. Detections at the instream PTISs have shown trends of age-0 and age-1 Steelhead Trout parr emigration from natal areas during summer and fall, in addition to the expected movement of parr and smolts in spring. Our data suggest that most fish from a cohort that migrate downstream will do so at age-1 for additional rearing in the subbasin. We have estimated that from 15% to 56% of parr tagged as age-0 fish in headwater areas make downstream migrations at age-1 for additional rearing (median = 29%). We have estimated that from 1% to 27% of Steelhead Trout parr, tagged as age-1 fish, make downstream migrations during fall (median = 3.5%): this is especially pronounced in the upper Wind River portion of the watershed (median 10%). These findings raise questions about parr rearing habitat and whether migrations are density- or habitat-quality driven, and answers to such questions are long-term goals of this study as active and passive habitat restoration occurs. Repeat sampling at sites in the subbasin within and between years has enabled assessment of juvenile Steelhead Trout growth patterns. Growth rates (relative change in weight) of age-0 PIT-tagged parr during summer have been similar across the subbasin, though slightly lower in the Trout Creek watershed (Trout Creek sites, 0.57 - 1.25%/day, Wind River sites = 0.94 – 2.48%/day). Summer growth rates have been lower for age-1 parr in the Trout Creek watershed than the upper Wind River watershed (Trout Creek sites, = 0.03 - 0.14%/day, Wind River sites = 0.05 – 0.19%/day). Yearly relative growth was similar across the subbasin for both age-0 and age-1 tagged parr. During 2024 range of mean daily relative change in weight from the previous year for age-0 tagged fish was: Trout Creek sites = 0.96 – 1.41%/day, Wind River sites = 0.80 – 1.30 %/day; and for age1 tagged fish was: Trout Creek sites = 0.37 - 0.50 %/day, Wind River sites = no age-1 tagged recaptures. Non-native Brook Trout are present in the subbasin, chiefly the Trout Creek watershed. Mean percent-of-catch that is Brook Trout, at four sample sites in Trout Creek, has declined from the period 1998 – 2003 to the period 2011 – 2024 (range of decrease = 19 - 82%). Percent-of-catch (of 64 samples, 52 < 10%; 3 > 20%) and number of Brook Trout at the Trout Creek sites from 2011 through 2024, though variable, have generally declined. Habitat restoration evaluation efforts are critical to ensure efficient use of money and resources but require long-term monitoring of population metrics. Detailed viable salmonid population and life-history data, such as that provided by PIT-tagging and instream PTIS networks inform fisheries policy and management and enable assessment of long-term effects of habitat restoration actions such as the removal of Hemlock Dam on Trout Creek and proposed major instream habitat restoration in the upper Wind River.

Washington↗

USGS2016

Effect of a levee setback on aquatic resources using two-dimensional flow and bioenergetics models

Watershed restoration is the focus of many resource managers and can include a multitude of restoration actions each with specific restoration objectives. For the White River flowing through the cities of Pacific and Sumner, Washington, a levee setback has been proposed to reconnect the river with its historical floodplain to help reduce flood risks, as well as provide increased habitat for federally listed species of salmonids. The study presented here documents the use of a modeling framework that integrates two-dimensional hydraulic modeling with process-based bioenergetics modeling for predicting how changes in flow from reconnecting the river with its floodplain affects invertebrate drift density and the net rate of energy intake of juvenile salmonids. Modeling results were calculated for flows of 25.9 and 49.3 cubic meters per second during the spring, summer, and fall. Predicted hypothetical future mean velocities and depths were significantly lower and more variable when compared to current conditions. The abundance of low energetic cost and positive growth locations for salmonids were predicted to increase significantly in the study reach following floodplain reconnection, particularly during the summer. This modeling framework presents a viable approach for evaluating the potential fisheries benefits of reconnecting a river to its historical floodplain that integrates our understanding of hydraulic, geomorphology, and organismal biology.

Washington↗

USGS2007

Systematic mapping of bedrock and habitats along the Florida Reef tract — Central Key Largo to Halfmoon Shoal (Gulf of Mexico)

The fragile coral reefs of the Florida Keys form the largest living coral reef ecosystem in the continental United States. Lining the shallow outer shelf approximately 5 to 7 km seaward of the keys, the reefs have national aesthetic and resource value. As recently as the 1970s, the coral reefs were the heart of a vibrant ecosystem. Since then, the health of all ecosystem components has declined markedly due to a variety of environmental stressors . Corals are succumbing to bleaching and diseases. Species that are the building blocks of solid reef framework are increasingly being replaced by species that do not construct reef framework. Algal proliferation is increasing competition for space and hard surfaces needed by coral larvae for settlement. Decline of the coral reef ecosystem has significant negative implications for economic vitality of the region, ranging from viability of the tourism industry attracted by the aesthetics to commercial fisheries drawn by the resources. At risk of loss are biologic habitats and reef resources, including interconnected habitats for endangered species in shoreline mangroves, productive nearshore marine and wetland nurseries, and economic offshore fisheries. In 1997, the U.S. Geological Survey's Coastal and Marine Geology Program undertook a comprehensive 7-year-long mission to consolidate, synthesize, and map new (1997) and existing geologic and biologic information into a digitized regional database and one-volume reference source on the geologic history of the Florida Keys reef tract (this report). The project was conducted in cooperation with the National Oceanic and Atmospheric Administration's National Marine Sanctuary Program. The purpose was to examine the natural evolution and demise of several coral reef ecosystems over the past 325,000 years, with an eye toward gaining a better understanding of the cause of the reef decline observed today. Scientific data and datasets presented in this report are intended for use by others in ongoing efforts to delineate which components of reef decline in the Florida Keys may be natural and which may be a result of human activities. Beyond scientific baseline datasets, this report also incorporates environmental, social, and historical aspects of the Florida Keys, including the impact of exploratory oil wells on benthic habitats off Florida.

Florida↗

USGS2011

Land area change in coastal Louisiana from 1932 to 2010

Coastal Louisiana wetlands make up the seventh largest delta on Earth, contain about 37 percent of the estuarine herbaceous marshes in the conterminous United States, and support the largest commercial fishery in the lower 48 States. These wetlands are in peril because Louisiana currently undergoes about 90 percent of the total coastal wetland loss in the continental United States. Documenting and understanding the occurrence and rates of wetland loss are necessary for effective planning, protection, and restoration activities. The analyses of landscape change presented in this report use historical surveys, aerial data, and satellite data to track landscape changes. Summary data are presented for 1932-2010; trend data are presented for 1985-2010. These later data were calculated separately because of concerns over the comparability of the 1932 and 1956 datasets (which are based on survey and aerial data, respectively) with the later datasets (which are all based on satellite imagery). These analyses show that coastal Louisiana has undergone a net change in land area of about -1,883 square miles (mi 2 ) from 1932 to 2010. This net change in land area amounts to a decrease of about 25 percent of the 1932 land area. Persistent losses account for 95 percent of this land area decrease; the remainder are areas that have converted to water but have not yet exhibited the persistence necessary to be classified as "loss." Trend analyses from 1985 to 2010 show a wetland loss rate of 16.57 mi 2 per year. If this loss were to occur at a constant rate, it would equate to Louisiana losing an area the size of one football field per hour. The use of 17 datasets plus the application of consistent change criteria in this study provide opportunities to better understand the timing and causal mechanisms of wetland loss that are critical for forecasting landscape changes in the future.

Louisiana↗

USGS2002

Isolation of thiaminase-positive bacteria from alewife

Evidence pointing to thiamine deficiency as a primary factor in early mortality syndrome in feral salmonids from the Great Lakes and New York's Finger Lakes continues to mount. Such deficiency is believed to be the result of the consumption of nontraditional forage fish, such as alewife Alosa pseudoharengus , that contain thiaminase activity. The source of thiaminase within these forage fish has not been reported. In this study, we report finding thiaminase-positive Paenibacillus thiaminolyticus and other Paenibacillaceae that are closely related to P. thiaminolyticus in the viscera of frozen alewives. Thiaminase-positive bacteria associated with alewife viscera have not previously been reported. Because viable thiaminase-positive cultures were found in only 25% of the fish, bacteria should be considered as only one potential source of thiaminase in alewives.

Transactions of the American Fisheries Society↗

USGS2011

Nomenclature of mitochondrial DNA haplotypes for Oncorhynchus mykiss

Congruence of genetic data is critical for comparative and collaborative studies on natural fish populations. A comprehensive list of reported mitochrondrial DNA haplotypes for Oncorhynchus mykiss generated using the S‐Phe/P2 primer set is presented as a resource for future investigations of this species.

Transactions of the American Fisheries Society↗

USGS1989

Effects of fire in the Northern Great Plains

This publication is a review of selected literature about prescribed burning in the Northern Great Plains (NGP) for management of wildlife. It also will be useful to other resource managers and researchers and to persons interested in the NGP. It is more 'descriptive' than 'interpretative.'The publication is a joint effort of the South Dakota State Cooperative Fish and Wildlife Research Unit (SDCFWRU), South Dakota State University, Brookings; the Northern Prairie Wildlife Research Center (NPWRC), Jamestown, N.D.; and the U.S. Fish and Wildlife Service (USFWS), Fergus Falls, Minn. Manuscript typing and library services were shared between SDCFWRU and NPWRC.This publication (EC 761) is the second of three SDSU Extension circulars on grassland fires. EC 760 is Prescribed burning guidelines in the Northern Great Plains; EC 762 is Annotated bibliography of fire literature relative to northern grasslands in South-Central Canada and North-Central United States and contains many more citations than presented in this publication. All three circulars may be obtained from either the Wildlife and Fisheries Sciences Department; SDSU Box 2206; ph (605) 688-6121; or from the Ag Communications Bulletin Room; SDSU Box 2231; ph (605) 688-5628; both in Brookings, S.D. 57007.

Report↗

USGS2011

Understanding the influence of predation by introduced fishes on juvenile salmonids in the Columbia River Basin: Closing some knowledge gaps. Interim Report of Research 2010

Project overview Predation on juvenile salmonids by fish in the Columbia River Basin (CRB) has impacted salmon survival and is a topic that has received considerable attention over the last three decades. Some of the earliest and most detailed research focused on the food habits, consumption rates, abundance, and distribution of predaceous northern pikeminnow Ptychocheilus oregonensis , smallmouth bass Micropterus dolomieu , walleye Sander vitreus , and channel catfish Ictalurus punctatus in John Day Reservoir (Beamesderfer and Rieman 1991; Poe et al. 1991; Vigg et al. 1991). This group of researchers also estimated the loss of juvenile salmonids to predation by some of these predators (Rieman et al. 1991). Since this pioneering effort, others have evaluated various aspects of predation-related mortality on juvenile salmonids in the CRB, focusing mostly on northern pikeminnow and smallmouth bass (e.g., Tabor et al. 1993; Zimmerman 1999; Naughton et al. 2004). Perhaps the most significant finding coming from this body of research was that the native northern pikeminnow was the dominant predator of juvenile salmonids in the CRB. Indeed, Beamesderfer et al. (1996) estimated that northern pikeminnow consumed about 16 million (8%) of the estimated 200 million juvenile salmonids emigrating annually in the CRB, far surpassing the consumption of smallmouth bass, walleye, and channel catfish combined. Because of this, large-scale management fisheries (i.e., the northern pikeminnow management program, or NPMP; see Rieman and Beamesderfer 1990; Beamesderfer et al. 1996) have been implemented in the CRB since 1990 to achieve a 10%–20% exploitation rate on northern pikeminnow and reduce predation on juvenile salmonids. The NPMP has been a success, resulting in up to 38% potential reductions in predation (Friesen and Ward 1999; Knutsen and Ward 1999; Ward and Zimmerman 1999;). In contrast to the NPMP, Oregon and Washington state fish and wildlife agencies manage and enhance recreational fisheries for smallmouth bass and walleye by implementing size and harvest limit regulations. Recently, many biologists and fish managers have become concerned about the impact of non-native predaceous fishes on juvenile salmonid survival. For example, Poe et al. (1994) warned that smallmouth bass, walleye, and channel catfish were expanding their populations in some areas, that these fish could be significant predators on juvenile salmonids, and that they may compete with northern pikeminnow for common prey items, resulting in higher consumption rates of salmonids by the native predator. Sanderson et al. (2009) reported that the impact of non-indigenous species (including piscivorous fishes) on salmon survival within the CRB can be severe and suggested that managing nonindigenous species may be imperative for salmon recovery. Assessing the current ecological impacts of introduced fishes throughout the CRB will fill information gaps associated with their impact on salmonid survival and contribute to the description of CRB food webs. In response to these recent concerns about the potential predatory impact of non-native piscivores on salmon survival, the Bonneville Power Administration (BPA) and the Columbia Basin Fish and Wildlife Authority (CBFWA) co-hosted a workshop to address predation on juvenile salmonids in the CRB by non-native fish (Halton 2008). The purpose of the workshop was to review, evaluate, and develop strategies to reduce predation by non-native fishes on juvenile salmonids. In the end, discussion at the workshop and at subsequent meetings considered two potential ideas to reduce predation by non-native fish on juvenile salmonids; (1) understanding the role of juvenile American shad Alosa sapidissima in the diet of non-native predators in the fall; and (2) the effects of localized, intense reductions of smallmouth bass in areas of particularly high salmonid predation. In this report, we describe initial efforts to understand the influence of juvenile American shad as a prey item for introduced predators in the middle Columbia River. Our first objective, addressed in Chapter 1, was to evaluate the efficacy of nonlethal methods to describe the physiological condition of smallmouth bass, walleye, and channel catfish from late summer through late fall. Such information will be used to understand the contribution of juvenile American shad to the energy reserves of predaceous fish prior to winter. In Chapter 2, we describe the results of some limited sampling to document the food habits of smallmouth bass, walleye, and channel catfish in three reservoirs of the middle Columbia River during late fall. Collectively, we hope to increase our understanding of the contribution of juvenile American shad to the diets of introduced predators and the contribution of this diet to their energy reserves, growth, and perhaps over-winter survival. Managers should be able to use this information for deciding whether to control the population of American shad in the CRB or for managing introduced predaceous fish in the CRB.

Oregon, Washington↗

USGS2024

Risk of capture is modified by hypoxia and interjurisdictional migration of Lake Whitefish (Coregonus clupeaformis)

Interjurisdictional migrations lead to seasonally changing patterns of exploitation risk, emphasizing the importance of spatially explicit approaches to fishery management. Understanding how risk changes along a migration route supports time-area based fishery management, but quantifying risk can be complicated when multiple fishing methods are geographically segregated and when bycatch species are considered. Further, habitat selection in dynamic environments can influence migration behavior, interacting with other management objectives such as water quality and habitat restoration. As a case study, we examined a novel acoustic telemetry data set for Lake Whitefish in Lake Erie, where they migrate through multiple spatial management units that are variably affected by seasonal hypoxia and host a variety of fisheries. Combining telemetry results with fishery catch and water quality monitoring, we demonstrate three exploitation risk scenarios: i) high risk due to high residency and high catch, ii) high risk due to high residency in time-areas with moderate catch, and iii) low risk due to residency in time-areas with low catch. Interestingly, occupation of low risk refugia was increased by the development of hypoxia in adjacent areas. Consequently, fishery management goals to sustainably manage other target species may be directly and indirectly linked to water quality management goals through Lake Whitefish.

Lake Erie↗

USGS1982

Gasometer: An inexpensive device for continuous monitoring of dissolved gases and supersaturation

The “gasometer” is a device that measures differential dissolved-gas pressures (δP) in water relative to barometric pressure (as does the “Weiss saturometer”), but operates continuously without human attention. The gasometer can be plumbed into a water-supply system and requires 8 liters/minute of water or more at 60 kilopascals. The gasometer's surfaces are nontoxic, and flow-through water can be used for fish culture. The gasometer may be connected to a small submersible pump and operated as a portable unit. The gasometer can activate an alarm system and thus protect fish from hyperbaric (supersaturation) or hypobaric gas pressures (usually due to low dissolved oxygen). Instructions are included for calculating and reporting data including the pressure and saturation of individual gases. Construction and performance standards are given for the gasometer. Occasional cleaning is required to remove biofouling from the gas-permeable tubing. PDF

Transactions of the American Fisheries Society↗

USGS2005

Managing water in the West: developing new tools for a critical resource

Rapid population growth in the Western United States over the last century has placed increasing strains on our water supplies and aquatic ecosystems. Historically, water rights have been used to determine the allocation of water in the West, but rules and regulations related to endangered species now often drive how water is released from reservoirs in large rivers such as the lower Colorado and the Columbia. In numerous smaller watersheds, communities are trying to balance the water necessary for human use, irrigation, and the conservation of ecosystems. To assist managers in the face of increasing complexity and uncertainty in water management decision-making, the Western Fisheries Research Center (WFRC) is involved in developing a new generation of integrative tools. Below are some examples of the types of tools that already exist within the WFRC.

Fact Sheet↗

USGS2005

The Columbia River Research Laboratory

The U.S. Geological Survey's Columbia River Research Laboratory (CRRL) was established in 1978 at Cook, Washington, in the Columbia River Gorge east of Portland, Oregon. The CRRL, as part of the Western Fisheries Research Center, conducts research on fishery issues in the Columbia River Basin. Our mission is to: 'Serve the public by providing scientific information to support the stewardship of our Nation's fish and aquatic resources...by conducting objective, relevant research'.

Washington↗

USGS2007

Longitudinal patterns of fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River, Oregon

The Lower Crooked River is a remarkable groundwater-fed stream flowing through vertical basalt canyons in the Deschutes River Valley ecoregion in central Oregon (Pater and others, 1998). The 9-mile section of the river between the Crooked River National Grasslands boundary near Ogden Wayside and river mile (RM) 8 is protected under the National Wild and Scenic Rivers Act (16 U.S.C. 1271-1287) for its outstandingly remarkable scenic, recreational, geologic, hydrologic, wildlife, and botanical values (ORVs), and significant fishery and cultural values. Groundwater springs flow directly out of the canyon walls into the Lower Crooked River and create a unique hydrologic setting for native coldwater fish, such as inland Columbia Basin redband trout (Oncorhynchus mykiss gairdneri). To protect and enhance the ORVs that are the basis for the wild and scenic designation, the Bureau of Land Management (BLM) has identified the need to evaluate, among other conditions, fish presence and habitat use of the Lower Crooked River. The results of this and other studies will provide a scientific basis for communication and cooperation between the BLM, Oregon Water Resources Department, Oregon Department of Fish and Wildlife (ODFW) and all water users within the basin. These biological studies initiated by the BLM in the region reflect a growing national awareness of the impacts of agricultural and municipal water use on the integrity of freshwater ecosystems. Biological surveys are needed to better understand the aquatic ecosystem of the Lower Crooked River. This baseline information will be valuable to public land managers whose task is to balance resource use while protecting the unique attributes (that is, ORVs) of the Lower Crooked River. The habitat requirements of coldwater fishes in this section of stream are of particular interest due to state and federal regulation of water temperature in order to protect and restore fish populations. Historical data on the distribution and abundance of stream fishes in the Lower Crooked River are limited to point observations by fishermen and local biologists because steep canyon walls have limited access to most of the river. Surveys of aquatic habitat (channel morphology and substrate composition) have been conducted for the BLM by the ODFW (Oregon Department of Fish and Wildlife, 1997), U.S. Forest Service (United States Forest Service, 2003), and the U.S. Fish and Wildlife Service (USFWS), but fish surveys using electrofishing gear have never been conducted in the isolated 11-mile section of the Crooked River Gorge, and visual observations with mask and snorkel have only been made at isolated point locations where hiking trails provide access to the river (K. Jones, Steve Marx, and Brett Hodgson, ODFW; P. Lickwar, USFWS; pers. comm.). Thus, there is a poor understanding of stream fish presence and distribution throughout Lower Crooked River. Information on fish assemblages is available for the Deschutes River basin and applies generally to the Lower Crooked River because the two rivers were connected historically (Zimmerman and Ratliff 2003). The construction of dams throughout the Deschutes River basin has eliminated historic runs of salmon and steelhead and prevented migration of bull trout and Pacific lamprey into the Crooked River system. Native fish species expected to occur in the Lower Crooked River include Columbia Basin redband trout ( Oncorhynchus mykiss gairdneri ), mountain whitefish ( Prosopium williamsoni ), sculpin ( Cottus spp.), two species of dace ( Rhinichthys spp.), two species of sucker ( Catostomus spp.), northern pikeminnow ( Ptychocheilus oregonensis ), chiselmouth ( Acrocheilus alutaceus ), and redside shiner ( Richardsonius balteatus ). Threespine stickleback ( Gasterosteus aculeatus ), a species native to western Oregon, also occurs in the basin but is believed to be introduced (D. Markle, Department of Fisheries and Wildlife, Oregon State University, personnel commun.). Extensive stocking of rainbow trout has contributed to a large population of naturalized fish of hatchery origin in the Lower Crooked River. Due to the difficulty of differentiating between wild redband trout and naturalized rainbow trout of hatchery origin, the general classification of rainbow trout ( Oncorhynchus mykiss ) is used throughout this report to describe the fish that were observed in the Lower Crooked River. Exotic fish species expected to occur in the Lower Crooked River include large- and smallmouth bass ( Micropterus spp.), yellow perch ( Perca flavescens ), and brown bullhead (Ameiurus nebulosis) (Zimmerman and Ratliff 2003). The goal of this project was to examine longitudinal patterns in fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River during summer conditions. Specific objectives were to (1) characterize the spatial distribution of native and non-native fishes, (2) describe variation in channel morphology, substrate composition, and water temperature, and (3) evaluate the associations between fishes, aquatic habitat, and water temperature.

Oregon↗

USGS2007

Geophysical mapping of oyster habitats in a shallow estuary: Apalachicola Bay, Florida

This report presents high-resolution geophysical data, interpretive maps, and a preliminary discussion about the oyster habitat and estuary-floor geology within Apalachicola Bay, Florida (fig. 1). During two research cruises, conducted in 2005 and 2006, approximately 230 km² of the bay floor were surveyed using interferometric-bathymetry, sidescan-sonar, and chirp seismic-reflection techniques. The research was conducted as part of a cooperative program between the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration Coastal Services Center (CSC), and the Apalachicola Bay National Estuarine Research Reserve. The Apalachicola Bay National Estuarine Research Reserve was established in 1979 to provide opportunities for long-term monitoring and research to provide a basis for more informed coastal management decisions for this estuary. Apalachicola Bay is the largest oyster fishery in Florida (Whitfield and Beaumariage, 1977), and the primary objective of this program is to develop a suite of maps that define oyster habitat distribution and estuary-floor geology within the bay. The resulting maps will assist in effective management of oyster resources and provide a reference geologic framework for future scientific and applied research.

Florida↗

USGS1999

An assessment of stream habitat and nutrients in the Elwha River basin: implications for restoration

The Elwha River was once famous for its 10 runs of anadromous salmon which included chinook that reportedly exceeded 45 kilograms. These runs either ceased to exist or were significantly depleted after the construction of the Elwha (1912) and Glines Canyon (1927) Dams, which resulted in the blockage of more than 113 kilometers of mainstem river and tributary habitat. In 1992, in response to the loss of the salmon runs in the Elwha River Basin, President George Bush signed the Elwha River Ecosystem and Fisheries Restoration Act, which authorizes the Secretary of the Interior to remove both dams for ecosystem restoration. The objective of this U.S. Geological Survey (USGS) study was to begin describing baseline conditions for assessing changes that will result from restoration. The first step was to review available physical, chemical, and biological information on the Elwha River Basin. We found that most studies have focused on anadromous fish and habitat and that little information is available on water quality, habitat classification, geomorphic processes, and riparian and aquatic biological communities. There is also a lack of sufficient data on baseline conditions for assessing future changes if restoration occurs. The second component of this study was to collect water-quality and habitat data, filling information gaps. This information will permit a better understanding of the relation between physical habitat and nutrient conditions and changes that may result from salmon restoration. We collected data in the fall of 1997 and found that the concentrations of nitrogen and phosphorous were generally low, with most samples having concentrations below detection limits. Detectable concentrations of nitrogen were associated with sites in the lower reach of the Elwha River, whereas the few detections of phosphorus were at sites throughout the basin. Nutrient data indicate that the Elwha River and its tributaries are oligotrophic. Results of the stream classification indicated that most of the habitat that would be usable by salmon is found in the mainstem of the Elwha River due to natural gradient barriers at the lower end of most tributaries. Habitat is diverse in the mainstem due to large woody debris accumulations and the existence of secondary channels. We concluded that restoring salmon runs to the Elwha River system will affect the ecosystem profoundly. Decaying carcasses of migrating salmon will be the source of large quantities of nutrients to the Elwha River. The complex instream habitat of the mainstem will enhance cycling of these nutrients because carcasses will be retained long enough to be assimilated thereby increasing primary and secondary production, size of immature salmonids, and overall higher salmon recruitment.

Washington↗

USGS2000

Seasonal movement of brown trout in a southern appalachian river

Radio telemetry was used to evaluate the seasonal movement, activity level, and home range size of adult brown trout Salmo trutta in the Chattooga River watershed, one of the southernmost coldwater stream systems in the United States. In all, 27 adult brown trout (262-452 mm total length) were successfully monitored from 16 November 1995 to 15 December 1996. During the day, adult brown trout were consistently found in small, well-established home ranges of less than 270 m in stream length. However, 8 of a possible 18 study fish made spawning migrations during a 2-week period in November 1996. The daytime locations of individual fish were restricted to a single pool or riffle-pool combination, and fish were routinely found in the same location over multiple sampling periods. Maximum upstream movement during spawning was 7.65 km, indicating that brown trout in the Chattooga River have the ability to move long distances. Spawning brown trout returned to their prespawning locations within a few days after spawning. Brown trout maintained larger home ranges in winter than in other seasons. When spawning-related movement was deleted from the analysis, brown trout moved more on a weekly basis in fall than in summer. Brown trout were more active in fall and winter than in spring and summer. Apart from spawning migrations, displacement from established home ranges was not observed for any fish in the study. Although summer water temperatures reached and exceeded reported upper thermal-preference levels, brown trout did not move to thermal refuge areas in nearby tributaries during the stressful summer periods.

Transactions of the American Fisheries Society↗

USGS2024

Pilot framework for fish habitat assessments across tidal and non tidal waters in the Patuxent River Basin

As part of the 2014 Chesapeake Bay Watershed Agreement, all Bay States and the District of Columbia have committed to improving the condition of the Bay, which includes a goal to achieve sustainable fisheries. One outcome under that broad goal is improved effectiveness of fish habitat conservation and preservation efforts. In support of that outcome, the U.S. Geological Survey Eastern Ecological Science Center (USGS-EESC) and the National Oceanic and Atmospheric Association’s National Centers for Coastal Ocean Science (NOAA-NCCOS) are actively developing datasets, methods, and analyses to conduct fish habitat assessments in the Chesapeake Bay watershed, guided by recommendations from a regional stakeholder workshop held by the Chesapeake Bay Program’s (CBP) Fish Habitat Action Team (FHAT) in 2018. The joint USGS and NOAA team has been collaborating on methods for conducting inland and estuarine assessments and exploring whether a seamless headwater to estuary assessment could be developed. The goals of this assessment are to benefit both State and Federal fisheries managers, help advance fisheries science, and provide beneficial information for the public. While past national and regional assessments (e.g. the National Fish Habitat Partnership National Assessment) treated inland and estuarine fish habitat conditions separately due to differences in environments, GIS data representation, and data availability, a seamless habitat assessment could be of value for a broad range of stakeholders as many fish species, several of which are invasive or under federal jurisdiction, use habitats across both inland and estuarine waters. This project developed a pilot framework, explored and tested methods necessary for a finer scale, seamless assessment across both inland and estuarine waters, and demonstrated its use. Although there was interest by the CBP FHAT for the generation of a Baywide fish habitat assessment that spanned tidal salt, tidal fresh, warm non-tidal and cold non-tidal waters, there are a myriad of implementation details and considerations around conducting a Baywide assessment across all four of these general habitat areas. Therefore, the practical need to conduct a tributary-specific pilot assessment arose. At the beginning of this pilot process, members of the FHAT were presented with a decision matrix to choose a study basin using factors such as data availability and tributary size. FHAT members chose the Patuxent River basin, which has been relatively well sampled and studied. Several spatial frameworks were considered before selection of an inclusive gridded framework for summary and analysis that represented inland drainage networks and landscape influences as well as estuarine bathymetry. A suite of landscape and in-water stressor variables were summarized into the framework and were largely generalized over time. In order to assess the viability of the framework, we chose to use species distribution modeling for each of the species to test the framework’s ability to predict habitat use of non-tidal resident, estuarine resident, and migratory species. Tessellated darter (Etheostoma olmstedi), American eel (Anguilla rostrata), and white perch (Morone americana) were chosen as illustrative fish species based on data availability, and differences in life history and habitat use. A nested modeling approach, which involved successive model runs at multiple scales (1000m, 100m, and 10m raster grids) was developed to examine differences in variable importance at different spatial scales and to enhance modeling efficiency. For white perch, a complementary modeling analysis was performed for variables available only in estuarine waters. For all testing, an ensemble modeling approach was conducted, using a suite of potential statistical techniques driven by model strength and variable predictive power. The statistical testing that we conducted was intended only to test the framework and modeling approach, and not to definitively predict all habitats where specific fish species might be present. The modeling we conducted to test the framework did have some limitations. For example, the spatial distribution of favorable habitat areas for white perch was likely influenced by the predominance of fish survey locations near the center channel of the river and the use of generalized in-water conditions. For all species, the use of juvenile and adult fish survey data limits the estimation of habitat use to those life stages. Despite such limitations of the data inputs and modeling approach, we found the framework could seamlessly predict fish habitat distribution across freshwater and tidal environments and integrate the influence of landscape stressors with local in-water factors. The developed framework presented to the Sustainable Fisheries Goal Implementation Team (GIT) and FHAT is informative and could potentially be used for other modeling applications in the Chesapeake Bay watershed and elsewhere. In particular the framework and modeling approach lend themselves to evaluating living resource distributions and underlying habitat conditions in shallow tidal waters and beyond, as recommended by the recent Comprehensive Evaluation of System Response (CESR) report from the Chesapeake Bay Program.

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USGS2005

Host Fish Identification and Early Life Thermal Requirements for the Federal Endangered Winged Mapleleaf Mussel

The winged mapleleaf mussel (Quadrula fragosa, WML) is a Federal endangered species historically inhabiting at least 34 river systems in 12 Midwestern states. Only four populations are currently known to exist, including one confirmed reproducing population in the St. Croix National Scenic Riverway (NSR) bordering Minnesota and Wisconsin. Recovery efforts are limited by a lack of life history information, particularly which species of fish serve as host to the mussel's parasitic larvae (glochidia). Since 1997, biologists at the University of Minnesota have tried to identify host fish for the WML. Department of the Interior colleagues working in western Wisconsin at the U.S. Fish and Wildlife Service's La Crosse Fishery Resources Office and Genoa National Fish Hatchery, the National Park Service's St. Croix NSR, and the U.S. Geological Survey's Upper Midwest Environmental Sciences Center (UMESC) in La Crosse joined the team in 2001 to expand and accelerate the laboratory host fish identification program by making use of the well-equipped aquatic research facilities at UMESC. We report on several WML early life history investigations conducted at UMESC since autumn 2003 to identify suitable host fish species and evaluate thermal requisites for the development of glochidia into free-living juvenile mussels.

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