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At least 487 records · Page 27Linked to original sources
USGS2023

Influence of a guide net on the presence and behavior of fish near the selective water withdrawal structure in Lake Billy Chinook, Oregon, 2022

Imaging sonar was used to assess the influence of a fish guidance net, installed at the entrances to the selective water withdrawal (SWW) intake structure, in the forebay of Round Butte Dam, Oregon, on behavior, abundance, and timing of fish during the spring of 2022. The purposes of the SWW are (1) to direct surface currents in the forebay to attract and collect downriver migrating juvenile salmonid smolts (Chinook salmon [ Oncorhynchus tshawytscha ], sockeye salmon [ O. nerka ], and steelhead [ O. mykiss ]) from Lake Billy Chinook and (2) to enable operators of the SWW to withdraw water from surface and benthic elevations in the reservoir to manage downriver water temperatures. Part of the evaluation to determine how well the structure performs at collecting juvenile salmonids is (1) to regularly assess how fish are approaching the entrance, and (2) determine if operational flows and the installation of a guidance (lead) net near the SWW structure entrance can be optimized to increase the attraction of smolts present in the forebay of Lake Billy Chinook. The goal of this study was to provide data about the effects of the installation of a lead net on the movements and behaviors of juvenile salmonids near the entrance to the SWW to help inform decisions to improve downstream passage solutions. Two imaging sonar units were deployed during the spring 2022 smolt out-migration period. One unit monitored fish movements near the south entrance and one unit monitored movements near the north entrance of the SWW, with the lead net between the two entrances. Both smolt and bull trout ( Salvelinus confluentus )-size fish were regularly observed near the entrances, with greater abundances observed at night, corresponding with greater discharge through the SWW, as opposed to during the day when discharge was reduced. Smolt-size fish groups were primarily observed near the interior halves of each SWW entrance, and greater abundances of fish were observed at the south entrance. Increased counts of bull trout-size fish coincided with the increased abundances of smolt-size fish. Overall, the results indicate that (1) smolt-size fish were more abundant near the entrance of the SWW during periods of increased discharge, (2) bull trout-size fish were present at the SWW, and (3) a greater percentage of smolt-size fish were observed directed toward the entrances of the SWW during periods of increased discharge. The addition of the lead net may assist in orienting fish toward the entrances to the SWW.

Oregon↗
USGS2012

Simulating potential structural and operational changes for Detroit Dam on the North Santiam River, Oregon, for downstream temperature management

Detroit Dam was constructed in 1953 on the North Santiam River in western Oregon and resulted in the formation of Detroit Lake. With a full-pool storage volume of 455,100 acre-feet and a dam height of 463 feet, Detroit Lake is one of the largest and most important reservoirs in the Willamette River basin in terms of power generation, recreation, and water storage and releases. The U.S. Army Corps of Engineers operates Detroit Dam as part of a system of 13 reservoirs in the Willamette Project to meet multiple goals, which include flood-damage protection, power generation, downstream navigation, recreation, and irrigation. A distinct cycle in water temperature occurs in Detroit Lake as spring and summer heating through solar radiation creates a warm layer of water near the surface and isolates cold water below. Controlling the temperature of releases from Detroit Dam, therefore, is highly dependent on the location, characteristics, and usage of the dam's outlet structures. Prior to operational changes in 2007, Detroit Dam had a well-documented effect on downstream water temperature that was problematic for endangered salmonid fish species, releasing water that was too cold in midsummer and too warm in autumn. This unnatural seasonal temperature pattern caused problems in the timing of fish migration, spawning, and emergence. In this study, an existing calibrated 2-dimensional hydrodynamic water-quality model [CE-QUAL-W2] of Detroit Lake was used to determine how changes in dam operation or changes to the structural release points of Detroit Dam might affect downstream water temperatures under a range of historical hydrologic and meteorological conditions. The results from a subset of the Detroit Lake model scenarios then were used as forcing conditions for downstream CE-QUAL-W2 models of Big Cliff Reservoir (the small reregulating reservoir just downstream of Detroit Dam) and the North Santiam and Santiam Rivers. Many combinations of environmental, operational, and structural options were explored with the model scenarios. Multiple downstream temperature targets were used along with three sets of environmental forcing conditions representing cool/wet, normal, and hot/dry conditions. Five structural options at Detroit Dam were modeled, including the use of existing outlets, one hypothetical variable-elevation outlet such as a sliding gate, a hypothetical combination of a floating outlet and a fixed-elevation outlet, and a hypothetical combination of a floating outlet and a sliding gate. Finally, 14 sets of operational guidelines for Detroit Dam were explored to gain an understanding of the effects of imposing different downstream minimum streamflows, imposing minimum outflow rules to specific outlets, and managing the level of the lake with different timelines through the year. Selected subsets of these combinations of operational and structural scenarios were run through the downstream models of Big Cliff Reservoir and the North Santiam and Santiam Rivers to explore how hypothetical changes at Detroit Dam might provide improved temperatures for endangered salmonids downstream of the Detroit-Big Cliff Dam complex. Conclusions that can be drawn from these model scenarios include: *The water-temperature targets set by the U.S. Army Corps of Engineers for releases from Detroit Dam can be met through a combination of new dam outlets or a delayed drawdown of the lake in autumn. *Spring and summer dam operations greatly affect the available release temperatures and operational flexibility later in the autumn. Releasing warm water during midsummer tends to keep more cool water available for release in autumn. *The ability to meet downstream temperature targets during spring depends on the characteristics of the available outlets. Under existing conditions, although warm water sometimes is present at the lake surface in spring and early summer, such water may not be available for release if the lake level is either well below or well above the spillway crest. *Managing lake releases to meet downstream temperature targets depends on having outlet structures that can access both (warm) lake surface water and (cold) deeper lake water throughout the year. The existing outlets at Detroit Dam do not allow near-surface waters to be released during times when the lake surface level is below the spillway (spring and autumn). *Using the existing outlets at Detroit Dam, lake level management is important to the water temperature of releases because it controls the availability and depth of water at the spillway. When lake level is lowered below the spillway crest in late summer, the loss of access to warm water at the lake surface can result in abrupt changes to release temperatures. *Because the power-generation intakes (penstocks) are 166 feet below the full-pool lake level, imposing minimum power production requirements at Detroit Dam limits the amount of warm surface water that can be expelled from the lake in midsummer, thereby postponing and amplifying warm outflows from Detroit Lake into the autumn spawning season. *Likewise, imposing minimum power production requirements at Detroit Dam in autumn can limit the amount of cool hypolimnetic water that is released from the lake, thereby limiting cool outflows from Detroit Lake during the autumn spawning season. *Model simulations indicate that a delayed drawdown of Detroit Lake in autumn would result in better control over release temperatures in the immediate downstream vicinity of Big Cliff Dam, but the reduced outflows necessary to retain more water in the lake in late summer are more susceptible to rapid heating downstream. *Compared to the existing outlets at Detroit Dam, floating or sliding-gate outlet structures can provide greater control over release temperatures because they provide better access to warm water at the lake surface and cooler water at depth. These conclusions can be grouped into several common themes. First, optimal and flexible management and achievement of downstream temperature goals requires that releases of warm water near the surface of the lake and cold water below the thermocline are both possible with the available dam outlets during spring, summer, and autumn. This constraint can be met to some extent with existing outlets, but only if access to the spillway is extended into autumn by keeping the lake level higher than called for by the current rule curve (the typical target water-surface elevation throughout the year). If new outlets are considered, a variable-elevation outlet such as a sliding gate structure, or a floating outlet in combination with a fixed-elevation outlet at sufficient depth to access cold water, is likely to work well in terms of accessing a range of water temperatures and achieving downstream temperature targets. Furthermore, model results indicate that it is important to release warm water from near the lake surface during midsummer. If not released downstream, the warm water will build up at the top of the lake as a result of solar energy inputs and the thermocline will deepen, potentially causing warm water to reach the depth of deeper fixed-elevation outlets in autumn, particularly when the lake level is drawn down to make room for flood storage. Delaying the drawdown in autumn can help to keep the thermocline above such outlets and preserve access to cold water. Although it is important to generate hydropower at Detroit Dam, minimum power-production requirements limit the ability of dam operators to meet downstream temperature targets with existing outlet structures. The location of the power penstocks below the thermocline in spring and most of summer causes the release of more cool water during summer than is optimal. Reducing the power-production constraint allows the temperature target to be met more frequently, but at the cost of less power generation. Finally, running the Detroit Dam, Big Cliff Dam, and North Santiam and Santiam River models in series allows dam operators to evaluate how different operational strategies or combinations of new dam outlets might affect downstream temperatures for many miles of critical endangered salmonid habitat. Temperatures can change quickly in these downstream reaches as the river exchanges heat with its surroundings, and heating or cooling of 6 degrees Celsius is not unusual in the 40–50 miles downstream of Big Cliff Dam. The results published in this report supersede preliminary results published in U.S. Geological Survey Open-File Report 2011-1268 (Buccola and Rounds, 2011). Those preliminary results are still valid, but the results in this report are more current and comprehensive.

Oregon↗
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↗
USGS2022

Assessment of habitat availability for juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in the Willamette River, Oregon

The Willamette River, Oregon, is home to two salmonid species listed as threatened under the Endangered Species Act, Upper WIllamette River spring Chinook salmon ( Oncorhynchus tshawytscha ) and Upper Willamette River winter steelhead ( O. mykiss ). Streamflow in the Willamette River is regulated by upstream dams, 13 of which are operated by the U.S. Army Corps of Engineers (USACE) as part of the Willamette Valley Project. In 2008, these dams were determined to have a deleterious effect on Endangered Species Act-listed salmonids, resulting in USACE taking actions to mitigate those effects. Mitigation actions included setting seasonal streamflow targets at various locations along the river to improve survival and migration of juvenile salmonids. Although these targets were established with the best available information at the time, recent data and models have advanced understanding of Willamette River bathymetric, hydraulic, and thermal conditions, allowing for a more robust analysis of the effect of streamflow on downstream habitat. This study integrates those recent advances to build high-resolution models of usable habitat for juvenile Chinook salmon and steelhead to assess variation in spatial and seasonal patterns of habitat availability. Specifically, this study develops detailed maps of habitat availability for juvenile Chinook salmon and steelhead for two size classes (fry and pre-smolt). Habitat availability is modeled in a three-step process whereby (1) two-dimensional hydraulic models are paired with literature-supplied data on habitat preferences to create spatially explicit maps of rearing habitats for a wide range of streamflows; (2) reach-specific relations between streamflow and habitat area are developed and paired with streamgage records to create habitat time series for 2011, 2015, and 2016, which reflect “cool and wet,” “hot and dry,” and “warm but average precipitation” conditions, respectively; (3) temperature models are coupled with literature-based thermal thresholds to determine time periods and locations along the river corridor when rearing habitat has optimal, harmful, or lethal temperature conditions; (4) finally, habitat availability is summarized at several spatial scales to characterize longitudinal and seasonal patterns. Findings show that modeled area of rearing habitat for Chinook salmon and steelhead responds non-uniformly to streamflow, where habitat in some reaches of the Willamette River consistently increase with additional streamflow, while in other reaches, habitat area decreases when streamflows increase from low to moderate flows. Modeled differences in flow-habitat relations are primarily explained by local geomorphology in each reach and resulting hydraulic conditions that arise with different streamflows. These are most pronounced when comparing laterally active, multi-channel reaches upstream from Corvallis with downstream reaches that are laterally stable with single-channel planforms. The reaches upstream from Corvallis generally have more habitat available per unit stream distance than downstream reaches, but all reaches display greatest amounts of habitat at the highest streamflows. Finally, results show that warm water temperature in summer greatly decreases the utility of habitat available to the focal species, particularly downstream from Corvallis. Together, these findings serve to inform flow management by characterizing spatial and seasonal patterns of habitat availability for juvenile spring Chinook salmon and winter steelhead and provide a quantitative assessment of the effects of streamflow on rearing habitat.

Oregon↗
USGS2024

Comparison of longitudinal stream temperature profiles and significant thermal features from airborne thermal infrared and float surveys of the Skykomish, Snoqualmie, and Middle Fork Snoqualmie Rivers, King and Snohomish Counties, Washington, summer 2020 and 2021

Summer water temperatures in the Skykomish, Snoqualmie, and Middle Fork Snoqualmie Rivers in western Washington have in recent decades exceeded the water temperature criteria for aquatic life uses set by the Washington Department of Ecology. This temperature increase is of particular concern because these rivers provide critical habitat for several salmonid populations, including Endangered Species Act-listed Chinook salmon ( Onchorhynchus tshawytscha ), steelhead trout ( O. mykiss ), and bull trout ( Salvelinus confluentus ), thus helping sustain Endangered Species Act-listed Southern Resident orcas ( Orcinus orca ). To inform salmonid restoration efforts within these rivers, this study used high-resolution thermal infrared (TIR) and three-band red, green, blue imagery acquired from repeated airborne surveys conducted in August 2020 and 2021 to (1) quantify longitudinal stream temperature profiles (LTPs) and (2) identify and characterize significant thermal features (STFs), including cold-water anomalies that could represent thermal refuges and serve as salmonid habitat. In addition, drag-probe water temperature surveys (“float surveys”) were performed on the Skykomish and Middle Fork Snoqualmie Rivers during August–September 2020 and on a segment of the Middle Fork Snoqualmie River in August 2021. These float surveys were intended to evaluate this thermal profiling method in comparison to airborne TIR surveys, by employing a novel method of processing float survey data to adjust for diurnal heating. The Middle Fork Snoqualmie River warmed about 7 degrees Celsius (°C) from upstream to downstream in the 2020 airborne TIR survey and 9 °C in the 2021 airborne TIR survey, and the Snoqualmie River warmed about 4 °C in both surveys. The water temperature of the Skykomish River cooled in the 2020 and 2021 surveys, primarily because of cold inflow from the Sultan River. The overall shapes of airborne TIR LTPs of the same river were similar in the 2020 and 2021 surveys, with increasing and decreasing gradients in temperature tending to be nearly parallel over the same reaches and abrupt changes in temperature typically identified at the same locations. A total of 854 STFs were identified in the 2020 TIR imagery, and 732 STFs were identified in the 2021 TIR imagery. Interannual persistence was detected in 36.4 to 61.3 percent of lateral groundwater, side channel, and small tributary STFs, depending on the river surveyed, and in 14.8 to 28.7 percent of hyporheic and diffuse groundwater STFs. Hyporheic flow was commonly detected at the downstream end of a riffle, but not often detected directly downstream from large woody debris. Shade from riparian vegetation did not reduce water temperatures but rather maintained the water temperature recorded just upstream from the shaded section. The adjusted average water temperature profiles from the float surveys were comparable to the LTPs derived from the airborne TIR surveys, with differences in temperature gradient primarily because the surveys were performed under different streamflow, radiation, and shading conditions. Though float surveys were found to be a valuable means of obtaining thermal profiles comparable to profiles obtained by airborne TIR surveys, one key advantage of airborne TIR surveys is that they may be used to precisely locate STFs over long distances, during a short survey duration, and in areas inaccessible to most watercraft.

Washington↗
USGS2003

Aquatic assemblages and their relation to temperature variables of least-disturbed streams in the Salmon River basin, central Idaho, 2001

In the late 1990s, Idaho’s established stream temperature criteria for the protection of coldwater biota and salmonid spawning were considered inadequate because the criteria did not agree with observed biological conditions in many instances and did not allow for variability in environmental condition or species diversity across a broad area such as the entire State of Idaho. In 2001, benthic invertebrate and fish assemblages in 34 least-disturbed streams in the Salmon River Basin, central Idaho, were evaluated in relation to stream temperature and other environmental variables. The Salmon River Basin retains watersheds that are minimally affected by human activities. These “natural” stream conditions provide a basis for deriving attainable stream temperatures that can be used to set new, and revise existing, water-quality criteria for stream habitats affected by human activities. During July through September 2001, data were collected to document the thermal regime of least-disturbed streams, characterize the distribution of aquatic biota at streams representing a gradient of temperature, and describe the relations between environmental variables and benthic invertebrate and fish assemblages. Nine stream temperature metrics were compared with the U.S. Environmental Protection Agency’s criterion of 10 ° C (degrees Celsius) for bull trout spawning and juvenile rearing. The maximum weekly-maximum temperature at all 33 sites where temperature data were available exceeded this criterion. The maximum daily-maximum temperature (MDMT) at 30 of the sites exceeded the Idaho Department of Environmental Quality (IDEQ) criterion of 13.0 ° C for the protection of salmonid spawning; and the maximum daily-average temperature at all 33 sites exceeded the 9.0 ° C criterion for the protection of salmonid spawning. The thermal regime at most sites did not exceed the IDEQ criteria for the protection of coldwater biota. Nine environmental variables—water-surface gradient, discharge, wetted channel width, width:depth ratio, aspect, total seasonal thermal input, open canopy, riparian canopy density, and elevation were selected for correlation with the nine stream temperature metrics. Elevation showed the strongest inverse correlation with the stream temperature metrics. Two hundred and one benthic invertebrate taxa from the 34 sampling sites were identified. The most abundant taxa were Baetis tricaudatus , Oligochaeta, Tvetenia bavarica gr., Acari, Rhithrogena , Cinygmula , Heterlimnius , Micropsectra , Eukiefferiella devonica gr., Drunella doddsi , and Cricotopus . Of the 201 benthic invertebrate taxa collected during this study, 57 taxa (present at a minimum of 5 sampling sites) were significantly correlated with one or more of the stream temperature metrics. Among the invertebrate taxa collected, 32 were identified as coldwater taxa. Of the coldwater taxa collected, Zapada oregonensis gr. showed the strongest inverse correlation with the stream temperature metrics and was collected at sites where maximum weekly-maximum temperature (based on date of sample and 6 days prior) ranged from 11.3 ° to 18.5 °C. Ten species of fish in the families Salmonidae, Cottidae, and Cyprinidae were collected. Two species (bull trout and chinook salmon) listed as threatened under the U.S. Fish and Wildlife Service Endangered Species Act were collected. Among all species, bull trout showed the strongest inverse correlation between relative fish abundance and stream temperature. Bull trout and juvenile bull trout densities were inversely correlated with stream temperature. The probability of occurrence of juvenile bull trout was significantly correlated with MDMT on the basis of results from a logistic regression model developed during this study. However, this model differed from a similar model developed by the U.S. Forest Service on the basis of regional data collected in the Pacific Northwest. The regression model based on data collected during this study showed higher probabilities of occurrence of bull trout at colder stream temperatures (10 ° to 15 ° C) and lower probabilities of occurrence at warmer stream temperatures (16 ° to 21 ° C) than did the model based on regional data. The model comparisons suggest that regional or local differences need to be considered when deriving stream temperature criteria.

Idaho↗
USGS2025

Histological progression and bacterial load dynamics of Renibacterium salmoninarum in Chinook salmon Oncorhynchus tshawytscha

Renibacterium salmoninarum , the cause of bacterial kidney disease (BKD), severely impacts salmonid populations. Much of our understanding of the BKD pathology in salmonids comes from evaluating fatal infections in wild populations or spawning Pacific Northwest salmonids. Our study investigated the histological progression and bacterial load dynamics of R. salmoninarum infection in Chinook salmon following intraperitoneal injection to enhance understanding of the disease’s dynamics. Seventy presmolt salmon were injected with the ATCC-33209 isolate of R. salmoninarum and monitored over 10 wk. Histological signs of disease were observed in spleen and liver tissues at 1 wk post-injection and in kidney tissues at 4 wk post-injection, with signs of disease increasing over time. Additionally, histopathological analysis revealed splenic and hepatic capsulitis (coelomitis), individual hepatocyte necrosis, progressive granulomatous hepatitis, splenitis, and nephritis with necrosis. Gram staining confirmed the presence of Gram-positive bacteria within macrophages and extracellularly in infected tissues. Quantitative PCR revealed significant increases in bacterial loads in both kidney and liver tissues over the study period, with higher bacterial loads observed in the kidney tissue. Bacterial load was strongly correlated with disease stage, with peak bacterial burdens coinciding with the most severe histological changes. Our study provides a comprehensive account of R. salmoninarum infection and disease progression in Chinook salmon after intraperitoneal injection.

Diseases of Aquatic Organisms↗
USGS1999

Influence of temperature and substrate on infection rate, triactinomyxon production, and release duration from eastern tubifex worms infected with Myxobolus cerebralis

Salmonid whirling disease is caused by Myxobolus cerebralis , a metazoan parasite with a two host life cycle involving salmonid fish a an aquatic oligochaete, Tubifex tubifex (Wolf, Markiw and Hiltunen, 1986). Whirling disease has been reported in 22 U.S. states with the greatest losses occurring in the salmonid fisheries of western and Midwestern states. Although whirling disease is endemic in the eastern United States, serious documented losses to wild populations have not been reported. Two high priority research needs identified in 1996 were a better understanding of how worm and parasite populations might differ from different geographic areas and how environmental factors affect the various stages of whirling disease. To begin to address these research needs we established "eastern" populations of worms, parasite and fish hosts. This abstract will present data on the effects of temperature and substrate upon eastern T. tubifex worms infected with an eastern isolate of M. cerebralis . The influences of these abiotic factors upon the ability to infect the worms and subsequently their ability to produce waterborne triactinomyxons.

Book↗
USGS2012

Hood River PIT-tag interrogation system efficiency study. Annual report of U.S. Geological Survey activities: November 2010-October 2011

Introduction During summer 2010, an agreement was made between the US Geological SurveyColumbia River Research Laboratory (USGS-CRRL) and the Confederated Tribes of the Warm Springs (CTWS) to operate an experimental Passive Integrated Transponder (PIT)-tag interrogation system (PTIS) near the mouth of the Hood River for a year and provide fishdetection efficiency estimates (Bonneville Power Administration (BPA) project number 1988- 053-03, contract number 50150). A previous agreement between Oregon Department of Fish and Wildlife (ODFW) and USGS-CRRL had funded materials acquisition, construction, and installation of the PTIS (BPA project number 1988-053-04, contract number 48684). The primary purpose of the project was to test the efficacy of a PTIS in the lower Hood River for providing data on returning adult salmonids to the Hood River as part of the Hood River Production Monitor and Evaluation project (HRPME). Because PIT tags are small, relatively inexpensive, carry no internal battery, and last through the lifespan of most fishes, they are commonly used in long term fish monitoring projects. They have been extensively used in the Columbia River basin to monitor salmonid behavior and survival through life stages and migration routes in the mainstem Columbia River (Skalski et al. 1998; Zabel and Achord 2004). Increasingly, PIT-tag detection equipment has been deployed in streams to investigate salmonid behavior (Zydlewski et al. 2001, 2006; Riley et al. 2003; Bond et al. 2007). Most of the detection systems deployed and evaluated to date have been in much smaller streams than the mainstem of the Hood River (Zydlewski et al. 2001, 2006; Bond et al. 2007; Horton et al. 2007; Connolly et al. 2008), but researchers are attempting to expand detection abilities to larger streams and rivers. Large streams and rivers can prove extremely challenging to monitor. Some systems have showed promise for contributing valuable detection data, others have proved less successful. A detection system in the Klamath River (Beeman et al. 2012), a site similar in size to the Hood River, suffered problems from cables being dislodged and high water that resulted in a detection efficiency estimate for juvenile coho salmon of less than 0.05. An additional USGS-CRRL task, under contract number 50150, was to build three antennas for use with Destron-Fearing 2001F-ISO PIT tag readers. These antennas would be 5 used at the East Fork Hood River Acclimation site. They would be placed in the outflow channel to inform managers about the number of PIT tagged steelhead smolts released to the Hood River after a period of acclimation when some mortality and predation might occur.

Oregon↗
USGS2015

Sea lamprey mark type, wounding rate, and parasite-host preference and abundance relationships for lake trout and other species in Lake Ontario

We examined how the frequency of attacks by Sea Lamprey on fishes in Lake Ontario varied in response to Sea Lamprey abundance and preferred host abundance (Lake Trout >432mm). For this analysis we assembled seven data sets. Two fishery independent surveys for Lake Trout: US Geological Survey (USGS)/New York State Department of Environmental Conservation (NYSDEC) south shore September gillnet assessment of adult Lake Trout (USGS/NYSDEC SGNS)( Lantry and Lantry 2011); and Ontario Ministry of Natural Resources (OMNR) monthly June-November community index gillnetting in northeastern Lake Ontario (OMNR CIS) (Ontario Ministry of Natural Resources 2011). One angler survey: NYSDEC April-September Fishing Boat Survey data collected along the south shore for Chinook and Coho salmon, and Rainbow and Brown trout (NYSDEC FBS) ( Lantry and Eckert 2012). Two spawning run datasets: OMNR north shore data including spring spawning runs of Rainbow Trout in the Ganaraska River and electroshocking data for fall spawning runs of Chinook and Coho salmon in the Credit River (Ontario Ministry of Natural Resources 2011); and NYSDEC data from the Salmon River on the southeastern shore including October spawning runs of Chinook and Coho salmon. One Sea Lamprey spawning survey: Department of Fisheries and Oceans Canada (DFO)/US Fish and Wildlife Service (USFWS) data for spawning-phase Sea Lamprey abundance collected from known spawning streams distributed throughout the Lake Ontario drainage basin (Mullet et al. 2003). One assessment of the abundance of dead Lake Trout: USGS/NYSDEC October-November bottom trawl collection of Lake Trout carcasses (Schneider et al. 1996). Annual patterns in A1, A2 and A3 wound stages did not track well in plots of wounding rates for the USGS/NYSDEC SGNS and correlations between A1 and later stages did not exist. A1 rates were not correlated to either Lake Trout abundance or Sea Lamprey numbers when considered alone, but were strongly correlated to the ratio between Sea Lamprey numbers and Lake Trout abundance (parasite/host ratio). While A2 and A3 rates were correlated to each other, neither was consistently correlated to any of the Lake Trout abundance or Sea Lamprey abundance parameters and sums of A1 to A3 rates did not improve correlations over those for A1 rates considered alone. Our analysis of the strain-specific susceptibility of Lake Trout to attack by Sea Lampreys extended the previous Schneider et al. (1996) analysis of three strains (SUP, CWL, and SEN) and 11 years of data 1982-1992 to an analysis of seven strains (SUP, CWL, SEN, JEN, LEW, ONT, and OXS) and two groups of unmarked fish (1983-1995 and 1996-2010) and included 18 more years of data through 2010. The susceptibility to attack for CWLs and SENs were below SUPs and nearly identical to the earlier values, new values for LEWs were greater than SUPS and values of unmarked Lake Trout prior to 1996 were unexpectedly greater than SUPs. By reexamining the Schneider et al. (1996) regression relationship between A1 wounding on Lake Trout and the incidence of Lake Trout carcasses recovered in fall bottom trawls (including three additional years of data), and substituting A1 wounding rate for total numbers of A1s observed which was used as the independent variable in the previous version, we were able to increase the variance explained by the relationship from an r2 of 0.60 to 0.88. Healing rate of wounds was explored by examining the monthly incidence of A1 and A2 wounds on Lake Trout from the OMNR CIS. Because wounding intensity varied between years and monthly sample size was frequently low, the ratio of A2 to A1s wounds was used to index how wounds accumulated or disappeared from the Lake Trout populations across seasons. The A2/A1 ratio decreased between June/July and October. A simple wounding model for Lake Trout was constructed to simulate the pattern of ratios by inflicting wounds on the population each month according to a predetermined distribution and including parameters for lethality (fixed distribution) and healing rate of A1 and A2 wounds (discretely varied between simulations). The best simulated representation (ratio size and monthly pattern) of the OMNR CIS data came from an A1 healing rate of 0.5 months and an A2 rate of 2 months. To examine whether alternate hosts provided reliable data to index damage caused by Sea Lampreys we compared September values of abundance and A1 wounding rates on Lake Trout, Sea Lamprey abundance, and the parasite/host ratio with NYSDEC Creel data for observations of Sea lampreys attached to sport-caught salmonids and to wounding observations for salmonids sampled in OMNR and NYSDEC spawning run assessments. Attachment frequency on NYSDEC Creel Chinook Salmon, Brown Trout, and Rainbow Trout were strongly correlated to all measures of Lake Trout abundance and wounding and to the parasite/host ratio. Chinook Salmon and Coho Salmon wounding observations for the NYSDEC Salmon River spawning run assessments and Rainbow Trout from the OMNR Ganaraska River spawning run assessment were strongly correlated to wounding measures for nearly all salmonids and to the parasite/host ratio.

Lake Ontario↗
USGS2010

Sediment management strategies associated with dam removal in the State of Washington

Different removal strategies are described for dams in three diverse drainage basins (Wind River, White Salmon River, and Elwha River basins) in the State of Washington (USA). The comparisons between the strategies offer the opportunity to track the effects of sediment resulting from dam decommissioning in the Pacific Northwest and to determine possible effects on socio-economically important species of anadromous salmonids. Hemlock Dam, located on Trout Creek and managed by the United States Forest Service, was removed from July to September 2009. To mitigate the effect on fish downstream (specifically, salmonids) and to minimize sediment aggradation downstream in the main-stem Wind River, the Forest Service chose to excavate the approximately 42,000 cubic meters of sediment entrapped behind the dam before removal of the dam. Thus, the reach of Trout Creek downstream of the dam will not be affected by a large, released pulse of accumulated sediment. In contrast, the scheduled removal of Condit Dam, located on the White Salmon River 30 kilometers to the east of Hemlock Dam, involves a different removal strategy. Condit Dam will be breached near its base in order to mobilize the 1.7 million cubic meters of trapped sediment during the reservoir drawdown in an effort to decrease the time needed for the downstream reach to return to normal levels of suspended sediment. Finally, the much-anticipated 2011 removal of two dams on the Elwha River on the Olympic Peninsula in northwestern Washington will take place over 2 years with progressive notches cut into the dams from the top down. Although some portion of reservoir sediment will be carried downstream by the river, the specific timing of notching will be adaptively managed to mitigate the effects of raised sediment concentration on fishes and people living downstream. With improved scientific understanding from these studies, future damremoval projects can be planned and executed with approaches that mitigate deleterious effectson salmonids.

Washington↗
USGS2016

Report A: Fish and habitat assessment in Rock Creek, Klickitat County, Washington, June 2013-December 2015

The U.S. Geological Survey (USGS) and the Yakama Nation have collaborated in the Rock Creek subbasin, southeastern, Washington since 2009 to assess steelhead (Oncorynchus mykiss) populations and habitat conditions. Rock Creek, flows south to the Columbia River at river kilometer (rkm) 368. During 2015, a habitat survey was conducted, and monitoring of Passive Integrated Transponder (PIT)-tagged salmonids in the Rock Creek subbasin continued. Two multiplexing PIT-tag interrogation systems (PTISs) were installed in Rock Creek in the fall of 2009 to evaluate timing and degree of salmonid movement, smolting success, stray rates, and other life history attributes. These have been monitored every year since, during the spring, fall, and winter months. Returning adult steelhead detection histories are summarized from past Rock Creek PIT-tagging efforts. Detection histories and detection efficiencies were used to estimate a smolt-to-adult return rate (SAR) for Rock Creek PIT-tagged steelhead (tagged from 2009 to 2012) that ranged from 2.2% to 5.5%. Additionally, a SAR was also estimated for Rock Creek PIT-tagged steelhead returning to Bonneville Dam, Columbia River (rkm 235). The SAR rate to Bonneville Dam was always higher (2.4% to 10.4%), indicating straying of adults to other sites for spawning potentially further upstream or in other tributaries, or pre-spawn mortality. Twenty-two Rock Creek PIT-tagged steelhead were detected returning to Rock Creek and 35 were detected at Bonneville Dam from past tagging efforts (2009 – 2012). Monitoring of the Rock Creek PTISs [Rock Creek Lower (RCL) and Rock Creek Squaw (RCS)] provide evidence for PIT-tagged salmonid use from fish tagged outside of Rock Creek subbasin (out-of-basin) origins. A total of 82 out-of-basin PIT-tagged fish have been detected at the Rock Creek PTISs since installation. The habitat survey was conducted in Rock Creek from September 16 to October 7, 2015. The survey started at rkm 2 and continued upstream to rkm 29.3, and included portions of the major tributaries, ranging from 1 to 9 rkm survey length upstream from their confluence. During the survey, we measured the lengths of all dry and non-pool wet sections, and for pools: the length, wetted width, average residual depth, maximum residual depth, and temperature. During the 2015 survey of Rock Creek, 38% of the river between rkm 2 and 29 was classified as dry, with a higher relative proportion (57%) of dry being in the lower river section (rkm 2-13) than the upper river section (33%, rkm 14-22). This was higher than during survey years 2010 to 2012, which ranged from 29% to 43% in the lower river. As a result of the increase in dry area the percent of non-pool wet habitat was less (22%) than previous years (range 34% to 43%), as well as the percent of pools (21%). However, more river kilometers were surveyed in the lower river section (rkm 2-13) than previous years. For the 2015 survey length (rkm 2 to 29), 19% was classified as pools and 43% was non-pool wet. This work informs potential restoration actions by identifying the persistent pools across years and in years of low water flow (i.e., 2015). This work also provides a baseline to evaluate effectiveness of future restoration actions. Potential restoration actions could include headwater and upland restoration to improve base flows and pool habitat enhancement, through increased structure and vegetation plantings for increased cover. The Rock Creek steelhead population remains to be an important cultural resource for the Rock Creek Band of the Yakama Nation Tribe. The Rock Creek steelhead population is part of the Cascades Eastern Slope major population group (MPG), one of four MPGs contributing to the Middle Columbia steelhead distinct population segment (DPS). The National Marine Fisheries Service recovery plan for Rock Creek (NMFS 2009a) identifies an overall biological recovery goal for Rock Creek steelhead to contribute to recovery of the Mid-Columbia D

Washington↗
USGS2018

Survival of whirling disease resistant rainbow trout fry in the wild: A comparison of two strains

Introduced pathogens can affect fish populations, and three main factors affect disease occurrence: the environment, host, and pathogen. Manipulating at least one of these factors is necessary for controlling disease. Myxobolus cerebralis , the parasite responsible for salmonid whirling disease, became established in Colorado during the 1990s and caused significant declines in wild Rainbow Trout Oncorhynchus mykiss populations. Attempts to re-establish Rainbow Trout have focused on manipulating salmonid host resistance. A Rainbow Trout strain known as GR × CRR was developed for stocking in Colorado by crossing a whirling-disease-resistant strain known as the German Rainbow Trout (GR) with the Colorado River Rainbow Trout (CRR). The GR × CRR fish exhibit resistance similar to that shown by GR, and survival and reproduction were expected to be similar to those of CRR. One disadvantage of stocking GR × CRR is that outcrossing and backcrossing could decrease resistance, and laboratory studies have indicated that this can occur. A potential disadvantage of stocking pure GR is lower survival due to domestication. To compare fry survival between the strains, a field experiment was conducted in 1.6-km reaches of nine Colorado streams. Each stream was stocked in August 2014 with 5,000 GR × CRR and 5,000 GR individuals. In October 2014, April 2015, and August 2015, apparent survival was assessed. Two laboratory predation experiments were also conducted. The field experiment revealed that short-term apparent survival was influenced by stream, and growth rate was influenced by strain and stream. However, after 12 months, there was no difference in apparent survival or growth rate between the GR and GR × CRR strains. Laboratory experiments showed that survival did not differ between the strains when confronted with Brown Trout Salmo trutta predation. Our results indicate that the GR strain is a viable option for stocking in streams where M. cerebralis is enzootic. Further evaluation is needed to determine whether GR fish will survive to maturity and reproduce.

Journal of Aquatic Animal Health↗
USGS2017

Transmission routes maintaining a viral pathogen of steelhead trout within a complex multi-host assemblage

This is the first comprehensive region wide, spatially explicit epidemiologic analysis of surveillance data of the aquatic viral pathogen infectious hematopoietic necrosis virus (IHNV) infecting native salmonid fish. The pathogen has been documented in the freshwater ecosystem of the Pacific Northwest of North America since the 1950s, and the current report describes the disease ecology of IHNV during 2000–2012. Prevalence of IHNV infection in monitored salmonid host cohorts ranged from 8% to 30%, with the highest levels observed in juvenile steelhead trout. The spatial distribution of all IHNV-infected cohorts was concentrated in two sub-regions of the study area, where historic burden of the viral disease has been high. During the study period, prevalence levels fluctuated with a temporal peak in 2002. Virologic and genetic surveillance data were analyzed for evidence of three separate but not mutually exclusive transmission routes hypothesized to be maintaining IHNV in the freshwater ecosystem. Transmission between year classes of juvenile fish at individual sites (route 1) was supported at varying levels of certainty in 10%–55% of candidate cases, transmission between neighboring juvenile cohorts (route 2) was supported in 31%–78% of candidate cases, and transmission from adult fish returning to the same site as an infected juvenile cohort was supported in 26%–74% of candidate cases. The results of this study indicate that multiple specific transmission routes are acting to maintain IHNV in juvenile fish, providing concrete evidence that can be used to improve resource management. Furthermore, these results demonstrate that more sophisticated analysis of available spatio-temporal and genetic data is likely to yield greater insight in future studies.

Idaho, Oregon, Washington↗
USGS2022

Dammed water quality — Longitudinal stream responses below beaver ponds in the Umpqua River Basin, Oregon

Beaver-related restoration (BRR) has gained popularity as a means of improving stream ecosystems, but the effects are not fully understood. Studies of dissolved oxygen (DO) and water temperature, key water quality metrics for salmonids, have demonstrated improved conditions in some cases, but warming and decreased DO have been more commonly reported in meta-analyses. These results point to the contingencies that can influence outcomes from BRR. We examined water quality related to beaver ponds in a diverse coastal watershed (Umpqua River Basin, OR, USA). We monitored water temperature 0–400 m above and below beaver ponds and at pond surfaces and bottoms across seven study sites from June through September of 2019. DO was also recorded at two sites at pond surfaces and pond bottoms. Downstream monthly mean daily maximum temperatures were warmer than upstream reference locations by up to 1.9°C at beaver dam outlets but this heating signal attenuated with downstream distance. Downstream warming was greatest in June and July and best predicted by pond bottom temperatures. DO at pond surfaces and bottoms were hypoxic (≤5 mg/L) for more than half of the 32-day monitoring period. Water temperatures increased for short distances below monitored beaver ponds and observed oxygen conditions within ponds were largely unsuitable for salmonid fishes. These findings contrast with some commonly stated expectations of BRR, and we recommend that managers consider these expectations prior to implementation. In some cases, project goals may override water quality concerns but in streams where temperature or DO restoration are objectives, managers may consider using BRR techniques with caution.

Oregon↗
USGS2018

River response to large‐dam removal in a Mediterranean hydroclimatic setting: Carmel River, California, USA

Dam removal provides a valuable opportunity to measure the fluvial response to changes in both sediment supply and the processes that shape channel morphology. We present the first study of river response to the removal of a large (32‐m‐high) dam in a Mediterranean hydroclimatic setting, on the Carmel River, coastal California, USA. This before‐after/control‐impact study measured changes in channel topography, grain size, and salmonid spawning habitat throughout dam removal and subsequent major floods. During dam removal, the river course was rerouted in order to leave most of the impounded sediment sequestered in the former reservoir and thus prevent major channel and floodplain aggradation downstream. However, a substantial sediment pulse occurred in response to base‐level fall, knickpoint migration, and channel avulsion through sediment in the former reservoir above the newly rerouted channel. The sediment pulse advanced ~3.5 km in the first wet season after dam removal, resulting in decreased riverbed grain size downstream of the dam site. In the second wet season after dam removal, high flows (including a 30‐year flood and two 10‐year floods) transported sediment >30 km downstream, filling pools and reducing cross‐channel relief. Deposition of gravel in the second wet season after dam removal enhanced salmonid spawning habitat downstream of the dam site. We infer that in dam removals where most reservoir sediment remains impounded and where high flows follow soon after dam removal, flow sequencing becomes a more important driver of geomorphic and fish‐habitat change than the dam removal alone.

California↗
USGS2019

Challenges in Columbia River fisheries conservation: Response to Duda et al.

The salmonid fisheries of the Columbia River Basin (CRB) have enormous socioeconomic, cultural, and ecological importance to numerous diverse stakeholders (e.g., state, federal, tribal, nonprofit), and there are a wide array of opinions and perspectives on how these fisheries should be managed. Although we appreciate Duda et al.’s commentary, it offers only one perspective of many in this context. The objective of our paper (Hand et al. 2018) was to provide justification for “the importance of social–ecological perspectives when communicating conservation values and goals, and the role of independent science in guiding management policy and practice for salmonids in the CRB”. However, we did not intend to strictly advocate for a single course of action, and the available space within our paper’s Panel 1 limited us from engaging in a thorough ecological debate.

Frontiers in Ecology and the Environment↗
USGS2019

Return of a giant: Coordinated conservation leads to the first wild reproduction of Lahontan Cutthroat Trout in the Truckee River in nearly a century

Many freshwater fish populations have been greatly reduced, with particular loss of migratory fishes. Recovering depleted populations is challenging as threats are often plentiful and complex, especially in arid environments where demands for water resources are high. Here, we describe how a collaborative, multifaceted approach has spurred natural reproduction—a major step towards Lahontan Cutthroat Trout Oncorhynchus clarkii henshawi (LCT) recovery in Pyramid Lake and the Truckee River, Nevada, once home to one of largest freshwater salmonids in North America. The factors limiting LCT were immense, including habitat fragmentation, degradation, and non‐native species attributes common in the declines of native salmonids. Yet for the first time in over 80 years and each year since 2014, adfluvial LCT have spawned in the lower Truckee River, resulting in the production of tens of thousands of young‐of‐year. The progress and positive trajectory towards recovery were driven by a holistic view of the Truckee River watershed beginning in the early 1990's that envisioned bringing numerous conservation building blocks together to expedite the conservation and recovery for the listed fishes of Pyramid Lake. Although additional challenges remain, the LCT recovery program in the Truckee River basin provides a template for the conservation of imperiled fishes.

Nevada↗