Search USGS⌕ Search

SEARCH · Search USGS

Results for “Salmonid”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources
USGS2015

Flow management and fish density regulate salmonid recruitment and adult size in tailwaters across western North America

Rainbow and brown trout have been intentionally introduced into tailwaters downriver of dams globally and provide billions of dollars in economic benefits. At the same time, recruitment and maximum length of trout populations in tailwaters often fluctuate erratically, which negatively affects the value of fisheries. Large recruitment events may increase dispersal downriver where other fish species may be a priority (e.g., endangered species). There is an urgent need to understand the drivers of trout population dynamics in tailwaters, in particular the role of flow management. Here, we evaluate how flow, fish density, and other physical factors of the river influence recruitment and mean adult length in tailwaters across western North America using data from 29 dams spanning 1-19 years. Rainbow trout recruitment was negatively correlated with high annual, summer, and spring flow and dam latitude, and positively correlated with high winter flow, sub-adult brown trout catch, and reservoir storage capacity. Brown trout recruitment was negatively correlated with high water velocity and daily fluctuations in flow (i.e., hydropeaking) and positively correlated with adult rainbow trout catch. Among these many drivers, rainbow trout recruitment was primarily correlated with high winter flow combined with low spring flow, whereas brown trout recruitment was most related to high water velocity. The mean lengths of adult rainbow and brown trout were influenced by similar flow and catch metrics. Length in both species was positively correlated with high annual flow but declined in tailwaters with high daily fluctuations in flow, high catch rates of conspecifics, and when large cohorts recruited to adult size. Whereas brown trout did not respond to the proportion of water allocated between seasons, rainbow trout length increased in rivers that released more water during winter than in spring. Rainbow trout length was primarily related to high catch rates of conspecifics, whereas brown trout length was mainly related to large cohorts recruiting to the adult size class. Species-specific responses to flow management are likely attributable to differences in seasonal timing of key life history events such as spawning, egg hatching, and fry emergence.

Ecological Applications↗
USGS2012

Detection probability of an in-stream passive integrated transponder (PIT) tag detection system for juvenile salmonids in the Klamath River, northern California, 2011

A series of in-stream passive integrated transponder (PIT) detection antennas installed across the Klamath River in August 2010 were tested using tagged fish in the summer of 2011. Six pass-by antennas were constructed and anchored to the bottom of the Klamath River at a site between the Shasta and Scott Rivers. Two of the six antennas malfunctioned during the spring of 2011 and two pass-through antennas were installed near the opposite shoreline prior to system testing. The detection probability of the PIT tag detection system was evaluated using yearling coho salmon implanted with a PIT tag and a radio transmitter and then released into the Klamath River slightly downstream of Iron Gate Dam. Cormack-Jolly-Seber capture-recapture methods were used to estimate the detection probability of the PIT tag detection system based on detections of PIT tags there and detections of radio transmitters at radio-telemetry detection systems downstream. One of the 43 PIT- and radio-tagged fish released was detected by the PIT tag detection system and 23 were detected by the radio-telemetry detection systems. The estimated detection probability of the PIT tag detection system was 0.043 (standard error 0.042). Eight PIT-tagged fish from other studies also were detected. Detections at the PIT tag detection system were at the two pass-through antennas and the pass-by antenna adjacent to them. Above average river discharge likely was a factor in the low detection probability of the PIT tag detection system. High discharges dislodged two power cables leaving 12 meters of the river width unsampled for PIT detections and resulted in water depths greater than the read distance of the antennas, which allowed fish to pass over much of the system with little chance of being detected. Improvements in detection probability may be expected under river discharge conditions where water depth over the antennas is within maximum read distance of the antennas. Improvements also may be expected if additional arrays of antennas are used.

California↗
USGS2012

Behavior and passage of juvenile salmonids during the evaluation of a behavioral guidance structure at Cowlitz Falls Dam, Washington, 2011

Executive Summary A radiotelemetry evaluation was conducted during April–October 2011 to describe movement patterns, forebay behavior, and passage of juvenile steelhead, coho salmon, and Chinook salmon at Cowlitz Falls Dam, Washington. The primary focus of the study was to describe fish behavior near a behavioral guidance structure (BGS) and floating surface collector (FSC) deployed upstream of Cowlitz Falls Dam. A secondary focus was to determine the proportion of tagged fish that were detected near spillbays 2 and 3 on the dam, because this location has been proposed for deploying weir boxes as an additional dam-based collection alternative in the future. Juvenile steelhead ( Oncorhynchus mykiss ), coho salmon ( Oncorhynchus kisutch ), and Chinook salmon ( Oncorhynchus tshawytscha ) were collected and tagged at the Cowlitz Falls Fish Collection Facility and transported upstream where they were released into the Cowlitz and Cispus Rivers. We radio-tagged and released 110 juvenile steelhead, 110 juvenile coho salmon, and 110 juvenile Chinook salmon and monitored their movements in and around the BGS/FSC complex, at the dam, and downstream of the dam. We used detection records and a Markov chain model to calculate probabilities of movement between specific areas in the forebay of Cowlitz Falls Dam. These areas are referred to as states and the Markov chain model was used to create a series of tables, called transition matrices, that contained estimated probabilities of movement between states. These probabilities were insightful for understanding how radio-tagged fish moved near the BGS, FSC, and spillbays. Most tagged fish (89–91 percent) moved downstream of release sites (9 or 22 rkm upstream of the dam) and were detected in the dam forebay during the study period. Tagged fish that encountered the BGS on their first approach to the dam were distributed across the forebay, which supports the concept of using a BGS to concentrate fish near a collector entrance in the dam forebay. We found that 14 percent of the steelhead, 18 percent of the coho salmon, and 17 percent of the Chinook salmon encountered the FSC discovery area without BGS guidance on their first trip through the forebay. The BGS guided 36 percent of the steelhead, 22 percent of the coho salmon, and 46 percent of the Chinook salmon to the FSC discovery area when fish first entered the forebay, which resulted in 40–63 percent (by species) of the tagged fish arriving at the FSC discovery area. Movement patterns along the BGS showed that fish were likely to guide along the device, but also demonstrated the tendency of fish to move under the BGS and downstream to Cowlitz Falls Dam. Differential distribution among sucker species within the Williamson River Delta and between the delta and adjacent lakes indicated that shortnose suckers likely benefited more from the restored Williamson River Delta than Lost River or Klamath largescale suckers ( Catostomus snyderi ). Catch rates in shallow-water habitats within the delta were higher for shortnose and Klamath largescale sucker larvae than for larval Lost River suckers in 2008, 2009, and 2010. Shortnose suckers also comprised the greatest portion of age-0 suckers captured in the Williamson River Delta in all 3 years of the study. The relative abundance of age-1 shortnose suckers was high in our catches compared to age-1 Lost River suckers in 2009 and 2010. Tagged fish that arrived at Cowlitz Falls Dam were distributed across the dam face but a high percentage of each species (65 percent of steelhead; 61 percent of coho salmon; 71 percent of Chinook salmon) arrived on the northern side of the dam. Movement probabilities near spillbays 1 and 4 showed a strong preference for tagged fish to move from the outer edges of the dam towards the center of the dam where they were detected at the debris barrier (range of probabilities = 0.690–0.841). We found that 76 percent of the steelhead, 61 percent of the coho salmon, and 92 percent of the Chinook salmon were detected at spillbays 2 or 3 during the study. This behavior supports the strategy of weir box deployments in spillbays 2 and 3 for future dam-based collection options. Tagged fish that arrived at the dam commonly moved upstream and were detected at the BGS or FSC discovery area. This behavior provided a secondary opportunity for fish to encounter the FSC discovery area and we found that in total, 72 percent of the steelhead, 48 percent of the coho salmon, and 92 percent of the Chinook salmon were detected near the FSC while residing in the forebay. Overall, 88 percent of the steelhead, 76 percent of the coho salmon, and 95 percent of the Chinook salmon that entered the forebay were detected near the FSC or in spillbays 2 and 3. Turbine passage was the most common passage route for tagged fish at Cowlitz Falls Dam during 2011. We found that 40 percent of the steelhead, 52 percent of the coho salmon, and 33 percent of the Chinook salmon passed through turbines. An additional 22 percent of the steelhead and 32 percent of the coho salmon passed through turbines or spillways when both passage routes were available. Fish collection numbers were relatively low during 2011 compared to long-term averages. In total, 37 percent of the steelhead, 14 percent of the coho salmon, and 23 percent of the Chinook salmon that entered the forebay were collected, primarily through collection flumes. The FSC collected a single radio-tagged fish (a Chinook salmon) in 2011.

Washington↗
USGS2012

Fish population and habitat analysis in Buck Creek, Washington, prior to recolonization by anadromous salmonids after the removal of Condit Dam

We assessed the physical and biotic conditions in the part of Buck Creek, Washington, potentially accessible to anadromous fishes. This creek is a major tributary to the White Salmon River upstream of Condit Dam, which was breached in October 2011. Habitat and fish populations were characterized in four stream reaches. Reach breaks were based on stream gradient, water withdrawals, and fish barriers. Buck Creek generally was confined, with a single straight channel and low sinuosity. Boulders and cobble were the dominant stream substrate, with limited gravel available for spawning. Large-cobble riffles were 83 percent of the available fish habitat. Pools, comprising 15 percent of the surface area, mostly were formed by bedrock with little instream cover and low complexity. Instream wood averaged 6—10 pieces per 100 meters, 80 percent of which was less than 50 centimeters in diameter. Water temperature in Buck Creek rarely exceeded 16 degrees Celsius and did so for only 1 day at river kilometer (rkm) 3 and 11 days at rkm 0.2 in late July and early August 2009. The maximum temperature recorded was 17.2 degrees Celsius at rkm 0.2 on August 2, 2009. Minimum summer discharge in Buck Creek was 3.3 cubic feet per second downstream of an irrigation diversion (rkm 3.1) and 7.7 cubic feet per second at its confluence with the White Salmon River. Rainbow trout ( Oncorhynchus mykiss ) was the dominant fish species in all reaches. The abundance of age-1 or older rainbow trout was similar between reaches. However, in 2009 and 2010, the greatest abundance of age-0 rainbow trout (8 fish per meter) was in the most downstream reach. These analyses in Buck Creek are important for understanding the factors that may limit fish abundance and productivity, and they will help identify and prioritize potential restoration actions. The data collected constitute baseline information of pre-dam removal conditions that will allow assessment of changes in fish populations now that Condit Dam has been removed and anadromous fish have an opportunity to recolonize Buck Creek.

Washington↗
USGS1979

Availability of supplemental water supplies at salmonid fish-propagation stations in Wisconsin

Supplemental water supplies are available at all the 12 fish-propagation stations. At seven of the stations water may be obtained by diverting or impounding streams. Ground water is available from glacial sand-and-gravel aquifers at all the stations and from sandstone aquifers at 7 of the 12 stations. Probable well yields range from 100 to 1,000 gallons per minute from the sand and gravel and from 50 to 1,000 gallons per minute from the sandstone. The response of pumping 1,600 gallons per minute from a ground-water source at Crystal Springs, Langlade, Nevin, and Osceola was estimated by a digital model. Estimated drawdown after 10 years of pumping ranged from 10 to 28 feet (6 to 35 percent of the saturated thickness of the aquifers).

Wisconsin↗
USGS2006

A thermal profile method to identify potential ground-water discharge areas and preferred salmonid habitats for long river reaches

The thermal regime of riverine systems is a major control on aquatic ecosystems. Ground water discharge is an important abiotic driver of the aquatic ecosystem because it provides preferred thermal structure and habitat for different types of fish at different times in their life history. In large diverse river basins with an extensive riverine system, documenting the thermal regime and ground-water discharge is difficult and problematic. A method was developed to thermally profile long (5-25 kilometers) river reaches by towing in a Lagrangian framework one or two probes that measure temperature, depth, and conductivity. One probe is towed near the streambed and, if used, a second probe is towed near the surface. The probes continuously record data at 1-3-second intervals while a Global Positioning System logs spatial coordinates. The thermal profile provides valuable information about spatial and temporal variations in habitat, and, notably, indicates ground-water discharge areas. This method was developed and tested in the Yakima River Basin, Washington, in summer 2001 during low flows in an extreme drought year. The temperature profile comprehensively documents the longitudinal distribution of a river's temperature regime that cannot be captured by fixed station data. The example profile presented exhibits intra-reach diversity that reflects the many factors controlling the temperature of a parcel of water as it moves downstream. Thermal profiles provide a new perspective on riverine system temperature regimes that represent part of the aquatic habitat template for lotic community patterns.

Scientific Investigations Report↗
USGS2013

Salmonids, stream temperatures, and solar loading--modeling the shade provided to the Klamath River by vegetation and geomorphology

The U.S. Geological Survey is studying approaches to characterize the thermal regulation of water and the dynamics of cold water refugia. High temperatures have physiological impacts on anadromous fish species. Factors affecting the presence, variability, and quality of thermal refugia are known, such as riverine and watershed processes, hyporheic flows, deep pools and bathymetric factors, thermal stratification of reservoirs, and other broader climatic considerations. This research develops a conceptual model and methodological techniques to quantify the change in solar insolation load to the Klamath River caused by riparian and floodplain vegetation, the morphology of the river, and the orientation and topographic characteristics of its watersheds. Using multiple scales of input data from digital elevation models and airborne light detection and ranging (LiDAR) derivatives, different analysis methods yielded three different model results. These models are correlated with thermal infrared imagery for ground-truth information at the focal confluence with the Scott River. Results from nonparametric correlation tests, geostatistical cross-covariograms, and cross-correlograms indicate that statistical relationships between the insolation models and the thermal infrared imagery exist and are significant. Furthermore, the use of geostatistics provides insights to the spatial structure of the relationships that would not be apparent otherwise. To incorporate a more complete representation of the temperature dynamics in the river system, other variables including the factors mentioned above, and their influence on solar loading, are discussed. With similar datasets, these methods could be applied to any river in the United States—especially those listed as temperature impaired under Section 303(d) of the Clean Water Act—or international riverine systems. Considering the importance of thermal refugia for aquatic species, these methods can help investigate opportunities for riparian restoration, identify problematic reaches unlikely to provide good habitat, and simulate changes to solar loading estimates from alternative landscape configurations.

California↗
USGS1993

Determination of buoyant density and sensitivity to chloroform and freon for the etiological agent of infectious salmonid anaemia

Plasma was collected from Atlantic salmon Salrno salar with acute infectious salmon anaemia (ISA) and used to challenge Atlantic salmon parr by intraperitoneal injection. Treatment of plasma with the lipid solvent, chloroform, showed that the etiological agent of ISA contained essential lipids, probably as a viral envelope. Some infectivity remained following treatment with freon. Injection challenges using fractions from equilibrium density gradient centrifugation of plasma from fish with acute ISA revealed a band of infectivity in the range 1.184 to 1.262 g cm-3. The band was believed to conta~n both complete ISA-virus particles and infectious particles lacking a complete envelope, nucleocapsid or genome. Density gradient centrifugation of infectious plasma for enrichment of the putative ISA virus appeared to offer a suitable method for obtaining virus-specific nucleic acid for use in the construction of cDNA libraries.

Diseases of Aquatic Organisms↗
USGS2021

Temperature variation and host immunity regulate viral persistence in a salmonid host

Environmental variation has important effects on host–pathogen interactions, affecting large-scale ecological processes such as the severity and frequency of epidemics. However, less is known about how the environment interacts with host immunity to modulate virus fitness within hosts. Here, we studied the interaction between host immune responses and water temperature on the long-term persistence of a model vertebrate virus, infectious hematopoietic necrosis virus (IHNV) in steelhead trout ( Oncorhynchus mykiss ). We first used cell culture methods to factor out strong host immune responses, allowing us to test the effect of temperature on viral replication. We found that 15 ∘ "> ∘ C water temperature accelerated IHNV replication compared to the colder 10 and 8 ∘ "> ∘ C temperatures. We then conducted in vivo experiments to quantify the effect of 6, 10, and 15 ∘ "> ∘ C water temperatures on IHNV persistence over 8 months. Fish held at 15 and 10 ∘ "> ∘ C were found to have higher prevalence of neutralizing antibodies compared to fish held at 6 ∘ "> ∘ C. We found that IHNV persisted for a shorter time at warmer temperatures and resulted in an overall lower fish mortality compared to colder temperatures. These results support the hypothesis that temperature and host immune responses interact to modulate virus persistence within hosts. When immune responses were minimized (i.e., in vitro) virus replication was higher at warmer temperatures. However, with a full potential for host immune responses (i.e., in vivo experiments) longer virus persistence and higher long-term virulence was favored in colder temperatures. We also found that the viral RNA that persisted at later time points (179 and 270 days post-exposure) was mostly localized in the kidney and spleen tissues. These tissues are composed of hematopoietic cells that are favored targets of the virus. By partitioning the effect of temperature on host and pathogen responses, our results help to better understand environmental drivers of host–pathogen interactions within hosts, providing insights into potential host–pathogen responses to climate change.

Pathogens↗
USGS1985

Comparative sensitivities of diagnostic procedures used to detect bacterial kidney disease in salmonid fishes

Kidney and spleen homogenates from each of 60 coho salmon ( Oncorhynchus kisutch ) and steelhead trout ( Salmo gairdneri ) were examined for detection of Renibacterium salmoninarum . The proportions of positives differed widely with the detection procedures used: in coho salmon, 5% were positive by the Gram-stain procedure, 10% by the direct fluorescent antibody test, 48% by bacteriological isolation, 65% by staphylococcal coagglutination, and 73% by counterimmunoelectrophoresis; in steelhead trout, 3% were positive by Gram-stain, 8.3% by fluorescent antibody, 17% by bacteriological isolation, and 67% by counterimmunoelectrophoresis. Renibacterium salmoninarum was not detected in either coho salmon or steelhead trout by immunodiffusion analysis.

Journal of Wildlife Diseases↗
USGS1986

Immunoblot assay: a rapid and sensitive method for identification of salmonid fish viruses

An immunoblot assay was used to identify the viruses of infectious pancreatic necrosis, infectious hematopoietic necrosis, and viral hemorrhagic septicemia. Viral antigen in infected cell culture supernatant was adsorbed onto nitrocellulose membrane or Whatman 541 filter paper and detected by enzyme-linked immunosorbent assay techniques. The immunoblot assay took less than 4 hr to perform and required no special instrumentation. Assays using cell culture supernatant fluids showed immunoblot sensitivity was 10 5 –10 6 PFU/ml. Assay sensitivity, determined using purified virus, is 0.85–4.0 ng of viral antigen. The immunoblot assay was used to detect and identify virus in cell culture fluids.

Journal of Wildlife Diseases↗
USGS1987

Immunization of salmonids against Yersinia ruckeri: Significance of humoral immunity and cross protection between serotypes

Brook trout ( Salvelinus fontinalis ) were immunized with bacterins containing either Serotype 1 or 2 isolates of Yersinia ruckeri to determine the relative degree of cross-protection afforded when the fish were challenged with the homologous or heterologous serotype. While fish immunized with pH-lysed bacterins produced highly specific agglutinins that did not cross-react with antigens derived from a heterologous serotype of Y. ruckeri all fish were protected against experimental challenge, regardless of which serotype was used for bacterin production and experimental challenge. Other experiments indicated that brook trout injected intraperitoneally with highly specific antibodies could not be passively immunized against experimental challenge.

Journal of Wildlife Diseases↗
USGS1994

Relationship between resistance of salmonids to furunculosis and recovery of Aeromonas salmonicida from external mucus

Fish were sampled at the Ed Weed State Fish Hatchery (South Hero, Vermont, USA) in September 1992. Aeromonas salmonicida was common, with concentrations as high as 10 5 to 10 7 colony-forming units per gram of mucus, and readily recovered from most mucus samples obtained from furunculosis-sensitive populations of brook trout ( Salvelinus fontinalis ), lake trout ( Salvelinus namaycush ), and Atlantic salmon (Salmo salar) . The pathogen was the predominant microorganism and accounted for greater than 85% of the total number of bacteria isolated from the mucus of these fish. By comparison, A. salmonicida was recovered only from two rainbow trout ( Oncorhynchus mykiss ), and bacterial frequencies did not exceed 10 3 colony-forming units per gram of mucus. The pathogen was not recovered from the mucus of steelhead ( O. mykiss ) or Rome brown trout ( Salmo trutta ) selectively bred for resistance to furunculosis, even though there was widespread contagion throughout the hatchery and fish were cultured on a common, unprotected water supply.

Journal of Wildlife Diseases↗