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Sample records for 4r-derivative salmonid fishes

  1. A review of infectious gill disease in marine salmonid fish.

    PubMed

    Mitchell, S O; Rodger, H D

    2011-06-01

    Infectious gill diseases of marine salmonid fish present a significant challenge in salmon-farming regions. Infectious syndromes or disease conditions affecting marine-farmed salmonids include amoebic gill disease (AGD), proliferative gill inflammation (PGI) and tenacibaculosis. Pathogens involved include parasites, such as Neoparamoeba perurans, bacteria, such as Piscichlamydia salmonis and Tenacibaculum maritimum, and viruses, such as the Atlantic salmon paramyxovirus (ASPV). The present level of understanding of these is reviewed with regard to risk factors, potential impacting factors, methods of best practice to mitigate infectious gill disease, as well as knowledge gaps and avenues for future research. PMID:21401646

  2. Polyphasic characterization of Aeromonas salmonicida isolates recovered from salmonid and non-salmonid fish

    USGS Publications Warehouse

    Diamanka, A.; Loch, T.P.; Cipriano, R.C.; Faisal, M.

    2013-01-01

    Michigan's fisheries rely primarily upon the hatchery propagation of salmonid fish for release in public waters. One limitation on the success of these efforts is the presence of bacterial pathogens, including Aeromonas salmonicida, the causative agent of furunculosis. This study was undertaken to determine the prevalence of A. salmonicida in Michigan fish, as well as to determine whether biochemical or gene sequence variability exists among Michigan isolates. A total of 2202 wild, feral and hatchery-propagated fish from Michigan were examined for the presence of A. salmonicida. The examined fish included Chinook salmon, Oncorhynchus tshawytscha (Walbaum), coho salmon, O. kisutcha (Walbaum), steelhead trout, O. mykiss (Walbaum), Atlantic salmon, Salmo salar L., brook trout, Salvelinus fontinalis (Mitchill), and yellow perch, Perca flavescens (Mitchill). Among these, 234 fish yielded a brown pigment-producing bacterium that was presumptively identified as A. salmonicida. Further phenotypic and phylogenetic analyses identified representative isolates as Aeromonas salmonicida subsp. salmonicida and revealed some genetic and biochemical variability. Logistic regression analyses showed that infection prevalence varied according to fish species/strain, year and gender, whereby Chinook salmon and females had the highest infection prevalence. Moreover, this pathogen was found in six fish species from eight sites, demonstrating its widespread nature within Michigan.

  3. Identification of Yersinia ruckeri from diseased salmonid fish by Fourier transform infrared spectroscopy.

    PubMed

    Wortberg, F; Nardy, E; Contzen, M; Rau, J

    2012-01-01

    Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), which mainly affects salmonid fish. Isolates of Y. ruckeri from diseased salmonid fish were obtained over a 6-year period from eight fish farms in the State of Baden-Württemberg, Southwest Germany. The strains were characterized by biochemical methods and Fourier transform infrared spectroscopy (FT-IR) combined with artificial neural network analysis. These methods were complemented by 16S rDNA sequencing for several isolates. The set of strains from these fish farms included sorbitol-positive, gelatinase-positive and non-motile Y. ruckeri. These variants were differentiated with an advanced FT-IR module, which is part of a higher-ranking method including more than 200 well-defined Yersinia strains against a background of more than 1000 other Gram-negative isolates. Validation of the newly constructed method yielded 97.4% of Y. ruckeri identified correctly on the species level. Thus, the FT-IR analysis enables distinction of all Y. ruckeri from other Yersinia species (e.g. fish-borne Y. enterocolitica) and other Enterobacteriaceae typically misidentified because of similar biochemical reaction profiles, especially Hafnia alvei. The differentiation of sorbitol-positive variants of Y. ruckeri using FT-IR was demonstrated. PMID:22103737

  4. Evolution of Ancient Functions in the Vertebrate Insulin-Like Growth Factor System Uncovered by Study of Duplicated Salmonid Fish Genomes

    PubMed Central

    Macqueen, Daniel J.; Garcia de la serrana, Daniel; Johnston, Ian A.

    2013-01-01

    Whole-genome duplication (WGD) was experienced twice by the vertebrate ancestor (2 rounds; 2R), again by the teleost fish ancestor (3R) and most recently in certain teleost lineages (4R). Consequently, vertebrate gene families are often expanded in 3R and 4R genomes. Arguably, many types of “functional divergence” present across 2R gene families will exceed that between 3R/4R paralogs of genes comprising 2R families. Accordingly, 4R offers a form of replication of 2R. Examining whether this concept has implications for molecular evolutionary research, we studied insulin-like growth factor (IGF) binding proteins (IGFBPs), whose six 2R family members carry IGF hormones and regulate interactions between IGFs and IGF1-receptors (IGF1Rs). Using phylogenomic approaches, we resolved the complete IGFBP repertoire of 4R-derived salmonid fishes (19 genes; 13 more than human) and established evolutionary relationships/nomenclature with respect to WGDs. Traits central to IGFBP action were determined for all genes, including atomic interactions in IGFBP–IGF1/IGF2 complexes regulating IGF–IGF1R binding. Using statistical methods, we demonstrate that attributes of these protein interfaces are overwhelming a product of 2R IGFBP family membership, explain 49–68% of variation in IGFBP mRNA concentration in several different tissues, and strongly predict the strength and direction of IGFBP transcriptional regulation under differing nutritional states. The results support a model where vertebrate IGFBP family members evolved divergent structural attributes to provide distinct competition for IGFs with IGF1Rs, predisposing different functions in the regulation of IGF signaling. Evolution of gene expression then acted to ensure the appropriate physiological production of IGFBPs according to their structural specializations, leading to optimal IGF-signaling according to nutritional-status and the endocrine/local mode of action. This study demonstrates that relatively recent

  5. Developments in the control of bacterial kidney disease of salmonid fishes

    USGS Publications Warehouse

    Elliott, D.G.; Pascho, R.J.; Bullock, G.L.

    1989-01-01

    Bacterial kidney disease of salmonid fishes, caused by Renibactenum salrnoninarum, was first reported more than 50 yr ago; nevertheless, large gaps persist in our knowledge of the infection - particularly in methods for its control. In the 1950's, principal control measures consisted of prophylactic or therapeutic feeding of sulfonamides, which were later supplanted by the antibiotic erythromycin. Chemotherapy has effected some reduction of mortality, but benefits are typically transient and mortality usually resumes after the drug is withdrawn. Some studies have indicated that diet composition affects the prevalence and severity of the disease. Although tests of chemotherapeutants and diet modification have continued, research emphasis has shifted partly toward prevention of the disease by breaking the infection cycle. It is now generally accepted that R. salrnoninarum can be transmitted both vertically and horizontally. Experimental evidence indicates that immersion of newly fertilized eggs in iodophor or erythromycin does not prevent vertical transmission. However, the injection of female salmon with erythromycin before they spawn shows promise as a practical means of interrupting vertical transmission. The results of attempts to prevent infection of juvenile salmonids by vaccination against bacterial kidney disease have been disappointing, thus underscoring a basic need for a better understanding of protective mechanisms in salmonids. The recent development of more sensitive and quantitative detection methods should aid in evaluating the efficacy of current and future control strategies.

  6. Olfactory sensitivity to bile acids in salmonid fishes.

    PubMed

    Døving, K B; Selset, R; Thommesen, G

    1980-02-01

    Monopolar DC-recordings were made simultaneously from two positions on the olfactory bulb of chars (Salmo alpinus L.) and graylings (Thymallus thymallu L.) using bile acids and amino acids as olfactory stimulants. The bile acids induced responses with characteristic spatial differences from those of the amino acids. The distribution of responses to bile acids indicated a neuronal activity in the medial part of the bulb. In contrast, amino acids elicit responses in the lateral part of the bulb. Taurine conjugated bile acids were up to 1 000 times more potent as olfactory stimuli than methionine. The results suggest that olfactory receptors are of two types, one responding to bile acids, the other to amino acids. 3 -alpha-hydroxysteroids are released from the fish into the water in quantities that suffice for detection by their olfactory system. The odorant potency of the bile acids, their evolutionary history and variability, together with their renowned adherent properties made them interesting candidates for specific signals in the acquatic environment. PMID:7376910

  7. Sex-biased dispersal in a salmonid fish.

    PubMed Central

    Hutchings, Jeffrey A; Gerber, Leah

    2002-01-01

    We tested the hypothesis that dispersal is sex biased in an unexploited population of brook trout, Salvelinus fontinalis, on Cape Race, Newfoundland, Canada. Based on the assumptions that trout are promiscuous and that reproductive success is limited primarily by either number of mates (males) or fecundity (females), we predicted that males would disperse greater distances than females. We also tested the hypothesis that trout populations comprise stationary and mobile individuals, predicting that males have greater mobility than females. Based on a mark-recapture study of 943 individually tagged fishes, 191 of which were recaptured over 5 years, we find strong support for our hypothesis of male-biased dispersal in brook trout. Averaged among all 11 resampling periods, males dispersed 2.5 times as far as females; during the spawning period only, male dispersal exceeded that by females almost fourfold. Both sexes were heterogeneous with respect to movement, with a lower incidence of mobility among females (29.6%) than males (41.1%); mobile males dispersed six times further than mobile females. We conclude that this sex bias reduces mate competition among male kin and decreases the probability that males will reproduce with related females. PMID:12495493

  8. Watershed processes, fish habitat, and salmonid distribution in the Tonsina River (Copper River watershed), Alaska

    NASA Astrophysics Data System (ADS)

    Booth, D. B.; Ligon, F. K.; Sloat, M. R.; Amerson, B.; Ralph, S. C.

    2007-12-01

    The Copper River watershed is a critical resource for northeastern Pacific salmon, with annual escapements in the millions. The Tonsina River basin, a diverse 2100-km2 tributary to the Copper River that supports important salmonid populations, offers an opportunity to integrate watershed-scale channel network data with field reconnaissance of physical processes and observed distribution of salmonid species. Our long-term goals are to characterize habitats critical to different salmonid life stages, describe the geologic context and current geologic processes that support those habitats in key channel reaches, and predict their watershed-wide distribution. The overarching motivation for these goals is resource conservation, particularly in the face of increased human activity and long-term climate change. Channel geomorphology within the Tonsina River basin reflects inherited glacial topography. Combinations of drainage areas, slopes, channel confinement, and sediment-delivery processes are unique to this environment, giving rise to channel "types" that are recognizable but that do not occur in the same positions in the channel network as in nonglaciated landscapes. We also recognize certain channel forms providing fish habitat without analog in a nonglacial landscape, notably relict floodplain potholes from once-stranded and long-melted ice blocks. Salmonid species dominated different channel types within the watershed network. Sockeye salmon juveniles were abundant in the low-gradient, turbid mainstem; Chinook juveniles were also captured in the lower mainstem, with abundant evidence of spawning farther downstream. Coho juveniles were abundant in upper, relatively large tributaries, even those channels with cobble-boulder substrates and minimal woody debris that provide habitats more commonly utilized by Chinook in low-latitude systems. More detailed field sampling also revealed that patterns of species composition and abundance appeared related to small

  9. An online database for IHN virus in Pacific Salmonid fish: MEAP-IHNV

    USGS Publications Warehouse

    Kurath, Gael

    2012-01-01

    The MEAP-IHNV database provides access to detailed data for anyone interested in IHNV molecular epidemiology, such as fish health professionals, fish culture facility managers, and academic researchers. The flexible search capabilities enable the user to generate various output formats, including tables and maps, which should assist users in developing and testing hypotheses about how IHNV moves across landscapes and changes over time. The MEAP-IHNV database is available online at http://gis.nacse.org/ihnv/ (fig. 1). The database contains records that provide background information and genetic sequencing data for more than 1,000 individual field isolates of the fish virus Infectious hematopoietic necrosis virus (IHNV), and is updated approximately annually. It focuses on IHNV isolates collected throughout western North America from 1966 to the present. The database also includes a small number of IHNV isolates from Eastern Russia. By engaging the expertise of the broader community of colleagues interested in IHNV, our goal is to enhance the overall understanding of IHNV epidemiology, including defining sources of disease outbreaks and viral emergence events, identifying virus traffic patterns and potential reservoirs, and understanding how human management of salmonid fish culture affects disease. Ultimately, this knowledge can be used to develop new strategies to reduce the effect of IHN disease in cultured and wild fish.

  10. Complete genome sequence of Yersinia ruckeri str. CSF007-82, etiologic agent of enteric redmouth disease in salmonid fish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present the complete, closed and finished chromosomal and extra-chromosomal genome sequences of Y. ruckeri strain CSF007-82, etiologic agent of enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a G+C content of 47.5% and encodes 3,530 predicted CDS, 7 ribosomal opero...

  11. A new value for mol percent guanine + cytosine of DNA for the salmonid fish pathogen Renibacterium salmoninarum.

    PubMed

    Banner, C R; Rohovec, J S; Fryer, J L

    1991-03-15

    The mol% G + C of DNA extracted from seven different isolates of Renibacterium salmoninarum was determined. Organisms studied were from selected geographical areas (U.S.A., Canada, England and France) and were isolated from five different species of salmonid fish. The mol% G + C was determined to be 55.5, higher than the currently reported value of 53. PMID:2044940

  12. Functional morphology and biomechanics of the tongue-bite apparatus in salmonid and osteoglossomorph fishes.

    PubMed

    Camp, Ariel L; Konow, Nicolai; Sanford, Christopher P J

    2009-05-01

    The tongue-bite apparatus and its associated musculoskeletal elements of the pectoral girdle and neurocranium form the structural basis of raking, a unique prey-processing behaviour in salmonid and osteoglossomorph fishes. Using a quantitative approach, the functional osteology and myology of this system were compared between representatives of each lineage, i.e. the salmonid Salvelinus fontinalis (N = 10) and the osteoglossomorph Chitala ornata (N = 8). Divergence was found in the morphology of the novel cleithrobranchial ligament, which potentially relates to kinematic differences between the raking lineage representatives. Salvelinus had greater anatomical cross-sectional areas of the epaxial, hypaxial and protractor hyoideus muscles, whereas Chitala had greater sternohyoideus and adductor mandibulae mass. Two osteology-based biomechanical models (a third-order lever for neurocranial elevation and a modified four-bar linkage for hyoid retraction) showed divergent force/velocity priorities in the study taxa. Salvelinus maximizes both force (via powerful cranial muscles) and velocity (through mechanical amplification) during raking. In contrast, Chitala has relatively low muscle force but more efficient force transmission through both mechanisms compared with Salvelinus. It remains unclear if and how behavioural modulation and specializations in the post-cranial anatomy may affect the force/velocity trade-offs in Chitala. Further studies of tongue-bite apparatus morphology and biomechanics in a broader species range may help to clarify the role that osteology and myology play in the evolution of behavioural diversity. PMID:19438765

  13. Functional morphology and biomechanics of the tongue-bite apparatus in salmonid and osteoglossomorph fishes

    PubMed Central

    Camp, Ariel L; Konow, Nicolai; Sanford, Christopher P J

    2009-01-01

    The tongue-bite apparatus and its associated musculoskeletal elements of the pectoral girdle and neurocranium form the structural basis of raking, a unique prey-processing behaviour in salmonid and osteoglossomorph fishes. Using a quantitative approach, the functional osteology and myology of this system were compared between representatives of each lineage, i.e. the salmonid Salvelinus fontinalis (N =10) and the osteoglossomorph Chitala ornata(N = 8). Divergence was found in the morphology of the novel cleithrobranchial ligament, which potentially relates to kinematic differences between the raking lineage representatives. Salvelinus had greater anatomical cross-sectional areas of the epaxial, hypaxial and protractor hyoideus muscles, whereas Chitala had greater sternohyoideus and adductor mandibulae mass. Two osteology-based biomechanical models (a third-order lever for neurocranial elevation and a modified four-bar linkage for hyoid retraction) showed divergent force/velocity priorities in the study taxa. Salvelinus maximizes both force (via powerful cranial muscles) and velocity (through mechanical amplification) during raking. In contrast, Chitala has relatively low muscle force but more efficient force transmission through both mechanisms compared with Salvelinus. It remains unclear if and how behavioural modulation and specializations in the post-cranial anatomy may affect the force/velocity trade-offs in Chitala. Further studies of tongue-bite apparatus morphology and biomechanics in a broader species range may help to clarify the role that osteology and myology play in the evolution of behavioural diversity. PMID:19438765

  14. Regulation of salmonid fish sperm motility by osmotic shock-induced water influx across the plasma membrane.

    PubMed

    Takei, Gen Leon; Mukai, Chinatsu; Okuno, Makoto

    2015-04-01

    The motility of salmonid fish sperm is initiated by a decrease in the extracellular K(+) concentration. However, our previous studies revealed that salmonid fish sperm motility could be initiated in the presence of an inhibitory concentration of K(+) by drastic osmotic shock induced by suspension in a hypertonic glycerol solution and subsequent dilution in a hypotonic solution (glycerol-treatment). In the present study, we examined if an osmotic shock-induced water influx is involved in the regulation of salmonid fish sperm motility. HgCl2, a common inhibitor of aquaporins (AQPs), decreased the duration of salmonid fish sperm motility. Dilution of sperm cells in a hypotonic solution increased the cellular volume, whereas HgCl2 inhibited such an increase in cellular volume. Furthermore, the expression of AQP 1a and 10 in rainbow trout testes was confirmed. In contrast, HgCl2 did not affect glycerol-treated sperm motility, indicating that AQPs are not involved in glycerol-treated sperm motility. We also explored the possibility of aquaporin-independent water influx in glycerol-treated sperm by assessing the sperm membrane permeability using propidium iodide. The plasma membrane of glycerol-treated sperm was considerably permeabilized. The cellular volume was decreased in a hypertonic glycerol solution and increased upon subsequent hypoosmotic shock, indicating an AQP-independent water flux across the plasma membrane upon glycerol-treatment. Taken together, these results showed that water influx across the plasma membrane via AQP is crucial for the maintenance of salmonid fish sperm motility under normal conditions, whereas water influx by osmotic shock-induced membrane permeation is critical for the initiation of glycerol-treated sperm motility. PMID:25522712

  15. Application of neural networks to prediction of fish diversity and salmonid production in the Lake Ontario basin

    USGS Publications Warehouse

    McKenna, James E., Jr.

    2005-01-01

    Diversity and fish productivity are important measures of the health and status of aquatic systems. Being able to predict the values of these indices as a function of environmental variables would be valuable to management. Diversity and productivity have been related to environmental conditions by multiple linear regression and discriminant analysis, but such methods have several shortcomings. In an effort to predict fish species diversity and estimate salmonid production for streams in the eastern basin of Lake Ontario, I constructed neural networks and trained them on a data set containing abiotic information and either fish diversity or juvenile salmonid abundance. Twenty percent of the original data were retained as a test data set and used in the training. The ability to extend these neural networks to conditions throughout the streams was tested with data not involved in the network training. The resulting neural networks were able to predict the number of salmonids with more than 84% accuracy and diversity with more than 73% accuracy, which was far superior to the performance of multiple regression. The networks also identified the environmental variables with the greatest predictive power, namely, those describing water movement, stream size, and water chemistry. Thirteen input variables were used to predict diversity and 17 to predict salmonid abundance.

  16. Complete genome sequence of Piscirickettsia salmonis LF-89 (ATCC VR-1361) a major pathogen of farmed salmonid fish.

    PubMed

    Pulgar, Rodrigo; Travisany, Dante; Zuñiga, Alejandro; Maass, Alejandro; Cambiazo, Verónica

    2015-10-20

    Piscirickettsia salmonis, the causative agent of salmonid rickettsial septicemia (SRS), is a significant threat to the healthy and sustainable production of salmonid farming industry. This Gram-negative bacterium, originally isolated from a coho salmon in Southern Chile, produces a systemic infection characterized by colonization of several fish organs. P. salmonis is able to infect, survive, and replicate inside salmonid macrophages however little is known about its mechanisms of pathogenesis. Here, we present the whole genome sequence and annotation of the P. salmonis reference strain LF-89 (ATCC VR-1361). The genome contains one circular chromosome of 3,184,851 bp and three plasmids, pPSLF89-1 (180,124 bp), pPSLF89-2 (33,516 bp) and pPSLF89-3 (51,573 bp). A total of 2850 protein-coding genes, 56 tRNAs and six copies of 5S-16S-23S rRNA. PMID:26220311

  17. Evaluation of Fish Passage Conditions for Juvenile Salmonids Using Sensor Fish at Detroit Dam, Oregon

    SciTech Connect

    Duncan, Joanne P.

    2010-01-29

    Fish passage conditions through two spillways at Detroit Dam on the North Santiam River in Oregon were evaluated by Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers (USACE), Portland District, using Sensor Fish devices. The objective of the study was to describe and compare passage exposure conditions through Spillbay 3 and Spillbay 6 at 1.5- and 3.5-ft gate openings, identifying potential fish injury regions of the routes. The study was performed in July 2009, concurrent with HI-Z balloon-tag studies by Normandeau Associates, Inc. Sensor Fish and live fish were deployed at elevations approximately 3 ft above structure at depths determined using a computational fluid dynamics model. Data collected were analyzed to estimate 1) exposure conditions, particularly exposure to severe collision and shear events by passage route sub-regions; 2) differences in passage conditions between passage routes; and 3) relationships to live-fish injury and mortality data estimates.

  18. Immunological characterization of a bacterial protein isolated from salmonid fish naturally infected with Piscirickettsia salmonis.

    PubMed

    Marshall, Sergio H; Conejeros, Pablo; Zahr, Marcela; Olivares, Jorge; Gómez, Fernando; Cataldo, Patricio; Henríquez, Vitalia

    2007-03-01

    The Salmon Rickettsia syndrome (SRS) remains a major infectious disease in the Chilean aquaculture. A limited number of Piscirickettsia salmonis proteins have been characterized so far for their use as potential candidates for vaccines studies. In this study, we identified and expressed a highly immunogenic protein of P. salmonis extracted by selective hydrophobicity from crude-cell macerates of naturally infected salmonid fish. One and two-D PAGE gels followed by Western blot analysis with a battery of polyclonal anti-P. salmonis antibodies have allowed the isolation of the target protein. Basic local alignment search (BLAST) done after partial sequencing of the pure protein identified it as a member of the heat-shock protein (HSP) family of prokaryotes. The protein, named ChaPs, was cloned as a single open reading frame encoding 545 amino acid residues with a predicted molecular mass of 57.3 kDa. The amplicon representing the entire novel gene was expressed in vitro in different heterologous systems: the PurePro Caulobacter crescentus expression system from where most of the characterization was attained, and also in the Escherichia coli BL-21 CodonPlus model for commercially potential purposes. The immunologic potential of ChaPs was determined with serum from naturally infected fish. PMID:17250933

  19. The potential impacts of migratory difficulty, including warmer waters and altered flow conditions, on the reproductive success of salmonid fishes.

    PubMed

    Fenkes, Miriam; Shiels, Holly A; Fitzpatrick, John L; Nudds, Robert L

    2016-03-01

    Climate change and urbanisation of watercourses affect water temperatures and current flow velocities in river systems on a global scale. This represents a particularly critical issue for migratory fish species with complex life histories that use rivers to reproduce. Salmonids are migratory keystone species that provide substantial economical value to ecosystems and human societies. Consequently, a comprehensive understanding of the effects of environmental stressors on their reproductive success is critical in order to ensure their continued abundance during future climatic change. Salmonids are capital breeders, relying entirely on endogenous energy stores to fuel return migration to their natal spawning sites and reproduction upon arrival. Metabolic rates and cost of transport en-route increase with temperature and at extreme temperatures, swimming is increasingly fuelled anaerobically, resulting in an oxygen debt and reduced capacity to recover from exhaustive exercise. Thermally challenged salmonids also produce less viable gametes, which themselves are affected by water temperature after release. Passage through hydrological barriers and temperature changes both affect energy expenditure. As a result, important energetic tradeoffs emerge between extra energy used during migration and that available for other facets of the reproductive cycle, such as reproductive competition and gamete production. However, studies identifying these tradeoffs are extremely sparse. This review focuses on the specific locomotor responses of salmonids to thermal and hydrological challenges, identifying gaps in our knowledge and highlighting the potential implications for key aspects of their reproduction. PMID:26603555

  20. The potential impacts of migratory difficulty, including warmer waters and altered flow conditions, on the reproductive success of salmonid fishes

    PubMed Central

    Fenkes, Miriam; Shiels, Holly A.; Fitzpatrick, John L.; Nudds, Robert L.

    2016-01-01

    Climate change and urbanisation of watercourses affect water temperatures and current flow velocities in river systems on a global scale. This represents a particularly critical issue for migratory fish species with complex life histories that use rivers to reproduce. Salmonids are migratory keystone species that provide substantial economical value to ecosystems and human societies. Consequently, a comprehensive understanding of the effects of environmental stressors on their reproductive success is critical in order to ensure their continued abundance during future climatic change. Salmonids are capital breeders, relying entirely on endogenous energy stores to fuel return migration to their natal spawning sites and reproduction upon arrival. Metabolic rates and cost of transport en-route increase with temperature and at extreme temperatures, swimming is increasingly fuelled anaerobically, resulting in an oxygen debt and reduced capacity to recover from exhaustive exercise. Thermally challenged salmonids also produce less viable gametes, which themselves are affected by water temperature after release. Passage through hydrological barriers and temperature changes both affect energy expenditure. As a result, important energetic tradeoffs emerge between extra energy used during migration and that available for other facets of the reproductive cycle, such as reproductive competition and gamete production. However, studies identifying these tradeoffs are extremely sparse. This review focuses on the specific locomotor responses of salmonids to thermal and hydrological challenges, identifying gaps in our knowledge and highlighting the potential implications for key aspects of their reproduction. PMID:26603555

  1. Pit-Tag Studies with Juvenile Salmonids at the Chandler Canal Fish Collection Facility, Yakima River : Annual Report 1990.

    SciTech Connect

    Ruehle, Thomas E.; McCutcheon, Clinton Scott

    1994-09-01

    Juvenile salmonid survival studies planned for the Yakima Basin will require the release and recapture of large numbers of marked fish. Before these studies can be implemented, information is needed about potential recovery rates of marked fish at proposed sampling sites. The type of mark employed and the efficiency of the equipment used to capture and examine fish for marks must be evaluated since accurate survival estimates depend on their reliability. Recovery rates are expected to vary with species and life stage as well as environmental factors such as river flow and water temperature. The purpose of this study was to assess the mark-recovery capabilities of the Chandler facility and a mobile juvenile fish trap installed temporarily at West Richland, Washington near the mouth of the Yakima River.

  2. Salmonid fish viruses and cell interactions at early steps of the infective cycle.

    PubMed

    de las Heras, A I; Rodríguez Saint-Jean, S; Pérez-Prieto, S I

    2008-07-01

    A flow cytometric virus-binding assay that directly visualizes the binding and entry of infectious pancreatic necrosis virus (IPNV), infectious haematopoietic necrosis virus (IHNV) and virus haemorrhagic septicaemia virus (VHSV) to several cell lines was established. The highest efficiency of binding was shown by the BF-2 cell line and this was used to study, at the attachment level, the interactions of these cells with salmonid fish viruses in coinfections, and to further determine if the earliest stage of the viral growth cycle could explain the previously described loss of infectivity of IHNV when IPNV is present. Our results demonstrated that IPNV binds to around 88% of cells either in single or dual infections, whereas IHNV attachment always decreased in the presence of any of the other viruses. VHSV binding was not affected by IPNV, but coinfection with IHNV reduced the percentage of virus-binding cells, which suggests competition for viral receptors or co-receptors. Internalization of the adsorbed IHNV was not decreased by coinfection with IPNV, so the hypothetical competence could be restricted to the binding step. Treatment of the cells with antiviral agents, such as amantadine or chloroquine, did not affect the binding of IPNV and VHSV, but reduced IHNV binding by more than 30%. Tributylamine affected viral binding of the three viruses to different degrees and inhibited IPNV or IHNV entry in a large percentage of cells treated for 30 min. Tributylamine also inhibited IHNV cytopathic effects in a dose-dependent manner, decreasing the virus yield by 4 log of the 50% endpoint titre, at 10 mm concentration. IPNV was also inhibited, but at a lower level. The results of this study support the hypothesis that IHNV, in contrast to VHSV or IPNV, is less efficient at completing its growth cycle in cells with a simultaneous infection with IPNV. It can be affected at several stages of viral infection and is more sensitive to the action of antiviral compounds. PMID

  3. Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes

    PubMed Central

    Faber-Hammond, Joshua J.; Phillips, Ruth B.; Brown, Kim H.

    2015-01-01

    Salmonids present an excellent model for studying evolution of young sex-chromosomes. Within the genus, Oncorhynchus, at least six independent sex-chromosome pairs have evolved, many unique to individual species. This variation results from the movement of the sex-determining gene, sdY, throughout the salmonid genome. While sdY is known to define sexual differentiation in salmonids, the mechanism of its movement throughout the genome has remained elusive due to high frequencies of repetitive elements, rDNA sequences, and transposons surrounding the sex-determining regions (SDR). Despite these difficulties, bacterial artificial chromosome (BAC) library clones from both rainbow trout and Atlantic salmon containing the sdY region have been reported. Here, we report the sequences for these BACs as well as the extended sequence for the known SDR in Chinook gained through genome walking methods. Comparative analysis allowed us to study the overlapping SDRs from three unique salmonid Y chromosomes to define the specific content, size, and variation present between the species. We found approximately 4.1 kb of orthologous sequence common to all three species, which contains the genetic content necessary for masculinization. The regions contain transposable elements that may be responsible for the translocations of the SDR throughout salmonid genomes and we examine potential mechanistic roles of each one. PMID:26112966

  4. Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes.

    PubMed

    Faber-Hammond, Joshua J; Phillips, Ruth B; Brown, Kim H

    2015-07-01

    Salmonids present an excellent model for studying evolution of young sex-chromosomes. Within the genus, Oncorhynchus, at least six independent sex-chromosome pairs have evolved, many unique to individual species. This variation results from the movement of the sex-determining gene, sdY, throughout the salmonid genome. While sdY is known to define sexual differentiation in salmonids, the mechanism of its movement throughout the genome has remained elusive due to high frequencies of repetitive elements, rDNA sequences, and transposons surrounding the sex-determining regions (SDR). Despite these difficulties, bacterial artificial chromosome (BAC) library clones from both rainbow trout and Atlantic salmon containing the sdY region have been reported. Here, we report the sequences for these BACs as well as the extended sequence for the known SDR in Chinook gained through genome walking methods. Comparative analysis allowed us to study the overlapping SDRs from three unique salmonid Y chromosomes to define the specific content, size, and variation present between the species. We found approximately 4.1 kb of orthologous sequence common to all three species, which contains the genetic content necessary for masculinization. The regions contain transposable elements that may be responsible for the translocations of the SDR throughout salmonid genomes and we examine potential mechanistic roles of each one. PMID:26112966

  5. Toll-like receptors in maraena whitefish: Evolutionary relationship among salmonid fishes and patterns of response to Aeromonas salmonicida.

    PubMed

    Altmann, Simone; Korytář, Tomáš; Kaczmarzyk, Danuta; Nipkow, Mareen; Kühn, Carsten; Goldammer, Tom; Rebl, Alexander

    2016-07-01

    Toll-like receptors (TLRs) interact directly with particular pathogenic structures and are thus highly important to innate immunity. The present manuscript characterises a suite of 14 TLRs in maraena whitefish (Coregonus maraena), a salmonid species with increasing importance for aquaculture. Whitefish TLRs were structurally and evolutionary analysed. The results revealed a close relationship with TLRs from salmonid fish species rainbow trout and Atlantic salmon. Profiling the baseline expression of TLR genes in whitefish indicated that mainly members of the TLR11 family were highly expressed across all investigated tissues. A stimulation model with inactivated Aeromonas salmonicida was used to induce inflammation in the peritoneal cavity of whitefish. This bacterial challenge induced the expression of pro-inflammatory cytokine genes and evoked a strong influx of granulated cells of myeloid origin into the peritoneal cavity. As a likely consequence, the abundance of TLR-encoding transcripts increased moderately in peritoneal cells, with the highest levels of transcripts encoding non-mammalian TLR22a and a soluble TLR5 variant. In the course of inflammation, the proportion of granulated cells increased in peripheral blood accompanied by elevated TLR copy numbers in spleen and simultaneously reduced TLR copy numbers in head kidney at day 3 post-stimulation. Altogether, the present study provides in-vivo evidence for relatively modest TLR response patterns, but marked trafficking of myeloid cells as an immunophysiological consequence of A. salmonicida inflammation in whitefish. The present results contribute to improved understanding of the host-pathogen interaction in salmonid fish. PMID:27131902

  6. Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray

    PubMed Central

    von Schalburg, Kristian R; Rise, Matthew L; Cooper, Glenn A; Brown, Gordon D; Gibbs, A Ross; Nelson, Colleen C; Davidson, William S; Koop, Ben F

    2005-01-01

    Background We have developed and fabricated a salmonid microarray containing cDNAs representing 16,006 genes. The genes spotted on the array have been stringently selected from Atlantic salmon and rainbow trout expressed sequence tag (EST) databases. The EST databases presently contain over 300,000 sequences from over 175 salmonid cDNA libraries derived from a wide variety of tissues and different developmental stages. In order to evaluate the utility of the microarray, a number of hybridization techniques and screening methods have been developed and tested. Results We have analyzed and evaluated the utility of a microarray containing 16,006 (16K) salmonid cDNAs in a variety of potential experimental settings. We quantified the amount of transcriptome binding that occurred in cross-species, organ complexity and intraspecific variation hybridization studies. We also developed a methodology to rapidly identify and confirm the contents of a bacterial artificial chromosome (BAC) library containing Atlantic salmon genomic DNA. Conclusion We validate and demonstrate the usefulness of the 16K microarray over a wide range of teleosts, even for transcriptome targets from species distantly related to salmonids. We show the potential of the use of the microarray in a variety of experimental settings through hybridization studies that examine the binding of targets derived from different organs and tissues. Intraspecific variation in transcriptome expression is evaluated and discussed. Finally, BAC hybridizations are demonstrated as a rapid and accurate means to identify gene content. PMID:16164747

  7. Influence of Habitat Modifications on Habitat Composition and Anadromous Salmonid Populations in Fish Creek, Oregon, 1983-1988 Annual Report.

    SciTech Connect

    Reeves, Gordon H.; Everest, Fred H.; Hohler, David B.

    1990-05-01

    Modification of degraded habitats to increase populations of anadromous salmonids is a major focus of management agencies throughout the Pacific Northwest. Millions of dollars are spent annually on such efforts. Inherent in implementing habitat improvements is the need for quantitative evaluation of the biological and physical effects of such work. Reeves et al. (in press), however, noted that such evaluations are rare, making it difficult to assess the true results of habitat work. While it is not economically possible to thoroughly evaluate every habitat project, it is essential that intensive evaluations be done on selected representative projects. One such evaluation program has been underway since 1982 on Fish Creek, a tributary of the Clackamas River near Estacada, OR. Habitat modification has been done by the USDA Forest Service, Estacada Ranger District, Mt. Hood National Forest with funding provided in part by the Bonneville Power Administration (BPA). The USDA Forest Service, Anadromous Fish Habitat Research Unit, Pacific Northwest Research Station (PNW), Corvallis, OR is charged with: (1) evaluating the biological and physical responses to habitat modifications on a basin scale; and (2) developing a cost-benefit analysis of the program. Preliminary results have been reported in a series of annual publications, Everest and Sedell 1983, 1984 and Everest et al. 1985, 1986, 1987, 1988. The objectives of this paper are to: (1) report 1988 observations of biological and physical changes in habitat, salmonid populations, and smolt production in Fish Creek, and (2) examine preliminary trends in fish habitat and populations related to habitat improvement over the period 1983-1988. We have prefaced the trends in the latter objective as preliminary because we believe it could take a minimum of 10 years before the full biological and physical responses to habitat work are realized. We therefore urge caution in interpreting these preliminary results.

  8. 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

    USGS Publications Warehouse

    Rose, Brien P.; Hansen, Gabriel S.; Mesa, Matthew G.

    2011-01-01

    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 pred

  9. Spiral swimming behavior due to cranial and vertebral lesions associated with Cytophaga psychrophila infections in salmonid fishes

    USGS Publications Warehouse

    Kent, M.L.; Groff, J.M.; Morrison, J.K.; Yasutake, W.T.; Holt, R.A.

    1989-01-01

    C. psychrophila infections of the cranium and anterior vertebrae in salmonid fishes were associated with ataxia, spiral swimming along the axis of the fish, and death. The syndrome was observed in 2-10% of underyearling coho salmon Oncorhynchus kisutch, rainbow troutSalmo gairdneri, and steelhead trout S. gairdneri at several private, state, and federal hatcheries in Washington and Oregon, USA, between 1963 and 1987. Affected fish did not recover and ultimately died. Histological examination consistently revealed subacute to chronic periostitis, osteitis, meningitis, and ganglioneuritis. Inflammation and periosteal proliferation of the anterior vertebrae at the junction of the vertebral column with the cranium with extension into the cranial case was a consistent feature. The adjacent nervous tissue, particularly the medulla, was often compressed by the proliferative lesion, and this may have caused the ataxia. Though bacteria were seldom observed in these lesions. C. psychrophilawas isolated in culture from the cranial cavity of all affected fish that were tested. Epidemiological observations suggested that this bacterium is the causative agent because the spiral swimming behaviour and lesions were observed only in populations that had recovered from acute C. psychrophila infections.

  10. An epidemic model for the interactions between thermal regime of rivers and transmission of Proliferative Kidney Disease in salmonid fish

    NASA Astrophysics Data System (ADS)

    Carraro, Luca; Bertuzzo, Enrico; Mari, Lorenzo; Gatto, Marino; Strepparava, Nicole; Hartikainen, Hanna; Rinaldo, Andrea

    2015-04-01

    Proliferative kidney disease (PKD) affects salmonid populations in European and North-American rivers. It is caused by the endoparasitic myxozoan Tetracapsuloides bryosalmonae, which exploits freshwater bryozoans (Fredericella sultana) and salmonids as primary and secondary hosts, respectively. Incidence and mortality, which can reach up to 90-100%, are known to be strongly related to water temperature. PKD has been present in brown trout population for a long time but has recently increased rapidly in incidence and severity causing a decline in fish catches in many countries. In addition, environmental changes are feared to cause PKD outbreaks at higher latitude and altitude regions as warmer temperatures promote disease development. This calls for a better comprehension of the interactions between disease dynamics and the thermal regime of rivers, in order to possibly devise strategies for disease management. In this perspective, a spatially explicit model of PKD epidemiology in riverine host metacommunities is proposed. The model aims at summarizing the knowledge on the modes of transmission of the disease and the life-cycle of the parasite, making the connection between temperature and epidemiological parameters explicit. The model accounts for both local population and disease dynamics of bryozoans and fish and hydrodynamic dispersion of the parasite spores and hosts along the river network. The model is time-hybrid, coupling inter-seasonal and intra-seasonal dynamics, the former being described in a continuous time domain, the latter seen as time steps of a discrete time domain. In order to test the model, a case study is conducted in river Wigger (Cantons of Aargau and Lucerne, Switzerland), where data about water temperature, brown trout and bryozoan populations and PKD prevalence are being collected.

  11. FishMORPH - An agent-based model to predict salmonid growth and distribution responses under natural and low flows

    PubMed Central

    Phang, S. C.; Stillman, R. A.; Cucherousset, J.; Britton, J. R.; Roberts, D.; Beaumont, W. R. C.; Gozlan, R. E.

    2016-01-01

    Predicting fish responses to modified flow regimes is becoming central to fisheries management. In this study we present an agent-based model (ABM) to predict the growth and distribution of young-of-the-year (YOY) and one-year-old (1+) Atlantic salmon and brown trout in response to flow change during summer. A field study of a real population during both natural and low flow conditions provided the simulation environment and validation patterns. Virtual fish were realistic both in terms of bioenergetics and feeding. We tested alternative movement rules to replicate observed patterns of body mass, growth rates, stretch distribution and patch occupancy patterns. Notably, there was no calibration of the model. Virtual fish prioritising consumption rates before predator avoidance replicated observed growth and distribution patterns better than a purely maximising consumption rule. Stream conditions of low predation and harsh winters provide ecological justification for the selection of this behaviour during summer months. Overall, the model was able to predict distribution and growth patterns well across both natural and low flow regimes. The model can be used to support management of salmonids by predicting population responses to predicted flow impacts and associated habitat change. PMID:27431787

  12. FishMORPH - An agent-based model to predict salmonid growth and distribution responses under natural and low flows.

    PubMed

    Phang, S C; Stillman, R A; Cucherousset, J; Britton, J R; Roberts, D; Beaumont, W R C; Gozlan, R E

    2016-01-01

    Predicting fish responses to modified flow regimes is becoming central to fisheries management. In this study we present an agent-based model (ABM) to predict the growth and distribution of young-of-the-year (YOY) and one-year-old (1+) Atlantic salmon and brown trout in response to flow change during summer. A field study of a real population during both natural and low flow conditions provided the simulation environment and validation patterns. Virtual fish were realistic both in terms of bioenergetics and feeding. We tested alternative movement rules to replicate observed patterns of body mass, growth rates, stretch distribution and patch occupancy patterns. Notably, there was no calibration of the model. Virtual fish prioritising consumption rates before predator avoidance replicated observed growth and distribution patterns better than a purely maximising consumption rule. Stream conditions of low predation and harsh winters provide ecological justification for the selection of this behaviour during summer months. Overall, the model was able to predict distribution and growth patterns well across both natural and low flow regimes. The model can be used to support management of salmonids by predicting population responses to predicted flow impacts and associated habitat change. PMID:27431787

  13. Utilization of soybean products in non-salmonid marine fish diets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current feeds for marine finfish are heavily dependend on fish meal and fish oil to meet their critical protein and lipid requirements. Due to the increased demand, uncertain availability, and rising costs of fish meal and oil, however, several ingredients of plant origin have been evaluated as pote...

  14. Morphology of certain viruses of Salmonid Fishes. I. in vitro studies of some viruses causing Hematopoietic Necrosis

    USGS Publications Warehouse

    Amend, Donald F.; Chambers, Velma C.

    1970-01-01

    An electron microscope study was performed on three virus isolates that caused hematopoietic necrosis in salmonid fishes: infectious hematopoietic necrosis (IHN), Oregon Sockeye Disease (OSD), and Sacramento River Chinook Salmon Disease (SRCD). All three isolates were examined by negative staining of fathead minnow (FHM) monolayer tissue culture concentrates and IHN virus was also examined in thin sections of FHM cells. Viruslike particles were observed in infected tissues, but similar structures were not found in uninfected cultures. All three isolates were bullet-shaped, but oval and truncated forms were also observed. Mean measurements of particles from IHN-virus-infected tissue were 158 × 90 mμ. They consisted of an outer coat 15 mμ thick, a core 60 mμ in diameter, subunits about 5 mμ, and an axial pore about 20 mμ in diameter. These particles also were seen budding from the cytoplasmic membrane. Similar particles from SRCD were 159 × 90 mμ and isolates from OSD were 181 × 91 mμ. The three isolates were morphologically indistinguishable from one another and the greater length of OSD was considered insignificant. IHN, SRCD, and OSD viruses were tentatively placed in the rhabdovirus group, but serological studies are needed to determine if they are antigenically identical or should be included as separate members. Biochemical and physical characteristics of these viruses and a comparison with other salmonid viruses is also discussed.

  15. Coupling between stress coping style and time of emergence from spawning nests in salmonid fishes: evidence from selected rainbow trout strains (Oncorhynchus mykiss).

    PubMed

    Andersson, Madelene Åberg; Khan, Uniza Wahid; Overli, Oyvind; Gjøen, Hans Magnus; Höglund, Erik

    2013-05-27

    Correlations between behavioral and physiological traits, often referred to as stress coping styles, have been demonstrated in numerous animal groups. Such trait variations often cluster in two contrasting styles, with animals characterized as either proactive or reactive. In natural populations of salmonid fishes, emergence from spawning nests, when fry establish a territory and shifts from exogenous to endogenous feeding, is a crucial niche shift with a high selection pressure. The timing of this event is correlated to behavioral and physiological traits such as aggression, boldness/shyness, dominance, and metabolic rate; resembling those of proactive and reactive stress coping styles. In farmed fish populations, however the relation between emergence and stress coping styles seems to be absent, an effect which has been related to lack of selection pressure during emergence. In the present study two rainbow trout strains genetically selected as LR (low-responsive) and HR (high-responsive) trout, characterized with proactive (LR) and reactive (HR) stress coping traits, was used to further investigate the relationship between the time of emergence and stress coping style in salmonid fishes. For this task LR and HR larvae were hatched in mixed batches, and thirty individuals from the earliest and latest 25% of emerging larvae were randomly collected. Thereafter, a line specific genetic marker was used to distinguish the proportion of LR and HR occurring in early and late fractions. The result demonstrates a higher proportion of LR fry in the early fraction in comparison to the HR fry, which emerged at a higher proportion during the late period. Early emerging individuals had larger yolk reserves at emergence, lending further support to a relationship between emergence times, yolk reserves at emergence and stress coping styles in salmonids. Smaller larval bodies in early compared to late emerging individuals suggest that this difference in yolk size reflects

  16. Chemical contaminants in fish feeds used in federal salmonid hatcheries in the USA

    USGS Publications Warehouse

    Maule, A.G.; Gannam, A.L.; Davis, J.W.

    2007-01-01

    Recent studies have demonstrated that fish feeds contain significant concentrations of contaminants, many of which can bioaccumulate and bioconcentrate in fish. Organochlorine (OC) contaminants are present in the fish oils and fish meals used in feed manufacture, and some researchers speculate that all fish feeds contain measurable levels of some contaminants. To determine the concentration of contaminants in feeds used in US Fish and Wildlife Service's National Fish Hatcheries, we systematically collected samples of feed from 11 cold-water fish hatcheries. All samples (collected from October 2001 to October 2003) contained at least one polychlorinated dibenzo-p-dioxin (PCDD), polychlorinated dibenzofuran (PCDF), polychlorinated biphenyl (PCB) congener, or dichlorodiphenyltrichloroethane (DDT) metabolite. Of the 55 samples in which they were analyzed 39 contained PCDDs, 24 contained PCDFs and 24 contained DDT or its metabolites. There were 10- to 150-fold differences in concentrations of total PCBs, PCDDs, PCDFs and DDT. Although PCBs were the most commonly detected contaminant in our study, concentrations (range: 0.07-10.46 ng g-1 wet weight) were low compared to those reported previously. In general, we also found lower levels of OCs than reported previously in fish feed. Perhaps most notable was the near absence of OC pesticides - except for DDT or its metabolites, and two samples containing hexachlorocyclohexane (HCH). While contaminant concentrations were generally low, the ecological impacts can not be determined without a measure of the bioaccumulation of these compounds in the fish and the fate of these compounds after the fish are released. ?? 2006 Elsevier Ltd. All rights reserved.

  17. Juvenile Salmonid Pit-Tag Studies at Prosser Dam and the Chandler Canal Fish Collection Facility, Yakima River, 1991 and 1992 Final Report.

    SciTech Connect

    Ruehle, Thomas E.; Sandford, Benjamin P.

    1996-01-01

    In 1991 and 1992, the National Marine Fisheries Service completed the second and third years of a 3-year study to estimate juvenile salmonid (Oncorhynchus spp.) timing and survival characteristics related to passage through the Prosser Dam complex, including the Chandler Canal and the Chandler fish collection facility, on the Yakima River. Yearling chinook (O. tshawyacha) and coho salmon (O. kisutch) were collected at the Chandler facility, PIT tagged, and released at various locations in the Yakima River, Chandler Canal, and the Chandler facility. Individual fish were subsequently detected at PIT-tag detection monitors at the Chandler facility and/or McNary Dam on the Columbia River. Survival through various reaches, PIT-tag detection efficiency, and Chandler Canal fish entrainment proportion parameters were estimated using maximum likelihood techniques. The research objectives in 1991 and 1992 were to: (1) assess the effects of passage through the Chandler Canal and the Chandler facility on the survival of juvenile salmonids, (2) determine the entrainment rate of juvenile salmonids into the Chandler Canal as a function of river flow, and (3) determine the efficiency and reliability of the PIT-tag monitoring system at the Chandler facility. The initial 1990 research plan was expanded in 1991 and 1992 to include several more release locations and many more release days.

  18. Linking ecosystems, food webs, and fish production: subsidies in salmonid watersheds

    USGS Publications Warehouse

    Wipfli, Mark S.; Baxter, Colden V.

    2010-01-01

    Physical characteristics of riverine habitats, such as large wood abundance, pool geometry and abundance, riparian vegetation cover, and surface flow conditions, have traditionally been thought to constrain fish production in these ecosystems. Conversely, the role of food resources (quantity and quality) in controlling fish production has received far less attention and consideration, though they can also be key productivity drivers. Traditional freshwater food web illustrations have typically conveyed the notion that most fish food is produced within the local aquatic habitat itself, but the concepts and model we synthesize in this article show that most fish food comes from external or very distant sources—including subsidies from marine systems borne from adult returns of anadromous fishes, from fishless headwater tributaries that transport prey to downstream fish, and from adjacent streamside vegetation and associated habitats. The model we propose further illustrates how key trophic pathways and food sources vary through time and space throughout watersheds. Insights into how food supplies affect fishes can help guide how we view riverine ecosystems, their structure and function, their interactions with marine and terrestrial systems, and how we manage natural resources, including fish, riparian habitats, and forests.

  19. MODELLING BIOACCUMULATION OF ORGANIC POLLUTANTS IN FISH WITH AN APPLICATION TO PCBS IN LAKE ONTARIO SALMONIDS

    EPA Science Inventory

    A model describing passive accumulatiOn of organic chemicals from the aqueous environment and contaminated food in fish is developed. This model considers both biological attributes of the fish and physicochemical properties of the chemical that determine diffusive exchange acros...

  20. Predation by Northern Pikeminnow and tiger muskellunge on juvenile salmonids in a high–head reservoir: Implications for anadromous fish reintroductions

    USGS Publications Warehouse

    Sorel, Mark H.; Hansen, Adam G.; Connelly, Kristin A.; Wilson, Andrew C.; Lowery, Erin D.; Beauchamp, David A.

    2016-01-01

    The feasibility of reintroducing anadromous salmonids into reservoirs above high-head dams is affected by the suitability of the reservoir habitat for rearing and the interactions of the resident fish with introduced fish. We evaluated the predation risk to anadromous salmonids considered for reintroduction in Merwin Reservoir on the North Fork Lewis River in Washington State for two reservoir use-scenarios: year-round rearing and smolt migration. We characterized the role of the primary predators, Northern Pikeminnow Ptychocheilus oregonensis and tiger muskellunge (Northern Pike Esox lucius × Muskellunge E. masquinongy), by using stable isotopes and stomach content analysis, quantified seasonal, per capita predation using bioenergetics modeling, and evaluated the size and age structures of the populations. We then combined these inputs to estimate predation rates of size-structured population units. Northern Pikeminnow of FL ≥ 300 mm were highly cannibalistic and exhibited modest, seasonal, per capita predation on salmonids, but they were disproportionately much less abundant than smaller, less piscivorous, conspecifics. The annual predation on kokanee Oncorhynchus nerka (in biomass) by a size-structured unit of 1,000 Northern Pikeminnow having a FL ≥ 300 mm was analogous to 16,000–40,000 age-0 spring Chinook Salmon O. tshawytscha rearing year-round, or 400–1,000 age-1 smolts migrating April–June. The per capita consumption of salmonids by Northern Pikeminnow having a FL ≥ 200 mm was relatively low, due in large part to spatial segregation during the summer and the skewed size distribution of the predator population. Tiger muskellunge fed heavily on Northern Pikeminnow, other nonsalmonids, and minimally on salmonids. In addition to cannibalism within the Northern Pikeminnow population, predation by tiger muskellunge likely contributed to the low recruitment of larger (more piscivorous) Northern Pikeminnow, thereby decreasing the risk of predation to

  1. Physiological response of some economically important freshwater salmonids to catch-and-release fishing

    USGS Publications Warehouse

    Wedemeyer, G.A.; Wydoski, R.S.

    2008-01-01

    Catch-and-release fishing regulations are widely used by fishery resource managers to maintain both the quantity and quality of sport fish populations. We evaluated blood chemistry disturbances in wild brook trout Salvelinus fontinalis, brown trout Salmo trutta, cutthroat trout Oncorhynchus clarkii, and Arctic grayling Thymallus arcticus that had been hooked and played for 1-5 min in waters of the intermountain western United States. A hatchery stock of brown trout was included for comparison. To assess time needed for recovery, additional test groups were played for 5 min and then released into net-pens, where they were held for up to 72 h. The osmoregulatory and metabolic disturbances associated with catch-and-release fishing under the conditions we tested were minimal and judged to be well within normal physiological tolerance limits. In fish that were held for recovery, the blood chemistry alterations that did occur appeared to be related to stress from confinement in the net-pens. Our results confirm the results of previous studies, showing that prerelease air exposure and handling cause more physiological stress than does either hooking per se or playing time. Fishery managers must be aware of the differences in the perceptions, attitudes, and values of different societal groups, some of which feel that catch-and-release fishing should be banned because it is cruel to the animals. On the basis of brain anatomy, it seems highly unlikely that fish experience pain in the same manner as humans experience it, because fish lack a neocortex, the brain structure that enables the sensation of pain in higher vertebrates. However, independent of the neurobiological argument, our results indicate that under conditions similar to those tested, fish subjected to catch and release are neither suffering nor particularly stressed. Improved education programs about the relatively benign physiological effects of catch-and-release fishing as a fishery management practice would

  2. Renibacterium salmoninarum, the causative agent of bacterial kidney disease in salmonid fish, detected by nested reverse transcription-PCR of 16S rRNA sequences.

    PubMed Central

    Magnússon, H B; Fridjónsson, O H; Andrésson, O S; Benediktsdóttir, E; Gudmundsdóttir, S; Andrésdóttir, V

    1994-01-01

    An assay based on reverse transcription and nested PCR amplification of hypervariable regions within the 16S rRNA sequence was used to specifically detect Renibacterium salmoninarum, the slowly growing causative agent of bacterial kidney disease in salmonid fish. This assay detected 1 to 10 bacteria per sample and took 1 to 2 days to perform. The assay was used to detect R. salmoninarum in ovarian fluid obtained from naturally infected fish. The assay was unreliable when it was used to examine kidney tissue. Images PMID:7529017

  3. Renibacterium salmoninarum, the causative agent of bacterial kidney disease in salmonid fish, detected by nested reverse transcription-PCR of 16S rRNA sequences.

    PubMed

    Magnússon, H B; Fridjónsson, O H; Andrésson, O S; Benediktsdóttir, E; Gudmundsdóttir, S; Andrésdóttir, V

    1994-12-01

    An assay based on reverse transcription and nested PCR amplification of hypervariable regions within the 16S rRNA sequence was used to specifically detect Renibacterium salmoninarum, the slowly growing causative agent of bacterial kidney disease in salmonid fish. This assay detected 1 to 10 bacteria per sample and took 1 to 2 days to perform. The assay was used to detect R. salmoninarum in ovarian fluid obtained from naturally infected fish. The assay was unreliable when it was used to examine kidney tissue. PMID:7529017

  4. Tetraploid production in salmonids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tetraploid induction is of interest to aquaculture and fisheries as part of a more efficient means of producing triploid fish by mating a tetraploid parent with a diploid parent (tetraploid-derived triploids). Tetraploid induction has previously been reported in salmonids including rainbow trout a...

  5. Changing technologies, ingredients and formulations to replace fish meal in salmonid diets.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the search for alternatives to fish meal in aquafeeds has been active for the last 30 years, efforts in the last decade have been intensified on a world wide scale. Multiple factors are driving these efforts and include regulatory concerns on the environmental effects of nutrient release, ...

  6. Experiments upon the control of Trichodiniasis of salmonid fishes by the prolonged recirculation of formalin solutions

    USGS Publications Warehouse

    1940-01-01

    In a search for more effective disinfectants to combat parasitic diseases of hatchery fish, the authors report results from a series of experiments designed to determine the toxicity of varying exposures to concentrations of formalin, sodium p-phenolsulphonate, ammonium sulphate, and sodium benzoate. Non-toxic concentrations of these disinfectants were tested, in addition to the usual hatchery methods of salt treatment and hand dipping in copper sulphate and acetic acid solutions, on No. 1 brook trout fingerlings which had been experimentally infected with the protozoan parasite Trichodina sp. (previously known as Cyclochaeta sp.).Of the disinfectants tested, only formalin completely removed all parasites. Salt treatment in a 5 per cent solution, by weight, as well as hand dipping in 1:500 acetic acid, failed to eradicate all parasites present, although a marked reduction in their numbers did occur. The hand dipping in a 1:2,000 copper sulphate solution was found to be without practical value for the removal of parasites.The authors recommend a prolonged treatment for sixty minutes by recirculating a 1:4,000 solution of formalin, or, where circumstances permit, a 120- to 150-minute exposure to a 1:6,000 concentration of formalin, as the most effective, most economical, and least toxic treatments for combating infections of Trichodina sp., and presumably those of other external parasites as well, among hatchery fish.

  7. Morphology of certain viruses of Salmonid fishes. II. In vivo studies of infectious Hematopoietic Necrosis Virus

    USGS Publications Warehouse

    Amend, Donald F.; Chambers, Velma C.

    1970-01-01

    Juvenile sockeye salmon (Oncorhynchus nerka) were injected with the infectious hematopoietic necrosis (IHN) virus, and tissue samples from the anterior kidney, spleen, liver, intestine, and pyloric caeca of moribund fish were prepared for electron microscopy. Bullet-shaped virus particles measuring 158 × 90 mμ were observed in the hematopoietic tissues of the anterior kidney and spleen. Virus particles were also observed in the outer connective tissues of the pancreas or pyloric caeca, or both. No virus was found in the intestine or liver. The healthy appearance of erythrocytes, reticular cells, and endothelial cells in necrotic areas of the spleen and anterior kidney, and the absence of lymphocytes in these areas, suggested that lymphocytes might be one source of the virus.

  8. Investigation of Head Burns in Adult Salmonids : Phase 1 : Examination of Fish at Lower Granite Dam, July 2, 1996. Final Report.

    SciTech Connect

    Elston, Ralph

    1996-08-01

    Head burn is a descriptive clinical term used by fishery biologists to describe exfoliation of skin and underlying connective tissue of the jaw and cranial region of salmonids, observed at fish passage facilities on the Columbia and Snake Rivers. The observations are usually made on upstream migrant adult salmon or steelhead. An expert panel, convened in 1996, to evaluate the risk and severity of gas bubble disease (GBD) in the Snake and Columbia River system believed that, while head burns appeared to be distinct from GBD, the relationship between dissolved gas saturation in the rivers and head burns was uncertain.

  9. Evaluation of commercially prepared transport systems for nonlethal detection of Aeromonas salmonicida in salmonid fish

    USGS Publications Warehouse

    Cipriano, R.C.; Bullock, G.L.

    2001-01-01

    In vitro studies indicated that commercially prepared transport systems containing Amies, Stuart's, and Cary-Blair media worked equally well in sustaining the viability of the fish pathogen Aeromonas salmonicida, which causes furunculosis. The bacterium remained viable without significant increase or decrease in cell numbers for as long as 48 h of incubation at 18-20??C in Stuart's transport medium; consequently, obtaining mucus samples in such tubes were comparable to on-site detection of A. salmonicida by dilution plate counts on Coomassie Brilliant Blue agar. In three different assays of 100 samples of mucus from Atlantic salmon Salmo salar infected subclinically with A. salmonicida, dilution counts conducted on-site proved more reliable for detecting the pathogen than obtaining the samples in the transport system. In the on-site assays, dilution counts detected the pathogen in 34, 41, and 22 samples, whereas this was accomplished in only 15, 15, and 3 of the respective samples when the transport system was used. In an additional experiment, Arctic char Salvelinus alpinus sustaining a frank epizootic of furunculosis were sampled similarly. Here, too, dilution counts were more predictive of the prevalence of A. salmonicida and detected the pathogen in 46 mucus samples; in comparison, only 6 samples collected by using the transport system were positive. We also observed that the transport system supported the growth of the normal mucus bacterial flora. Particularly predominant among these were motile aeromonads and Pseudomonas fluorescens. In studies of mixed culture growth, two representatives of both of the latter genera of bacteria outgrew A. salmonicida - in some cases, to the total exclusion of the pathogen itself.

  10. Evaluating Adaptive Divergence Between Migratory and Nonmigratory Ecotypes of a Salmonid Fish, Oncorhynchus mykiss

    PubMed Central

    Hale, Matthew C.; Thrower, Frank P.; Berntson, Ewann A.; Miller, Michael R.; Nichols, Krista M.

    2013-01-01

    Next-generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. The use of these two approaches in parallel is especially attractive in nonmodel organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a nonmodel fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and nonmigratory ecotypes and to further our understanding about the genetic basis of migration. Restriction site-associated DNA (RAD) tag sequencing was used to identify single-nucleotide polymorphisms (SNPs) in migrant and resident O. mykiss from two systems, one in Alaska and the other in Oregon. A total of 7920 and 6755 SNPs met filtering criteria in the Alaska and Oregon data sets, respectively. Population genetic tests determined that 1423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Previous linkage mapping studies that used RAD DNA tag SNPs were available to determine the position of 1990 markers. Several significant SNPs are located in genome regions that contain quantitative trait loci for migratory-related traits, reinforcing the importance of these regions in the genetic basis of migration/residency. Annotation of genome regions linked to significant SNPs revealed genes involved in processes known to be important in migration (such as osmoregulatory function). This study adds to our growing knowledge on adaptive divergence between migratory and nonmigratory ecotypes of this species; across studies, this complex trait appears to be controlled by many loci of small effect, with some in common, but many loci not shared between populations studied. PMID:23797103

  11. Denaturing gradient gel electrophoresis for nonlethal detection of Aeromonas salmonicida in salmonid mucus and its potential for other bacterial fish pathogens.

    PubMed

    Quinn, Robert A; Stevenson, Roselynn M W

    2012-05-01

    Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA was used to nonlethally detect Aeromonas salmonicida and other bacteria in salmonid skin mucus. Mucus samples from wild spawning coho salmon (Oncorhynchus kisutch) with endemic A. salmonicida and from cultured lake trout (Salvelinus namaycush) were tested by PCR-DGGE and were compared with mucus culture on Coomassie brilliant blue agar and internal organ culture. PCR-DGGE gave a highly reproducible 4-band pattern for 9 strains of typical A. salmonicida, which was different from other Aeromonas spp. Aeromonas salmonicida presence in mucus was evident as a band that comigrated with the bottom band of the A. salmonicida 4-band pattern and was verified by sequencing. PCR-DGGE found 36 of 52 coho salmon positive for A. salmonicida, compared with 31 positive by mucus culture and 16 by organ culture. Numerous other bacteria were detected in salmonid mucus, including Pseudomonas spp., Shewanella putrefaciens, Aeromonas hydrophila and other aeromonads. However, Yersinia ruckeri was not detected in mucus from 27 lake trout, but 1 fish had a sorbitol-positive Y. ruckeri isolated from organ culture. Yersinia ruckeri seeded into a mucus sample suggested that PCR-DGGE detection of this bacterium from mucus was possible. PCR-DGGE allows nonlethal detection of A. salmonicida in mucus and differentiation of some Aeromonas spp. and has the potential to allow simultaneous detection of other pathogens present in fish mucus. PMID:22506865

  12. Predation by Resident Fish on Juvenile Salmonids in John Day Reservoir: Final Report, 1983-1986: Volume 1, Final Report of Research.

    SciTech Connect

    Poe, Thomas P.; Rieman, Bruce E.

    1988-07-01

    In 1982 the NPPC included in its Fish and Wildlife Program a measure that called for studies ''... to investigate juvenile salmon and steelhead losses to predators while these fish are migrating through Columbia and Snake River reservoirs.'' In the same year the Bonneville Power Administration (BPA) funded ODFW and FWS to conduct collaborative studies to estimate the number of juvenile salmonids lost to predators in John Day Reservoir. Also included as study objectives were: (1) a description of the importance of predation losses relative to mortality at the dam and total reservoir mortality; (2) a description of how predation losses might vary (spatially and temporally); and (3) recommendations of measures to control predation on smolts. We studied four species of predator: northern squawfish, walleye, smallmouth bass, and channel catfish. We selected John Day Reservoir as the study site because the following factors led us to believe if predation was a problem in any reservoir, it would be most obvious there because: (1) the reservoir is an important subyearling chinook rearing area; (2) passage and residualism of juvenile salmonids were considered a problem there; and (3) substantial populations of predators were known to reside in the reservoir. Individual reports were processed separately for the data base.

  13. Differences in detection of Aeromonas salmonicida in covertly infected salmonid fishes by the stress-inducible furunculosis test and culture-based assays

    USGS Publications Warehouse

    Cipriano, R.C.; Ford, L.A.; Smith, D.R.; Schachte, J.H.; Petrie, C.J.

    1997-01-01

    Accurate detection of Aeromonas salmonicida subsp. salmonicida (the cause of furunculosis disease) in covertly infected salmonids is difficult and is a cause of concern for those involved in fish health inspection and resource management programs. In this study, we examined populations of brook trout Salvelinus fontinalis, Atlantic salmon Salmo salar, and lake trout Salvelinus namaycush that previously sustained natural episodes of furunculosis. Consequently, the sampled fish were presumed to harbor latent infections. Mucus, gill, liver, kidney, heart, spleen, and intestine samples (N = 100 fish per group sampled) were processed and examined by (1) direct dilution counts and (2) quadrant streaking after a 48-h pre-enrichment in trypticase soy broth (TSB). Another subsample of fish from each group was then subjected to stress-inducible furunculosis tests. Stress tests detected A. salmonicida in three of four groups of fish that were examined whereas the pathogen was detected in only two of the groups analyzed with culture-based assays. Although pre-enrichment in TSB enhanced detection within internal sampling sites including the liver, heart, spleen, and kidney, enrichment did not enhance detection from mucus, gill, or intestinal samples.

  14. Vaccination against salmonid bacterial kidney disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial kidney disease (BKD) of salmonid fishes, caused by Renibacterium salmoninarum, has presented challenges for development of effective vaccines, despite several decades of research. The only vaccine against BKD that is commercially licensed is an injectable preparation containing live cells ...

  15. Biochemical and antigenic properties of the first isolates of infectious hematopoietic necrosis virus from salmonid fish in Europe

    USGS Publications Warehouse

    Arkush, K.D.; Bovo, G.; deKinkelin, P.; Winton, J.R.; Wingfield, W.H.; Hedrick, R.P.

    1989-01-01

    The first isolates of infectious hematopoietic necrosis virus (IHNV) recovered from rainbow trout Oncorhynchus mykiss (formerly Salmo gairdneri) in France and Italy were compared to six representative strains from North America by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of virion polypeptides and neutralization by monoclonal antibodies (MAbs). All three IHNV isolates from Europe had similar polypeptide profiles when compared by SDS-PAGE. An analysis of the antigenic relatedness of the European isolates to representative strains from North America showed that they were clearly different from viruses obtained from salmonids in California. The RB/B5 MAb, which was developed against virus isolated from adult steelhead (anadromous rainbow trout) reared in central Oregon, neutralized all isolates examined. The 193–110/B4 MAb, developed against IHNV isolated from infected yearling rainbow trout in southern Idaho, neutralized all isolates tested except those from California. The SRCV/A4 MAb, developed against Sacramento River chinook virus (SRCV) isolated from adult spring chinook salmon O. tshawytscha in central California, was the least reactive, and strong neutralization was observed only with the SRCV strain of IHNV from California. However, partial reactivity of the virus isolates from France with the SRCV/A4 MAb distinguished them from the virus recovered from salmonids in Italy.

  16. Antiviral activity of casein and αs2 casein hydrolysates against the infectious haematopoietic necrosis virus, a rhabdovirus from salmonid fish.

    PubMed

    Rodríguez Saint-Jean, S; De las Heras, A; Carrillo, W; Recio, I; Ortiz-Delgado, J B; Ramos, M; Gomez-Ruiz, J A; Sarasquete, C; Pérez-Prieto, S I

    2013-05-01

    Salmonid fish viruses, such as infectious haematopoietic necrosis virus (IHNV), are responsible for serious losses in the rainbow trout and salmon-farming industries, and they have been the subject of intense research in the field of aquaculture. Thus, the aim of this work is to study the antiviral effect of milk-derived proteins as bovine caseins or casein-derived peptides at different stages during the course of IHNV infection. The results indicate that the 3-h fraction of casein and α(S2) -casein hydrolysates reduced the yield of infectious IHNV in a dose-dependent manner and impaired the production of IHNV-specific antigens. Hydrolysates of total casein and α(S2) -casein target the initial and later stages of viral infection, as demonstrated by the reduction in the infective titre observed throughout multiple stages and cycles. In vivo, more than 50% protection was observed in the casein-treated fish, and the kidney sections exhibited none of the histopathological characteristics of IHNV infection. The active fractions from casein were identified, as well as one of the individual IHNV-inhibiting peptides. Further studies will be required to determine which other peptides possess this activity. These findings provide a basis for future investigations on the efficacy of these compounds in treating other viral diseases in farmed fish and to elucidate the underlying molecular mechanisms of action. However, the present results provide convincing evidence in support of a role for several milk casein fractions as suitable candidates to prevent and treat some fish viral infections. PMID:23167612

  17. Predation by Resident Fish on Juvenile Salmonids in John Day Reservoir: Final Report, 1983-1986: Volume 2: Supplemental Papers and Data Documentation.

    SciTech Connect

    Poe, Thomas P.; Rieman, Bruce E.

    1988-07-01

    In 1982 the NPPC included in its Fish and Wildlife Program measure that called for studies ''... to investigate juvenile salmon and steelhead losses to predators while these fish are migrating through Columbia and Snake River reservoirs.'' In the same year the Bonneville Power Administration (BPA) funded ODFW and FWS to conduct collaborative studies to estimate the number of juvenile salmoids lost to predators in John Day Reservoir. Also included as study objectives were: (1) a description of the importance of predation losses relative to mortality at the dam and total reservoir mortality; (2) a description of how predation losses might vary (spatially and temporally); and (3) recommendations of measures to control predation on smolts. We studied four species of predator; northern squawfish, walleye, smallmouth bass, and channel catfish. We selected John Day Reservoir as the study site because the following factors led us to believe if predation was a problem in any reservoir, it would be most obvious there because: (1) the reservoir is an important subyearling chinook rearing area; (2) passage and residualism of juvenile salmonids were considered a problem there; and (3) substantial populations of predators were known to reside in the reservoir. Individual reports were processed separately for the data base.

  18. [Epidemiology of infectious hematopoietic necrosis (IHN) of salmonid fish in France: study of the course of natural infection by combined use of viral and seroneutralization test and eradication attempts].

    PubMed

    Hattenberger-Baudouy, A M; Danton, M; Merle, G; de Kinkelin, P

    1995-01-01

    Infectious haematopoietic necrosis (IHN), a rhabdoviral infection of salmonid fish, was considered to be an exotic disease in Europe until it was recognized in France and Italy in 1987. In France, the existence of this new condition led the authorities in charge of animal health to order epidemiological studies to be undertaken. These studies were based upon virological, serological and experimental diagnostic methods and also encompassed disease eradication attempts. Studies were conducted at 7 fish farming sites, involved 1,545 salmonid fish, of which 848 were sacrificed, and represented 262 virological examinations and 1,782 serum neutralization tests. The presence of the IHN virus was detected in the 7 trout farm fish populations that were located in 5 regions, one of which was situated 600 km from the place where the first isolation of IHN virus was made. Moreover, 6 out of 7 rainbow trout populations reared in these farms also harboured viral haemorrhagic septicaemia virus (VHSV) often resulting in overt disease. Rainbow trout was the only salmonid fish species found infected with IHN. Overt infection, which was observed in fish ageing less than 2,200 degrees-days, always occurred at water temperatures below 14 degrees C, and the younger fish were more susceptible (mortality rate > or = 80%). Although the IHN virus is easily isolable from fish undergoing overt infection, it was hardly detectable in survivors until they were adults, at which stage the virus was shedded via sexual products which constituted suitable materials for virological examination and disease transmission assays. Survivors of overt and dormant IHN infection developed consistent immune response and special attention was paid to neutralizing antibodies (NAb) to IHN virus. The detection of such NAb in fish from infected farming sites or other NAb from presumably IHN-free sites, correlated fairly well with the presence and further detection of IHN virus among such fish populations. Our data

  19. Molecular cloning and sequence analysis of the gene coding for the 57-kDa major soluble antigen of the salmonid fish pathogen Renibacterium salmoninarum.

    PubMed

    Chien, M S; Gilbert, T L; Huang, C; Landolt, M L; O'Hara, P J; Winton, J R

    1992-09-15

    The complete sequence coding for the 57-kDa major soluble antigen of the salmonid fish pathogen, Renibacterium salmoninarum, was determined. The gene contained an opening reading frame of 1671 nucleotides coding for a protein of 557 amino acids with a calculated M(r) value of 57,190. The first 26 amino acids constituted a signal peptide. The deduced sequence for amino acid residues 27-61 was in agreement with the 35 N-terminal amino acid residues determined by microsequencing, suggesting the protein is synthesized as a 557-amino acid precursor and processed to produce a mature protein of M(r) 54,505. Two regions of the protein contained imperfect direct repeats. The first region contained two copies of an 81-residue repeat, the second contained five copies of an unrelated 25-residue repeat. Also, a perfect inverted repeat (including three in-frame UAA stop codons) was observed at the carboxyl-terminus of the gene. PMID:1383085

  20. Combining Bioenergetic Responses of Fish to Thermal Regimes and Productivity in Reservoirs: Implications for Conservation and Re-Introduction of Anadromous Salmonids

    NASA Astrophysics Data System (ADS)

    Beauchamp, D.

    2014-12-01

    Temperature, food availability, and predation risk form vertical gradients determining growth and survival for fish in lakes and reservoirs. These gradients change on inter-annual, seasonal, and diel temporal scales and are strongly influenced by climatic variability, conflicting water demands and management. Temperatures associated with optimal growth and energy loss vary both among life stages and species of fish, but the quantity and quality of available food resources can significantly alter these thermal responses. Greater understanding of how water management affects the timing, magnitude, and duration of thermal stratification, and how key species and their supporting aquatic resources respond can improve strategies for development and operation of water storage facilities within the context of localized environmental and ecological constraints. An emerging trend for coldwater reservoirs in the Pacific Northwest has been to re-introduce anadromous salmon above historically impassable dams. Thermal regimes and the existing ecological communities in the reservoirs and tributary habitats above these dams will determine the seasonal importance of lotic and lentic habitats for rearing or migration corridors. The feasibility of reservoir rearing and migration can be evaluated by combining mass- and species-specific thermal growth response curves with temporal dynamics in the vertical and longitudinal thermal structure of reservoirs and associated distribution of food resources (primarily zooplankton). The value of reservoirs as rearing habitats or migration corridors could be compared with coincident tributary conditions to predict the likely temporal-spatial distribution of optimal conditions for growth and survival of different species or life stages of salmonids within the watershed and how these conditions might change under different climatic or water management scenarios.

  1. Introduced northern pike consumption of salmonids in Southcentral Alaska

    USGS Publications Warehouse

    Sepulveda, Adam J.; Rutz, David S.; Dupuis, Aaron W; Shields, Patrick A; Dunker, Kristine J.

    2015-01-01

    The impacts of introduced northern pike (Esox lucius) on salmonid populations have attracted much attention because salmonids are popular subsistence, sport and commercial fish. Concern over the predatory effects of introduced pike on salmonids is especially high in Southcentral Alaska, where pike were illegally introduced to the Susitna River basin in the 1950s. We used pike abundance, growth, and diet estimates and bioenergetics models to characterise the realised and potential consumptive impacts that introduced pike (age 2 and older) have on salmonids in Alexander Creek, a tributary to the Susitna River. We found that juvenile salmonids were the dominant prey item in pike diets and that pike could consume up to 1.10 metric tons (realised consumption) and 1.66 metric tons (potential consumption) of juvenile salmonids in a summer. Age 3–4 pike had the highest per capita consumption of juvenile salmonids, and age 2 and age 3–4 pike had the highest overall consumption of juvenile salmonid biomass. Using historical data on Chinook salmon and pike potential consumption of juvenile salmonids, we found that pike consumption of juvenile salmonids may lead to collapsed salmon stocks in Alexander Creek. Taken together, our results indicate that pike consume a substantial biomass of juvenile salmonids in Alexander Creek and that coexistence of pike and salmon is unlikely without management actions to reduce or eliminate introduced pike.

  2. Development of a polymerase chain reaction diagnostic assay for Ceratomyxa shasta, a myxosporean parasite of salmonid fish.

    PubMed

    Palenzuela, O; Trobridge, G; Bartholomew, J L

    1999-04-15

    A diagnostic procedure based on the polymerase chain reaction (PCR) was developed for the myxosporean parasite Ceratomyxa shasta. Three sets of oligonucleotide primers were designed to specifically amplify C. shasta ribosomal RNA genes and several parameters of the assay were tested and optimised. A simple protocol for the processing of fish tissue samples was also developed. In a single round, 20 microliters volume reaction the optimised procedure allows the detection of 50 fg of purified C. shasta genomic DNA, or 0.01 spore from a seeded fish intestine sample. This protocol is considerably faster, cheaper and more reliable than any previous diagnostic procedure for a myxosporean parasite, and can be an invaluable tool for the monitoring of early and/or subclinical C. shasta infections in wild and cultured salmon populations. PMID:10349552

  3. Rising from the ashes: Changes in salmonid fish assemblages after 30 months of the Puyehue-Cordon Caulle volcanic eruption.

    PubMed

    Lallement, Mailén; Macchi, Patricio J; Vigliano, Pablo; Juarez, Santiago; Rechencq, Magalí; Baker, Matthew; Bouwes, Nicolaas; Crowl, Todd

    2016-01-15

    Events such as volcanic eruptions may act as disturbance agents modifying the landscape spatial diversity and increasing environmental instability. On June 4, 2011 the Puyehue-Cordon Caulle volcanic complex located on Chile (2236 m.a.s.l., 40° 02' 24" S- 70° 14' 26" W) experience a rift zone eruption ejecting during the first day 950 million metric tons into the atmosphere. Due to the westerly winds predominance, ash fell differentially upon 24 million ha of Patagonia Argentinean, been thicker deposits accumulated towards the West. In order to analyze changes on stream fish assemblages we studied seven streams 8, 19 and 30 months after the eruption along the ash deposition gradient, and compare those data to pre eruption ones. Habitat features and structure of the benthic macroinvertebrate food base of fish was studied. After the eruption, substantial environmental changes were observed in association with the large amount of ash fallout. In western sites, habitat loss due to ash accumulation, changes in the riparian zone and morphology of the main channels were observed. Turbidity was the water quality variable which reflected the most changes throughout time, with NTU values decreasing sharply from West to East sites. In west sites, increased Chironomid densities were recorded 8 months after the initial eruption as well as low EPT index values. These relationships were reversed in the less affected streams farther away from the volcano. Fish assemblages were greatly influenced both by habitat and macroinvertebrate changes. The eruption brought about an initial sharp decline in fish densities and the almost total loss of young of the year in the most western streams affecting recruitment. This effect diminished rapidly with distance from the emission center. Thirty months after the eruption, environmental changes are still occurring as a consequence of basin wide ash remobilization and transport. PMID:26473706

  4. Linking spatially distributed biogeochemical data with a two-host life-cycle pathogen:A model of whirling disease dynamics in salmonid fishes in the Intermountain West

    NASA Astrophysics Data System (ADS)

    Fytilis, N.; Lamb, R.; Stevens, L.; Morrissey, L. A.; Kerans, B.; Rizzo, D. M.

    2010-12-01

    Fish diseases are often caused by waterborne parasites, making them ideal systems for modeling the non-linear relationships between biogeochemical features and disease dynamics. Myxobolus cerebralis, the causative agent of whirling disease, has been a major contributor to the loss of wild rainbow trout populations in numerous streams within the Intermountain West (Colorado, Idaho, Montana, Utah, Wyoming). The parasite alternates between an invertebrate and vertebrate host, being transmitted between the sediment feeding worm T.Tubifex and salmonid fishes. A greater understanding of the linkage between biological stream integrity, geomorphic features, water quality parameters and whirling disease risk is needed to improve current management techniques. Biodiversity and abundance of the worm communities are influenced by biogeochemical features and linked to disease severity in fish. We collected and identified ~700 worms from eight sites using molecular genetic probes and a taxonomic key. Additionally, ~1700 worms were identified using only a taxonomic key. Our work examines the links between worm community structure and biogeochemical features. We use a modified Self-Organizing-Map (SOM), which is a non-parametric clustering method based on an artificial neural network (ANN). Clustering methods are particularly attractive for exploratory data analyses because they do not require either the target number of groupings or the data structure be specified at the outset. ANN clustering methods have been shown to be more robust and to account for more data variability than traditional methods when applied to clustering geo-hydrochemical and microbiological datasets. The SOM highlights spatial variation of worm community structure between sites; and is used in tandem with expert knowledge (Lamb and Kerans) of local worm communities and a Madison River, MT physiochemical dataset (GIS-derived layers, water quality parameters). We iteratively clustered the physiochemical data

  5. First in-depth analysis of the novel Th2-type cytokines in salmonid fish reveals distinct patterns of expression and modulation but overlapping bioactivities.

    PubMed

    Wang, Tiehui; Johansson, Petronella; Abós, Beatriz; Holt, Amy; Tafalla, Carolina; Jiang, Youshen; Wang, Alex; Xu, Qiaoqing; Qi, Zhitao; Huang, Wenshu; Costa, Maria M; Diaz-Rosales, Patricia; Holland, Jason W; Secombes, Christopher J

    2016-03-01

    IL-4 and IL-13 are closely related canonical type-2 cytokines in mammals and have overlapping bioactivities via shared receptors. They are frequently activated together as part of the same immune response and are the signature cytokines produced by T-helper (Th)2 cells and type-2 innate lymphoid cells (ILC2), mediating immunity against extracellular pathogens. Little is known about the origin of type-2 responses, and whether they were an essential component of the early adaptive immune system that gave a fitness advantage by limiting collateral damage caused by metazoan parasites. Two evolutionary related type-2 cytokines, IL-4/13A and IL-4/13B, have been identified recently in several teleost fish that likely arose by duplication of an ancestral IL-4/13 gene as a consequence of a whole genome duplication event that occurred at the base of this lineage. However, studies of their comparative expression levels are largely missing and bioactivity analysis has been limited to IL-4/13A in zebrafish. Through interrogation of the recently released salmonid genomes, species in which an additional whole genome duplication event has occurred, four genomic IL-4/13 loci have been identified leading to the cloning of three active genes, IL-4/13A, IL-4/13B1 and IL-4/13B2, in both rainbow trout and Atlantic salmon. Comparative expression analysis by real-time PCR in rainbow trout revealed that the IL-4/13A expression is broad and high constitutively but less responsive to pathogen-associated molecular patterns (PAMPs) and pathogen challenge. In contrast, the expression of IL-4/13B1 and IL-4/13B2 is low constitutively but is highly induced by viral haemorrhagic septicaemia virus (VHSH) infection and during proliferative kidney disease (PKD) in vivo, and by formalin-killed bacteria, PAMPs, the T cell mitogen PHA, and the T-cell cytokines IL-2 and IL-21 in vitro. Moreover, bioactive recombinant cytokines of both IL-4/13A and B were produced and found to have shared but also distinct

  6. First in-depth analysis of the novel Th2-type cytokines in salmonid fish reveals distinct patterns of expression and modulation but overlapping bioactivities

    PubMed Central

    Wang, Tiehui; Johansson, Petronella; Abós, Beatriz; Holt, Amy; Tafalla, Carolina; Jiang, Youshen; Wang, Alex; Xu, Qiaoqing; Qi, Zhitao; Huang, Wenshu; Costa, Maria M.; Diaz-Rosales, Patricia; Holland, Jason W.; Secombes, Christopher J.

    2016-01-01

    IL-4 and IL-13 are closely related canonical type-2 cytokines in mammals and have overlapping bioactivities via shared receptors. They are frequently activated together as part of the same immune response and are the signature cytokines produced by T-helper (Th)2 cells and type-2 innate lymphoid cells (ILC2), mediating immunity against extracellular pathogens. Little is known about the origin of type-2 responses, and whether they were an essential component of the early adaptive immune system that gave a fitness advantage by limiting collateral damage caused by metazoan parasites. Two evolutionary related type-2 cytokines, IL-4/13A and IL-4/13B, have been identified recently in several teleost fish that likely arose by duplication of an ancestral IL-4/13 gene as a consequence of a whole genome duplication event that occurred at the base of this lineage. However, studies of their comparative expression levels are largely missing and bioactivity analysis has been limited to IL-4/13A in zebrafish. Through interrogation of the recently released salmonid genomes, species in which an additional whole genome duplication event has occurred, four genomic IL-4/13 loci have been identified leading to the cloning of three active genes, IL-4/13A, IL-4/13B1 and IL-4/13B2, in both rainbow trout and Atlantic salmon. Comparative expression analysis by real-time PCR in rainbow trout revealed that the IL-4/13A expression is broad and high constitutively but less responsive to pathogen-associated molecular patterns (PAMPs) and pathogen challenge. In contrast, the expression of IL-4/13B1 and IL-4/13B2 is low constitutively but is highly induced by viral haemorrhagic septicaemia virus (VHSH) infection and during proliferative kidney disease (PKD) in vivo, and by formalin-killed bacteria, PAMPs, the T cell mitogen PHA, and the T-cell cytokines IL-2 and IL-21 in vitro. Moreover, bioactive recombinant cytokines of both IL-4/13A and B were produced and found to have shared but also distinct

  7. Preliminary characterization of a virus causing infectious anemia among stocks of salmonid fish in the western United States

    USGS Publications Warehouse

    Arakawa, C.K.; Hursh, D.A.; Lannan, C.N.; Rohovec, J.S.; Winton, J.R.

    1989-01-01

    Since 1982, anemias occurring in stocks of yearling coho (Oncorhynchus kisutch) and chinook salmon (Oncorhynchus tshawytscha) have been associated with serious losses at hatcheries in the Pacific Northwest, USA. The anemia is often accompanied by infections with external fungus (e.g. Saprolegnia) or the bacterial pathogens Cytophaga psychrophila or Renibacterium salmoninarum (Holt and Rohovec 1984, Leek 1987). The losses associated with the anemia are thought to be caused by these secondary infections.Blood smears that were made from anemic fish and stained with Giemsa or pinacyanol chloride showed erythrocytic inclusions ranging in size from 1 to 8 um and varying in number per cell. Thin sections of infected red blood cells (RBC) examined by electron microscopy revealed virus particles approximately 70 nm in diameter. The virions were scattered in the cytoplasm of the RBC or contained within membrane bound organelles. These virus particles were morphologically distinct from the iridovirus, erythrocytic necrosis virus (ENV), which is also associated with anemia (Holt and Rohovec 1984, Leek 1987). Evidence suggests that the etiological agent of this new anemic disease, termed erythrocytic inclusion body syndrome (EIBS) by Leek (1987), is a previously undescribed virus infecting salmon. The purpose of this study was to experimentally transmit the disease to healthy fish, to determine the blood parameters associated with infection, and to investigate the nature of the virus associated with EIBS.

  8. Detection of Renibacterium salmoninarum, the Causative Agent of Bacterial Kidney Disease in Salmonid Fish, from Pen-Cultured Coho Salmon.

    PubMed

    Sakai, M; Kobayashi, M

    1992-03-01

    The detection of Renibacterium salmoninarum antigen from pen-cultured coho salmon was attempted. Flounder (Limanda herzensteini) (n = 24), greenling (Hexagrammos otakii) (n = 5), Japanese sculpin (Cottus japonicus) (n = 1), and flathead (Platycephalus indicus) (n = 22) captured by fishing around coho salmon net pens were examined for the presence of R. salmoninarum antigen by an indirect dot blot assay and by an indirect fluorescent-antibody technique using polyclonal and monoclonal antibodies. R. salmoninarum antigen was detected from kidney samples of one greenling and six flathead. Moreover, 86 scallops (Patinopecten yessoensis) were hung from the edge of the net pen for 50 days, and R. salmoninarum antigen was demonstrated in 31 samples by the indirect dot blot assay and the indirect fluorescent-antibody technique. PMID:16348666

  9. Detection of Renibacterium salmoninarum, the Causative Agent of Bacterial Kidney Disease in Salmonid Fish, from Pen-Cultured Coho Salmon

    PubMed Central

    Sakai, Masahiro; Kobayashi, Masanori

    1992-01-01

    The detection of Renibacterium salmoninarum antigen from pen-cultured coho salmon was attempted. Flounder (Limanda herzensteini) (n = 24), greenling (Hexagrammos otakii) (n = 5), Japanese sculpin (Cottus japonicus) (n = 1), and flathead (Platycephalus indicus) (n = 22) captured by fishing around coho salmon net pens were examined for the presence of R. salmoninarum antigen by an indirect dot blot assay and by an indirect fluorescent-antibody technique using polyclonal and monoclonal antibodies. R. salmoninarum antigen was detected from kidney samples of one greenling and six flathead. Moreover, 86 scallops (Patinopecten yessoensis) were hung from the edge of the net pen for 50 days, and R. salmoninarum antigen was demonstrated in 31 samples by the indirect dot blot assay and the indirect fluorescent-antibody technique. PMID:16348666

  10. Persistence of Salmonid Redds

    NASA Astrophysics Data System (ADS)

    Buffington, J. M.; Buxton, T.; Fremier, A. K.; Hassan, M. A.; Yager, E.

    2013-12-01

    The construction of redds by spawning salmonids modifies fluvial processes in ways that are beneficial to egg and embryo survival. Redd topography induces hyporheic flow that oxygenates embryos incubating within the streambed and creates form drag that reduces bed mobility and scour of salmonid eggs. Winnowing of fine material during redd construction also coarsens the streambed, increasing bed porosity and hyporheic flow and reducing bed mobility. In addition to the biological benefits, redds may influence channel morphology by altering channel hydraulics and bed load transport rates depending on the size and extent of redds relative to the size of the channel. A key question is how long do the physical and biological effects of redds last? Field observations indicate that in some basins redds are ephemeral, with redd topography rapidly erased by subsequent floods, while in other basins, redds can persist for years. We hypothesize that redd persistence is a function of basin hydrology, sediment supply, and characteristics of the spawning fish. Hydrology controls the frequency and magnitude of bed mobilizing flows following spawning, while bed load supply (volume and caliber) controls the degree of textural fining and consequent bed mobility after spawning, as well as the potential for burial of redd features. The effectiveness of flows in terms of their magnitude and duration depend on hydroclimate (i.e., snowmelt, rainfall, or transitional hydrographs), while bed load supply depends on basin geology, land use, and natural disturbance regimes (e.g., wildfire). Location within the stream network may also influence redd persistence. In particular, lakes effectively trap sediment and regulate downstream flow, which may promote long-lived redds in stream reaches below lakes. These geomorphic controls are modulated by biological factors: fish species (size of fish controls size of redds and magnitude of streambed coarsening); life history (timing of spawning and

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

    PubMed

    Dibble, Kimberly L; Yackulic, Charles B; Kennedy, Theodore A; Budy, Phaedra

    2015-12-01

    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, subadult 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

  12. Multilocus variable-number tandem-repeat genotyping of Renibacterium salmoninarum, a bacterium causing bacterial kidney disease in salmonid fish

    PubMed Central

    2013-01-01

    Background Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, is a bacterial disease of fish, which is both geographically widespread and difficult to control. Previously, application of various molecular typing methods has failed to reliably discriminate between R. salmoninarum isolates originating from different host species and geographic areas. The current study aimed to utilize multilocus variable number tandem repeats (VNTR) to investigate inter-strain variation of R. salmoninarum to establish whether host-specific populations exist in Atlantic salmon and rainbow trout respectively. Such information would be valuable in risk assessment of transmission of R. salmoninarum in a multispecies aquaculture environment. Results The present analysis utilizing sixteen VNTRs distinguished 17 different haplotypes amongst 41 R. salmoninarum isolates originating from Atlantic salmon and rainbow trout in Scotland, Norway and the US. The VNTR typing system revealed two well supported groups of R. salmoninarum haplotypes. The first group included R. salmoninarum isolates originating from both Atlantic salmon and rainbow trout circulating in Scottish and Norwegian aquaculture, in addition to the type strain ATCC33209T originating from Chinook salmon in North America. The second group comprised isolates found exclusively in Atlantic salmon, of mainly wild origin, including isolates NCIB1114 and NCIB1116 associated with the original Dee disease in Scotland. Conclusions The present study confirmed that VNTR analysis can be successfully applied to discriminate R. salmoninarum strains. There was no clear distinction between isolates originating from Atlantic salmon and rainbow trout as several haplotypes in group 1 clustered together R. salmoninarum isolates from both species. These findings indicate a potential exchange of pathogens between Atlantic salmon and rainbow trout in Scottish and Norwegian aquaculture during the last 20 years. In a scenario of

  13. Some myxosporidia found in Pacific Northwest salmonids

    USGS Publications Warehouse

    Yasutake, W.T.; Wood, E.M.

    1957-01-01

    During the histological examination of a group of wild and hatchery salmonids undescribed sporazoans were frequently observed. This was not unexpected, since Myxosporidia are typical fish parasites (Kudo, 1920). Myxidium were observed in kidney tubules, Cholromyxum in glomeruli, and Myxobous in the spinal cord and on epidermal scales. The present paper will deal with the description and indentification of these unclassified Myxosporodia.

  14. Freshwater aspects of anadromous salmonid enhancement

    USGS Publications Warehouse

    Gould, Rowan W.

    1982-01-01

    Freshwater enhancement of anadromous salmonid populations has been practiced in the United States and Canada since the late 1800's. Reduction of natural spawning habitat and increasing fishing pressure make artificial enhancement a possible alternative to declining populations. Enhancement of anadromous salmonids involved improvement of the natural environment and reducing natural mortality. Methods of enhancement include fishways, spawning and rearing channels, stream rehabilitation, lake fertilization, environmental management, and artificial propagation techniques. Five Pacific salmon species and steelhead trout are commonly enhanced, primarily in watershed entering the Pacific Ocean and Great Lakes. Enhancement efforts contribute heavily to a commercial and sport industry realizing over $1.5 billion.

  15. High diversity of bacterial pathogens and antibiotic resistance in salmonid fish farm pond water as determined by molecular identification employing 16S rDNA PCR, gene sequencing and total antibiotic susceptibility techniques.

    PubMed

    Moore, John E; Huang, Junhua; Yu, Pengbo; Ma, Chaofeng; Moore, Peter Ja; Millar, Beverley C; Goldsmith, Colin E; Xu, Jiru

    2014-10-01

    The aim of this study was to examine the microbiological and related parameters (antibiotic resistance and pathogen identification) of water at two salmonid fish farms in Northern Ireland. Total Bacterial Counts at the Movanagher Fish Farm was 1730 colony forming units (cfu)/ml water (log10 3.24cfu/ml) and 3260cfu/ml (log10 3.51cfu/ml) at the Bushmills Salmon Station. Examination of resulting organisms revealed 10 morphological phenotypes, which were subsequently sequenced to determine their identification. All these organisms were Gram-negative and no Gram-positive organisms were isolated from any water sample. From these phenotypes, eight different genera were identified including Acinetobacter, Aeromonas, Chryseobacterium, Erwinia, Flavobacterium, Pseudomonas and Rheinheimera. One unnamed novel taxon was identified from water at the Movanagher Fish Farm, belonging to the genus Acinetobacter and has been tentatively named Acinetobacter movanagherensis. No other novel taxa were observed. All but one of these environmental organisms (Erwinia) are potential pathogens of fish disease. Total antibiotic resistance was observed to varying degrees in water specimens. The most resistant populations were observed in water taken from the Bushmills Salmon Station inlet, followed by water from the Movanagher Fish Farm. No resistance was observed against tetracycline and there was only one occurrence of resistance against ciprofloxacin. Overall, this study indicates that potential fish pathogens made up the majority of environmental organisms identified, even in the absence of recorded fish disease. There was also relatively high levels of total antibiotic resistance in the bacterial water populations examined, where tetracycline was the only antibiotic with zero resistance. These data indicate that the threat of bacterial disease is relatively close due to the indigenous colonization of farm water and that husbandry standards should be maintained at a high standard to avert

  16. Introduced northern pike predation on salmonids in southcentral Alaska

    USGS Publications Warehouse

    Sepulveda, Adam J.; Rutz, David S.; Ivey, Sam S.; Dunker, Kristine J.; Gross, Jackson A.

    2013-01-01

    Northern pike (Esox lucius) are opportunistic predators that can switch to alternative prey species after preferred prey have declined. This trophic adaptability allows invasive pike to have negative effects on aquatic food webs. In Southcentral Alaska, invasive pike are a substantial concern because they have spread to important spawning and rearing habitat for salmonids and are hypothesised to be responsible for recent salmonid declines. We described the relative importance of salmonids and other prey species to pike diets in the Deshka River and Alexander Creek in Southcentral Alaska. Salmonids were once abundant in both rivers, but they are now rare in Alexander Creek. In the Deshka River, we found that juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) dominated pike diets and that small pike consumed more of these salmonids than large pike. In Alexander Creek, pike diets reflected the distribution of spawning salmonids, which decrease with distance upstream. Although salmonids dominated pike diets in the lowest reach of the stream, Arctic lamprey (Lampetra camtschatica) and slimy sculpin (Cottus cognatus) dominated pike diets in the middle and upper reaches. In both rivers, pike density did not influence diet and pike consumed smaller prey items than predicted by their gape-width. Our data suggest that (1) juvenile salmonids are a dominant prey item for pike, (2) small pike are the primary consumers of juvenile salmonids and (3) pike consume other native fish species when juvenile salmonids are less abundant. Implications of this trophic adaptability are that invasive pike can continue to increase while driving multiple species to low abundance.

  17. Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling

    PubMed Central

    2010-01-01

    Background Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing) and mapped using family-based indels/SNPs in rainbow trout (RT)(Oncorhynchus mykiss), Arctic charr (AC)(Salvelinus alpinus), and Atlantic salmon (AS)(Salmo salar) mapping panels. Results Clock1 duplicates mapped to linkage groups RT-8/-24, AC-16/-13 and AS-2/-18. Clock3/NPAS2-like genes mapped to RT-9/-20, AC-20/-43, and AS-5. Most of these linkage group regions containing the Clock gene duplicates were derived from the most recent 4R whole genome duplication event specific to the salmonids. These linkage groups contain quantitative trait loci (QTL) for life history and growth traits (i.e., reproduction and cell cycling). Comparative synteny analyses with other model teleost species reveal a high degree of conservation for genes in these chromosomal regions suggesting that functionally related or co-regulated genes are clustered in syntenic blocks. For example, anti-müllerian hormone (amh), regulating sexual maturation, and ornithine decarboxylase antizymes (oaz1 and oaz2), regulating cell cycling, are contained within these syntenic blocks. Conclusions Synteny analyses indicate that regions homologous to major life-history QTL regions in salmonids contain many candidate genes that are likely to influence reproduction and cell cycling. The order of these genes is highly conserved across the vertebrate species examined, and as such, these genes may make up a functional cluster of genes that are likely co-regulated. CLOCK, as a transcription factor, is found within this block and therefore has the potential to cis-regulate the processes influenced by these genes. Additionally, clock-controlled genes (CCGs) are located in other life-history QTL regions within salmonids suggesting that

  18. Design and evaluation of a unique RT-qPCR assay for diagnostic quality control assessment that is applicable to pathogen detection in three species of salmonid fish

    PubMed Central

    2013-01-01

    Background The detection of pathogens at early stages of infection is a key point for disease control in aquaculture. Therefore, accurate diagnostic procedures are a must. Real-time PCR has been a mainstay in diagnostics over the years due to its speed, specificity, sensitivity, reproducibility and throughput; as such, real-time PCR is a target for improvement. Nevertheless, to validate a novel diagnostic tool, correct setup of the assay, including proper endogenous controls to evaluate the quantity and quality of the samples and to detect possible sample degradation, is compulsory. This work aims to design a unique RT-qPCR assay for pathogen detection in the three salmonid species reared in Chile. The assay uses elongation factor 1 alpha as the single endogenous control, thus avoiding the need for multiple endogenous controls, as well as multiple validations and non-comparable quality control parameters. Results The in vivo and in vitro analyses of samples from Salmo salar, Oncorhynchus mykiss and Oncorhynchus kisutch showed that when primers were accurately selected to target conserved regions of the elongation factor 1 alpha (ELF1α) gene, a single novel RT-qPCR assay yielding similar and reproducible Ct values between the three species could be designed. The opposite occurred when an assay originally designed for Salmo salar was tested in samples from the two species of the genus Oncorhynchus. Conclusions Here, we report the design and evaluation of an accurate trans-species RT-qPCR assay that uses the elongation factor 1 alpha (ELF1α) gene as an endogenous control and is applicable for diagnostic purposes in samples obtained from the three salmonid species reared in Chile. PMID:24040749

  19. Drug resistance in sea lice: a threat to salmonid aquaculture.

    PubMed

    Aaen, Stian Mørch; Helgesen, Kari Olli; Bakke, Marit Jørgensen; Kaur, Kiranpreet; Horsberg, Tor Einar

    2015-02-01

    Sea lice are copepod ectoparasites with vast reproductive potential and affect a wide variety of fish species. The number of parasites causing morbidity is proportional to fish size. Natural low host density restricts massive parasite dispersal. However, expanded salmon farming has shifted the conditions in favor of the parasite. Salmon farms are often situated near wild salmonid migrating routes, with smolts being particularly vulnerable to sea lice infestation. In order to protect both farmed and wild salmonids passing or residing in the proximity of the farms, several measures are taken. Medicinal treatment of farmed fish has been the most predictable and efficacious, leading to extensive use of the available compounds. This has resulted in drug-resistant parasites occurring on farmed and possibly wild salmonids. PMID:25639521

  20. Physiological Assessment and Behavioral Interaction of Wild and Hatchery Juvenile Salmonids : The Relationship of Fish Size and Growth to Smoltification in Spring Chinook Salmon.

    SciTech Connect

    Beckman, Brian R.; Larsen, Donald A.; Lee-Pawlak, Beeda; Dickhoff, Walton W.

    1996-10-01

    Experiments were performed to determine the relative influence of size and growth rate on downstream migratory disposition and physiology in yearling spring chinook salmon (Oncorhynchus tshawtscha) smolts. A group of juvenile chinook salmon was size graded into small and large categories with half the fish in each group reared at an elevated temperature, resulting in four distinct treatment groups: Large Warm (LW), Large Cool (LC), Small Warm (SW), and Small Cool (SC). Fish from warm-water treatment groups displayed significantly higher growth rates than cool-water groups. Fish were tagged and released into a natural creek where downstream movement was monitored. For each of the two releases, fish that migrated past a weir within the first 5 days postrelease had significantly higher spring growth rates than fish that did not migrate within that period. Significant differences in length for the same fish were only found in the second release. Also for the second release, fish from the warm water treatment groups were recovered in higher proportions than fish from cool water groups. The results indicate that increased growth rate in the spring has a positive relation to downstream migratory disposition. Furthermore, there is a relation between smolt size and migration; however, this relation is weaker than that found between growth rate and migration.

  1. Proceedings from a Workshop on Ecological Carrying Capacity of Salmonids in the Columbia River Basin : Measure 7.1A of the Northwest Power Planning Council`s 1994 Fish and Wildlife Program : Report 3 of 4, Final Report.

    SciTech Connect

    Johnson, Gary E.; Neitzel, D.A.; Mavros, William V.

    1996-05-01

    This report contains the proceedings of a workshop held during 1995 in Portland, Oregon. The objective of the workshop was to assemble a group of experts that could help us define carrying capacity for Columbia River Basin salmonids. The workshop was one activity designed to answer the questions asked in Measure 7.1A of the Council`s Fish and Wildlife Program. Based, in part, on the information we learned during the workshop we concluded that the approach inherent in 7.1A will not increase understanding of ecology, carrying capacity, or limiting factors that influence salmon under current conditions. Measure 7.1A requires a definition of carrying capacity and a list of determinants (limiting factors) of capacity. The implication or inference then follows that by asking what we know and do not know about the determinants will lead to research that increases our understanding of what is limiting salmon survival. It is then assumed that research results will point to management actions that can remove or repair the limiting factors. Most ecologists and fisheries scientists that have studied carrying capacity clearly conclude that this approach is an oversimplification of complex ecological processes. To pursue the capacity parameter, that is, a single number or set of numbers that quantify how many salmon the basin or any part of the basin can support, is meaningless by itself and will not provide useful information.

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

    USGS Publications Warehouse

    Allen, M. Brady; Burkhardt, Jeanette; Munz, Carrie; Connolly, Patrick J.

    2012-01-01

    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

  3. Characteristics of current international trade of live salmonid eggs.

    PubMed

    Jansen, M; McLeary, R

    1996-06-01

    World trade in live salmonid embryos (eyed eggs) has grown in response to increased global salmon production, particularly in South America, and parallels international trade in farmed salmonid products. Rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar) and coho salmon (O. kisutch) are the most commercially important species. In 1992, the Food and Agriculture Organization of the United Nations estimated world production of rainbow trout at 300,000 tonnes, while the production of Atlantic salmon was estimated at 250,000 tonnes and coho salmon at 50,000 tonnes. One can estimate that roughly 3 billion, 150 million and 30 million eggs, respectively, were required to produce this yield. Broodstock are cultivated world-wide, using a wide variety of water sources, including the marine environment, riverine water containing anadromous fish, and ground water free of migrating fish. As many as 70% of all coho eggs are derived from feral fish. Approximately 50% of all commercial salmonid eyed eggs are produced in Europe, and approximately 15% are produced in the state of Washington, United States of America. Conditions which are ideal for commercial salmonid grow-out are not necessarily ideal for the cultivation of salmonid broodstock; this is one reason why international egg trade is necessary. The trend of current salmonid health regulations is towards facilitating egg commerce on a regional level, in an attempt to control disease transmission. Regulations controlling egg importation often include pathogens which are not vertically transmitted. This serves only to increase egg prices, in compensation for the cost of laboratory tests. Genetic improvements have been the cornerstone of increasing commercial production of all agricultural commodities. Fish health regulations are sometimes instituted in an effort to protect the local industry, but in fact they act more often to restrict the flow of genetic material and may actually serve to reduce industry

  4. Spawning salmon and the fitness of stream-dwelling fishes: Marine-derived nutrients show saturating effects on growth and energy storage in juvenile salmonids

    USGS Publications Warehouse

    Rinella, D.J.; Wipfli, M.S.; Stricker, C.A.; Heintz, R.

    2012-01-01

    We examined how marine-derived nutrients (MDN), in the form of spawning Pacific salmon, influenced the nutritional status and d15N of stream-dwelling fishes. We sampled juvenile coho salmon (Oncorhynchus kisutch) and Dolly Varden (Salvelinus malma) during spring and fall from 11 south-central Alaskan streams that ranged widely in spawning salmon biomass (0.1–4.7 kg•m–2). Growth rate (as indexed by RNA–DNA ratios), energy density, and d15N enrichment in spring-sampled fishes increased with spawner biomass, indicating the persistence of spawner effects more than 6 months after salmon spawning. Point estimates suggest that spawner effects on nutrition were substantially greater for coho salmon than Dolly Varden (268% and 175% greater for growth and energy, respectively), indicating that both species benefitted physiologically, but that juvenile coho salmon accrued more benefits than Dolly Varden. Although the data were less conclusive for fall- than spring-sampled fish, they do suggest spawner effects were also generally positive during fall, soon after salmon spawned. In a follow-up analysis where growth rate and energy density were modeled as a function of d15N enrichment, results suggested that both increased with MDN assimilation, especially in juvenile coho salmon. Our results support the importance of salmon runs to the nutritional ecology of stream-dwelling fishes.

  5. The relationship between productivities of salmonids and forest stands in northern California watersheds

    USGS Publications Warehouse

    Frazey, S.L.; Wilzbach, M.A.

    2007-01-01

    Productivities of resident salmonids and upland and riporian forests in 22 small watersheds of coastal northern California were estimated and compared to determine whether: 1) upland site productivity predicted riparian site productivity; 2) either upland or riparian site productivity predicted salmonid productivity; and 3) other parameters explained more of the variance in salmonid productivity. Upland and riparian site productivities were estimated using Site Index values for redwood (Sequoia sempervirens) and red alder (Alnus rubra), respectively. Salmonid productivity was indexed by back-calculated length at age 1 of the largest individuals sampled and by total biomass. Upland and riparian site indices were correlated, but neither factor contributed to the best approximating models of salmonid productivity. Total salmonid biomass was best described by a positive relationship with drainage area. Length of dominant fish was best described by a positive relationship with percentage of hardwoods within riparian areas, which may result from nutrient and/or litter subsidies provided by red older. The inability of forest productivity to predict salmon productivity may reflect insufficient variation in independent variables, limitations of the indices, and the operation of other factors affecting salmonid production. The lack of an apparent relationship between upland conifer and salmonid productivity suggests that management of land for timber productivity and component streams for salmonid production in these sites will require separate, albeit integrated, management strategies.

  6. The footprint of salmonids on river morphology

    NASA Astrophysics Data System (ADS)

    Hassan, M. A.; Tonina, D.

    2012-12-01

    Female salmonids dig a pit in the streambed where they lay their eggs, which then cover with sediment from a second pit forming an egg nest call redd. This formation results in a shape resembling a dune with an amplitude, which is the vertical difference between bottom of the pit and crest of the hump, varying from few centimetres (for small fish, chum or sockeye salmon) to tenths of a meter (for large fish, Chinook salmon). During redd construction, salmonids alter streambed topography, winnow away fine sediment and mix streambed material within a layer as thick as 50 cm, for the large chinook salmon. The spawning activities may result in additional roughness at the local scale due to redds. However, redd construction may smooth large-scale topography reducing roughness due the macro-bedform. These topographical changes vary streambed roughness, which in turn may affect shear stress distribution. Redds have been suggested to increase the overall flow resistance due to form drag resulting in lower grain shear stress and less particle mobility. However, the mixing of the sediment could prevent armouring of the streambed surface allowing higher than with armouring sediment transport. Here, we use detailed pre- and post-spawning bathymetries coupled with accurate 2-dimensional hydraulic numerical modelling to test which of these two effects has potentially more impact on sediment transport. Our results show that topographical roughness added by sockeye salmons, which build small redds with 15cm amplitude and 1 meter wavelength (longitudinal length of a redd), has negligible effect on shear stress at the reach-scale and limited at the local scale. Conversely, sediment mixing has an important effect on reducing armouring, increasing sediment mobility, which results in potentially more sediment transport in reaches with than without redds. Consequently, salmonid bioturbation due to mass-spawning fish can be a dominant element for sediment transport in mountain drainage

  7. Immunological and Therapeutic Strategies against Salmonid Cryptobiosis

    PubMed Central

    Woo, Patrick T. K.

    2010-01-01

    Salmonid cryptobiosis is caused by the haemoflagellate, Cryptobia salmositica. Clinical signs of the disease in salmon (Oncorhynchus spp.) include exophthalmia, general oedema, abdominal distension with ascites, anaemia, and anorexia. The disease-causing factor is a metalloprotease and the monoclonal antibody (mAb-001) against it is therapeutic. MAb-001 does not fix complement but agglutinates the parasite. Some brook charr, Salvelinus fontinalis cannot be infected (Cryptobia-resistant); this resistance is controlled by a dominant Mendelian locus and is inherited. In Cryptobia-resistant charr the pathogen is lysed via the Alternative Pathway of Complement Activation. However, some charr can be infected and they have high parasitaemias with no disease (Cryptobia-tolerant). In infected Cryptobia-tolerant charr the metalloprotease is neutralized by a natural antiprotease, α2 macroglobulin. Two vaccines have been developed. A single dose of the attenuated vaccine protects 100% of salmonids (juveniles and adults) for at least 24 months. Complement fixing antibody production and cell-mediated response in vaccinated fish rise significantly after challenge. Fish injected with the DNA vaccine initially have slight anaemias but they recover and have agglutinating antibodies. On challenge, DNA-vaccinated fish have lower parasitaemias, delayed peak parasitaemias and faster recoveries. Isometamidium chloride is therapeutic against the pathogen and its effectiveness is increased after conjugation to antibodies. PMID:20052385

  8. Immunological and therapeutic strategies against salmonid cryptobiosis.

    PubMed

    Woo, Patrick T K

    2010-01-01

    Salmonid cryptobiosis is caused by the haemoflagellate, Cryptobia salmositica. Clinical signs of the disease in salmon (Oncorhynchus spp.) include exophthalmia, general oedema, abdominal distension with ascites, anaemia, and anorexia. The disease-causing factor is a metalloprotease and the monoclonal antibody (mAb-001) against it is therapeutic. MAb-001 does not fix complement but agglutinates the parasite. Some brook charr, Salvelinus fontinalis cannot be infected (Cryptobia-resistant); this resistance is controlled by a dominant Mendelian locus and is inherited. In Cryptobia-resistant charr the pathogen is lysed via the Alternative Pathway of Complement Activation. However, some charr can be infected and they have high parasitaemias with no disease (Cryptobia-tolerant). In infected Cryptobia-tolerant charr the metalloprotease is neutralized by a natural antiprotease, alpha2 macroglobulin. Two vaccines have been developed. A single dose of the attenuated vaccine protects 100% of salmonids (juveniles and adults) for at least 24 months. Complement fixing antibody production and cell-mediated response in vaccinated fish rise significantly after challenge. Fish injected with the DNA vaccine initially have slight anaemias but they recover and have agglutinating antibodies. On challenge, DNA-vaccinated fish have lower parasitaemias, delayed peak parasitaemias and faster recoveries. Isometamidium chloride is therapeutic against the pathogen and its effectiveness is increased after conjugation to antibodies. PMID:20052385

  9. Gill diseases of cultured salmonids in Ontario.

    PubMed Central

    Daoust, P Y; Ferguson, H W

    1983-01-01

    Between 1977 and 1981, the Fish Pathology Laboratory of the Ontario Veterinary College received 239 cases from trout farms of southern Ontario, 51 (21.3%) of which had diseased gills. Branchial lesions in 86.3% of these 51 cases were characterized by marked lamellar epithelial hyperplasia with epithelial hypertrophy and lamellar fusion. Filamentous bacteria were seen on the surface of the branchial filaments and lamellae in 68.6% of the cases. Our observations highlight the importance of gill diseases as a production problem of farmed salmonids in southern Ontario. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 8. Fig. 9. PMID:6416657

  10. Glochidiosis of salmonid fishes. IV. Humoral and tissue responses of coho and chinook salmon to experimental infection with Margaritefera Margaritifera (L. ) (Pelecypoda: Margaritanidae)

    SciTech Connect

    Meyers, T.R.; Millemann, R.E.; Fustish, C.A.

    1980-01-01

    Coho salmon (Oncorhynchus kisutch) are more resistant than chinook salmon (O. tshawytscha) to experimental infection with the glochidia of the freshwater mussel Margaritifera margaritifera. Histological sections of gills from coho salmon 16 hr postinfection (p.i.) showed that parasite encystment either did not occur or had progressed incompletely, which accounted for the loss of many glochidia from the gills. The remaining encysted glochidia were sloughed within 2 days (p.i.) by a well-developed hyperplasia. On chinook salmon, the parasites developed normally with no sloughing or hyperplasia. Analysis of blood samples taken from coho salmon at intervals during the infection showed significant increases in hematocrit, hemoglobin, the mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and leukocyte numbers when compared with control fish. In infected chinook salmon only the hematocrit, erythrocyte numbers, and MCV increased while the MCHC decreased. Total plasma protein increased in coho salmon but decreased in chinook salmon during infection. Glochidial antibodies were demonstrated in the blood plasma of coho and chinook salmon 8 to 12 wk p.i. Fewer glochidia attached to the excised gills of coho salmon than to the gills of chinook salmon. Also, the in vitro survival time of parasites in mucus and plasma from coho salmon was less than in the same chinook salmon fluids.

  11. Vaccine Adjuvants in Fish Vaccines Make a Difference: Comparing Three Adjuvants (Montanide ISA763A Oil, CpG/Poly I:C Combo and VHSV Glycoprotein) Alone or in Combination Formulated with an Inactivated Whole Salmonid Alphavirus Antigen.

    PubMed

    Thim, Hanna L; Villoing, Stéphane; McLoughlin, Marian; Christie, Karen Elina; Grove, Søren; Frost, Petter; Jørgensen, Jorunn B

    2014-01-01

    Most commercial vaccines offered to the aquaculture industry include inactivated antigens (Ag) formulated in oil adjuvants. Safety concerns are related to the use of oil adjuvants in multivalent vaccines for fish, since adverse side effects (e.g., adhesions) can appear. Therefore, there is a request for vaccine formulations for which protection will be maintained or improved, while the risk of side effects is reduced. Here, by using an inactivated salmonid alphavirus (SAV) as the test Ag, the combined use of two Toll-like receptor (TLR) ligand adjuvants, CpG oligonucleotides (ODNs) and poly I:C, as well as a genetic adjuvant consisting of a DNA plasmid vector expressing the viral haemorrhagic septicaemia virus (VHSV) glycoprotein (G) was explored. VHSV-G DNA vaccine was intramuscularly injected in combination with intraperitoneal injection of either SAV Ag alone or combined with the oil adjuvant, Montanide ISA763, or the CpG/polyI:C combo. Adjuvant formulations were evaluated for their ability to boost immune responses and induce protection against SAV in Atlantic salmon, following cohabitation challenge. It was observed that CpG/polyI:C-based formulations generated the highest neutralizing antibody titres (nAbs) before challenge, which endured post challenge. nAb responses for VHSV G-DNA- and oil-adjuvanted formulations were marginal compared to the CpG/poly I:C treatment. Interestingly, heat-inactivated sera showed reduced nAb titres compared to their non-heated counterparts, which suggests a role of complement-mediated neutralization against SAV. Consistently elevated levels of innate antiviral immune genes in the CpG/polyI:C injected groups suggested a role of IFN-mediated responses. Co-delivery of the VHSV-G DNA construct with either CpG/polyI:C or oil-adjuvanted SAV vaccine generated higher CD4 responses in head kidney at 48 h compared to injection of this vector or SAV Ag alone. The results demonstrate that a combination of pattern recognizing receptor (PRR

  12. Osmoregulatory actions of the GH/IGF axis in non-salmonid teleosts

    USGS Publications Warehouse

    Mancera, J.M.; McCormick, S.D.

    1998-01-01

    Salmonid fishes provided the first findings on the influence of the growth hormone (GH)/insulin-like growth factor I (IGF-I) axis on osmoregulation in teleost fishes. Recent studies on non-salmonid species, however, indicate that this physiological action of the GH/IGF-I axis is not restricted to salmonids or anadromous fishes. GH-producing cells in the pituitary of fish acclimated to different salinities show different degrees of activation depending on the species studied. Plasma GH levels either increase or do not change after transfer of fish from freshwater to seawater. Treatment with GH or IGF-I increases salinity tolerance and/or increases gill Na+,K+-ATPase activity of killifish (Fundulus heteroclitus), tilapia (Oreochromis mossambicus and Oreochromis niloticus) and striped bass (Morone saxatilis). As in salmonids, a positive interaction between GH and cortisol for improving hypoosmoregulatory capacity has been described in tilapia (O. mossambicus). Research on the osmoregulatory role of the GH/IGF-I axis is derived from a small number of teleost species. The study of more species with different osmoregulary patterns will be necessary to fully clarify the osmoregulatory role of GH/IGF-I axis in fish. The available data does suggest, however, that the influence of the GH/IGF-I axis on osmoregulation may be a common feature of euryhalinity in teleosts. Copyright (C) 1998 Elsevier Science Inc.

  13. Fish mycobacteriosis (Tuberculosis)

    USGS Publications Warehouse

    Parisot, T.J.; Wood, J.W.

    1959-01-01

    The etiologic agent for the bacterial disease, "fish tuberculosis" (more correctly "mycobacteriosis"), was first observed in carp in 189& from a pond in France. Subsequently similar agents have been isolated from or observed in fish in fresh water, salt water, and brackish water, in fish in aquaria, hatcheries, and natural habitat~ (wild populations of fish). The disease has been recognized as an important infection among hatchery reared salmonid fishes on the West Coast of the United States, and in aquarium fishes such as the neon tetra, the Siamese fighting fish, and in salt water fish held in zoological displays.

  14. Prevention and control of viral diseases of salmonids

    USGS Publications Warehouse

    Amend, Donald F.

    1976-01-01

    Three viral diseases of salmonids are of worldwide concern: infectious pancreatic necrosis (IPN) viral hemorrhagic septicemia (VHS), and infectious hematopoietic necrosis (IHN). Six principal approaches are being used to prevent or control these diseases: 1) preventing contact o the pathogen with the host, 2) environmental manipulation, 3) immunization, 4) chemotherapy, 5 selective breeding for disease resistance, and 6) reducing stress conditions which augment disease conditions. Preventing the introduction of a pathogen into a new stock of fish has been accomplished mainly by implementing stringent laws to prevent transport of infected fish into uninfected areas. Stocks of fish already infected are sometimes destroyed, and the hatchery is disinfected and restocked with fish free of specific pathogens. Environmental manipulation (elevated water temperature) has been successfully used to control IHN. Chemotherapeutics such as povidone-iodine for IPN and benzipyrene for IHN show promise of controlling mortalities; however, the practicality of using these drugs to eliminate the carrier fish has not been evaluated. Salmonids are capable of developing immune responses to viruses; however, development of effective vaccines, selective breeding for disease resistance, and identification of stress conditions which augment disease are still in the experimental phase.

  15. Assessing Success of Instream Structures for Salmonid Stream Restoration

    NASA Astrophysics Data System (ADS)

    Whiteway, S.; Biron, P.

    2009-05-01

    Stream restoration is a billion dollar industry in North America; despite this expenditure there remain questions regarding the effectiveness of current techniques such as the installation of instream structures. Assessing the effect that such structures have on physical habitat and on salmonid density are key ways of determining project success. The objectives of this research were to assess the impact of instream structures on physical habitat in the Nicolet River (Quebec) and to analyze physical habitat and fish density data from many stream restoration projects in North America. Results of intensive surveys of the Nicolet River show that the installation of weirs and deflectors results in a greater frequency of pools. These pools have significantly greater depths, lower velocities, larger sediment size and higher percent cover than those without structures. Meta analysis of data from 187 stream restoration projects in North America also show significant increases in percent pool area, average depth, and percent cover as well as decreases in channel width following the installation of structures. The physical changes observed in the Nicolet River resulted in improved trout habitat, as measured by applying habitat preference curves, but uneven stocking practices and fishing pressure confounded attempts to verify differences in trout density based on presence or absence of structures. The meta analysis, however, shows significant increases in salmonid density, measured as fish/m2, following the installation of structures. On average, density increased by 161%. Different structure types result in significantly different changes in physical habitat, with weir structures providing the largest density increase. Multiple linear regression analysis reveals that the combination of change in relative pool area and in width is the best predictor of change in salmonid density (r2=0.511). Instream structures are significantly more successful at increasing brook trout density

  16. Cryptobia (Trypanoplasma) salmositica and salmonid cryptobiosis.

    PubMed

    Woo, P T K

    2003-01-01

    Salmonid cryptobiosis is caused by Cryptobia (Trypanoplasma) salmositica. The haemoflagellate has been reported from all species of Pacific Oncorhynchus spp. on the west coast of North America. It is normally transmitted by the freshwater leech, Piscicola salmositica, in streams and rivers, and sculpins, Cottus spp., are considered important reservoir hosts. The pathogen can also survive on the body surface of fish because it has a contractile vacuole to osmoregulate when the fish is in fresh water. This allows for direct transmission between fish, especially in aquaculture facilities. The parasite divides rapidly by binary fission in the blood to cause disease, the severity of which is directly related to parasitaemia. Cryptobia salmositica has a mitochondrium and it normally undergoes aerobic respiration; however, if its mitochondrium is damaged it will switch to glycolysis. Its glycolytic enzymes and catalase are contained in glycosomes. Cysteine protease is a metabolic enzyme, and its neutralization inhibits oxygen consumption and multiplication of the parasite. An important virulent factor in cryptobiosis is a secretory metalloprotease. The protective mechanism involves production of complement fixing antibodies, phagocytosis by macrophages, and cell-mediated cytotoxicity. Recovered fish are protected, probably for life as the immunity is non-sterile. Clinical signs of the disease include anaemia, anorexia, splenomegaly, general oedema and abdominal distension with ascites. The metabolism and swimming performance of infected fish are significantly reduced and the bioenergetic cost of the disease is very considerable. Fish are susceptible to hypoxia and their immune system is depressed during acute cryptobiosis. Severity of the disease and mortality rates vary significantly between species and stocks of salmon. Protective strategies include selective breeding of Cryptobia-resistant fish. This is innate resistance to infection and it is controlled by a dominant

  17. Grande Ronde Basin Fish Habitat Enhancement Project : 1998 Annual Report.

    SciTech Connect

    McGowan, Vance R.; Powell, Russ M.

    1999-05-01

    The primary goal of ''The Grande Ronde Basin Fish Habitat Improvement Project'' is to access, create, improve, protect, and restore reparian and instream habitat for anadromous salmonids, thereby maximizing opportunities for natural fish production within the basin.

  18. Minimally Invasive Detection of Piscirickettsia salmonis in Cultivated Salmonids via the PCR

    PubMed Central

    Marshall, Sergio; Heath, Sekou; Henríquez, Vitalia; Orrego, Cristián

    1998-01-01

    The attributes of the PCR allowed implementation of an assay for specific detection of Piscirickettsia salmonis from a few microliters of fish serum. This opens the way to less invasive modes of sampling for this microbial pathogen in salmonids. PMID:9687475

  19. Avian Predation on Juvenile Salmonids in the Lower Columbia River: 1997 Annual Report.

    SciTech Connect

    Roby, Daniel D.; Craig, David P.; Collis, Ken; Adamany, Stephanie L.

    1998-09-01

    The authors initiated a field study in 1997 to assess the impacts of fish-eating colonial waterbirds (i.e., terns, cormorants, and gulls) on the survival of juvenile salmonids in the lower Columbia River. Here the authors present results from the 1998 breeding season, the second field season of work on this project. The research objectives in 1998 were to: (1) determine the location, size, nesting chronology, nesting success, and population trajectories of breeding colonies of fish-eating birds in the lower Columbia River; (2) determine diet composition of fish-eating birds, including taxonomic composition and energy content of various prey types; (3) estimate forage fish consumption rates, with special emphasis on juvenile salmonids, by breeding adults and their young; (4) determine the relative vulnerabilit2048 different groups of juvenile salmonids to bird predation; (5) identify foraging range, foraging strategies, and habitat utilization by piscivorous waterbirds; and (6) test the feasibility of various alternative methods for managing avian predation on juvenile salmonids and develop recommendations to reduce avian predation, if warranted by the results.

  20. Avian Predation on Juvenile Salmonids in the Lower Columbia River: 1998 Annual Report.

    SciTech Connect

    Collis, Ken; Adamany, Stephanie; Roby, Daniel D.; Craig, David P.; Lyons, Donald E.

    2000-04-01

    The authors initiated a field study in 1997 to assess the impacts of fish-eating colonial waterbirds (i.e., terns, cormorants, and gulls) on the survival of juvenile salmonids in the lower Columbia River. Here the authors present results from the 1998 breeding season, the second field season of work on this project. The research objectives in 1998 were to: (1) determine the location, size, nesting chronology, nesting success, and population trajectories of breeding colonies of fish-eating birds in the lower Columbia River; (2) determine diet composition of fish-eating birds, including taxonomic composition and energy content of various prey types; (3) estimate forage fish consumption rates, with special emphasis on juvenile salmonids, by breeding adults and their young; (4) determine the relative vulnerability of different groups of juvenile salmonids to bird predation; (5) identify foraging range, foraging strategies, and habitat utilization by piscivorous waterbirds; and (6) test the feasibility of various alternative methods for managing avian predation on juvenile salmonids and develop recommendations to reduce avian predation, if warranted by the results.

  1. Factors associated with the incidence of bacterial gill disease in salmonid lots reared in Ontario, Canada government hatcheries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial gill disease (BGD) (causative agent: Flavobacterium branchiophilum) has been a persistent problem in early-rearing salmonids in the Ontario Ministry of Natural Resources (OMNR) fish hatchery system. Retrospective epidemiological investigations of BGD diagnoses and treatments in OMNR fish h...

  2. Sublethal toxicity of chlorpyrifos to salmonid olfaction after hypersaline acclimation.

    PubMed

    Maryoung, Lindley A; Blunt, Brian; Tierney, Keith B; Schlenk, Daniel

    2015-04-01

    Salmonid habitats can be impacted by several environmental factors, such as salinization, which can also affect salmonid tolerance to anthropogenic stressors, such as pesticides. Previous studies have shown that hypersaline acclimation enhances the acute toxicity of certain organophosphate and carbamate pesticides to euryhaline fish; however, sublethal impacts have been far less studied. The current study aims to determine how hypersaline acclimation and exposure to the organophosphate chlorpyrifos (CPF) impact salmonid olfaction. Combined acclimation and exposure to CPF was shown to impact rainbow trout olfaction at the molecular, physiological, and behavioral levels. Concurrent exposure to hypersalinity and 0.5μg/L CPF upregulated four genes (chloride intracellular channel 4, G protein zgc:101761, calcium calmodulin dependent protein kinase II delta, and adrenergic alpha 2C receptor) that inhibit olfactory signal transduction. At the physiological level, hypersalinity and chlorpyrifos caused a decrease in sensory response to the amino acid l-serine and the bile salt taurocholic acid. Combined acclimation and exposure also negatively impacted behavior and reduced the avoidance of a predator cue (l-serine). Thus, acclimation to hypersaline conditions and exposure to environmentally relevant concentrations of chlorpyrifos caused an inhibition of olfactory signal transduction leading to a decreased response to odorants and impairment of olfactory mediated behaviors. PMID:25697678

  3. Virulence of Renibacterium salmoninarum to salmonids

    USGS Publications Warehouse

    Starliper, C.E.; Smith, D.R.; Shatzer, T.

    1997-01-01

    Virulence of Renibacterium salmoninarum isolates representing five origins was evaluated in eight salmonid hosts; four origins were of Lake Michigan and the fifth was of the Pacific Northwest. The species type strain, ATCC (American Type Culture Collection) 33209, was also included. Each isolate was grown in a kidney disease medium (KDM2) supplemented with 1 % ATCC 33209 culture metabolite; serial 10-fold dilutions were prepared, and groups of fish were challenged by intraperitoneal injection with 0.1 mL of each dilution. A 70-d observation period followed, and bacterial kidney disease (BKD) was diagnosed by the fluorescent antibody technique. Virulence of isolates was quantified as a dose lethal to 50% of fish (LD50) for each host–isolate challenge. In the first set of experiments, 23 isolates were used to challenge groups of brook trout Salvelinus fontinalis. The mean LD50 was 1.087 x 106 colony-forming units per milliliter (cfu/mL; SD = 2.022 x 106), and the LD50 values ranged from 8.457 x 106 to 2.227 x 104 cfu/mL. Analysis of variance to evaluate the effect of isolate origin on virulence in brook trout revealed no significant difference (F = 1.502; P = 0.243). Susceptibilities of the other salmonid hosts were evaluated by challenge with six isolates of R. salmoninarum representing each origin and the species type strain. For many of the host–isolate challenge combinations, time to death was highly dependent on the dilution (number of bacteria) injected. In general, the isolates MCO4M, B26, and A34 (all of Lake Michigan origin) tended to be more virulent. Also, LD50 values were dispersed throughout a wider range among the more susceptible hosts. Lake trout Salvelinus namaycush, rainbow trout Oncorhynchus mykiss, and brook trout were relatively resistant to challenge with the strains, whereas coho salmon O. kisutch, domestic Atlantic salmon Saltno salar, and chinook salmon O. tshawytscha were relatively susceptible. Another challenge evaluated the effect of

  4. Salmon lice – impact on wild salmonids and salmon aquaculture

    PubMed Central

    Torrissen, O; Jones, S; Asche, F; Guttormsen, A; Skilbrei, O T; Nilsen, F; Horsberg, T E; Jackson, D

    2013-01-01

    Salmon lice, Lepeophtheirus salmonis, are naturally occurring parasites of salmon in sea water. Intensive salmon farming provides better conditions for parasite growth and transmission compared with natural conditions, creating problems for both the salmon farming industry and, under certain conditions, wild salmonids. Salmon lice originating from farms negatively impact wild stocks of salmonids, although the extent of the impact is a matter of debate. Estimates from Ireland and Norway indicate an odds ratio of 1.1:1-1.2:1 for sea lice treated Atlantic salmon smolt to survive sea migration compared to untreated smolts. This is considered to have a moderate population regulatory effect. The development of resistance against drugs most commonly used to treat salmon lice is a serious concern for both wild and farmed fish. Several large initiatives have been taken to encourage the development of new strategies, such as vaccines and novel drugs, for the treatment or removal of salmon lice from farmed fish. The newly sequenced salmon louse genome will be an important tool in this work. The use of cleaner fish has emerged as a robust method for controlling salmon lice, and aquaculture production of wrasse is important towards this aim. Salmon lice have large economic consequences for the salmon industry, both as direct costs for the prevention and treatment, but also indirectly through negative public opinion. PMID:23311858

  5. Incorporating spatial context into the analysis of salmonid habitat relations

    USGS Publications Warehouse

    Torgersen, Christian E.; Baxter, Colden V.; Ebersole, J.L.; Gresswell, Bob

    2012-01-01

    In this response to the chapter by Lapointe (this volume), we discuss the question of why it is so difficult to predict salmonid-habitat relations in gravel-bed rivers and streams. We acknowledge that this cannot be an exhaustive treatment of the subject and, thus, identify what we believe are several key issues that demonstrate the necessity of incorporating spatial context into the analysis of fish-habitat data. Our emphasis is on spatial context (i.e., scale and location), but it is important to note that the same principles may be applied with some modification to temporal context, which is beyond the scope of this chapter.

  6. Effects of Hatchery Rearing on the Structure and Function of Salmonid Mechanosensory Systems.

    PubMed

    Brown, Andrew D; Sisneros, Joseph A; Jurasin, Tyler; Coffin, Allison B

    2016-01-01

    This paper reviews recent studies on the effects of hatchery rearing on the auditory and lateral line systems of salmonid fishes. Major conclusions are that (1) hatchery-reared juveniles exhibit abnormal lateral line morphology (relative to wild-origin conspecifics), suggesting that the hatchery environment affects lateral line structure, perhaps due to differences in the hydrodynamic conditions of hatcheries versus natural rearing environments, and (2) hatchery-reared salmonids have a high proportion of abnormal otoliths, a condition associated with reduced auditory sensitivity and suggestive of inner ear dysfunction. PMID:26610951

  7. Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin; 1996 Annual Report.

    SciTech Connect

    Knapp, Suzanne M.; Kern, J. Chris; Carmichael, Richard W.

    1997-01-01

    This is the second year report of a multi-year project that monitors the outmigration and survival of hatchery and naturally-produced juvenile salmonids in the lower Umatilla River. This project supplements and complements ongoing or completed fisheries projects in the Umatilla River basin. Knowledge gained on outmigration and survival will assist researchers and managers in adapting hatchery practices, flow enhancement strategies, canal operations, and supplementation and enhancement efforts for natural and restored fish populations. The authors also report on tasks related to evaluating juvenile salmonid passage at Three Mile Falls Dam and West Extension Canal.

  8. Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin; 1995 Annual Report.

    SciTech Connect

    Knapp, Suzanne M.; Cameron, William A.; Shapleigh, Stacey L.

    1995-12-01

    This is the first year report of a multi-year project that monitors the outmigration and survival of hatchery and naturally produced juvenile salmonids in the lower Umatilla River. This project supplements and complements ongoing or completed fisheries projects in the Umatilla river basin. Knowledge gained on outmigration and survival will assist researchers and managers in adapting hatchery practices, flow enhancement strategies, canal operations, and supplementation and enhancement efforts for natural fish populations. This project also completed tasks related to evaluating juvenile salmonid passage at Three Mile Falls Dam and West Extension Canal.

  9. Vaccination against pancreas disease in Atlantic salmon, Salmo salar L., reduces shedding of salmonid alphavirus.

    PubMed

    Skjold, Pål; Sommerset, Ingunn; Frost, Petter; Villoing, Stephane

    2016-01-01

    Salmon pancreas disease virus, often referred to as salmonid alphavirus (SAV), causes pancreas disease (PD) in European salmonids. SAV transmits horizontally from fish shedding virus into the water and ocean currents are believed to be a main contributor of viral spread between marine farms. Vaccination against PD is previously shown to reduce mortality and severity of clinical PD. In this study, we demonstrate that vaccination against PD significantly reduces viral shedding from infected individuals. The results suggest that PD vaccination can be an important tool to reduce the infection pressure, a known key risk for PD outbreaks at neighbouring farms. PMID:27496170

  10. Piscine reovirus in wild and farmed salmonids in British Columbia, Canada: 1974-2013.

    PubMed

    Marty, G D; Morrison, D B; Bidulka, J; Joseph, T; Siah, A

    2015-08-01

    Piscine reovirus (PRV) was common among wild and farmed salmonids in British Columbia, western Canada, from 1987 to 2013. Salmonid tissues tested for PRV by real-time rRT-PCR included sections from archived paraffin blocks from 1974 to 2008 (n = 363) and fresh-frozen hearts from 2013 (n = 916). The earliest PRV-positive sample was from a wild-source steelhead trout, Oncorhynchus mykiss (Walbaum), from 1977. By histopathology (n = 404), no fish had lesions diagnostic for heart and skeletal muscle inflammation (HSMI). In some groups, lymphohistiocytic endocarditis affected a greater proportion of fish with PRV than fish without PRV, but the range of Ct values among affected fish was within the range of Ct values among unaffected fish. Also, fish with the lowest PRV Ct values (18.4-21.7) lacked endocarditis or any other consistent lesion. From 1987 to 1994, the proportion of PRV positives was not significantly different between farmed Atlantic salmon, Salmo salar L. (44% of 48), and wild-source salmonids (31% of 45). In 2013, the proportion of PRV positives was not significantly different between wild coho salmon, Oncorhynchus kisutch (Walbaum), sampled from British Columbia (5.0% of 60) or the reference region, Alaska, USA (10% of 58). PMID:25048977

  11. Modeling Food Delivery Dynamics For Juvenile Salmonids Under Variable Flow Regimes

    NASA Astrophysics Data System (ADS)

    Harrison, L.; Utz, R.; Anderson, K.; Nisbet, R.

    2010-12-01

    Traditional approaches for assessing instream flow needs for salmonids have typically focused on the importance of physical habitat in determining fish habitat selection. This somewhat simplistic approach does not account for differences in food delivery rates to salmonids that arise due to spatial variability in river morphology, hydraulics and temporal variations in the flow regime. Explicitly linking how changes in the flow regime influences food delivery dynamics is an important step in advancing process-based bioenergetic models that seek to predict growth rates of salmonids across various life-stages. Here we investigate how food delivery rates for juvenile salmonids vary both spatially and with flow magnitude in a meandering reach of the Merced River, CA. We utilize a two-dimensional (2D) hydrodynamic model and discrete particle tracking algorithm to simulate invertebrate drift transport rates at baseflow and a near-bankfull discharge. Modeling results indicate that at baseflow, the maximum drift density occurs in the channel thalweg, while drift densities decrease towards the channel margins due to the process of organisms settling out of the drift. During high-flow events, typical of spring dam-releases, the invertebrate drift transport pathway follows a similar trajectory along the high velocity core and the drift concentrations are greatest in the channel centerline, though the zone of invertebrate transport occupies a greater fraction of the channel width. Based on invertebrate supply rates alone, feeding juvenile salmonids would be expected to be distributed down the channel centerline where the maximum predicted food delivery rates are located in this reach. However, flow velocities in these channel sections are beyond maximum sustainable swimming speeds for most juvenile salmonids. Our preliminary findings suggest that a lack of low velocity refuge may prevent juvenile salmonids from deriving energy from the areas with maximum drift density in this

  12. Invasive salmonids and lake order interact in the decline of puye grande Galaxias platei in western Patagonia lakes.

    PubMed

    Correa, Cristian; Hendry, Andrew P

    2012-04-01

    Salmonid fishes, native to the northern hemisphere, have become naturalized in many austral countries and appear linked to the decline of native fishes, particularly galaxiids. However, a lack of baseline information and the potential for confounding anthropogenic stressors have led to uncertainty regarding the association between salmonid invasions and galaxiid declines, especially in lakes, as these have been much less studied than streams. We surveyed 25 lakes in the Aysén region of Chilean Patagonia, including both uninvaded and salmonid-invaded lakes. Abundance indices (AI) of Galaxias platei and salmonids (Salmo trutta and Oncorhynchus mykiss) were calculated using capture-per-unit-effort data from gillnets, minnow traps, and electrofishing. We also measured additional environmental variables, including deforestation, lake morphometrics, altitude, and hydrological position (i.e., lake order). An information-theoretic approach to explaining the AI of G. platei revealed that by far the strongest effect was a negative association with the AI of salmonids. Lake order was also important, and using structural equation modeling, we show that this is an indirect effect naturally constraining the salmonid invasion success in Patagonia. Supporting this conclusion, an analysis of an independent data set from 106 mountain lakes in western Canada showed that introduced salmonids are indeed less successful in low-order lakes. Reproductive failure due to insufficient spawning habitat and harsh environmental conditions could be the cause of these limits to salmonid success. The existence of this effect in Chilean Patagonia suggests that low-order lakes are likely to provide natural ecological refugia for G. platei. Finally, pristine, high-order lakes should be actively protected as these have become rare and irreplaceable unspoiled references of the most diverse, natural lake ecosystems in Patagonia. PMID:22645814

  13. Acute phase proteins in salmonids: evolutionary analyses and acute phase response.

    PubMed

    Jensen, L E; Hiney, M P; Shields, D C; Uhlar, C M; Lindsay, A J; Whitehead, A S

    1997-01-01

    Inflammation induces dramatic changes in the biosynthetic profile of the liver, leading to increased serum concentrations of positive acute phase (AP) proteins and decreased concentrations of negative AP proteins. Serum amyloid A (SAA) and the pentraxins C-reactive protein (CRP) and serum amyloid P component (SAP) are major AP proteins: their serum levels can rise by 1000-fold, indicating that they play a critical role in defense and/or the restoration of homeostasis. We have cloned SAA and a SAP-like pentraxin from salmonid fish species. The salmonid SAA shares approximately 70% amino acid identity with mammalian AP SAA. When salmonids are challenged with an AP stimulus, i.e., Aeromonas salmonicida, SAA responds dramatically as a major AP reactant. The salmonid pentraxin shows approximately 40% amino acid identity to both mammalian SAP and CRP. Evolutionary analysis suggests the presence of only a single such protein in teleosts and lower animal species. Surprisingly, the salmonid pentraxin behaves as a negative AP reactant, reminiscent of the SAP-like Syrian hamster female protein, in that hepatic mRNA concentrations decline to 50% of prestimulus levels. This study reinforces the hypothesis that SAA induction is an essential and universal feature of the vertebrate AP response and that it represents part of an ancient host defense system. Conversely, the species-dependent heterogeneity of pentraxin expression during the vertebrate AP response supports the possibility that its most important ancestral (and perhaps present) function is not related to its AP behavior. PMID:8977214

  14. Increased Levels of Harvest and Habitat Law Enforcement and Public Awareness for Anadromous Salmonids and Resident Fish in the Columbia River Basin -- Demonstration Period, 1992--1994, Final Report.

    SciTech Connect

    NeSmith, Frank; Long, Mack; Matthews, Dayne

    1995-06-01

    This report was funded by the Bonneville Power Administration (BPA), US Department of Energy, as part of BPA`s program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric facilities on the Columbia River and its tributaries. Illegal harvest and violation of habitat protection regulations are factors affecting the survival of many native species of anadromous and resident fish in the Columbia Basin.

  15. Predicting recolonization patterns and interactions between potamodromous and anadromous salmonids in response to dam removal in the Elwha River, Washington State, USA

    USGS Publications Warehouse

    Brenkman, S.J.; Pess, G.R.; Torgersen, C.E.; Kloehn, K.K.; Duda, J.J.; Corbett, S.C.

    2008-01-01

    The restoration of salmonids in the Elwha River following dam removal will cause interactions between anadromous and potamodromous forms as recolonization occurs in upstream and downstream directions. Anadromous salmonids are expected to recolonize historic habitats, and rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) isolated above the dams for 90 years are expected to reestablish anadromy. We summarized the distribution and abundance of potamodromous salmonids, determined locations of spawning areas, and mapped natural barriers to fish migration at the watershed scale based on data collected from 1993 to 2006. Rainbow trout were far more abundant than bull trout throughout the watershed and both species were distributed up to river km 71. Spawning locations for bull trout and rainbow trout occurred in areas where we anticipate returning anadromous fish to spawn. Nonnative brook trout were confined to areas between and below the dams, and seasonal velocity barriers are expected to prevent their upstream movements. We hypothesize that the extent of interaction between potamodromous and anadromous salmonids will vary spatially due to natural barriers that will limit upstream-directed recolonization for some species of salmonids. Consequently, most competitive interactions will occur in the main stem and floodplain downstream of river km 25 and in larger tributaries. Understanding future responses of Pacific salmonids after dam removal in the Elwha River depends upon an understanding of existing conditions of the salmonid community upstream of the dams prior to dam removal.

  16. Transporting juvenile salmonids around dams impairs adult migration.

    PubMed

    Keefer, Matthew L; Caudill, Christopher C; Peery, Christopher A; Lee, Steven R

    2008-12-01

    Mitigation and ecosystem-restoration efforts may have unintended consequences on both target and nontarget populations. Important effects can be displaced in space and time, making them difficult to detect without monitoring at appropriate scales. Here, we examined the effects of a mitigation program for juvenile salmonids on subsequent adult migration behaviors and survival. Juvenile chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) were collected and uniquely tagged with passive integrated transponder (PIT) tags at Lower Granite Dam (Washington State, USA) on the Snake River and were then either transported downstream in barges in an effort to reduce out-migration mortality or returned to the river as a control group. Returning adults were collected and radio-tagged at Bonneville Dam (Washington-Oregon, USA) on the Columbia River 1-3 years later and then monitored during approximately 460 km of their homing migrations. The proportion of adults successfully homing was significantly lower, and unaccounted loss and permanent straying into non-natal rivers was higher, for barged fish of both species. On average, barged fish homed to Lower Granite Dam at rates about 10% lower than for in-river migrants. Barged fish were also 1.7-3.4 times more likely than in-river fish to fall back downstream past dams as adults, a behavior strongly associated with lower survival. These results suggest that juvenile transport impaired adult orientation or homing abilities, perhaps by disrupting sequential imprinting processes during juvenile out-migration. While juvenile transportation has clear short-term juvenile-survival benefits, the delayed effects that manifest in adult stages illustrate the need to assess mitigation success throughout the life cycle of target organisms, i.e., the use of fitness-based measures. In the case of Snake River salmonids listed under the Endangered Species Act, the increased straying and potential associated genetic and demographic

  17. Histology of salmonid testes during maturation.

    PubMed

    Dziewulska, Katarzyna; Domagała, Józef

    2003-03-01

    the cells completed spermatogenesis. At the end of maturation, vacuoles, up to 18.9 microm in final diameter (brown trout), appeared in the Sertoli cells. The vacuoles were visible in the lobule wall epithelium for a prolonged period of time. In most salmonid individuals examined, the reproductive cycles were observed to overlap. In some fish, the preparation for another cycle began very early, i.e., at the and of preceding spermatogenesis, which had not been observed before. Gonad maturation in some males was incomplete. PMID:14666143

  18. Weirs: Counting and sampling adult salmonids in streams and rivers

    USGS Publications Warehouse

    Zimmerman, Christian E.; Zabkar, Laura M.

    2007-01-01

    Weirs—which function as porous barriers built across stream—have long been used to capture migrating fish in flowing waters. For example, the Netsilik peoples of northern Canada used V-shaped weirs constructed of river rocks gathered onsite to capture migrating Arctic char Salvelinus alpinus (Balikci 1970). Similarly, fences constructed of stakes and a latticework of willow branches or staves were used by Native Americans to capture migrating salmon in streams along the West Coast of North America (Stewart 1994). In modern times, weirs have also been used in terminal fisheries and to capture brood fish for use in fish culture. Weirs have been used to gather data on age structure, condition, sex ratio, spawning escapement, abundance, and migratory patterns of fish in streams. One of the critical elements of fisheries management and stock assessment of salmonids is a count of adult fish returning to spawn. Weirs are frequently used to capture or count fish to determine status and trends of populations or direct inseason management of fisheries; generally, weirs are the standard against which other techniques are measured. To evaluate fishery management actions, the number of fish escaping to spawn is often compared to river-specific target spawning requirements (O’Connell and Dempson 1995). A critical factor in these analyses is the determination of total run size (O’Connell 2003). O’Connell compared methods of run-size estimation against absolute counts from a rigid weir and concluded that, given the uncertainty of estimators, the absolute counts obtained at the weir wer significantly better than modeled estimates, which deviated as much as 50–60% from actual counts. The use of weirs is generally restricted to streams and small rivers because of construction expense, formation of navigation barriers, and the tendency of weirs to clog with debris, which can cause flooding and collapse of the structure (Hubert 1996). When feasible, however, weirs are

  19. Predicted redistribution of Ceratomyxa shasta genotypes with salmonid passage in the Deschutes River, Oregon.

    PubMed

    Stinson, Matthew E T; Bartholomew, Jerri L

    2012-12-01

    A series of dams on the Deschutes River, Oregon, act as migration barriers that segregate the river system into upper and lower basins. Proposed fish passage between basins would reunite populations of native potamodromous fish and allow anadromous fish of Deschutes River origin access to the upper basin. We assessed the potential redistribution of host-species-specific genotypes (O, I, II, III) of the myxozoan parasite Ceratomyxa shasta that could occur with fish passage and examined the influence of nonnative fish on genotype composition. To determine the present distribution of the parasite genotypes, we exposed eight salmonid species-three native and five stocked for sport fishing-in present and predicted anadromous salmonid habitats. We monitored fish for infection by C. shasta and sequenced a section of the parasite ribosomal DNA gene from fish and water samples to determine parasite genotype. Genotype O was present in both upper and lower basins and detected only in steelhead Oncorhynchus mykiss. Genotype I was spatially limited to the lower basin, isolated predominantly from Chinook salmon O. tshawytscha, and lethal for this species only. Genotype II was detected in both basins and in multiple species, but only as a minor component of the infection. Genotype III was also present in both basins, had a wide host range, and caused mortality in native steelhead and multiple nonnative species. Atlantic salmon Salmo salar and kokanee O. nerka were the least susceptible to infection by any genotype of C. shasta. Our findings confirmed the host-specific patterns of C. shasta infections and indicated that passage of Chinook salmon would probably spread genotype I into the upper Deschutes River basin, but with little risk to native salmonid populations. PMID:23146111

  20. Feeding response by northern squawfish to a hatchery release of juvenile salmonids in the Clearwater River, Idaho

    USGS Publications Warehouse

    Shively, R.S.; Poe, T.P.; Sauter, S.T.

    1996-01-01

    We collected gut contents from northern squawfish Ptychocheilus oregonensis captured in the Clearwater River, Idaho, 0–6 km from its confluence with the Snake River, following the release of 1.1 million yearling chinook salmon Oncorhynchus tshawytscha from the Dworshak National Fish Hatchery. Before the hatchery release, northern squawfish gut contents (by weight) in the study area were 38% crayfish Pacifastacus spp., 26% insects, 19% nonsalmonid fish, and 16% wheat kernels Triticum spp. Juvenile salmonids constituted 54% of gut contents about 24 h after the hatchery release, 78% after 5 d, and 86% after 7 d. The mean number of salmonids per gut (1.2) after release was higher than typically seen in guts from northern squawfish collected in mid-reservoir areas away from hydroelectric dams on the Snake and Columbia rivers. Length-frequency distributions of juvenile salmonids eaten and those captured in a scoop trap 4 km upstream of the study area indicated that northern squawfish were selectively feeding on the smaller individuals. We attribute the high rates of predation in the study area to the artificially high density of juvenile salmonids resulting from the hatchery release and to the physical characteristics of the study area in which the river changed from free flowing to impounded. Our results suggest that northern squawfish can quickly exploit hatchery releases of juvenile salmonids away from release sites in the Columbia River basin.

  1. Assessment of Salmonids and their Habitat Conditions in the Walla Walla River Basin within Washington, 2001 Annual Report.

    SciTech Connect

    Mendel, Glen Wesley; Trump, Jeremy; Karl, David

    2002-12-01

    Concerns about the decline of native salmon and trout populations have increased among natural resource managers and the public in recent years. As a result, a multitude of initiatives have been implemented at the local, state, and federal government levels. These initiatives include management plans and actions intended to protect and restore salmonid fishes and their habitats. In 1998 bull trout (Salvelinus confluentus) were listed under the Endangered Species Act (ESA), as ''Threatened'', for the Walla Walla River and its tributaries. Steelhead (Oncorhynchus mykiss) were listed as ''Threatened'' in 1999 for the mid-Columbia River and its tributaries. These ESA listings emphasize the need for information about these threatened salmonid populations and their habitats. The Washington Department of Fish and Wildlife (WDFW) is entrusted with ''the preservation, protection, and perpetuation of fish and wildlife....[and to] maximize public recreational or commercial opportunities without impairing the supply of fish and wildlife (WAC 77.12.010).'' In consideration of this mandate, the WDFW submitted a proposal in December 1997 to the Bonneville Power Administration (BPA) for a study to assess salmonid distribution, relative abundance, genetics, and the condition of salmonid habitats in the Walla Walla River basin. The primary purposes of this project are to collect baseline biological and habitat data, to identify major data gaps, and to draw conclusions whenever possible. The study reported herein details the findings of the 2001 field season (March to November, 2001).

  2. A prospective matched nested case-control study of bacterial gill disease outbreaks in Ontario, Canada government salmonid hatcheries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Early-rearing salmonids in Ontario, Canada government fish hatcheries have been persistently affected by bacterial gill disease (BGD), and outbreaks at these locations have often been associated with high morbidity and mortality. The causative agent of BGD, Flavobacterium branchiophilum, is consider...

  3. Predicting the Total Abundance of Resident Salmonids within the Willamette River Basin, Oregon - a Macroecological Modeling Approach

    EPA Science Inventory

    I present a simple, macroecological model of fish abundance that was used to estimate the total number of non-migratory salmonids within the Willamette River Basin (western Oregon). The model begins with empirical point estimates of net primary production (NPP in g C/m2) in fore...

  4. Rearing unit-level factors associated with bacterial gill disease treatment in two Ontario, Canada government salmonid hatcheries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Early-rearing salmonids in Ontario Ministry of Natural Resources (OMNR)fish hatcheries have been consistently affected by bacterial gill disease (BGD)(causative agent: Flavobacterium branchiophilum) for many years. Separate retrospective epidemiological investigations of BGD treatments at two OMNR f...

  5. Adsorption to fish sperm of vertically transmitted fish viruses

    USGS Publications Warehouse

    Mulcahy, D.; Pascho, R.J.

    1984-01-01

    More than 99 percent of a vertically transmitted fish rhabdovirus, infectious hematopoietic necrosis virus, was removed from suspension in less than 1 minute by adsorption to the surface membrane of sperm from two genera of salmonid fishes. The vertically transmitted, infectious pancreatic necrosis virus adsorbed to a lesser degree, but no adsorption occurred with a second fish rhabdovirus that is not vertically transmitted. Such adsorption may be involved in vertical transmission of these viruses.

  6. Tolerance of developing salmonid eggs and fry to nitrate exposure

    USGS Publications Warehouse

    Kincheloe, John W.; Wedemeyer, Gary A.; Koch, David L.

    1979-01-01

    This paper reports on tests which show significant effects on early salmonid life stages of nitrates at levels commonly found in groundwaters in geographical areas that are influenced by fertilizer application. It has long been known, from fish cultural experience, that in certain site specific locations, chronic problems can be expected with salmonid egg development and early fry mortality. However, fingerlings which survive usually grow normally. A complete explanation is lacking although several environmental factors have been proposed to account for this phenomenon. One, which has so far received little attention, is that nitrate levels in the ground and surface waters of many areas have been increasing significantly over historical background levels. Ammonia, urea, and other potential sources of nitrate can enter natural waters from a variety of sources, such as domestic or industrial sewage, animal feedlots, or seepage and return flows from agricultural lands. The latter may be the largest contributor, since billions of tons of nitrate fertilizers are applied to agricultural crops on a worldwide basis each year. In addition, intensive forest management techniques include the aerial application of nitrate fertilizer to increase the yield of wood products, while range management practices call for use of nitrates to increase forage production. The nitrate that is not taken up by plants ultimately appears in ground or surface waters.

  7. Influences of Stocking Salmon Carcass Analogs on Salmonids in Klickitat River Tributaries, 2001-2005 Completion Report.

    SciTech Connect

    Zendt, Joe; Sharp, Bill

    2006-09-01

    This report describes the work completed by the Yakama Nation Fisheries Program (YNFP) in the Klickitat subbasin in south-central Washington under BPA innovative project No.200105500--Influences of stocking salmon carcass analogs on salmonids in Columbia River Tributaries. Salmon carcasses historically provided a significant source of marine-derived nutrients to many stream systems in the Columbia basin, and decreased run sizes have led to a loss of this nutrient source in many streams. Partners in this project developed a pathogen-free carcass analog and stocked the analogs in streams with the following objectives: restoring food availability to streams with reduced anadromous salmon returns; mimicking the natural pathways and timing of food acquisition by salmonids; minimizing unintended negative ecological effects; and increasing the growth and survival of salmonids. In the Klickitat subbasin, carcass analogs were stocked in two streams in 2002 and 2003; a third stream was used as a control. Salmonid fish abundance, growth, and stomach contents were monitored in all three streams before and after carcass analog placement. Fish, invertebrate, and periphyton samples were also collected for stable isotope analysis (to determine if nutrients from carcass analogs were incorporated into the stream food web). Water quality samples were also collected to determine if nutrient overloading occurred in streams. Significant differences in growth were found between fish in treated and untreated stream reaches. Fish in treatment reaches exhibited higher instantaneous growth rates approximately one month after the first carcass analog stocking. Stomach contents sampling indicated that salmonid fish routinely consumed the carcass analog material directly, and that stomach fullness of fish in treatment reaches was higher than in untreated reaches in the first few weeks following carcass analog stockings. No significant differences were detected in fish abundance between

  8. Gas Bubble Trauma Monitoring and Research of Juvenile Salmonids, 1994-1995 Progress Report.

    SciTech Connect

    Hans, Karen M.

    1997-07-01

    This report describes laboratory and field monitoring studies of gas bubble trauma (GBT) in migrating juvenile salmonids in the Snake and Columbia rivers. The first chapter describes laboratory studies of the progression of GBT signs leading to mortality and the use of the signs for GBT assessment. The progression and severity of GBT signs in juvenile salmonids exposed to different levels of total dissolved gas (TDG) and temperatures was assessed and quantified. Next, the prevalence, severity, and individual variation of GBT signs was evaluated to attempt to relate them to mortality. Finally, methods for gill examination in fish exposed to high TDG were developed and evaluated. Primary findings were: (1) no single sign of GBT was clearly correlated with mortality, but many GBT signs progressively worsened; (2) both prevalence and severity of GBT signs in several tissues is necessary; (3) bubbles in the lateral line were the earliest sign of GBT, showed progressive worsening, and had low individual variation but may develop poorly during chronic exposures; (4) fin bubbles had high prevalence, progressively worsened, and may be a persistent sign of GBT; and (5) gill bubbles appear to be the proximate cause of death but may only be relevant at high TDG levels and are difficult to examine. Chapter Two describes monitoring results of juvenile salmonids for signs of GBT. Emigrating fish were collected and examined for bubbles in fins and lateral lines. Preliminary findings were: (1) few fish had signs of GBT, but prevalence and severity appeared to increase as fish migrated downstream; (2) there was no apparent correlation between GBT signs in the fins, lateral line, or gills; (3) prevalence and severity of GBT was suggestive of long-term, non-lethal exposure to relatively low level gas supersaturated water; and (4) it appeared that GBT was not a threat to migrating juvenile salmonids. 24 refs., 26 figs., 3 tabs.

  9. Impact of Beaver Dams on Abundance and Distribution of Anadromous Salmonids in Two Lowland Streams in Lithuania

    PubMed Central

    Virbickas, Tomas; Stakėnas, Saulius; Steponėnas, Andrius

    2015-01-01

    European beaver dams impeded movements of anadromous salmonids as it was established by fishing survey, fish tagging and redd counts in two lowland streams in Lithuania. Significant differences in abundancies of other litophilic fish species and evenness of representation by species in the community were detected upstream and downstream of the beaver dams. Sea trout parr marked with RFID tags passed through several successive beaver dams in upstream direction, but no tagged fish were detected above the uppermost dam. Increase in abundances of salmonid parr in the stream between the beaver dams and decrease below the dams were recorded in November, at the time of spawning of Atlantic salmon and sea trout, but no significant changes were detected in the sections upstream of the dams. After construction of several additional beaver dams in the downstream sections of the studied streams, abundance of Atlantic salmon parr downstream of the dams decreased considerably in comparison with that estimated before construction. PMID:25856377

  10. Impact of beaver dams on abundance and distribution of anadromous salmonids in two lowland streams in Lithuania.

    PubMed

    Virbickas, Tomas; Stakėnas, Saulius; Steponėnas, Andrius

    2015-01-01

    European beaver dams impeded movements of anadromous salmonids as it was established by fishing survey, fish tagging and redd counts in two lowland streams in Lithuania. Significant differences in abundancies of other litophilic fish species and evenness of representation by species in the community were detected upstream and downstream of the beaver dams. Sea trout parr marked with RFID tags passed through several successive beaver dams in upstream direction, but no tagged fish were detected above the uppermost dam. Increase in abundances of salmonid parr in the stream between the beaver dams and decrease below the dams were recorded in November, at the time of spawning of Atlantic salmon and sea trout, but no significant changes were detected in the sections upstream of the dams. After construction of several additional beaver dams in the downstream sections of the studied streams, abundance of Atlantic salmon parr downstream of the dams decreased considerably in comparison with that estimated before construction. PMID:25856377

  11. Virucidal activity of two Iodophors to salmonid viruses

    USGS Publications Warehouse

    Amend, Donald F.; Pietsch, John P.

    1972-01-01

    Wescodyne® and Betadine®, organic iodine complexes, were compared in vitro for virucidal activity against infectious hematopoietic necrosis (IHN), infectious pancreatic necrosis (IPN), and viral hemorrhagic septicemia (VHS) viruses. Both iodophors were about equally effective on all three viruses. Each iodophor completely destroyed IHN virus within 30 sec at 12 ppm iodine, and was not affected by water hardness. Virucidal activity, however, was reduced at pH levels above 8.0 and in the presence of organic matter. Wescodyne was also compared with seven disinfectants commonly used in fish hatcheries, for virucidal properties against IHN virus. Wescodyne and chlorine were the only disinfectants to completely destroy the virus. Either Wescodyne or Betadine would effectively destroy the salmonid viruses at less than 25 ppm iodine within 5 min in solutions near neutrality.

  12. Tradeoffs for Efficiently Passing Juvenile Salmonids through Bonneville Dam on the Lower Columbia River

    SciTech Connect

    Ploskey, Gene R.; Weiland, Mark A.; Kim, Jina

    2008-12-01

    We analyzed five years of route-specific fish-passage data acquired by fixed-aspect hydroacoustic sampling of juvenile salmonids passing downstream through Bonneville Dam. High passage effectiveness of surface-flow outlets relative to the spillway and turbines suggests that juvenile salmonids are preferentially selecting surface outlets over adjacent turbines. Seasonal estimates showed that median combined effectiveness of surface-flow outlets (7.8) was 7.1 times higher than that of the spillway (1.1) and 9.8 times higher than that of turbines (0.8). Islands prevent the spillway from attracting fish from either powerhouse, something that may occur at other projects. Regressions indicated that percent flow passing a specific route explained from 50 to 97% of fish-passage variation, and relations were useful for evaluating fish-passage alternatives. Fitted curves for surface-passage routes, including the sluiceway at Powerhouse 1 (B1) and Powerhouse 2 (B2) were much steeper at low percent low (2-15%) than were curves for the spillway or turbines. Regressions indicate that increasing surface-flow percentages of B1 flow from 1% to 10% could increase B1 sluiceway-passage efficiency from 40% to 83%. Increasing B2 flow to the B2 sluiceway from 4% to 15% could increase fish passage from 31% to 62%. Without spill, about 50% of fish passed by non-turbine routes.

  13. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

    PubMed Central

    Macqueen, Daniel J.; Johnston, Ian A.

    2014-01-01

    Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification. PMID:24452024

  14. Identifying when tagged fishes have been consumed by piscivorous predators: application of multivariate mixture models to movement parameters of telemetered fishes

    USGS Publications Warehouse

    Romine, Jason G.; Perry, Russell W.; Johnston, Samuel V.; Fitzer, Christopher W.; Pagliughi, Stephen W.; Blake, Aaron R.

    2013-01-01

    Mixture models proved valuable as a means to differentiate between salmonid smolts and predators that consumed salmonid smolts. However, successful application of this method requires that telemetered fishes and their predators exhibit measurable differences in movement behavior. Our approach is flexible, allows inclusion of multiple track statistics and improves upon rule-based manual classification methods.

  15. Invasion versus isolation: trade-offs in managing native salmonids with barriers to upstream movement.

    PubMed

    Fausch, Kurt D; Rieman, Bruce E; Dunham, Jason B; Young, Michael K; Peterson, Douglas P

    2009-08-01

    Conservation biologists often face the trade-off that increasing connectivity in fragmented landscapes to reduce extinction risk of native species can foster invasion by non-native species that enter via the corridors created, which can then increase extinction risk. This dilemma is acute for stream fishes, especially native salmonids, because their populations are frequently relegated to fragments of headwater habitat threatened by invasion from downstream by 3 cosmopolitan non-native salmonids. Managers often block these upstream invasions with movement barriers, but isolation of native salmonids in small headwater streams can increase the threat of local extinction. We propose a conceptual framework to address this worldwide problem that focuses on 4 main questions. First, are populations of conservation value present (considering evolutionary legacies, ecological functions, and socioeconomic benefits as distinct values)? Second, are populations vulnerable to invasion and displacement by non-native salmonids? Third, would these populations be threatened with local extinction if isolated with barriers? And, fourth, how should management be prioritized among multiple populations? We also developed a conceptual model of the joint trade-off of invasion and isolation threats that considers the opportunities for managers to make strategic decisions. We illustrated use of this framework in an analysis of the invasion-isolation trade-off for native cutthroat trout (Oncorhynchus clarkii) in 2 contrasting basins in western North America where invasion and isolation are either present and strong or farther away and apparently weak. These cases demonstrate that decisions to install or remove barriers to conserve native salmonids are often complex and depend on conservation values, environmental context (which influences the threat of invasion and isolation), and additional socioeconomic factors. Explicit analysis with tools such as those we propose can help managers make

  16. Potential for dissemination of the nonnative salmonid parasite Myxobolus cerebralis in Alaska.

    PubMed

    Arsan, E Leyla; Bartholomew, Jerri L

    2008-09-01

    Myxobolus cerebralis, the myxozoan parasite responsible for whirling disease in salmonids, was first introduced into the United States in 1958 and has since spread across the country, causing severe declines in wild trout populations in the intermountain western United States. The recent detection of the parasite in Alaska is further evidence of the species' capability to invade and colonize new habitat. This study qualitatively assesses the risk of further spread and establishment of M. cerebralis in Alaska. We examine four potential routes of dissemination: human movement of fish, natural dispersal by salmonid predators and straying salmon, recreational activities, and commercial seafood processing. Potential for establishment was evaluated by examining water temperatures, spatial and temporal overlap of hosts, and the distribution and genetic composition of the oligochaete host, Tubifex tubifex. The most likely pathway of M. cerebralis transport in Alaska is human movement of fish by stocking. The extent of M. cerebralis infection in Alaskan salmonid populations is unknown, but if the parasite becomes dispersed, conditions are appropriate for establishment and propagation of the parasite life cycle in areas of south-central Alaska. The probability of further establishment is greatest in Ship Creek, where the abundance of susceptible T. tubifex, the presence of susceptible rainbow trout Oncorhynchus mykiss, and the proximity of this system to the known area of infection make conditions particularly suitable for spread of the parasite. PMID:18942590

  17. Effect of Total Dissolved Solids on Fertilization and Development of Two Salmonid Species.

    PubMed

    Baker, Josh A; Elphick, James R; McPherson, Cathy A; Chapman, Peter M

    2015-10-01

    Some studies have shown that the early life stages of salmonids are particularly sensitive to elevated concentrations of total dissolved solids (TDS). We evaluated the effect of TDS released in treated effluent into Snap Lake (Northwest Territories, Canada) by the Snap Lake Diamond Mine on two salmonids native to Snap Lake: Salvenius namaycush (lake trout) and Thymallus arcticus (Arctic grayling). Exposures encompassed the embryo-alevin-fry early life stages and extended to 142 days for lake trout and 69 days for Arctic grayling. Such extended testing is uncommon with these two species. Two exposures were conducted with each species, one initiated prior to fertilization, and the other subsequent to fertilization. Fertilization, survival, and growth were not adversely affected for either species by TDS at concentrations >1400 mg/L, with the exception of survival of lake trout, which produced an LC20 of 991 mg/L in one test, and >1484 mg/L in the second test. For the specific TDS composition tested, which was dominated by chloride (45 %-47 %) and calcium (20 %-21 %), the early life stages of these two fish species were relatively insensitive. Although some authors have suggested lower TDS regulatory limits for salmonid early life stages, our study indicates that this is not necessary, at least for these two fish species and for the specific ionic composition tested. PMID:26134075

  18. Lake Michigan: effects of exploitation, introductions, and eutrophication on the salmonid community

    USGS Publications Warehouse

    Wells, LaRue; McLain, Alberton L.

    1972-01-01

    Lake Michigan surface area is 22,400 square miles and its main depth is 276 ft. Its fauna is generally typical of North American oligotrophic lakes. The original fish populations included 10 coregonines and one salmonine. The lake whitefish, the lake herring, and the lake trout were most abundant. Man's activities have caused great changes in the lake in the past 120 years. Although changes in water chemistry and in the lower biota have been generally modest (except locally), those in salmonid communities have been vast. Exploitation, exotic fish species (especially the sea lamprey and alewife), and accelerated eutrophication and other pollution, all have played a role in bringing about the modifications (mostly marked declines in abundance) in salmonid communities. Commercial exploitation was largely responsible for the changes in the salmonid communities before the invasion of the lamprey (1936), although eutrophication and other pollution, and alterations of spawning streams, also were important. The lamprey and alewife (first reported in 1949), however, have exerted a greater impact than the other factors in recent decades.

  19. Sluiceway Operations to Pass Juvenile Salmonids at The Dalles Dam, Columbia River, USA

    SciTech Connect

    Johnson, Gary E.; Khan, Fenton; Skalski, J. R.; Klatte, Bernard A.

    2013-11-20

    Existing ice and trash sluiceways are commonly used to pass juvenile salmonids downstream at hydropower dams through a benign, non-turbine route. At The Dalles Dam on the Columbia River, managers undertook optimizing operations of sluiceway weirs to maximize survival of juvenile salmonids at the powerhouse. We applied fixed-location hydroacoustic methods to compare fish passage rates and sluiceway efficiencies for two weir configurations during 2004 and 2005: three weirs versus six weirs, located at the mid- versus east powerhouse, respectively. We also analyzed horizontal distributions of passage at the sluiceway and turbines and the effects of operating turbines beneath open sluiceway gates to provide supporting data relevant to operations optimization. Based on the findings, we recommend the following for long-term operations for the sluiceway at The Dalles Dam: open six rather than three sluiceway weirs to take advantage of the maximum hydraulic capacity of the sluiceway; open the three weirs above the western-most operating main turbine unit (MU) and the three weirs at MU 8 where turbine passage rates are relatively high; operate the turbine units below open sluiceway weirs as a standard procedure; operate the sluiceway 24 h/d year-round to maximize its benefits to juvenile salmonids; and use the same operations for spring and summer emigrants. These operational concepts are transferable to dams where sluiceway surface flow outlets are used protect downstream migrating fishes.

  20. Efficacy of passive sand filtration in reducing exposure of salmonids to the actinospore of Myxobolus cerebralis.

    PubMed

    Nehring, R Barry; Thompson, Kevin G; Taurman, Karen; Atkinson, William

    2003-12-01

    The aquatic oligochaete Tubifex tubifex parasitized by Myxobolus cerebralis releases triactinomyxon (TAM) actinospores that can infect some species of salmonids and cause salmonid whirling disease. Silica sand was tested as a filtration medium for removal of TAMs from water containing the parasite. Laboratory tests indicated sand filtration removed > 99.99% of TAMs. In 2 different field tests, groups of 1 mo old rainbow trout Oncorhynchus mykiss were exposed for 2 wk to filtered and unfiltered water from a spring-fed pond enzootic for M. cerebralis. In November 2000, the exposure dose was estimated as between 3 and 5 TAMs fish(-1). During a March 2001 exposure, the estimated dose was between 286 and 404 TAMs fish(-1). Fish were held for 6 mo post exposure (p.e.) in laboratory aquaria for observation and evidence of clinical signs of whirling disease. We used 4 diagnostic techniques to assess the prevalence and severity of infection by M. cerebralis among fish exposed to filtered and unfiltered water. These included polymerase chain reaction (PCR) for genomic DNA of the parasite, histological evaluation for tissue damage, tissue digestion for quantification of cranial myxospores of the parasite, and total non-sampling mortality that occurred over 6 mo p.e. All diagnostic tests verified that the prevalence and severity of infection was significantly reduced among fish in treatment groups exposed to filtered water compared to those exposed to unfiltered water in both the low-dose and high-dose exposures. PMID:14735924

  1. Gas Bubble Disease Monitoring and Research of Juvenile Salmonids : Annual Report 1996.

    SciTech Connect

    Maule, Alec G.; Beeman, John W.; Hans, Karen M.; Mesa, M.G.; Haner, P.; Warren, J.J.

    1997-10-01

    This document describes the project activities 1996--1997 contract year. This report is composed of three chapters which contain data and analyses of the three main elements of the project: field research to determine the vertical distribution of migrating juvenile salmonids, monitoring of juvenile migrants at dams on the Snake and Columbia rivers, and laboratory experiments to describe the progression of gas bubble disease signs leading to mortality. The major findings described in this report are: A miniature pressure-sensitive radio transmitter was found to be accurate and precise and, after compensation for water temperature, can be used to determine the depth of tagged-fish to within 0.32 m of the true depth (Chapter 1). Preliminary data from very few fish suggest that depth protects migrating juvenile steelhead from total dissolved gas supersaturation (Chapter 1). As in 1995, few fish had any signs of gas bubble disease, but it appeared that prevalence and severity increased as fish migrated downstream and in response to changing gas supersaturation (Chapter 2). It appeared to gas bubble disease was not a threat to migrating juvenile salmonids when total dissolved gas supersaturation was < 120% (Chapter 2). Laboratory studies suggest that external examinations are appropriate for determining the severity of gas bubble disease in juvenile salmonids (Chapter 3). The authors developed a new method for examining gill arches for intravascular bubbles by clamping the ventral aorta to reduce bleeding when arches were removed (Chapter 3). Despite an outbreak of bacterial kidney disease in the experimental fish, the data indicate that gas bubble disease is a progressive trauma that can be monitored (Chapter 3).

  2. Effect of Multiple Turbine Passage on Juvenile Snake River Salmonid Survival

    SciTech Connect

    Ham, Kenneth D.; Anderson, James J.; Vucelick, Jessica A.

    2005-10-14

    This report describes a study conducted by Pacific Northwest National Laboratory to identify populations of migrating juvenile salmonids with a potential to be impacted by repeated exposure to turbine passage conditions. This study is part of a research program supported by the U.S. Department of Energy Wind/Hydropower Program. The program's goal is to increase hydropower generation and capacity while enhancing environmental performance. Our study objective is to determine whether the incremental effects of turbine passage during downstream migration impact populations of salmonids. When such a potential is found to exist, a secondary objective is to determine what level of effect of passing multiple turbines is required to decrease the number of successful migrants by 10%. This information will help identify whether future laboratory or field studies are feasible and design those studies to address conditions that present the greatest potential to improve dam survival and thus benefit fish and power generation.

  3. Physiological Assessment of Wild and Hatchery Juvenile Salmonids : Final Report, 2003.

    SciTech Connect

    Larsen, Donald A.; Beckman, Brian R.; Dickhoff, Walton W.

    2003-08-01

    It is generally held that hatchery-reared salmonids are of inferior quality and have lower smolt-to-adult survival compared to naturally-reared salmon. The overall objectives of the work performed under this contract were the following: (1) Characterize the physiology and development of naturally rearing juvenile salmonids to: (2) Allow for the design of effective rearing programs for producing wild-like smolts in supplementation and production hatchery programs. (3) Examine the relationship between growth rate and size on the physiology and migratory performance of fish reared in hatchery programs. (4) Examine the interaction of rearing temperature and feed rate on the growth and smoltification of salmon for use in producing a more wild-like smolt in hatchery programs.

  4. Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Lookout Point Dam, 2010

    SciTech Connect

    Khan, Fenton; Johnson, Gary E.; Royer, Ida M.; Hughes, James S.; Fischer, Eric S.; Trott, Donna M.; Ploskey, Gene R.

    2011-07-01

    This report presents the results of an evaluation of juvenile salmonid passage and distribution at Lookout Point Dam (LOP) on the Middle Fork Willamette River. The study was conducted by the Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers, Portland District (USACE). The goal of the study was to provide fish passage and distribution data to support decisions on long-term measures to enhance downstream passage at LOP and others dams in USACE’s Willamette Valley Project in response to the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. During the year-long study period - February 1, 2010 to January 31, 2011the objectives of the hydroacoustic evaluation of fish passage and distribution at LOP were to: 1. Estimate passage rates, run timing, horizontal distribution, and diel distribution at turbine penstock intakes for smolt-size fish. 2. Estimate passage rates, run timing and diel distribution at turbine penstock intakes for small-size fish. 3. Estimate passage rates and run timing at the regulating outlets for smolt-size fish. 4. Estimate vertical distribution of smolt-size fish in the forebay near the upstream face of the dam. The fixed-location hydroacoustic technique was used to accomplish the objectives of this study. Transducers (420 kHz) were deployed in each penstock intake, above each RO entrance, and on the dam face; a total of nine transducers (2 single-beam and 7 split-beam) were used. We summarize the findings from the hydroacoustic evaluation of juvenile salmonid passage and distribution at LOP during February 2010 through January 2011 as follows. • Fish passage rates for smolt-size fish (> ~90 mm) were highest during December-January and lowest in mid-summer through early fall. • During the entire study period, an estimated total of 142,463 fish ± 4,444 (95% confidence interval) smolt

  5. A synthesis of tagging studies examining the behaviour and survival of anadromous salmonids in marine environments.

    PubMed

    Drenner, S Matthew; Clark, Timothy D; Whitney, Charlotte K; Martins, Eduardo G; Cooke, Steven J; Hinch, Scott G

    2012-01-01

    This paper synthesizes tagging studies to highlight the current state of knowledge concerning the behaviour and survival of anadromous salmonids in the marine environment. Scientific literature was reviewed to quantify the number and type of studies that have investigated behaviour and survival of anadromous forms of Pacific salmon (Oncorhynchus spp.), Atlantic salmon (Salmo salar), brown trout (Salmo trutta), steelhead (Oncorhynchus mykiss), and cutthroat trout (Oncorhynchus clarkii). We examined three categories of tags including electronic (e.g. acoustic, radio, archival), passive (e.g. external marks, Carlin, coded wire, passive integrated transponder [PIT]), and biological (e.g. otolith, genetic, scale, parasites). Based on 207 papers, survival rates and behaviour in marine environments were found to be extremely variable spatially and temporally, with some of the most influential factors being temperature, population, physiological state, and fish size. Salmonids at all life stages were consistently found to swim at an average speed of approximately one body length per second, which likely corresponds with the speed at which transport costs are minimal. We found that there is relatively little research conducted on open-ocean migrating salmonids, and some species (e.g. masu [O. masou] and amago [O. rhodurus]) are underrepresented in the literature. The most common forms of tagging used across life stages were various forms of external tags, coded wire tags, and acoustic tags, however, the majority of studies did not measure tagging/handling effects on the fish, tag loss/failure, or tag detection probabilities when estimating survival. Through the interdisciplinary application of existing and novel technologies, future research examining the behaviour and survival of anadromous salmonids could incorporate important drivers such as oceanography, tagging/handling effects, predation, and physiology. PMID:22431962

  6. A Synthesis of Tagging Studies Examining the Behaviour and Survival of Anadromous Salmonids in Marine Environments

    PubMed Central

    Drenner, S. Matthew; Clark, Timothy D.; Whitney, Charlotte K.; Martins, Eduardo G.; Cooke, Steven J.; Hinch, Scott G.

    2012-01-01

    This paper synthesizes tagging studies to highlight the current state of knowledge concerning the behaviour and survival of anadromous salmonids in the marine environment. Scientific literature was reviewed to quantify the number and type of studies that have investigated behaviour and survival of anadromous forms of Pacific salmon (Oncorhynchus spp.), Atlantic salmon (Salmo salar), brown trout (Salmo trutta), steelhead (Oncorhynchus mykiss), and cutthroat trout (Oncorhynchus clarkii). We examined three categories of tags including electronic (e.g. acoustic, radio, archival), passive (e.g. external marks, Carlin, coded wire, passive integrated transponder [PIT]), and biological (e.g. otolith, genetic, scale, parasites). Based on 207 papers, survival rates and behaviour in marine environments were found to be extremely variable spatially and temporally, with some of the most influential factors being temperature, population, physiological state, and fish size. Salmonids at all life stages were consistently found to swim at an average speed of approximately one body length per second, which likely corresponds with the speed at which transport costs are minimal. We found that there is relatively little research conducted on open-ocean migrating salmonids, and some species (e.g. masu [O. masou] and amago [O. rhodurus]) are underrepresented in the literature. The most common forms of tagging used across life stages were various forms of external tags, coded wire tags, and acoustic tags, however, the majority of studies did not measure tagging/handling effects on the fish, tag loss/failure, or tag detection probabilities when estimating survival. Through the interdisciplinary application of existing and novel technologies, future research examining the behaviour and survival of anadromous salmonids could incorporate important drivers such as oceanography, tagging/handling effects, predation, and physiology. PMID:22431962

  7. System-Wide Significance of Predation on Juvenile Salmonids in Columbia and Snake River Reservoirs : Annual Report 1992.

    SciTech Connect

    Petersen, James H.; Poe, Thomas P.

    1993-12-01

    Northern squawfish (Ptychocheilus oregonensis) predation on juvenile salmonids was characterized during 1992 at ten locations in the Columbia River below Bonneville Dam and at three locations in John Day Reservoir. During the spring and summer, 1,487 northern squawfish were collected in the lower Columbia River and 202 squawfish were sampled in John Day Reservoir. Gut content data, predator weight, and water temperature were used to compute a consumption index (CI) for northern squawfish, and overall diet was also described. In the Columbia River below Bonneville Dam, northern squawfish diet was primarily fish (spring 69%; summer 53%), most of which were salmonids. Salmonids were also the primary diet component in the Bonneville Dam tailrace, John Day Dam forebay, and the McNary Dam tailrace. Crustaceans were the dominant diet item at the John Day mid-reservoir location, although sample sizes were small. About half of the non-salmonid preyfish were sculpins. The consumption index (CI) of northern squawfish was generally higher during summer than during spring. The highest CI`s were observed during summer in the tailrace boat restricted zones of Bonneville Dam (CI = 7.8) and McNary Dam (CI = 4.6). At locations below Bonneville Dam, CI`s were relatively low near Covert`s Landing and Rooster Rock, higher at four locations between Blue Lake and St. Helens, and low again at three downriver sites (Kalama, Ranier, and Jones Beach). Northern squawfish catches and CI`s were noticeably higher throughout the lower Columbia compared to mid-reservoir sites further upriver sampled during 1990--92. Predation may be especially intense in the free-flowing section of the Columbia River below Bonneville Dam. Smallmouth bass (Micropterus dolomieui; N = 198) ate mostly fish -- 25% salmonids, 29% sculpins, and 46% other fish. Highest catches of smallmouth bass were in the John Day Dam forebay.

  8. Evaluation of Juvenile Fish Bypass and Adult Fish Passage Facilities at Water Diversions on the Umatilla River; 1994 Annual Report.

    SciTech Connect

    Knapp, Suzanne M.

    1995-01-01

    We report on our progress from October 1993 through September 1994 in evaluating juvenile salmonid bypass facilities and juvenile salmonid passage through ladder facilities, and investigating passage conditions for juvenile fish at diversion dam facilities on the lower Umatilla River in northeastern Oregon. We also report on our progress in evaluating adult salmonid passage at and between dams on the lower Umatilla River and upriver migration using radio telemetry. Two principal studies are also included. Report A (ODFW): To evaluate the juvenile salmonid bypass facilities a Feed and Furnish canals, juvenile salmonid passage through fish ladders at Stanfield, Feed Canal, Westland, and Three Mile Falls dams, and the juvenile salmonid trap and haul procedures at Westland Canal. To investigate passage conditions at all passage facilities. Report B (CTUIR): To examine the passage of adult salmonids past diversions in the lower Umatilla River and their movement in the upper river after transport, using radio telemetry, and to assess factors for successful homing. These studies are part of a program to rehabilitate anadromous fish stocks in the Umatilla River Basin, including restoration of coho salmon (Oncorhynchus kisutch) and chinook salmon (Oncorhynchus tshawytscha), as well as enhancement of summer steelhead (Oncorhynchus mykiss).

  9. Synthesis of Juvenile Salmonid Passage Studies at The Dalles Dam, Volume II, 2001-05

    SciTech Connect

    Johnson, Gary E.; Beeman, John W.; Duran, Ian; Puls, Andrew

    2007-08-15

    The overall goal of juvenile salmonid research at The Dalles Dam is to provide data to inform decisions on strategies to improve smolt survival rates at the project. Survival improvement strategies address the three primary passage routes at The Dalles Dam -- spillway, sluiceway, and turbines – with the general intent to increase spill and sluice passage and decrease turbine passage. Since the review by Ploskey et al. (2001a) of research during 1982-2000 at The Dalles Dam, the Corps funded over $20M of research in at least 39 studies during 2001-2006. The purpose of the current review is to synthesize juvenile salmonid passage data at The Dalles Dam (TDA) collected from 2001 through 2006. The data we synthesize comes from numerous research techniques employed to address particular study objectives at The Dalles Dam. The suite of techniques includes acoustic and radio telemetry, acoustic cameras, acoustic Doppler current profilers, balloon tags, computational fluid dynamics models, drogues, fixed and mobile hydroacoustics, fyke nets, physical scale models, PIT-tags, sensor fish, sonar trackers, and underwater video. Hydraulic data involves flow patterns and water velocities. Biological data involve forebay approach paths and residence times, horizontal and diel distributions, passage efficiencies and effectiveness, fish behaviors, tailrace egress and predation rates, and route-specific and total project survival rates. Data for 2001-2006 are synthesized in this report to provide, in conjunction with Ploskey et al. (2001a), resources for engineers, biologists, and dam operators to use when making decisions about fish protection measures for juvenile salmonids at The Dalles Dam. This review covers the major fish passage research efforts during 2001-2006 and includes sections on the Environmental Setting, Forebay and Project Passage Studies, Spill Studies, Sluiceway Studies, Turbine Studies, Smolt Survival Studies, and a Discussion.

  10. Non-native salmonids affect amphibian occupancy at multiple spatial scales

    USGS Publications Warehouse

    Pilliod, David S.; Hossack, Blake R.; Bahls, Peter F.; Bull, Evelyn L.; Corn, Paul Stephen; Hokit, Grant; Maxell, Bryce A.; Munger, James C.; Wyrick, Aimee

    2010-01-01

    Aim The introduction of non-native species into aquatic environments has been linked with local extinctions and altered distributions of native species. We investigated the effect of non-native salmonids on the occupancy of two native amphibians, the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), across three spatial scales: water bodies, small catchments and large catchments. Location Mountain lakes at ≥ 1500 m elevation were surveyed across the northern Rocky Mountains, USA. Methods We surveyed 2267 water bodies for amphibian occupancy (based on evidence of reproduction) and fish presence between 1986 and 2002 and modelled the probability of amphibian occupancy at each spatial scale in relation to habitat availability and quality and fish presence. Results After accounting for habitat features, we estimated that A. macrodactylum was 2.3 times more likely to breed in fishless water bodies than in water bodies with fish. Ambystoma macrodactylum also was more likely to occupy small catchments where none of the water bodies contained fish than in catchments where at least one water body contained fish. However, the probability of salamander occupancy in small catchments was also influenced by habitat availability (i.e. the number of water bodies within a catchment) and suitability of remaining fishless water bodies. We found no relationship between fish presence and salamander occupancy at the large-catchment scale, probably because of increased habitat availability. In contrast to A. macrodactylum, we found no relationship between fish presence and R. luteiventris occupancy at any scale. Main conclusions Our results suggest that the negative effects of non-native salmonids can extend beyond the boundaries of individual water bodies and increase A. macrodactylum extinction risk at landscape scales. We suspect that niche overlap between non-native fish and A. macrodactylum at higher elevations in the northern Rocky

  11. Turbulence Investigation and Reproduction for Assisting Downstream Migrating Juvenile Salmonids, Part I of II, 2001-2002 Final Report.

    SciTech Connect

    Hotchkiss, Rollin H.

    2002-12-01

    Turbulence in gravel bed rivers plays a critical role in most stream processes including contaminant and nutrient transport, aquatic habitat selection, and natural channel design. While most hydraulic designs and fluid models are based on bulk velocity, migrating juvenile salmon experience and react to the temporally varied turbulent fluctuations. Without properly understanding and accounting for the continuous turbulent motions proper fishway design and guidance are impossible. Matching temporally varied flow to fish reactions is the key to guiding juvenile salmonids to safe passageways. While the ideal solution to fish guidance design would be to use specific fluid action-fish reaction mechanisms, such concrete cause and effect relations have not been established. One way to approach the problem of guidance is to hypothesize that in an environment lacking obvious bulk flow cues (like the reservoir environment), turbulent flow conditions similar to those experienced by juvenile salmonids in natural migration corridors will be attractive to juvenile salmonids. Proof of this hypothesis requires three steps: (1) gathering data on turbulence characteristics in natural migration corridors, (2) reproduction of the turbulence parameters in a controlled environment, and (3) testing the reproduced turbulence on actively migrating juvenile salmonids for increased passage efficiencies. The results from the third step have not been finalized, therefore this report will focus on understanding turbulent processes in gravel bed rivers and reproduction of turbulence in controlled environments for use in fish passage technologies. The purposes of this report are to (1) present data collected in natural gravel bed rivers, (2) present a simple method for reproduction of appropriate turbulence levels in a controlled environment, (3) compare these results to those from one prototype surface collector (PSC), and (4) discuss the implications on fish passage design.

  12. Assessment of Salmonids and their Habitat Conditions in the Walla Walla River Basin of Washington : 2000 Annual Report.

    SciTech Connect

    Mendel, Glen Wesley; Karl, David; Coyle, Terrence

    2001-11-01

    Concerns about the decline of native salmon and trout populations have increased among natural resource managers and the public in recent years. As a result, a multitude of initiatives have been implemented at the local, state, and federal government levels. These initiatives include management plans and actions intended to protect and restore salmonid fishes and their habitats. In 1998 bull trout were listed under the Endangered Species Act (ESA), as ''Threatened'', for the Walla Walla River and its tributaries. Steelhead were listed as ''Threatened'' in 1999 for the mid-Columbia River and its tributaries. These ESA listings emphasize the need for information about the threatened salmonid populations and their habitats. The Washington Department of Fish and Wildlife (WDFW) is entrusted with ''the preservation, protection, and perpetuation of fish and wildlife....[and to] maximize public recreational or commercial opportunities without impairing the supply of fish and wildlife (WAC 77. 12.010).'' In consideration of this mandate, the WDFW submitted a proposal in December 1997 to the Bonneville Power Administration (BPA) for a study to assess salmonid distribution, relative abundance, genetics, and the condition of their habitats in the Walla Walla River basin. The primary purposes of this project are to collect baseline biological and habitat data, to identify major data gaps, and to draw conclusions whenever possible. The study reported herein details the findings of the 2000 field season (March to November, 2000).

  13. River profile controls on channel morphology, debris flow disturbance, and the spatial extent of salmonids in steep mountain streams

    NASA Astrophysics Data System (ADS)

    May, Christine L.; Lisle, Thomas E.

    2012-12-01

    In the geologically and topographically diverse mountain ranges of the Pacific Northwest, a broad-scale means of prioritizing salmonid habitat conservation areas based on geomorphic process domains is examined. We propose that steepness and concavity indices derived from the relation between drainage area and channel slope provide a means of identifying basins that express different reach-scale morphologies, fish habitat capacity, and risk of episodic disturbance. Strongly concave river profiles that develop in mountainous terrain indicate that almost all of the relief in the drainage network occurs in headwater streams. In these basins a large proportion of the channel network has low-gradient morphologies, which provide favorable habitat for many salmonid species. The severity of pulse disturbances is also reduced because low-gradient main stem channels inhibit debris flow conveyance, and in these networks the distribution of fish can expand into tributaries, allowing for a spatial spreading of risk. In contrast, rivers with poorly concave or steeper profiles have a greater abundance of high gradient reaches that limit the distribution of fish to a small portion of the channel network and facilitate debris flow-passage. The combined influence of a limited spatial distribution of fish and an increased risk of debris flows may cause populations in these basins to be less resilient to pulse disturbances. A case example from the Klamath Mountains, an area with broad variation in the steepness and concavity of river profiles, was used to develop this approach and aid conservation planning for imperiled populations of anadromous salmonids.

  14. Impacts of hypersaline acclimation on the acute toxicity of the organophosphate chlorpyrifos to salmonids.

    PubMed

    Maryoung, Lindley A; Lavado, Ramon; Schlenk, Daniel

    2014-07-01

    Acclimation to hypersaline conditions enhances the acute toxicity of certain thioether organophosphate and carbamate pesticides in some species of euryhaline fish. As the organophosphate chlorpyrifos is commonly detected in salmonid waterways, the impacts of hypersaline conditions on its toxicity were examined. In contrast to other previously examined pesticides, time to death by chlorpyrifos was more rapid in freshwater than in hypersaline water (16ppth). The median lethal time (LT50) after 100μg/L chlorpyrifos exposure was 49h (95% CI: 31-78) and 120h (95% CI: 89-162) for rainbow trout (Oncorhynchus mykiss) in freshwater and those acclimated to hypersaline conditions, respectively. Previous studies with hypersaline acclimated fish indicated induction of xenobiotic metabolizing enzymes that may detoxify chlorpyrifos. In the current study, chlorpyrifos metabolism was unaltered in liver and gill microsomes of freshwater and hypersaline acclimated fish. Acetylcholinesterase inhibition in brain and bioavailability of chlorpyrifos from the aqueous exposure media were also unchanged. In contrast, mRNA expression of neurological targets: calcium calmodulin dependent protein kinase II delta, chloride intracellular channel 4, and G protein alpha i1 were upregulated in saltwater acclimated fish, consistent with diminished neuronal signaling which may protect animals from cholinergic overload associated with acetylcholinesterase inhibition. These results indicate targets other than acetylcholinesterase may contribute to the altered toxicity of chlorpyrifos in salmonids under hypersaline conditions. PMID:24799192

  15. Hydraulic features of Engineered Log Jams (ELJs) and their influence on salmonid behavior

    NASA Astrophysics Data System (ADS)

    Rice, W. D.; Fetter, D.; Somerville, G.; Tullos, D. D.; Palacijo, J.

    2010-12-01

    In an effort to recreate channel complexity and habitat, construction of Engineered Log Jams (ELJs) is increasing, yet questions remain regarding their effectiveness due to lack of observations of hydraulics and fish use around these structures. To address this limitation, we surveyed four different forms of engineered log jams in western Oregon. The structures and near-structure stream environments were surveyed for bathymetry, instrumented with an Acoustic Doppler Stream Profiler (ADCP) to measure velocities, and snorkeled to observe the behavior of salmonids. Further, tensor visualization of stream velocities were constructed to investigate circulation and flow patterns in and around the ELJ structures. We found that more complex structures created a more varied bottom profile, while simpler structures resulted in more simple pools. However, all log jams did increase the diversity of flow patterns, with areas of high and low velocity that appeared to influence fish behavior. Variation in the size of salmonids was related to greater variation in the velocity, and fish behavior (feeding, aggression) was observed to vary within the pools. Our results provide preliminary evidence of the influence of engineered structures on the diversity and versatility of fish habitat.

  16. Influences of Stocking Salmon Carcass Analogs on Salmonids in Yakima River Tributaries, 2001-2002 Technical Report.

    SciTech Connect

    Pearsons, Todd N.; Johnson, Christopher L.

    2003-04-01

    The benefits that marine derived nutrients from adult salmon carcasses provide to juvenile salmonids are increasingly being recognized. Current estimates suggest that only 6-7% of marine-derived nitrogen and phosphorus that were historically available to salmonids in the Pacific Northwest are currently available. Food limitation may be a major constraint limiting the restoration of salmonids. A variety of methods have been proposed to offset this nutrient deficit including: allowing greater salmon spawning escapement, stocking hatchery salmon carcasses, and stocking inorganic nutrients. Unfortunately, each of these methods has some ecological or socio-economic shortcoming. We intend to overcome many of these shortcomings by making and evaluating a pathogen free product that simulates a salmon carcass (analog). Abundant sources of marine derived nutrients are available such as fish offal from commercial fishing and salmon carcasses from hatcheries. However, a method for recycling these nutrients into a pathogen free analog that degrades at a similar rate as a natural salmon carcass has never been developed. We endeavored to (1) develop a salmon carcass analog that will increase the food available to salmonids, (2) determine the pathways that salmonids use to acquire food from analogs, and (3) determine the benefits to salmonids and the potential for application to salmonid restoration. We used a before-after-control-impact-paired design in six tributaries of the upper Yakima basin to determine the utility of stocking carcass analogs. Our preliminary results suggest that the introduction of carcass analogs into food-limited streams can be used to restore food pathways previously provided by anadromous salmon. The analogs probably reproduced both of the major food pathways that salmon carcasses produce: direct consumption and food chain enhancement. Trout and salmon fed directly on the carcass analogs during the late summer and presumably benefited from the increased

  17. River Temperature Dynamics and Habitat Characteristics as Predictors of Salmonid Abundance using Fiber-Optic Distributed Temperature Sensing

    NASA Astrophysics Data System (ADS)

    Gryczkowski, L.; Gallion, D.; Haeseker, S.; Bower, R.; Collier, M.; Selker, J. S.; Scherberg, J.; Henry, R.

    2011-12-01

    Salmonids require cool water for all life stages, including spawning and growth. Excessive water temperature causes reduced growth and increased disease and mortality. During the summer, salmonids seek local zones of cooler water as a refuge from elevated temperatures. They also prefer specific habitat features such as boulders and overhanging vegetation. The purpose of this study is to determine whether temperature dynamics or commonly measured fish habitat metrics best explain salmonid abundance. The study site was a 2-kilometer reach of the Walla Walla River near Milton-Freewater, OR, USA, which provides habitat for the salmonids chinook salmon (Oncorhynchus tshawytscha), steelhead/rainbow trout (Oncorhynchus mykiss), mountain whitefish (Prosopium williamsoni), and the endangered bull trout (Salvelinus confluentus). The Walla Walla River is listed as an impaired water body under section 303(d) of the Clean Water Act due to temperature. The associated total maximum daily load (TMDL) calls for temperatures to be below 18 °C at all times for salmonid rearing and migration; however, river temperatures surpassed 24 °C in parts of the study reach in 2009. The two largest factors contributing to the warmer water are reduced riparian vegetation, which decreases shading and increases direct solar radiation, and decreased summer flows caused by diversions and irrigation for agriculture. Fiber-optic distributed temperature sensing has emerged as a unique and powerful tool for ecological applications because of its high spatial and temporal resolution. In this study, meter-scale temperature measurements were obtained at 15-minute intervals along the length of the study reach, allowing for the detection and quantification of cold water inflows during the summer of 2009. The cold water inflows were classified as groundwater or hyporheic sources based on the diurnal temperature patterns. Snorkel surveys were conducted in mid-July and mid-August, 2009 to enumerate salmonid

  18. Determine the Influence of Time Held in “Knockdown” Anesthesia on Survival and Stress of Surgically Implanted Juvenile Salmonids

    SciTech Connect

    Woodley, Christa M.; Wagner, Katie A.; Knox, Kasey M.

    2012-01-31

    The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed for the U.S. Army Corp of Engineers Portland District (USACE) to address questions related to survival and performance measures of juvenile salmonids as they pass through the Federal Columbia River Power System (FCRPS). Researchers using JSATS acoustic transmitters (ATs) were tasked with standardizing the surgical implantation procedure to ensure that the stressors of handling and surgery on salmonids were consistent and less likely to cause effects of tagging in survival studies. Researchers questioned whether the exposure time in 'knockdown' anesthesia (or induction) to prepare fish for surgery could influence the survival of study fish (CBSPSC 2011). Currently, fish are held in knockdown anesthesia after they reach Stage 4 anesthesia until the completion of the surgical implantation of a transmitter, varies from 5 to 15 minutes for studies conducted in the Columbia Basin. The Columbia Basin Surgical Protocol Steering Committee (CBSPSC ) expressed concern that its currently recommended 10-minute maximum time limit during which fish are held in anesthetic - tricaine methanesulfonate (MS-222, 80 mg L-1 water) - could increase behavioral and physiological costs, and/or decrease survival of outmigrating juvenile salmonids. In addition, the variability in the time fish are held at Stage 4 could affect the data intended for direct comparison of fish within or among survival studies. Under the current recommended protocol, if fish exceed the 10-minute time limit, they are to be released without surgical implantation, thereby increasing the number of fish handled and endangered species 'take' at the bypass systems for FCRPS survival studies.

  19. Relationship between channel morphology and foraging habitat for stream salmonids: Effects of body size

    NASA Astrophysics Data System (ADS)

    Cienciala, P.; Hassan, M. A.

    2014-12-01

    Channel morphology and dynamics strongly influence fish populations in running waters by defining habitat template for movement, spawning, incubation, and foraging. In this research we adopted a modeling approach to investigate how body size controls the relationship between salmonid fish and their foraging habitat in streams. Body size is a fundamental ecological parameter which affects resource acquisition, locomotory costs, metabolic rates, and competitive abilities. We focus on two specific questions. First, we examined how distinct types of channel morphology and associated flow fields shape specific growth potential for different body size classes of trout. Second, we modeled these fish-habitat relationships in a size-structured population in the presence of intraspecific competition. In the latter scenario, fish may not be able to occupy energetically optimal foraging habitat and the predicted specific growth potential may differ from the intrinsic habitat quality. To address the research questions, we linked a 2D hydrodynamic model with a bioenergetic foraging model for drift-feeding trout. Net energy intake, simulated for four study reaches with different channel morphology, was converted into maps of specific growth rate potential. We extended this model by including a component that enabled us to estimate territory size for fish of a given body size and account for the effects of competition on spatial distribution of fish. The predictions that emerge from our simulations highlight that fish body size is an important factor that determines the relationship between channel morphology and the quality of foraging habitat. The results also indicate that distinct types of channel morphology may give rise to different energetic conditions for different body size classes of drift-feeding salmonids.

  20. Detection of salmonid alphavirus RNA in Celtic and Irish Sea flatfish.

    PubMed

    McCleary, S; Giltrap, M; Henshilwood, K; Ruane, N M

    2014-04-23

    Pancreas disease (PD) caused by the salmonid alphavirus (SAV) has been the most significant cause of mortalities in Irish farmed salmon Salmo salar L. over the past decade. SAV is a single-strand positive-sense RNA virus, originally thought to be unique to salmonids, but has recently been detected using real-time RT-PCR in a number of wild non-salmonid fish. In the present report, 610 wild flatfish (common dab Limanda limanda, plaice Pleuronectes platessa and megrim Lepidorhombus whiffiagonis) were caught from the Irish and Celtic Seas and screened for SAV using real-time RT-PCR and sequencing. In general, a very low prevalence was recorded in common dab and plaice, except for 1 haul in Dublin Bay where 25% of common dab were SAV-positive. SAV sequence analysis supported the fact that real-time RT-PCR detections were specific and further characterised the detected viruses within SAV Subtype I, the predominant subtype found in farmed salmon in Ireland. PMID:24781791

  1. RESEARCH PLAN: LANDSCAPE AND WATERSHED INFLUENCES ON WILD SALMON AND FISH ASSEMBLAGES IN OREGON COASTAL STREAMS

    EPA Science Inventory

    This document is a Research Plan. In the Pacific Northwest (PNW), many populations of wild anadromous salmonids are in serious decline. Landscape change, water pollution, introduced predators, fishing, hydropower development, hatcheries, disadvantageous ocean conditions, and ot...

  2. USE OF COLD FLOODPLAIN MARGIN HABITATS BY A STREAM FISH ASSEMBLAGE

    EPA Science Inventory

    We studied the effects of temperature and other habitat characteristics on fish assemblages and their distribution among coldwater patches potentially functioning as "coldwater refugia" for salmonids. Potential coldwater refugia in alluvial segments of the Grande Ronde River of ...

  3. Factors influencing the survival of outmigrating juvenile salmonids through multiple dam passages: an individual-based approach.

    PubMed

    Elder, Timothy; Woodley, Christa M; Weiland, Mark A; Strecker, Angela L

    2016-08-01

    Substantial declines of Pacific salmon populations have occurred over the past several decades related to large-scale anthropogenic and climatic changes in freshwater and marine environments. In the Columbia River Basin, migrating juvenile salmonids may pass as many as eight large-scale hydropower projects before reaching the ocean; however, the cumulative effects of multiple dam passages are largely unknown. Using acoustic transmitters and an extensive system of hydrophone arrays in the Lower Columbia River, we calculated the survival of yearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) passing one, two, or three dams. We applied a unique index of biological characteristics and environmental exposures, experienced by each fish individually as it migrated downstream, in order to examine which factors most influence salmonid survival. High outflow volumes led to involuntary spill in 2011 and created an environment of supersaturated dissolved gas concentrations. In this environment, migrating smolt survival was strongly influenced by barometric pressure, fish velocity, and water temperature. The effect of these variables on survival was compounded by multiple dam passages compared to fish passing a single dam. Despite spatial isolation between dams in the Lower Columbia River hydrosystem, migrating smolt appear to experience cumulative effects akin to a press disturbance. In general, Chinook salmon and steelhead respond similarly in terms of survival rates and responses to altered environmental conditions. Management actions that limit dissolved gas concentrations in years of high flow will benefit migrating salmonids at this life stage. PMID:27547362

  4. Rate of disappearance of gas bubble trauma signs in juvenile salmonids

    USGS Publications Warehouse

    Hans, K.M.; Mesa, M.G.; Maule, A.G.

    1999-01-01

    To assess the rate of disappearance of gas bubble trauma (GBT) signs in juvenile salmonids, we exposed spring chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss to water containing high levels of dissolved gas supersaturation (DGS) for a time period sufficient to induce signs of GBT, reduced the DGS to minimal levels, and then sampled fish through time to document changes in severity of GBT. Because of the tendency of GBT signs to dissipate at different rates, we conducted trials focusing on emboli (bubbles) in the gill filaments and lateral line and separate trials that focused on bubbles in the external surfaces (fins, eyes, and opercula). Bubbles in gill filaments dissipated almost completely within 2 h after transfer of fish to water of nearly normal DGS (104%), whereas bubbles in the lateral line dissipated to negligible levels within 5 h. Bubbles on external surfaces were more persistent through time than they were in gill filaments and the lateral line. Although typically dissipating to low levels within 48 h, external bubbles sometimes remained for 4 d. Assuming a direct relation exists between easily observable signs and direct mortality, our results suggest that fish can recover quickly from the potentially lethal effects of DGS once they move from water with high DGS to water of almost normal gas saturation. These results should be of fundamental importance to fishery managers interpreting the results of monitoring for the severity and prevalence of GBT in juvenile salmonids in the Columbia River system and perhaps elsewhere.

  5. Holding of juvenile salmonids for surgical implantation of electronic tags: a review and recommendations

    SciTech Connect

    Oldenburg, Eric W.; Colotelo, Alison HA; Brown, Richard S.; Eppard, M. B.

    2011-01-01

    Many telemetry based studies require that fish be sampled from the wild and then held for some amount of time both prior to and after the implantation of a transmitter. However, the effects of such holding (or the lack thereof) are often overlooked. Pre-surgical holding often occurs to facilitate logistical needs of research projects and as an attempt to minimize negative physiological effects due to capture and handling stress. Further, post-surgical holding time and conditions greatly influence the physiological state of fish prior to being returned to the wild. This paper reviews pertinent studies pertaining to the effects of surgical holding on the behavior, physiology, and survival of fishes, with particular emphasis on juvenile salmonids. The effects of individual aspects of surgical holding such as stressors, time, holding conditions and water quality are also examined. Recommendations regarding certain aspects of surgical holding (e.g., holding duration) are offered with a goal of reducing bias related to the surgical process. Pre- and post-surgical holding times of 18–36 h are suggested as a general guideline for juvenile salmonids.

  6. Pathogenesis of experimental salmonid alphavirus infection in vivo: an ultrastructural insight.

    PubMed

    Herath, Tharangani K; Ferguson, Hugh W; Weidmann, Manfred W; Bron, James E; Thompson, Kimberly D; Adams, Alexandra; Muir, Katherine F; Richards, Randolph H

    2016-01-01

    Salmonid alphavirus (SAV) is an enveloped, single-stranded, positive sense RNA virus belonging to the family Togaviridae. It causes economically devastating disease in cultured salmonids. The characteristic features of SAV infection include severe histopathological changes in the heart, pancreas and skeletal muscles of diseased fish. Although the presence of virus has been reported in a wider range of tissues, the mechanisms responsible for viral tissue tropism and for lesion development during the disease are not clearly described or understood. Previously, we have described membrane-dependent morphogenesis of SAV and associated apoptosis-mediated cell death in vitro. The aims of the present study were to explore ultrastructural changes associated with SAV infection in vivo. Cytolytic changes were observed in heart, but not in gill and head-kidney of virus-infected fish, although they still exhibited signs of SAV morphogenesis. Ultrastructural changes associated with virus replication were also noted in leukocytes in the head kidney of virus-infected fish. These results further describe the presence of degenerative lesions in the heart as expected, but not in the gills and in the kidney. PMID:26743442

  7. Comparative Performance of Acoustic-tagged and PIT-tagged Juvenile Salmonids

    SciTech Connect

    Hockersmith, Eric E.; Brown, Richard S.; Liedtke, Theresa L.

    2008-02-01

    Numerous research tools and technologies are currently being used to evaluate fish passage and survival to determine the impacts of the Federal Columbia River Power System (FCRPS) on endangered and threatened juvenile salmonids, including PIT tags, balloon tags, hydroacoustic evaluations, radio telemetry, and acoustic telemetry. Each has advantages and disadvantages, but options are restricted in some situations because of limited capabilities of a specific technology, lack of detection capability downstream, or availability of adequate numbers of fish. However, there remains concern about the comparative effects of the tag or the tagging procedure on fish performance. The recently developed Juvenile Salmonid Acoustic Telemetry System (JSATS) acoustic transmitter is the smallest active acoustic tag currently available. The goal of this study was to determine whether fish tagged with the JSATS acoustic-telemetry tag can provide unbiased estimates of passage behavior and survival within the performance life of the tag. We conducted both field and laboratory studies to assess tag effects. For the field evaluation we released a total of 996 acoustic-tagged fish in conjunction with 21,026 PIT-tagged fish into the tailrace of Lower Granite Dam on 6 and 13 May. Travel times between release and downstream dams were not significantly different for the majority of the reaches between acoustic-tagged and PIT-tagged fish. In addition to the field evaluation, a series of laboratory experiments were conducted to determine if growth and survival of juvenile Chinook salmon surgically implanted with acoustic transmitters is different than untagged or PIT tagged juvenile Chinook salmon. Only yearling fish with integrated and non-integrated transmitters experienced mortalities, and these were low (<4.5%). Mortality among sub-yearling control and PIT-tag treatments ranged up to 7.7% while integrated and non-integrated treatments had slightly higher rates (up to 8.3% and 7

  8. Comparison of infectious hematopoietic necrosis in natural and experimental infections of spawning salmonids by infectivity and immunohistochemistry

    USGS Publications Warehouse

    Yamamoto, T.; Arakawa, C.K.; Batts, W.N.; Winton, J.R.

    1989-01-01

    Infectious hematopoietic necrosis (IHN) continues to be a serious virus disease of salmonids with epizootics recorded in both wild and hatchery populations (Williams and Amend 1976; Carlisle et al 1979; Groberg and Fryer 1983; Saft and Pratt 1986; Traxler 1987; Follett et al 1987; Meyers et al 1988). While originally enzootic in western North America, the virus appears to be spreading further (Sano et al 1977; de Kinkelin et al 1987; Bovo et al 1987). In hatchery outbreaks occurring in regions where the virus is not enzootic, it is often possible to trace the virus to the importation of infected fingerlings or contaminated eggs. In regions where the virus is widespread among stocks of fish, the source of virus infection is more difficult to establish particularly in watersheds where there are anadromous salmonids. Although salmonid fish surviving infection as fry and returning from the ocean to spawn are considered to be parental carriers of IHNV, there is very little data to support this hypothesis. Amend (1975) in the study of rainbow trout reported that in a population surviving infection and assayed a few years later found that a few trout were carrying virus. This is the study often cited as evidence for the carrier status of returning salmonids. LaPatra et al (1987) presented data that indicated IHNV has been transmitted horizontally through water from adult chinook salmon (Oncorhynchus tshawytscha) to adult coho salmon (O. kisutch) at a hatchery in northern California. They suggested that horizontal transmission may be an important means for perpetuating IHN. However, the actual mechanisms for persistence and transmission of IHN among fish in a watershed is likely to be complex and involve multiple species and age groups as well as intermediate vectors and/or reservoirs.

  9. Significance of Selective Predation and Development of Prey Protection Measures for Juvenile Salmonids in the Columbia and Snake River Reservoirs: Annual Progress Report, February 1991-February 1992.

    SciTech Connect

    Poe, Thomas P.

    1992-12-31

    This document is the 1991 annual report of progress for the Bonneville Power Administration (BPA) research Project conducted by the US Fish and Wildlife Service (FWS). Our approach was to present the progress achieved during 1991 in a series of separate reports for each major project task. Each report is prepared in the format of a scientific paper and is able to stand alone, whatever the state of progress or completion. This project has two major goals. One is to understand the significance of selective predation and prey vulnerability by determining if substandard juvenile salmonids (dead, injured, stressed, diseased, or naive) are more vulnerable to predation by northern squawfish, than standard or normal juvenile salmonids. The second goal is to develop and test prey protection measures to control predation on juvenile salmonids by reducing predator-smolt encounters or predator capture efficiency.

  10. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1987 Annual Report.

    SciTech Connect

    Fryer, John L.

    1989-01-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration has been conducting a study concerning the epidemiology and control of three fish pathogens which cause major disease problems in salmonids of the Columbia River basin. The pathogens studied include Cera to myxa Shasta, the myxosporean parasite which causes ceratomyxosis; Renibacterium salmoninarum, the bacterium which is the etiological agent of bacterial kidney disease; and the rhabdovirus which causes infectious hematopoietic necrosis (IHN). During this project, the host and geographic range of C. Shasta have been more precisely determined and the known geographic range has been significantly expanded. The effects of the parasite on fish migrating through the Columbia River and on their introduction into salt water have been examined. Similar studies have been conducted with R. salmoninarum and it has been shown that bacterial kidney disease occurs at all life stages of salmonids and is responsible for mortality in both fresh and salt water. It has also been demonstrated that different isolates of R. salmoninarum have different antigenic composition. Results of demonstration projects designed to control IHN by using UV treated water for early rearing of salmonid fry were equivocal. The scope of the project was considerably narrowed and focused during the past two years The project has concentrated on a study concerning the biology of C. Shasta and the identification of potential chemotherapeutants for control of bacterial kidney disease. The emphasis of work on C. Shasta has been its pathogenesis. This aspect of the parasite has been investigated using histopathologic and immunologic methodology. Mode of transmission, the nature of the infectious stage, and potential intermediate hosts of the parasite have also been areas of active research. Classes of chemotherapeutants with the highest potential for efficacy against R. salmoninarum have been

  11. Migratory Behavior and Survival of Juvenile Salmonids in the Lower Columbia River and Estuary in 2009

    SciTech Connect

    McMichael, Geoffrey A.; Harnish, Ryan A.; Bellgraph, Brian J.; Carter, Jessica A.; Ham, Kenneth D.; Titzler, P. Scott; Hughes, Michael S.

    2010-08-01

    The study reported herein was funded as part of the Anadromous Fish Evaluation Program, which is managed by the U.S. Army Corps of Engineers (USACE). The Anadromous Fish Evaluation Program study code is EST P 02 01: A Study of Salmonid Survival and Behavior through the Columbia River Estuary Using Acoustic Tags. The study was conducted by the Pacific Northwest National Laboratory (PNNL) and National Oceanic and Atmospheric Administration (NOAA) Fisheries for the USACE Portland District. Estimated survival of acoustic-tagged juvenile Chinook salmon and steelhead through the lower Columbia River and estuary in 2009 was lowest in the final 50 km of the estuary. Probability of survival was relatively high (>0.90) for yearling and subyearling Chinook salmon from the Bonneville Dam forebay (rkm 236) to Three-tree Point (rkm 49.6). Survival of juvenile Chinook salmon declined sharply through the lower 50 km of the estuary. Acoustic-tagged steelhead smolts did not survive as well as juvenile Chinook salmon between Bonneville Dam and the mouth of the Columbia River. Steelhead survival began to decline farther upstream (at rkm 86) relative to that of the Chinook salmon stocks. Subyearling Chinook salmon survival decreased markedly as the season progressed. It remains to be determined whether later migrating subyearling Chinook salmon are suffering increasing mortality as the season progresses or whether some portion of the apparent loss is due to fish extending their freshwater residence. This study provided the first glimpse into what promises to be a very informative way to learn more about how juvenile salmonid passage experiences through the FCRPS may influence their subsequent survival after passing Bonneville Dam. New information regarding the influence of migration pathway through the lower 50 km of the Columbia River estuary on probability of survival of juvenile salmonids, combined with increased understanding regarding the foraging distances and time periods of

  12. Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin, Annual Report 1999-2000.

    SciTech Connect

    Knapp, Suzanne M.; Carmichael, Richard W.; Ehlers, Danette L.

    2002-04-01

    This is the sixth annual report of a multi-year project that monitors the outmigration and survival of hatchery and natural juvenile salmonids in the lower Umatilla River. This project supplements and complements ongoing or completed fisheries projects in the Umatilla River basin. Knowledge gained on outmigration and survival assists researchers and managers in adapting hatchery practices, flow enhancement strategies, canal and fish ladder operations, and supplementation and enhancement efforts for natural and restored fish populations. Findings from this study also measure the success of upriver habitat improvement projects and provide an overall evaluation of the Umatilla River fisheries restoration program.

  13. Comparing visual prey detection among species of piscivorous salmonids: effects of light and low turbidities

    USGS Publications Warehouse

    Mazur, Michael M.; Beauchamp, David A.

    2003-01-01

    Differences in reaction distance to prey fish by piscivorous salmonids can alter predator–prey interactions under different visual conditions. We compared reaction distances of three piscivorous salmonids commonly found in western lakes: cutthroat trout, Oncorhynchus clarki utah, rainbow trout, O. mykiss, and the nonnative lake char, Salvelinus namaycush. Reaction distances to salmonid prey were measured as functions of light and turbidity in a controlled laboratory setting. In addition, predation rates and swimming speeds of lake char preying on juvenile cutthroat trout were measured experimentally under a range of light levels. Reaction distances for cutthroat trout and rainbow trout increased rapidly as light levels increased, reaching relatively constant reaction distances at higher light levels. Reaction distances for lake char were similar to cutthroat trout and rainbow trout at the lower light levels; however, lake char reaction distances continued to increase with increasing light intensity to asymptote at distances 65% higher than those for both cutthroat and rainbow trout. Predation rates by lake char were low for the darkest light levels, increased rapidly under low light levels (0.50–0.75 lx), and then declined to an intermediate rate at all higher light levels. Swimming speeds by lake char also increased rapidly from extremely low light conditions to a peak and declined to an intermediate level at light levels above 1.00 lx. These results suggest that, above the saturation intensity threshold, piscivorous lake char react to fish prey at greater distances than do cutthroat trout and rainbow trout. These differences may help explain the decline of native trout following the introductions of nonnative lake char in lakes and reservoirs of western North America.

  14. Juvenile anadromous salmonid production in upper Columbia River side channels with different levels of hydrological connection

    USGS Publications Warehouse

    Martens, Kyle D.; Connolly, Patrick J.

    2014-01-01

    We examined the contribution of three types of side channels based on their hydrologic connectivity (seasonally disconnected, partially connected, and connected) to production of juvenile anadromous salmonids. Juvenile steelhead Oncorhynchus mykiss and Chinook Salmon O. tshawytscha were found in all three of these side channel types and in each year of the study. Upon connection with the main stem at high flows, the seasonally disconnected side channels experienced an emptying out of the previous year's fish while filling with young-of-year fish during the 2- to 4-month period of hydrologic connection. There were no differences between the densities of juvenile steelhead and Chinook Salmon and the rate of smolts produced among the three types of side channels. Recently reintroduced Coho Salmon O. kisutch had sporadic presence and abundance in partially and connected side channels, but the smolt production rate was over two times that of steelhead and Chinook Salmon in seasonally disconnected side channels. Within seasonally disconnected side channels, young-of-year salmonids in deep pools (≥100 cm) had greater survival than those in shallow pools (<100 cm). Densities of juvenile steelhead in all side channel types were similar to those in tributaries and were higher than in main-stem lateral margins. Juvenile Chinook Salmon densities were higher in side channels than in both tributary and main-stem lateral margins. Our results suggest that improving quality of pool habitat within seasonally disconnected side channels can result in improved survival for juvenile anadromous salmonids during the period of disconnection. Habitat improvement in these seasonally disconnected side channels should be recognized as a worthy restoration strategy, especially when full connectivity of side channels may not be a feasible target (e.g., through lack of water availability) or when full connectivity may present too high a risk (e.g., flooding, stream capture, bank

  15. Juvenile salmonid use of freshwater emergent wetlands in the floodplain and its implications for conservation management

    USGS Publications Warehouse

    Henning, J.A.; Gresswell, R.E.; Fleming, I.A.

    2006-01-01

    A recent trend of enhancing freshwater emergent wetlands for waterfowl and other wildlife has raised concern about the effects of such measures on juvenile salmonids. We undertook this study to quantify the degree and extent of juvenile Pacific salmon Oncorhynchus spp. utilization of enhanced and unenhanced emergent wetlands within the floodplain of the lower Chehalis River, Washington, and to determine the fate of the salmon using them. Enhanced emergent wetlands contained water control structures that provided an outlet for fish emigration and a longer hydroperiod for rearing than unenhanced wetlands. Age-0 and age-1 coho salmon O. kisutch were the most common salmonid at all sites, enhanced wetlands having significantly higher age-1 abundance than unenhanced wetlands that were a similar distance from the main-stem river. Yearling coho salmon benefited from rearing in two enhanced wetland habitats, where their specific growth rate and minimum estimates of survival (1.43%/d by weight and 30%; 1.37%/d and 57%) were comparable to those in other side-channel rearing studies. Dissolved oxygen concentrations decreased in emergent wetlands throughout the season and approached the limits lethal to juvenile salmon by May or June each year. Emigration patterns suggested that age-0 and age-1 coho salmon emigrated as habitat conditions declined. This observation was further supported by the results of an experimental release of coho salmon. Survival of fish utilizing emergent wetlands was dependent on movement to the river before water quality decreased or stranding occurred from wetland desiccation. Thus, our results suggest that enhancing freshwater wetlands via water control structures can benefit juvenile salmonids, at least in the short term, by providing conditions for greater growth, survival, and emigration. ?? Copyright by the American Fisheries Society 2006.

  16. Isolation and Characterization of Salmonid CD4+ T Cells.

    PubMed

    Maisey, Kevin; Montero, Ruth; Corripio-Miyar, Yolanda; Toro-Ascuy, Daniela; Valenzuela, Beatriz; Reyes-Cerpa, Sebastián; Sandino, Ana María; Zou, Jun; Wang, Tiehui; Secombes, Christopher J; Imarai, Mónica

    2016-05-15

    This study reports the isolation and functional characterization of rainbow trout (Oncorhynchus mykiss) CD4-1(+) T cells and the establishment of an IL-15-dependent CD4-1(+) T cell line. By using Abs specific for CD4-1 and CD3ε it was possible to isolate the double-positive T cells in spleen and head kidney. The morphology and the presence of transcripts for T cell markers in the sorted CD4-1(+)CD3ε(+) cells were studied next. Cells were found to express TCRα, TCRβ, CD152 (CTLA-4), CD154 (CD40L), T-bet, GATA-3, and STAT-1. The sorted CD4-1(+) T cells also had a distinctive functional attribute of mammalian T lymphocytes, namely they could undergo Ag-specific proliferation, using OVA as a model Ag. The OVA-stimulated cells showed increased expression of several cytokines, including IFN-γ1, IL-4/13A, IL-15, IL-17D, IL-10, and TGF-β1, perhaps indicating that T cell proliferation led to differentiation into distinct effector phenotypes. Using IL-15 as a growth factor, we have selected a lymphoid cell line derived from rainbow trout head kidney cells. The morphology, cell surface expression of CD4-1, and the presence of transcripts of T cell cytokines and transcription factors indicated that this is a CD4-1(+) T cell line. To our knowledge, this is the first demonstration of the presence of CD4-1(+)CD3ε(+) T cells in salmonids. As in mammals, CD4-1(+) T cells may be the master regulators of immune responses in fish, and therefore these findings and the new model T cell line developed will contribute to a greater understanding of T cell function and immune responses in teleost fish. PMID:27053758

  17. Migratory Behavior and Survival of Juvenile Salmonids in the Lower Columbia River, Estuary, and Plume in 2010

    SciTech Connect

    McMichael, Geoffrey A.; Harnish, Ryan A.; Skalski, John R.; Deters, Katherine A.; Ham, Kenneth D.; Townsend, Richard L.; Titzler, P. Scott; Hughes, Michael S.; Kim, Jin A.; Trott, Donna M.

    2011-09-01

    Uncertainty regarding the migratory behavior and survival of juvenile salmonids passing through the lower Columbia River and estuary after negotiating dams on the Federal Columbia River Power System (FCRPS) prompted the development and application of the Juvenile Salmon Acoustic Telemetry System (JSATS). The JSATS has been used to investigate the survival of juvenile salmonid smolts between Bonneville Dam (river kilometer (rkm) 236) and the mouth of the Columbia River annually since 2004. In 2010, a total of 12,214 juvenile salmonids were implanted with both a passive integrated transponder (PIT) and a JSATS acoustic transmitter. Using detection information from JSATS receiver arrays deployed on dams and in the river, estuary, and plume, the survival probability of yearling Chinook salmon and steelhead smolts tagged at John Day Dam was estimated form multiple reaches between rkm 153 and 8.3 during the spring. During summer, the survival probability of subyearling Chinook salmon was estimated for the same reaches. In addition, the influence of routes of passage (e.g., surface spill, deep spill, turbine, juvenile bypass system) through the lower three dams on the Columbia River (John Day, The Dalles, and Bonneville) on juvenile salmonid smolt survival probability from the dams to rkm 153 and then between rkm 153 and 8.3 was examined to increase understanding of the immediate and latent effects of dam passage on juvenile salmon survival. Similar to previous findings, survival probability was relatively high (>0.95) for most groups of juvenile salmonids from the Bonneville Dam tailrace to about rkm 50. Downstream of rkm 50 the survival probability of all species and run types we examined decreased markedly. Steelhead smolts suffered the highest mortality in this lower portion of the Columbia River estuary, with only an estimated 60% of the tagged fish surviving to the mouth of the river. In contrast, yearling and subyearling Chinook salmon smolts survived to the mouth

  18. Assessing Juvenile Salmonid Passage Through Culverts: Field Research in Support of Protocol Development

    SciTech Connect

    Williams, Greg D.; Evans, Nathan R.; Pearson, Walter H.; Southard, John A.

    2001-10-30

    The primary goal of our research this spring/ summer was to refine techniques and examine scenarios under which a standardized protocol could be applied to assess juvenile coho salmon (O. kisutch) passage through road culverts. Field evaluations focused on capture-mark- recapture methods that allowed analysis of fish movement patterns, estimates of culvert passability, and potential identification of cues inducing these movements. At this stage, 0+ age coho salmon fry 30 mm to 65 mm long (fork length) were the species and age class of interest. Ultimately, the protocol will provide rapid, statistically rigorous methods for trained personnel to perform standardized biological assessments of culvert passability to a number of juvenile salmon species. Questions to be addressed by the research include the following: ? Do hydraulic structures such as culverts restrict habitat for juvenile salmonids? ? How do existing culverts and retrofits perform relative to juvenile salmonid passage? ? Do some culvert characteristics and hydraulic conditions provide better passage than others? ? Does the culvert represent a barrier to certain size classes of fish? Recommendations addressed issues of study site selection, initial capture, marking, recapture/observations, and estimating movement.

  19. Salmonid alphavirus replication in mosquito cells: towards a novel vaccine production system

    PubMed Central

    Hikke, Mia C; Verest, Marjan; Vlak, Just M; Pijlman, Gorben P

    2014-01-01

    Salmonid alphavirus (SAV) causes pancreas disease and sleeping disease in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) and confers a major burden to the aquaculture industry. A commercial inactivated whole virus vaccine propagated in a salmon cell line at low temperature provides effective protection against SAV infections. Alphaviruses (family Togaviridae) are generally transmitted between vertebrate hosts via blood-sucking arthropod vectors, typically mosquitoes. SAV is unique in this respect because it can be transmitted directly from fish to fish and has no known invertebrate vector. Here, we show for the first time that SAV is able to complete a full infectious cycle within arthropod cells derived from the Asian tiger mosquito Aedes albopictus. Progeny virus is produced in C6/36 and U4.4. cells in a temperature-dependent manner (at 15°C but not at 18°C), can be serially passaged and remains infectious to salmonid Chinook salmon embryo cells. This suggests that SAV is not a vertebrate-restricted alphavirus after all and may have the potential to replicate in invertebrates. The current study also shows the ability of SAV to be propagated in mosquito cells, thereby possibly providing an alternative SAV production system for vaccine applications. PMID:24418177

  20. Liquid fat, a potential abiotic vector for horizontal transmission of salmonid alphavirus?

    PubMed

    Stene, A; Hellebø, A; Viljugrein, H; Solevåg, S E; Devold, M; Aspehaug, V

    2016-05-01

    Viral diseases represent serious challenge in marine farming of Atlantic salmon (Salmo salar L). Pancreas disease (PD) caused by a salmonid alphavirus (SAV) is by far the most serious in northern Europe. To control PD, it is necessary to identify virus transmission routes. One aspect to consider is whether the virus is transported as free particles or associated with potential vectors. Farmed salmonids have high lipid content in their tissue which may be released into the environment from decomposing dead fish. At the seawater surface, the effects of wind and ocean currents are most prominent. The aim of this study was primarily to identify whether the lipid fraction leaking from dead infected salmon contains SAV. Adipose tissue from dead SAV-infected fish from three farming sites was submerged in beakers with sea water in the laboratory and stored at different temperature and time conditions. SAV was identified by real-time RT-PCR in the lipid fractions accumulating at the water surface in the beakers. SAV-RNA was also present in the sea water. Lipid fractions were transferred to cell culture, and viable SAV was identified. Due to its hydrophobic nature, fat with infective pathogenic virus at the surface may contribute to long-distance transmission of SAV. PMID:25952607

  1. Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Detroit Dam, 2011

    SciTech Connect

    Khan, Fenton; Royer, Ida M.; Johnson, Gary E.; Ham, Kenneth D.

    2012-11-15

    Pacific Northwest National Laboratory evaluated juvenile salmonid passage and distribution at Detroit Dam (DET) on the North Santiam River, Oregon for the U.S. Army Corps of Engineers (USACE) to provide data to support decisions on long-term measures to enhance downstream passage at DET and others dams in USACE’s Willamette Valley Project. This study was conducted in response to regulatory requirements necessitated by the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. The goal of the study was to provide information of juvenile salmonid passage and distribution at DET from February 2011 through February 2012. The results of the hydroacoustic study provide new and, in some cases, first-ever data on passage estimates, run timing, distributions, and relationships between fish passage and environmental variables at the dam. This information will inform management decisions on the design and development of surface passage and collection devices to help restore Chinook salmon populations in the North Santiam River watershed above DET. During the entire study period, an estimated total of 182,526 smolt-size fish (±4,660 fish, 95% CI) passed through turbine penstock intakes. Run timing peaked in winter and early spring months. Passage rates were highest during late fall, winter and early spring months and low during summer. Horizontal distribution for hours when both turbine units were operated simultaneously indicated Unit 2 passed almost twice as much fish as Unit 1. Diel distribution for smolt-size fish during the study period was fairly uniform, indicating fish were passing the turbines at all times of the day. A total of 5,083 smolt-size fish (± 312 fish, 95% CI) were estimated passed via the spillway when it was open between June 23 and September 27, 2011. Daily passage was low at the spillway during the June-August period, and

  2. Hydroacoustic Evaluation of Juvenile Salmonid Passage and Distribution at Lookout Point Dam, 2010

    SciTech Connect

    Khan, Fenton; Johnson, Gary E.; Royer, Ida M.; Hughes, James S.; Fischer, Eric S.; Trott, Donna M.; Ploskey, Gene R.

    2012-05-31

    Pacific Northwest National Laboratory evaluated juvenile salmonid passage and distribution at Lookout Point Dam (LOP) on the Middle Fork Willamette River for the U.S. Army Corps of Engineers, Portland District (USACE), to provide data to support decisions on long-term measures to enhance downstream passage at LOP and others dams in USACE's Willamette Valley Project. This study was conducted in response to the listing of Upper Willamette River Spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River steelhead (O. mykiss) as threatened under the Endangered Species Act. We conducted a hydroacoustic evaluation of juvenile salmonid passage and distribution at LOP during February 2010 through January 2011. Findings from this 1 year of study should be applied carefully because annual variation can be expected due to variability in adult salmon escapement, egg-to-fry and fry-to-smolt survival rates, reservoir rearing and predation, dam operations, and weather. Fish passage rates for smolt-size fish (> {approx}90 mm and < 300 mm) were highest during December-January and lowest in mid-summer through early fall. Passage peaks were also evident in early spring, early summer, and late fall. During the entire study period, an estimated total of 142,463 fish {+-} 4,444 (95% confidence interval) smolt-size fish passed through turbine penstock intakes. Of this total, 84% passed during December-January. Run timing for small-size fish ({approx}65-90 mm) peaked (702 fish) on December 18. Diel periodicity of smolt-size fish showing crepuscular peaks was evident in fish passage into turbine penstock intakes. Relatively few fish passed into the Regulating Outlets (ROs) when they were open in summer (2 fish/d) and winter (8 fish/d). Overall, when the ROs were open, RO efficiency (RO passage divided by total project passage) was 0.004. In linear regression analyses, daily fish passage (turbines and ROs combined) for smolt-size fish was significantly related to project

  3. Hydroacoustic Assessment of Downstream Migrating Salmonids at the Dalles Dam in Spring and Summer, 1985 Final Report.

    SciTech Connect

    Steig, Tracy W.; Johnson, Ward R.

    1986-02-15

    A hydroacoustic study of downstream migrating salmon and steelhead was conducted at The Dalles Dam. The primary objective was to estimate the effectiveness of the spillway and sluiceway in passing downstream migrants. The secondary goals were to provide information on the horizontal, vertical, and temporal distributions of downstream migrants. June 1, and the summer season was from July 1 to August 15, 1985. Nineteen transducers were deployed to monitor turbine, spillway, and sluiceway locations. The 10 h instantaneous spill effectiveness results showed that spill passed fish more efficiently during the summer study than during the spring study. During the period May 1-31 when the turbines, spillway, and sluiceway were all operating consistently, the sluiceway was found to be the most efficient method of passing fish on a percent flow basis. During the summer study, after the termination of spill, the sluiceway and turbines passed almost equal percentages of fish. The run timing during the spring showed steadily increasing numbers of fish until the peak of the run on May 16. Another, smaller peak occurred on May 20. Thereafter, passage gradually decreased through the end of the spring study. The spring run consisted of yearling chinook, steelhead and sockeye juvenile salmonids. During the summer study, fish passage gradually decreased, except for minor peaks near the beginning of the study. The summer migration consisted primarily of subyearling chinook juvenile salmonids.

  4. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1983 Annual Report.

    SciTech Connect

    Fryer, John L.

    1984-11-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration conducted a study relating to the epidemiology and control of three fish diseases of salmonids in the Columbia River Basin. These three diseases were ceratomyxosis which is caused by the myxosporidan parasite Ceratomyxa shasta, bacterial kidney disease, the etiological agent of which is Renibacterium salmoninarum, and infectious hematopoietic necrosis, which is caused by a rhabdovirus. Each of these diseases is highly destructive and difficult or impossible to treat with antimicrobial agents. The presence of ceratomyxosis in rainbow trout exposed at McNary and Little Goose Dams extends the range of this disease about 200 miles further up the Columbia River and into the Snake River drainage. Wallowa steelhead trout were less resistant to this disease than other upriver stocks tested. Juvenile salmonids entering the Columbia River estuary were collected periodically between May to September, 1983. Nine percent of the beach seined chinook salmon and 5, 11 and 12%, respectively, of the purse seined coho and chinook salmon and steelhead trout were infected with Ceratomyxa shasta. Experiments indicated ceratomyxosis progresses in salt water at the same rate as in fresh water once the fish have become infected. These data indicate a longer exposure to infective stages of C. shasta than previously identified and that approximately 10% of the migrating salmonids are infected and will probably die from this organism after entering salt water. Since sampling began in 1981 the bacterial kidney disease organism, Renibacterium salmoninarum, has been detected by the fluorescent antibody test in seven salmonid species caught in the open ocean off the coasts of Washington and Oregon. The bacterium has been found primarily in chinook salmon (11%) with lesions in 2.5% of these fish. This disease was also detected at levels ranging from 17% in coho salmon to 25% in chinook

  5. Effects of Catch-and-Release Angling on Salmonids at Elevated Water Temperatures

    SciTech Connect

    Boyd, James W.; Guy, Christopher S.; Horton, Travis; Leathe, Steven A.

    2010-08-01

    Few studies have assessed catch and release mortality of salmonids at water temperatures ≥23°C, despite predictions of warming stream temperatures due to climate change. In addition, the effects of diel temperature fluctuations on salmonid mortality have largely been ignored in catch and release angling studies. The primary objective of this study was to measure catch and release mortality of rainbow trout Oncorhynchus mykiss, brown trout Salmo trutta, and mountain whitefish Prosopium williamsoni in three water temperature treatments; when daily maximum water temperatures were cool (<20°C), warm (20 to 22.9°C), and hot ( 23°C). A secondary objective was to assess catch and release mortality of salmonids angled in morning and evening within water-temperature treatments. These objectives were related to Montana Fish, Wildlife and Parks’ Drought Fishing Closure Policy (DFCP). Angling (fly-fishing only) occurred in the Gallatin and Smith rivers. All angled fish were confined to in-stream holding cages and monitored for mortality for 72 h. Mortality of rainbow trout peaked at 16% in the Gallatin River and 9% in the Smith River during the hot treatment. Mortality of brown trout was less than 5% in all water-temperature treatments in both rivers. Mountain whitefish mortality peaked at 28% in the hot treatment in the Smith River. No mortality for any species occurred in either river when daily maximum water temperatures were <20°C. Mortality of rainbow trout peaked at 16% in the evening hot treatment in the Smith River. Mortality of brown trout and mountain whitefish was not related to time of day. The catch and release mortality values presented here likely represent fishing mortality given that most anglers in southwest Montana practice catch and release angling. The mortality values we observed were lower than predicted (< 30%), given reports in the literature. The difference is likely related to the in situ nature of the study and periods of cooler water

  6. Ichthyophonus-induced cardiac damage: a mechanism for reduced swimming stamina in salmonids

    USGS Publications Warehouse

    Kocan, R.; LaPatra, S.; Gregg, J.; Winton, J.; Hershberger, P.

    2006-01-01

    Swimming stamina, measured as time-to-fatigue, was reduced by approximately two-thirds in rainbow trout experimentally infected with Ichthyophonus. Intensity of Ichthyophonus infection was most severe in cardiac muscle but multiple organs were infected to a lesser extent. The mean heart weight of infected fish was 40% greater than that of uninfected fish, the result of parasite biomass, infiltration of immune cells and fibrotic (granuloma) tissue surrounding the parasite. Diminished swimming stamina is hypothesized to be due to cardiac failure resulting from the combination of parasite-damaged heart muscle and low myocardial oxygen supply during sustained aerobic exercise. Loss of stamina in Ichthyophonus-infected salmonids could explain the poor performance previously reported for wild Chinook and sockeye salmon stocks during their spawning migration. ?? 2006 Blackwell Publishing Ltd.

  7. The contribution of molecular epidemiology to the understanding and control of viral diseases of salmonid aquaculture

    PubMed Central

    2011-01-01

    Molecular epidemiology is a science which utilizes molecular biology to define the distribution of disease in a population (descriptive epidemiology) and relies heavily on integration of traditional (or analytical) epidemiological approaches to identify the etiological determinants of this distribution. The study of viral pathogens of aquaculture has provided many exciting opportunities to apply such tools. This review considers the extent to which molecular epidemiological studies have contributed to better understanding and control of disease in aquaculture, drawing on examples of viral diseases of salmonid fish of commercial significance including viral haemorrhagic septicaemia virus (VHSV), salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV). Significant outcomes of molecular epidemiological studies include: Improved taxonomic classification of viruses A better understanding of the natural distribution of viruses An improved understanding of the origins of viral pathogens in aquaculture An improved understanding of the risks of translocation of pathogens outwith their natural host range An increased ability to trace the source of new disease outbreaks Development of a basis for ensuring development of appropriate diagnostic tools An ability to classify isolates and thus target future research aimed at better understanding biological function While molecular epidemiological studies have no doubt already made a significant contribution in these areas, the advent of new technologies such as pyrosequencing heralds a quantum leap in the ability to generate descriptive molecular sequence data. The ability of molecular epidemiology to fulfil its potential to translate complex disease pathways into relevant fish health policy is thus unlikely to be limited by the generation of descriptive molecular markers. More likely, full realisation of the potential to better explain viral transmission pathways will be dependent on the ability to assimilate and

  8. Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin, Annual Report 2000-2001.

    SciTech Connect

    White, Tara C.; Jewett, Shannon M.; Hanson, Josh T.

    2003-04-11

    This is the seventh year of a multi-year project, monitoring the outmigration and survival of juvenile salmonids in the lower Umatilla River. This project both supplements and complements ongoing and completed work within the Umatilla River basin. Knowledge gained on juvenile outmigration and survival assists researchers and managers in adapting hatchery practices, flow enhancement strategies, canal and fish ladder operations, and supplementation and enhancement efforts of natural and restored fish populations. Findings from this study also measure the success of upriver habitat improvement projects and provide an overall evaluation of the Umatilla River fisheries restoration program. The general objectives for 2001 were to: (1) Estimate migrant abundance and survival and determine migration parameters of PIT-tagged hatchery and natural juvenile salmonids; (2) Monitor natural production and estimate overall abundance of pacific lamprey, chinook and coho salmon and summer steelhead; (3) Assess the condition and health of migrants and determine length-frequency distributions through time; (4) Investigate the effects of canal and fishway operations and environmental conditions on fish migration and survival; (5) Investigate and implement improved tag monitoring capabilities; and (6) Participate in planning and coordination activities within the basin and disseminate results. More specifically, 2001 objectives included the ongoing evaluation of migrant abundance and survival of tagged hatchery fish groups from various species-specific hatchery, rearing, acclimation and release strategies; fourth year reach survival results; continuation of transport evaluation studies; outmigrant monitoring and estimation of natural abundance, and further investigation of the effects of canal operations, environmental factors, fish condition and health on migration, abundance and survival. Some of the key findings for 2001 are: (1) A significant decline in outmigrant abundance of

  9. Testing Geomorphic Controls on Salmonid Spawning Habitat

    NASA Astrophysics Data System (ADS)

    Pfeiffer, A.; Finnegan, N. J.

    2014-12-01

    The physical architecture of a landscape, as recorded in topography, is a major factor driving the spatial distribution of river habitat within a catchment. For this reason, predictive geomorphic models for fluvial characteristics, particularly grain size, have been suggested as possible contributors to salmonid habitat identification efforts. However, to our knowledge, no work has been done to both implement geomorphic predictions of reach-scale grain size and then test those predictions with salmonid habitat use data. We present a physically-based, empirically calibrated approach to predicting grain size distributions from high resolution LiDAR (Light Detection and Ranging)-derived topographic data. This approach builds on previous efforts in that it predicts the full grain size distribution, rather than just median grain size, and incorporates an empirically calibrated shear stress partitioning factor. We use the predicted grain size distributions to calculate the fraction of the bed area movable by salmon of a given size, which we then compare to 7 years of steelhead trout and coho salmon spawning survey data for a 77 km2 watershed along the central California Coast. We find that grain size explains the paucity of spawning in the upper reaches of the drainage, but does not explain variation within the mainstem. In order to explain the residuals in spawning within the mainstem, we turn to the spacing of riffle bedforms. Field surveys of riffle spacing explain 64% of the variation in spawning in these reaches, suggesting that spawning is ultimately limited by the availability of riffles. Because riffle spacing varies systematically with channel width, we show that predicting riffle spacing is feasible with LiDAR data. Taken together, these findings highlight both the value and limitations of a grain-size focused approach to habitat prediction, and suggest that such approaches should be used in concert with predictions of channel bed morphology.

  10. Estimated loss of juvenile salmonids to predation by northern squawfish, walleyes, and smallmouth bass in John Day Reservoir, Columbia River. [Oncorhynchus spp. ; Ptychocheilus oregonensis; Stizostedion vitreum; Micropterus dolomieu; O. tshawytscha

    SciTech Connect

    Rieman, B.E.; Beamesderfer, R.C. ); Vigg, S.; Poe, T.P. )

    1991-07-01

    The authors estimated the loss of juvenile salmonids Oncorhynchus spp. to predation by northern squawfish Ptychocheilus oregonensis, walleyes Stizostedion vitreum, and smallmouth bass Micropterus dolomieu in John Day Reservoir during 1983-1986. Their estimates were based on measures of daily prey consumption, predator numbers, and numbers of juvenile salmonids entering the reservoir during the April-August period of migration. They estimated the mean annual loss was 2.7 million juvenile salmonids. Northern squawfish were responsible for 78% of the total loss; walleyes accounted for 13% and smallmouth bass for 9%. Twenty-one percent of the loss occurred in a small area immediately below McNary Dam at the head of John Day Reservoir. The authors estimated that the three predator species consumed 14% of all juvenile salmonids that entered the reservoir. Mortality changed by month and increased late in the migration season. Monthly mortality estimates ranged from 7% in June and 61% in August. Mortality from predation was highest for chinook salmon O. tshawytscha, which migrated in July and August. Despite uncertainties in the estimates, it is clear that predation by resident fish predators can easily account for previously explained mortality of out-migrating juvenile salmonids. Alteration of the Columbia River by dams and a decline in the number of salmonids could have increased the fraction of mortality caused by predation over what is was in the past.

  11. Mortality and weight loss of Atlantic salmon, Salmon salar L., experimentally infected with salmonid alphavirus subtype 2 and subtype 3 isolates from Norway.

    PubMed

    Taksdal, T; Jensen, B Bang; Böckerman, I; McLoughlin, M F; Hjortaas, M J; Ramstad, A; Sindre, H

    2015-12-01

    Pancreas disease (PD) caused by salmonid alphavirus (SAV) has a significant negative economic impact in the salmonid fish farming industry in northern Europe. Until recently, only SAV subtype 3 was present in Norwegian fish farms. However, in 2011, a marine SAV 2 subtype was detected in a fish farm outside the PD-endemic zone. This subtype has spread rapidly among fish farms in mid-Norway. The PD mortality in several farms has been lower than expected, although high mortality has also been reported. In this situation, the industry and the authorities needed scientific-based information about the virulence of the marine SAV 2 strain in Norway to decide how to handle this new situation. Atlantic salmon post-smolts were experimentally infected with SAV 2 and SAV 3 strains from six different PD cases in Norway. SAV 3-infected fish showed higher mortality than SAV 2-infected fish. Among the SAV 3 isolates, two isolates gave higher mortality than the third one. At the end of the experiment, fish in all SAV-infected groups had significantly lower weight than the uninfected control fish. This is the first published paper on PD to document that waterborne infection produced significantly higher mortality than intraperitoneal injection. PMID:25322679

  12. Sensitivity of salmonid freshwater life history in western US streams to future climate conditions.

    PubMed

    Beer, W Nicholas; Anderson, James J

    2013-08-01

    We projected effects of mid-21st century climate on the early life growth of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in western United States streams. Air temperature and snowpack trends projected from observed 20th century trends were used to predict future seasonal stream temperatures. Fish growth from winter to summer was projected with temperature-dependent models of egg development and juvenile growth. Based on temperature data from 115 sites, by mid-21st century, the effects of climate change are projected to be mixed. Fish in warm-region streams that are currently cooled by snow melt will grow less, and fish in suboptimally cool streams will grow more. Relative to 20th century conditions, by mid-21st century juvenile salmonids' weights are expected to be lower in the Columbia Basin and California Central Valley, but unchanged or greater in coastal and mountain streams. Because fish weight affects fish survival, the predicted changes in weight could impact population fitness depending on other factors such as density effects, food quality and quantity changes, habitat alterations, etc. The level of year-to-year variability in stream temperatures is high and our analysis suggests that identifying effects of climate change over the natural variability will be difficult except in a few streams. PMID:23640715

  13. Surface Flow Outlets to Protect Juvenile Salmonids Passing through Hydropower Dams

    SciTech Connect

    Johnson, Gary E.; Dauble, Dennis D.

    2006-10-27

    We reviewed results of research conducted by engineers and biologists over the past 50 years related to development of surface flow outlets (SFOs) for juvenile salmonids that migrate downstream past hydropower dams. An SFO is a non-turbine, water-efficient passage route with an overflow structure through which flow and fish pass over a dam. Our review covered 69 SFOs in Europe and North America. We identified five main types of SFOs ? low-flow bypass/sluices, high-flow sluices, forebay collectors, powerhouse retrofits, and surface spills. Most low-flow bypass/sluices are sited in Europe and on the east coast of North America, where mean annual project discharge and hydropower production for the dams we reviewed were 95 m3/s and 15 MW, respectively. The other four SFO types are found at dams on the west coast of North America with 2184 m3/s mean annual discharge and 788 MW mean output. A conceptual framework based on fish behavior and hydraulics for different regions of a hydropower project was developed to evaluate SFO performance. For all SFO types, fish collection efficiency averaged 54%, with an average effectiveness ratio of 17:1 (fish to inflow). Surface flow outlet technology can meet the goal of concurrent anadromous fish protection and hydropower generation.

  14. Comparing Remote Sensing Techniques in Detecting Salmonid Habitat, Salmon River, Oregon

    NASA Astrophysics Data System (ADS)

    Shintani, C. M.

    2015-12-01

    Many restoration projects in the Pacific Northwest are implemented to improve habitat quality, quantity, and complexity for fish. Although numerous engineered log structures have been constructed in the hopes of achieving these goals, relatively few projects have been rigorously monitored to determine their success. This research seeks to compare the utility and application between photogrammetric and spectral depth approaches in detecting fish habitat in order to determine which method is more accurate and affordable for monitoring channel bathymetry. While each of these techniques has been individually studied, previous research has not directly compared and quantified their differences. Channel bathymetry data were collected by combining pre- and post-restoration digital photographs of the Salmon River in Northeast Clackamas County, Oregon, using structure-from-motion (SfM). The resulting 3D point cloud will be used to estimate water depths using photogrammetry and spectral depth. The photogrammetric method applies a refraction correction to the extracted water depth from the SfM topography to derive water depth. A regression between the surveyed water depth values and digital number values of surface pixels will derive depth. The resulting water depths from these two methods will be compared to the surveyed water depths for their accuracy and precision, particularly in critical salmonid habitats. The quantification of these differences will be an important contribution to river restoration science as it will allow for more accurate measurement and monitoring of changes in fish habitat. In the future, these data will be used in an eco-hydraulic River2D model to simulate changes in salmonid habitat availability after restoration.

  15. Columbia River System Operation Review : Final Environmental Impact Statement, Appendix C: Anadromous Fish and Juvenile Fish Transportation.

    SciTech Connect

    Columbia River System Operation Review

    1995-11-01

    This Appendix C of the Final Environmental Impact Statement for the Columbia River System discusses impacts on andromous fish and juvenile fish transportation. The principal andromous fish in the Columbia basin include salmonid species (Chinook, coho, and sockeye salmon, and steelhead) and nonsalmoinid andromous species (sturgeon, lamprey, and shad). Major sections in this document include the following: background, scope and process; affected environment for salmon and steelhead, shaded, lamprey, sturgeon; study methods; description of alternatives: qualitative and quantitative findings.

  16. Levels of Renibacterium salmoninarum antigens in resident and anadromous salmonids in the River Ellidaár system in Iceland.

    PubMed

    Kristmundsson, Á; Árnason, F; Gudmundsdóttir, S; Antonsson, T

    2016-06-01

    In relation to stock enhancement programmes, wild salmon broodfish have been routinely screened for the presence of Renibacterium salmoninarum antigens (Rs-Ag) for decades. A sudden increase in the prevalence of Rs-Ag experienced caused extensive problems to this industry as eggs from positive fish are discarded. The prevalence and level of Rs-Ag were examined in resident and anadromous salmonids in the River Ellidaár system and the progress of Rs-Ag in a cohort of salmon followed. Both prevalence and Rs-Ag levels were high in resident salmonids and emigrating salmon smolts in the river system. When the smolts re-entered their home river as adults the following summer, they were almost free of Rs-Ag, but the longer they stayed in the river, the more Rs-Ag they acquired; the majority being positive at spawning. This study demonstrates a high level of Rs-Ag in salmonids in the River Ellidaár system which significantly reduces in the salmon during its seawater phase. Accordingly, it seems ideal to sample salmon broodfish as soon as possible after ascending the river and subsequently transfer to Rs-free environment for storage until stripping, which could result in lower Rs-prevalence and minimize the problems that stock enhancement programmes have faced due to Rs-positive wild broodfish. PMID:26275672

  17. MHC evolution in three salmonid species: a comparison between class II alpha and beta genes.

    PubMed

    Gómez, Daniela; Conejeros, Pablo; Marshall, Sergio H; Consuegra, Sofia

    2010-08-01

    The genes of the major histocompatibility complex (MHC) are amongst the most variable in vertebrates and represent some of the best candidates to study processes of adaptive evolution. However, despite the number of studies available, most of the information on the structure and function of these genes come from studies in mammals and birds in which the MHC class I and II genes are tightly linked and class II alpha exhibits low variability in many cases. Teleost fishes are among the most primitive vertebrates with MHC and represent good organisms for the study of MHC evolution because their class I and class II loci are not physically linked, allowing for independent evolution of both classes of genes. We have compared the diversity and molecular mechanisms of evolution of classical MH class II alpha and class II beta loci in farm populations of three salmonid species: Oncorhynchus kisutch, Oncorhynchus mykiss and Salmo salar. We found single classical class II loci and high polymorphism at both class II alpha and beta genes in the three species. Mechanisms of evolution were common for both class II genes, with recombination and point mutation involved in generating diversity and positive selection acting on the peptide-binding residues. These results suggest that the maintenance of variability at the class IIalpha gene could be a mechanism to increase diversity in the MHC class II in salmonids in order to compensate for the expression of one single classical locus and to respond to a wider array of parasites. PMID:20521040

  18. The phylogeography of salmonid proliferative kidney disease in Europe and North America.

    PubMed Central

    Henderson, Matthew; Okamura, Beth

    2004-01-01

    Salmonid proliferative kidney disease (PKD) is caused by the myxozoan Tetracapsuloides bryosalmonae. Given the serious and apparently growing impact of PKD on farmed and wild salmonids, we undertook a phylogeographic study to gain insights into the history of genealogical lineages of T. bryosalmonae in Europe and North America, and to determine if the global expansion of rainbow trout farming has spread the disease. Phylogenetic analyses of internal transcribed spacer 1 sequences revealed a clade composed of all North American sequences plus a subset of Italian and French sequences. High genetic diversity in North America and the absence of genotypes diagnostic of the North American clade in the rest of Europe imply that southern Europe was colonized by immigration from North America; however, sequence divergence suggests that this colonization substantially pre-dated fisheries activities. Furthermore, the lack of southern European lineages in the rest of Europe, despite widespread rainbow trout farming, indicates that T. bryosalmonae is not transported through fisheries activities. This result strikingly contrasts with the commonness of fisheries-related introductions of other pathogens and parasites and indicates that fishes may be dead-end hosts. Our results also demonstrate that European strains of T. bryosalmonae infect and induce PKD in rainbow trout introduced to Europe. PMID:15306294

  19. Breeding salmonids for feed efficiency in current fishmeal and future plant-based diet environments

    PubMed Central

    Quinton, Cheryl D; Kause, Antti; Koskela, Juha; Ritola, Ossi

    2007-01-01

    The aquaculture industry is increasingly replacing fishmeal in feeds for carnivorous fish with soybean meal (SBM). This diet change presents a potential for genotype-environment (G × E) interactions. We tested whether current salmonid breeding programmes that evaluate and select within fishmeal diets also improve growth and efficiency on potential future SBM diets. A total of 1680 European whitefish from 70 families were reared with either fishmeal- or SBM-based diets in a split-family design. Individual daily gain (DG), daily feed intake (DFI) and feed efficiency (FE) were recorded. Traits displayed only weak G × E interactions as variances and heritabilities did not differ substantially between the diets, and cross-diet genetic correlations were near unity. In both diets, DFI exhibited moderate heritability and had very high genetic correlation with DG whereas FE had low heritability. Predicted genetic responses demonstrated that selection to increase DG and FE on the fishmeal diet lead to favourable responses on the SBM diet. Selection for FE based on an index including DG and DFI achieved at least double FE gain versus selection on DG alone. Therefore, current breeding programmes are improving the biological ability of salmonids to use novel plant-based diets, and aiding the aquaculture industry to reduce fishmeal use. PMID:17612482

  20. CHEMICAL RISKS TO THREATENED AND ENDANGERED FISH SPECIES AT CONCENTRATIONS BELOW WATER QUALITY CRITERIA: IS IT FEASIBLE TO ENSURE PROTECTION OF INDIVIDUALS

    EPA Science Inventory

    The USGS Laboratory in Columbia, Missouri has evaluated the acute sensitivities of 17 threatened and endangered fish species (including three salmonids), to five different chemicals (carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin). The results of these studie...

  1. Prevalence of infectious salmon anaemia virus (ISAV) in wild salmonids in western Norway.

    PubMed

    Plarre, H; Devold, M; Snow, M; Nylund, A

    2005-08-01

    Studies of infectious salmon anaemia virus (ISAV), an important pathogen of farmed salmon in Norway, Scotland, the Faeroe Islands, Ireland, Canada, the USA and Chile, suggest that natural reservoirs for this virus can be found on both sides of the North Atlantic. Based on existing information about ISAV it is believed to be maintained in wild populations of trout and salmon in Europe. It has further been suggested that ISAV is transmitted between wild hosts, mainly during their freshwater spawning phase in rivers, and that wild salmonids, mainly trout, are possible carriers of benign wild-type variants of ISAV. Change in virulence is probably a result of deletions of amino acid segments from the highly polymorphic region (HPR) of benign wild-type isolates after transmission to farmed salmon. Hence, it has been suggested that the frequency of new outbreaks of ISA in farmed salmon could partly reflect natural variation in the prevalence of ISAV in wild populations of salmonids. The aims of the present study were to screen for ISAV in wild salmonids during spawning in rivers and to determine the pathogenicity of resultant isolates from wild fish. Tissues from wild salmonids were screened by RT-PCR and real-time PCR. The prevalence of ISAV in wild trout Salmo trutta varied from 62 to 100% between tested rivers in 2001. The prevalence dropped in 2002, ranging from 13 to 36% in the same rivers and to only 6% in 2003. All ISAV were nonpathogenic when injected into disease-free Atlantic salmon, but were capable of propagation, as indicated by subsequent viral recovery. However, non-pathogenic ISAV has also been found in farmed salmon, where a prevalence as high as 60% has been registered, but with no mortalities occurring. Based on the results of the present and other studies, it must be concluded that vital information about the importance of wild and man-made reservoirs for the emergence of ISA in salmon farming is still lacking. This information can only be gained by

  2. Salmonid redd dewatering: What do we know

    SciTech Connect

    Becker, C D; Neitzel, D A

    1983-11-01

    Dewatering of salmonid spawning areas causes abrupt changes in the intergravel environment that may lead to extensive losses of development phases while intergravel in redds. Information on tolerance to dewatering and the extent of physicochemical changes in the gravel during dewatering can be used to assess potential impacts and to design and implement effective mitigation methods. Studies with fall chinook salmon are summarized, and the comparisons are made with results from available literature. Potentially useful methods of mitigation are mentioned. We found that prehatch phases (cleavage eggs and embryos) can be dewatered for several successive days and survive, but posthatch phases (eleutheroembryos and alevins) usually die within 24 hours. Survival of prehatch phases during extended dewatering requires maintenance of favorable intergravel temperature and moisture levels. Elevated temperatures (up to 22/sup 0/C) can be tolerated for up to 8 hours without direct adverse effects, but freezing temperatures (/sup -/1.0/sup 0/C or below) are lethal. Dewatered gravels must remain sufficient moisture to provide near 100% humidity for egg and embryo survival. In field situations, physicochemical conditions that limit survival in dewatered gravels include residual flow, temperature, gravel size and composition, and dissolved oxygen. Biological variables such as alevin behavior and certain species characteristics also influence survival. 29 refs., 6 figs.

  3. Density, aggregation, and body size of northern pikeminnow preying on juvenile salmonids in a large river

    USGS Publications Warehouse

    Petersen, J.H.

    2001-01-01

    Predation by northern pikeminnow Ptychocheilus oregonensis on juvenile salmonids Oncorhynchus spp. occurred probably during brief feeding bouts since diets were either dominated by salmonids (>80% by weight), or contained other prey types and few salmonids (<5%). In samples where salmonids had been consumed, large rather than small predators were more likely to have captured salmonids. Transects with higher catch-per-unit of effort of predators also had higher incidences of salmonids in predator guts. Predators in two of three reservoir areas were distributed more contagiously if they had preyed recently on salmonids. Spatial and temporal patchiness of salmonid prey may be generating differences in local density, aggregation, and body size of their predators in this large river.

  4. Vertical transmission of Tetracapsuloides bryosalmonae (Myxozoa), the causative agent of salmonid proliferative kidney disease.

    PubMed

    Abd-Elfattah, Ahmed; Fontes, Inês; Kumar, Gokhlesh; Soliman, Hatem; Hartikainen, Hanna; Okamura, Beth; El-Matbouli, Mansour

    2014-04-01

    The freshwater bryozoan, Fredericella sultana, is the main primary host of the myxozoan endoparasite, Tetracapsuloides bryosalmonae which causes proliferative kidney disease (PKD) of salmonid fish. Because spores that develop in bryozoan colonies are infectious to fish, bryozoans represent the ultimate source of PKD. Bryozoans produce numerous seed-like dormant stages called statoblasts that enable persistence during unfavourable conditions and achieve long-distance dispersal. The possibility that T. bryosalmonae may undergo vertical transmission via infection of statoblasts has been the subject of much speculation since this is observed in close relatives. This study provides the first evidence that such vertical transmission of T. bryosalmonae is extensive by examining the proportions of infected statoblasts in populations of F. sultana on two different rivers systems and confirms its effectiveness by demonstrating transmission from material derived from infected statoblasts to fish hosts. Vertical transmission in statoblasts is likely to play an important role in the infection dynamics of both bryozoan and fish hosts and may substantially contribute to the widespread distribution of PKD. PMID:24229733

  5. An assessment of salmon farms and wild salmonids as sources of Lepeophtheirus salmonis (Krøyer) copepodids in the water column in Loch Torridon, Scotland.

    PubMed

    Penston, M J; Davies, I M

    2009-01-01

    Wild salmonids and farmed salmon can both be sources of Lepeophtheirus salmonis (Krøyer, 1838) larvae. Farmed salmon smolts free of L. salmonis infections are stocked in sea cages and may subsequently contract L. salmonis infections, probably from wild fish. The contribution of gravid L. salmonis at Atlantic salmon, Salmo salar L., farms to populations of L. salmonis larvae in the water column has in the past been based on estimated parameters, such as louse fecundity. This present study augments these calculations by combining empirical data on densities of infective L. salmonis copepodids in the field with estimates of the number of gravid L. salmonis on farmed and wild salmonids in Loch Torridon. Data collected between 2002 and 2007 show a significant correlation between mean densities of L. salmonis copepodids recovered in the water column and the numbers of gravid L. salmonis at the local salmon farms. Generally, the farms with greatest numbers of salmon were observed to have stronger correlations with densities of copepodids in the water than the farms with fewer fish. The study suggests that louse management approaches, e.g. treatment trigger levels, need to take account of individual farm biomass, or numbers of fish. This study highlights the importance of control of L. salmonis on salmon farms for the co-existence of both wild salmonid populations and the aquaculture industry. PMID:19245632

  6. Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast

    PubMed Central

    Siah, Ahmed; Morrison, Diane B.; Fringuelli, Elena; Savage, Paul; Richmond, Zina; Johns, Robert; Purcell, Maureen K.; Johnson, Stewart C.; Saksida, Sonja M.

    2015-01-01

    Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period. PMID:26536673

  7. Pathways of Barotrauma in Juvenile Salmonids Exposed to Simulated Hydroturbine Passage: Boyle’s Law vs. Henry’s Law

    SciTech Connect

    Brown, Richard S.; Pflugrath, Brett D.; Colotelo, Alison HA; Brauner, Colin J.; Carlson, Thomas J.; Deng, Zhiqun; Seaburg, Adam

    2012-06-01

    On their seaward migration, juvenile salmonids commonly pass hydroelectric dams. Fish passing by the turbine blade may experience rapid decompression, the severity of which can be highly variable and may result in a number of barotraumas. The mechanisms of these injuries can be due to expansion of existing bubbles or gases coming out of solution; governed by Boyle’s Law and Henry’s Law, respectively. This paper combines re-analysis of published data with new experiments to gain a better understanding of the mechanisms of injury and mortality for fish experiencing rapid decompression associated with hydroturbine passage. From these data it appears that the majority of decompression related injuries are due to the expansion of existing bubbles in the fish, particularly the expansion and rupture of the swim bladder. This information is particularly useful for fisheries managers and turbine manufacturers, demonstrating that reducing the rate of swim bladder ruptures by reducing the frequency of occurrence and severity of rapid decompression during hydroturbine passage could reduce the rates of injury and mortality for hydroturbine passed juvenile salmonids.

  8. Piscine reovirus: Genomic and molecular phylogenetic analysis from farmed and wild salmonids collected on the Canada/US Pacific Coast

    USGS Publications Warehouse

    Siah, Ahmed; Morrison, Diane B.; Fringuelli, Elena; Savage, Paul S.; Richmond, Zina; Purcell, Maureen K.; Johns, Robert; Johnson, Stewart C.; Sakasida, Sonja M.

    2015-01-01

    Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

  9. Evolutionary consequences of habitat loss for Pacific anadromous salmonids

    PubMed Central

    McClure, Michelle M; Carlson, Stephanie M; Beechie, Timothy J; Pess, George R; Jorgensen, Jeffrey C; Sogard, Susan M; Sultan, Sonia E; Holzer, Damon M; Travis, Joseph; Sanderson, Beth L; Power, Mary E; Carmichael, Richard W

    2008-01-01

    Large portions of anadromous salmonid habitat in the western United States has been lost because of dams and other blockages. This loss has the potential to affect salmonid evolution through natural selection if the loss is biased, affecting certain types of habitat differentially, and if phenotypic traits correlated with those habitat types are heritable. Habitat loss can also affect salmonid evolution indirectly, by reducing genetic variation and changing its distribution within and among populations. In this paper, we compare the characteristics of lost habitats with currently accessible habitats and review the heritability of traits which show correlations with habitat/environmental gradients. We find that although there is some regional variation, inaccessible habitats tend to be higher in elevation, wetter and both warmer in the summer and colder in the winter than habitats currently available to anadromous salmonids. We present several case studies that demonstrate either a change in phenotypic or life history expression or an apparent reduction in genetic variation associated with habitat blockages. These results suggest that loss of habitat will alter evolutionary trajectories in salmonid populations and Evolutionarily Significant Units. Changes in both selective regime and standing genetic diversity might affect the ability of these taxa to respond to subsequent environmental perturbations. Both natural and anthropogenic and should be considered seriously in developing management and conservation strategies. PMID:25567633

  10. Juvenile salmonid migratory behavior at the mouth of the Columbia River and within the plume

    SciTech Connect

    McMichael, Geoffrey A.; O'Toole, Amanda C.; Harnish, Ryan A.; Trott, Donna M.

    2013-01-01

    A total of 8,159 acoustic-tagged salmonid smolts were detected at the mouth of the Columbia River. Of the fish detected at the mouth, 14% of yearling Chinook salmon, 9% of steelhead, and 22% of subyearling Chinook salmon were detected on a sparse array deployed in the Columbia River plume. Chinook salmon smolts decreased travel rate as they left the river and entered the plume, while steelhead increased travel rate. Chinook salmon also spent more time in the transitional area between the river mouth and plume as compared to steelhead. In early spring, yearling Chinook salmon and steelhead predominately migrated past the plume array towards the edge of the shelf and to the south. Later in the season, yearling Chinook salmon and steelhead smolts tended to migrate out of the river mouth in a northerly direction. Subyearling Chinook salmon migrated predominately past the portion of the plume array to the north of the river mouth.

  11. Global climate change and effects on Pacific Northwest salmonids: An exploratory case study

    SciTech Connect

    Shankle, S.A.

    1990-09-01

    Recently, a number of papers have addressed global warming and freshwater fisheries. The recent report to Congress by the US Environmental Protection Agency included an analysis of potential effects of global warming on fisheries of the Great Lakes, California, and the Southeast. In California, the report stated that salinity increases in the San Francisco Bay could enhance the abundance of marine fish species, while anadromous species could be adversely affected. This paper discusses global climate changes and the effects on Pacific Northwest Salmonids. The impacts of climate change or Spring Chinook production in the Yakima Sub-basin was simulated using a computer modeling system developed for the Northwest Power planning council. 35 refs., 1 fig., 1 tab.

  12. Histopathology and ultrastructure of ocular lesions associated with gas bubble disease in salmonids.

    PubMed

    Speare, D J

    1990-11-01

    Ocular lesions associated with natural and experimental outbreaks of gas bubble disease (GBD) in commercial salmonids were assessed histologically and by scanning electron microscopy. Small gas emboli were first detected in the choroid gland of the posterior uvea. In subacute and chronic cases, bubble size increased markedly and localization in retrobulbar and periocular sites was favoured. During the acute phase of GBD, ocular lesions were limited to anatomical displacement of tissue and local degeneration of compressed tissues around the perimeter of bubbles. Subacute sequelae included the formation of anterior synechia, lens cataract, and suppurative panophthalmitis. During chronic stages, when large retrobulbar bubbles had caused severe exophthalmia, there was stretching of the optic nerve and of retinal blood vessels and severe distortion of the posterior aspects of the globe. The sequential development, pathogenesis and persistence of ocular lesions associated with GBD in fish are discussed. PMID:2079557

  13. Turbulence Investigation and Reproduction for Assisting Downstream Migrating Juvenile Salmonids, Part II of II; Effects of Induced Turbulence on Behavior of Juvenile Salmon, 2001-2005 Final Report.

    SciTech Connect

    Perry, Russell W.; Farley, M. Jared; Hansen, Gabriel S.

    2005-07-01

    Passage through dams is a major source of mortality of anadromous juvenile salmonids because some populations must negotiate up to eight dams in Columbia and Snake rivers. Dams cause direct mortality when fish pass through turbines, but dams may also cause indirect mortality by altering migration conditions in rivers. Forebays immediately upstream of dams have decreased the water velocity of rivers and may contribute substantially to the total migration delay of juvenile salmonids. Recently, Coutant (2001a) suggested that in addition to low water velocities, lack of natural turbulence may contribute to migration delay by causing fish to lose directional cues. Coutant (2001a) further hypothesized that restoring turbulence in dam forebays may reduce migration delay by providing directional cues that allow fish to find passage routes more quickly (Coutant 2001a). Although field experiments have yielded proof of the concept of using induced turbulence to guide fish to safe passage routes, little is known about mechanisms actually causing behavioral changes. To test hypotheses about how turbulence influences movement and behavior of migrating juvenile salmonids, we conducted two types of controlled experiments at Cowlitz Falls Dam, Washington. A common measure of migration delay is the elapsed time between arrival at, and passage through, a dam. Therefore, for the first set of experiments, we tested the effect of induced turbulence on the elapsed time needed for fish to traverse through a raceway and pass over a weir at its downstream end (time trial experiment). If turbulence helps guide fish to passage routes, then fish should pass through the raceway quicker in the presence of appropriately scaled and directed turbulent cues. Second, little is known about how the physical properties of water movement provide directional cues to migrating juvenile salmonids. To examine the feasibility of guiding fish with turbulence, we tested whether directed turbulence could guide

  14. Hydroacoustic Evaluation of Juvenile Salmonid Passage at The Dalles Dam Sluiceway, 2005

    SciTech Connect

    Johnson, Gary E.; Khan, Fenton; Hedgepeth, J; Mueller, Robert P.; Rakowski, Cynthia L.; Richmond, Marshall C.; Serkowski, John A.; Skalski, John R.

    2006-06-01

    The U.S. Army Corps of Engineers Portland District engaged the Pacific Northwest National Laboratory to evaluate fish passage at The Dalles Dam powerhouse in 2005. The goal of the study was to provide information on smolt passage that will inform decisions on long-term measures and operations to enhance sluiceway passage and reduce turbine passage to improve smolt survival at the dam. The study addressed one of the main programs dedicated to improving juvenile salmonid survival at The Dalles Dam: Surface Flow Bypass. The study objectives (see below) were met using a combination of hydroacoustic and hydraulic data. The study incorporated fixed-location hydroacoustic methods across the entire powerhouse, with especially intense sampling using multiple split-beam transducers at all sluiceway portals. We did not sample fish passage at the spillway in 2005. In the sluiceway nearfield, we used an acoustic camera to track fish movements. The fish data were interpreted with hydraulic data from a computational fluid dynamics (CFD) model. Fish passage data were collected in the framework of an “experiment” using a randomized block design (3-day treatments; two treatments) to compare two sluiceway operational configurations: Sluice 2+5 and Sluice 2+19 (six gates open for each configuration). Total project outflow was 76% of the 10-year average for spring and 71% of the 10-year average for summer. Based on these findings, we make the following recommendations: 1) The sluice should be operated 24 h/d from April until November. 2) Open six rather than three sluice gates to take advantage of the maximum hydraulic capacity of the sluiceway. 3) Open the three gates above the western-most operating main turbine unit and the three gates at MU 8 where turbine passage rates are relatively high. 4) Operate the turbine units below open sluice gates as a standard fish operations procedure. 5) Develop hydraulic and entrance enhancements to the sluiceway to tap the potential of The

  15. Computer program for sample sizes required to determine disease incidence in fish populations

    USGS Publications Warehouse

    Ossiander, Frank J.; Wedemeyer, Gary

    1973-01-01

    A computer program is described for generating the sample size tables required in fish hatchery disease inspection and certification. The program was designed to aid in detection of infectious pancreatic necrosis (IPN) in salmonids, but it is applicable to any fish disease inspection when the sampling plan follows the hypergeometric distribution.

  16. Isolation and characterization of Flavobacterium columnare strains infecting fishes inhabiting the Laurentian Great Lakes basin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flavobacterium columnare, the etiological agent of columnaris disease, causes significant losses in fish worldwide. In this study, F. columnare infection prevalence was assessed in representative Great Lakes fish species. Over 2,000 wild, feral, and hatchery-propagated salmonids, percids, centrarc...

  17. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1986 Annual Report.

    SciTech Connect

    Fryer, John L.

    1986-12-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration conducted a study relating to the epidemiology and control of three fish diseases of salmonids in the Columbia River Basin. These three diseases were ceratomyxosis caused by the myxosporidan parasite Ceratomyxa Shasta, bacterial kidney disease, the causative agent Renibacterium salmoninarum, and infectious hematopoietic necrosis, caused by a rhabdovirus. Each of these diseases is highly destructive and difficult or impossible to treat with antimicrobial agents. The geographic range of the infectious stage of C. Shasta has been extended to include the Snake River to the Oxbow and Hells Canyon Dams. These are the farthest upriver sites tested. Infections of ceratomyxosis were also initiated in the east fork of the Lewis River and in the Washougal River in Washington. Laboratory studies with this parasite failed to indicate that tubeficids are required in its life cycle. Bacterial kidney disease has been demonstrated in all life stages of salmonids: in the eggs, fry, smolts, juveniles and adults in the ocean, and in fish returning to fresh water. Monoclonal antibodies produced against R. salmoninarum demonstrated antigenic differences among isolates of the bacterium. Monoclonal antibodies also showed antigens of R. salmoninarum which are similar to those of a wide variety of gram positive and gram negative bacteria. A demonstration project at Round Butte Hatchery showed U V treatment to be an effective method for reducing the microbial population of the water supply and could reduce risks of IHNV. Tangential flow filtration was used successfully to concentrate IHNV from environmental water. At Round Butte Hatchery the carrier rate of IHNV in adults was very low and there was no subsequent mortality resulting from IHN in juveniles.

  18. Sustaining salmonid populations: A caring understanding of naturalness of taxa

    USGS Publications Warehouse

    Nielsen, J.L.; Regier, H.A.

    2004-01-01

    Species of the family of Salmonidae occur naturally in Northern Hemisphere waters that remain clear and cool to cold in summer. For purposes of reproduction, salmonids generally behaviorally respond to the currents of streams and lakes in recently glaciated areas. For feeding and maturation, many larger species migrate into existing systems of large lakes, seas, and oceans. The subfamilies include Salmoninae, Coregoninae, and Thymallinae. In many locales and regions of the hemisphere, numerous species of these subfamilies evolved and self-organized into species flocks or taxocenes of bewildering complexity. For example, any individual species may play different or unique ecological roles in different taxocenes. The northern Pacific and Atlantic Ocean ecosystems, with their seas and tributaries, each contained a metacomplex of such taxocenes that, in their natural state some centuries ago, resembled each other but differed in many ways. Humans have valued all species of this family for subsistence, ceremonial, naturalist, gustatory, angling, and commercial reasons for centuries. Modern progressive humans (MPHs), whose industrial and commercial enterprises have gradually spread over this hemisphere in recent time, now affect aquatic ecosystems at all scales from local to global. These human effects mingle in complex ways that together induce uniquely natural salmonid taxocenes to disintegrate with the loss of species, including those groups least tolerant to human manipulations, but extending more recently to those taxa more adapted to anthropogenic change. As we leave the modern era, dominated by MPHs, will we find ways to live sustainably with salmonid taxocenes that still exhibit self-organizational integrity, or will only individual, isolated populations of salmonid species, derived from those most tolerant of MPHs, survive? To achieve future sustainability of salmonids, we suggest implementation of a search for intuitive knowledge based on faith in the wisdom of

  19. A riverscape perspective of Pacific salmonids and aquatic habitats prior to large-scale dam removal in the Elwha River, Washington, USA

    USGS Publications Warehouse

    Brenkman, S.J.; Duda, J.J.; Torgersen, C.E.; Welty, E.; Pess, G.R.; Peters, R.; McHenry, M.L.

    2012-01-01

     Dam removal has been increasingly proposed as a river restoration technique. In 2011, two large hydroelectric dams will be removed from Washington State’s Elwha River. Ten anadromous fish populations are expected to recolonise historical habitats after dam removal. A key to understanding watershed recolonisation is the collection of spatially continuous information on fish and aquatic habitats. A riverscape approach with an emphasis on biological data has rarely been applied in mid-sized, wilderness rivers, particularly in consecutive years prior to dam removal. Concurrent snorkel and habitat surveys were conducted from the headwaters to the mouth (rkm 65–0) of the Elwha River in 2007 and 2008. This riverscape approach characterised the spatial extent, assemblage structure and patterns of relative density of Pacific salmonids. The presence of dams influenced the longitudinal patterns of fish assemblages, and species richness was the highest downstream of the dams, where anadromous salmonids still have access. The percent composition of salmonids was similar in both years for rainbow trout, Oncorhynchus mykiss (Walbaum), coastal cutthroat trout, Oncorhynchus clarkii clarkii (Richardson) (89%; 88%), Chinook salmon, Oncorhynchus tshawytscha (Walbaum) (8%; 9%), and bull trout, Salvelinus confluentus (Suckley) (3% in both years). Spatial patterns of abundance for rainbow and cutthroat trout (r = 0.76) and bull trout (r = 0.70) were also consistent between years. Multivariate and univariate methods detected differences in habitat structure along the river profile caused by natural and anthropogenic factors. The riverscape view highlighted species-specific biological hotspots and revealed that 60–69% of federally threatened bull trout occurred near or below the dams. Spatially continuous surveys will be vital in evaluating the effectiveness of upcoming dam removal projects at restoring anadromous salmonids.

  20. Hydroacoustic Evaluation of Juvenile Salmonid Passage at The Dalles Dam Spillway, 2006

    SciTech Connect

    Johnson, Gary E.; Khan, Fenton; Skalski, John R.; Rakowski, Cynthia L.; Richmond, Marshall C.; Serkowski, John A.

    2007-05-24

    The objective of this study was to determine detailed vertical, horizontal, intensive, and diel distributions of juvenile salmonid passage at the spillway at The Dalles Dam from April 12 to July16, 2006. These data are being applied in the Spillway Improvements Program to position release pipes for direct injury and mortality studies and to provide baseline data for assessment of the vortex suppression devices scheduled for deployment in 2007. We estimated fish distributions from hydroacoustic data collected with split-beam transducers arrayed across Bays 1 through 9 and 14. Spill at ~20 kcfs per bay was bulked at Bays 1-6, although the other bays were opened at times during the study to maintain a 40% spill percentage out of total project discharge. The vertical distribution of fish was skewed toward the surface during spring, but during summer, passage peaked at 2-3 m above the spillway ogee. Fish passage rates (number per hour) and fish densities (number per kcfs) were highest at Bay 6, followed by passage at Bay 5. This result comports with spillway horizontal distribution data from radio telemetry and hydroacoustic studies in 2004. The vertical and horizontal distribution of fish passage at bays 5 and 6 was much more variable during spring than summer and more variable at bay 5 than bay 6. Diel distribution data revealed that fish passage was highest during 0600-0700 h in spring; otherwise passage was reasonably uniform on a diel basis. This study substantiates the purpose of the spillway vortex suppression device to re-distribute downstream migrants away from Bay 6 toward Bays 1-5.

  1. Applying Selective Breeding And Vaccination To Improve Fish Health

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infectious disease causes substantial economic loss in aquaculture. In an effort to reduce loss, selective breeding of animals with superior disease resistance is being increasingly utilized as a component within fish health management plans. Selective breeding is especially applicable to salmonid ...

  2. Fish distribution studies near N Reactor, Summer 1983

    SciTech Connect

    Dauble, D.D.; Page, T.L.

    1984-06-01

    This report summarizes field studies that were initiated in July 1983 to provide estimates of the relative distribution of late-summer outmigrant juvenile salmonids and juvenile resident fish upstream of the N Reactor 009 Outfall. Chinook salmon are among the fish species most sensitive to thermal effects, and impacts to the juvenile outmigrant populations are of particular concern to state and federal regulatory and fisheries management agencies. Therefore, the distribution studies were conducted from late July through September, a period when high ambient river temperatures and low river flows make these salmonid populations most susceptible to thermal effects. In addition, data were not available on the spatial distribution of outmigrant juvenile chinook salmon in late summer. Information on the relative distribution of resident fish populations was also gathered. Previous studies of midstream distribution of juvenile resident fish were limited to a description of ichthyoplankton populations (Beak Consultants, Inc. 1980 Page et al. 1982), and no data were available on vertical or horizontal distribution of juvenile resident fish species near N Reactor. Relative densities and spatial distribution estimates of juvenile salmonid and resident fish species will be used in conjunction with laboratory thermal effects studies (Neitzel et al. 1984) and with plume characterization studies (Ecker et al. 1983) to assess potential impacts of thermal discharge on fish populations near N Reactor.

  3. SALMOD: a population model for salmonids: user's manual. Version W3

    USGS Publications Warehouse

    Bartholow, John; Heasley, John; Laake, Jeff; Sandelin, Jeff; Coughlan, Beth A.K.; Moos, Alan

    2002-01-01

    SALMOD is a computer model that simulates the dynamics of freshwater salmonid populations, both anadromous and resident. The conceptual model was developed in a workshop setting (Williamson et al. 1993) using fish experts concerned with Trinity River chinook restoration. The model builds on the foundation laid by similar models (see Cheslak and Jacobson 1990). The model’s premise that that egg and fish mortality are directly related to spatially and temporally variable micro- and macrohabitat limitations, which themselves are related to the timing and amount of streamflow and other meteorological variables. Habitat quality and capacity are characterized by the hydraulic and thermal properties of individual mesohabitats, which we use as spatial “computation units” in the model. The model tracks a population of spatially distinct cohorts that originate as gees and grow from one life stage to another as a function of local water temperature. Individual cohorts either remain in the computational unit in which they emerged or move, in whole or in part, to nearby units (see McCormick et al. 1998). Model processes include spawning (with red superimposition and incubation losses), growth (including egg maturation), mortality, and movement (freshet-induced, habitat-induced, and seasonal). Model processes are implemented such that the user (modeler) has the ability to more-or-less program the model on the fly to create the dynamics thought to animate the population. SALMOD then tabulates the various causes of mortality and the whereabouts of fish.

  4. The Salmonid Rivers Observatory Network: Defining Reference Conditions for Salmon Rivers Around the Pacific.

    NASA Astrophysics Data System (ADS)

    Chilcote, S. D.; Stanford, J. A.

    2008-12-01

    The Salmonid Rivers Observatory River Project (SaRON) is a multi-year, multi-disciplinary project which has been assessing the state of intact, pristine salmon rivers around the Pacific Rim. The goal of this research is to illuminate the natural ecological functions of these dynamic and diverse systems as well as use the information to describe targets for restoration of impacted rivers. Our research has shown that the Shifting Habitat Mosaic (SHM) of unconstrained floodplain reaches is important in structuring the freshwater and riparian components of salmon ecosystems. The amount and productivity of available habitat in flood plains is a primary control on salmon abundance. Our research around the Pacific Rim has found that channel complexity is correlated with salmon abundance. Juvenile fish density linearly increased, R2=0.95, with a greater number of channel separations and returns. Some rivers with high habitat values had low salmon abundances. For example, the Kitlope River in British Columbia has channel complexity, 0.09 nodes per square km of watershed area, showing high habitat availability. Thus, our model predicted 3.48 fish per square meter but measured values 0.56 fishes per square meter. Paleolimnological study demonstrated a legacy over-harvest in this system, explaining the discrepancy between the actual and reference value. These results will be establishing reference values and ranges in natural variation.

  5. Outplanting Anadromous Salmonids, A Lilterature Study.

    SciTech Connect

    Smith, Eugene M.

    1985-10-01

    This paper presents a list of more than 200 references on topics associated with offstation releases of hatchery stocks of anadromous fish used to supplement or reestablish wild rearing. The narrative briefly reviews influences of genetics, rearing density of fish in the natural environment, survival rates observed from outplanted stocks, and estimation procedures for stocking rates and rearing densities. We have attempted to summarize guidelines and recommendations for fishery managers to consider. Based on tagging studies, a typical smolt release from a Willamette River hatchery would return 0.29% of the smolts to the stream of release as adults. Catch to escapement ratios for adult Willamette chinook vary widely between broods, but on average two fish are caught for each fish that escapes. The catch is about evenly divided between offshore and freshwater harvest. British Columbia is the primary location of offshore harvest, and the lower Willamette River is the primary location of freshwater harvest. Review of departmental policy indicates that only Willamette stock spring chinook are currently acceptable for use in a proposed outplant study within the Willamette basin. Further, most Oregon Department of Fish and Wildlife district management biologists would prefer not to transfer any stocks of spring chinook between drainage subbasins. State fishery managers identified 16 Willamette basin streams as being suitable for supplementation with spring chinook from hatcheries. We reviewed the potential for rearing salmon in reservoirs throughout the basin. Use of the Carmen-Smith spawning channel, which was constructed on the upper McKenzie River in 1960, has generally declined with the decline in populations of chinook salmon in this river. The Carmen-Smith channel still provides a spawning place for those relatively few adult chinook that still return each year, but more fishery benefits may result from other uses of this facility. 7 figs., 8 tabs.

  6. Significance of Selective Predation and Development of Prey Protection Measures for Juvenile Salmonids in the Columbia and Snake River Reservoirs: Annual Report, February 1992-February 1993.

    SciTech Connect

    Poe, Thomas P.; Gadomski, Dena M.

    1994-09-01

    This document is the 1992 annual report of progress for the Bonneville Power Administration (BPA) research Project No. 82-003 conducted by the U.S. Fish and Wildlife Service (FWS), the Oregon Cooperative Fishery Research Unit (OCFRU), and the Idaho Cooperative Fish and Wildlife Research Unit (ICFWRU). The approach was to present the progress achieved during 1992 in a series of separate reports for each major project task. Each report is prepared in the format of a scientific paper and is able to stand alone, whatever the state of progress or completion. Reports 1, 2, and 4 consist of the Abstract only (journal papers were submitted in lieu of reports). This project has two major goals. One is to understand the significance of selective predation and prey vulnerability by determining if substandard juvenile salmonids (dead, injured, stressed, diseased, or naive) are more vulnerable to predation by northern squawfish, Ptychocheilus oregonensis, than standard or normal juvenile salmonids. The second goal is to develop and test prey protection measures to control predation on juvenile salmonids by reducing predator-smolt encounters or predator capture efficiency. Separate abstracts have been submitted to the database for the seven articles in this report.

  7. Movements and Distribution of Northern Squawfish Downstream of Lower Snake River Dams Relative to the Migration of Juvenile Salmonids, 1992-1993 Completion Report.

    SciTech Connect

    Isaak, D.J.; Bjornn, T.C.

    1996-03-01

    Northern squawfish Ptychocheilus oregonensis movements were monitored downstream of two lower Snake River dams during the juvenile salmonid migrations of 1992 and 1993. During a high flow year in 1993, the abundance of squawfish in the tailrace of Lower Granite Dam peaked in July, after the majority of juveniles had moved past Lower Granite Dam, and peak abundance was inversely related to river discharge. Few squawfish moved into the tailrace of Ice Harbor Dam in 1993 because of the extended period of spill. Distributions of squawfish in the tailrace of Lower Granite Dam varied between and within years and shifted in response to changing prey densities, flow patterns, water temperature, and diel cycles, but fish consistently used low velocity habitats. Data from Ice Harbor Dam is less extensive, but squawfish distributions there appeared to be affected by changing flow patterns and fish used low velocity habitats. The changes in distribution and abundance of squawfish in tailrace areas are evidence that predation on seaward migrating salmonids depends on the timing of migration and size and timing of runoff. Juvenile salmonids migrating in the spring and early summer will probably be less affected by squawfish predation in tailrace areas than salmon that migrate later in the summer.

  8. Assessment of Salmonids and Their Habitat Conditions in the Walla Walla River Basin within Washington, Annual Report 2002-2003.

    SciTech Connect

    Mendel, Glen; Trump, Jeremy; Gembala, Mike

    2003-09-01

    This study began in 1998 to assess salmonid distribution, relative abundance, genetics, and the condition of salmonid habitats in the Walla Walla River basin. Stream flows in the Walla Walla Basin continue to show a general trend that begins with a sharp decline in discharge in late June, followed by low summer flows and then an increase in discharge in fall and winter. Manual stream flow measurements at Pepper bridge showed an increase in 2002 of 110-185% from July-September, over flows from 2001. This increase is apparently associated with a 2000 settlement agreement between the U.S. Fish and Wildlife Service (USFWS) and the irrigation districts to leave minimum flows in the river. Stream temperatures in the Walla Walla basin were similar to those in 2001. Upper montane tributaries maintained maximum summer temperatures below 65 F, while sites in mid and lower Touchet and Walla Walla rivers frequently had daily maximum temperatures well above 68 F (high enough to inhibit migration in adult and juvenile salmonids, and to sharply reduce survival of their embryos and fry). These high temperatures are possibly the most critical physiological barrier to salmonids in the Walla Walla basin, but other factors (available water, turbidity or sediment deposition, cover, lack of pools, etc.) also play a part in salmonid survival, migration, and breeding success. The increased flows in the Walla Walla, due to the 2000 settlement agreement, have not shown consistent improvements to stream temperatures. Rainbow/steelhead (Oncorhynchus mykiss) trout represent the most common salmonid in the basin. Densities of Rainbow/steelhead in the Walla Walla River from the Washington/Oregon stateline to Mojonnier Rd. dropped slightly from 2001, but are still considerably higher than before the 2000 settlement agreement. Other salmonids including; bull trout (Salvelinus confluentus), chinook salmon (Oncorhynchus tshawytscha), mountain whitefish (Prosopium williamsoni), and brown trout (Salmo

  9. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most wide...

  10. Physiological levels of testosterone kill salmonid leukocytes in vitro

    USGS Publications Warehouse

    Slater, C.H.; Schreck, C.B.

    1997-01-01

    Adult spring chinook salmon (Oncorhynchus tshawytscha) elaborate high plasma concentrations of testosterone during sexual maturation, and these levels of testosterone have been shown to reduce the salmonid immune response in vitro. Our search for the mechanism of testosterone's immunosuppressive action has led to the characterization of an androgen receptor in salmonid leukocytes. In the present study we examined the specific effects that testosterone had on salmonid leukocytes. Direct counts of viable leukocytes after incubation with and without physiological levels of testosterone demonstrate a significant loss of leukocytes in cultures exposed to testosterone. At least 5 days of contact with testosterone was required to produce significant immunosuppression and addition of a 'conditioned media' (supernatant from proliferating lymphocytes not exposed to testosterone) did not reverse the immunosuppressive effects of testosterone. These data lead us to conclude that testosterone may exert its immunosuppressive effects by direct action on salmonid leukocytes, through the androgen receptor described, and that this action leads to the death of a significant number of these leukocytes.

  11. Removal of small dams and its influence on physical habitat for salmonids in a Norwegian river

    NASA Astrophysics Data System (ADS)

    Fjeldstad, Hans-Petter; Barlaup, Bjørn; Stickler, Morten; Alfredsen, Knut; Gabrielsen, Sven-Erik

    2010-05-01

    While research and implementation of upstream migration solutions is extensive, and indeed often successful, full scale restoration projects and investigations of their influence on fish biology are rare in Norway. Acid deposition in Norwegian catchments peaked in the 1980's and resulted in both chronically and episodically acidified rivers and Salmonids in River Nidelva, one of the largest cathments in southern Norway, where extinct for decades. During this period hydropower development in the river paid limited attention to aquatic ecology. Weirs were constructed for esthetic purposes in the late 1970's and turned a 3 km stretch into a lake habitat, well suited for lake dwelling fish species, but unsuited for migration, spawning and juvenile habitat for salmonids. Since 2005, continuous liming to mitigate acidification has improved the water quality and a program for reintroduction of Atlantic salmon has been implemented. We used hydraulic modeling to plan the removal of two weirs on a bypass reach of the river. The 50 meters wide concrete weirs were blasted and removed in 2007, and ecological monitoring has been carried out in the river to assess the effect of weir removal. Topographic mapping, hydraulic measurements and modeling, in combination with biological surveys before and after the removal of the weirs, has proved to represent a powerful method for design of physical habitat adjustments and assessing their influence on fish biology. The model results also supported a rapid progress of planning and executing of the works. While telemetry studies before weir removal suggested that adult migration past the weirs was delayed with several weeks the fish can now pass the reach with minor obstacles. Spawning sites were discovered in the old bed substrate and were occupied already the first season after water velocities increased to suitable levels for spawning. Accordingly, the densities of Atlantic salmon juveniles have shown a marked increased after the

  12. Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin, Annual Report 2001-2002.

    SciTech Connect

    White, Tara C.; Hanson, Josh T.; Jewett, Shannon M.

    2004-01-01

    The year of 2002 represented the eighth year of a multi-year project, monitoring the outmigration and survival of juvenile salmonids in the lower Umatilla River. This project both supplements and complements various ongoing and completed work within the Umatilla River basin. Knowledge gained on juvenile outmigration and survival assists researchers and managers in adapting hatchery practices, flow enhancement strategies, canal and fish ladder operations, and supplementation and enhancement efforts of natural and restored fish populations. Findings from this study also assist in assessment of the success of upriver habitat improvement projects and provide an overall evaluation of the Umatilla River fisheries restoration program. General project objectives include: Evaluation of the outmigration and survival of natural and hatchery juvenile salmonids in the lower Umatilla River, in an effort to enhance the understanding of migration characteristics, survival bottlenecks, species interactions and effects of management strategies. Specific objectives for 2002 included: (1) Operation of the remote interrogation system at Three Mile Falls Dam, West Extension Canal; (2) Design of improved PIT tag detection capabilities at Three Mile Falls Dam east bank adult fish ladder; (3) Estimates of migrant abundance, migration timing and in-basin survival of tagged juvenile salmonids representing various hatchery, rearing, acclimation and release strategies; (4) Monitoring of abundance and trends in natural production of salmon, steelhead and pacific lamprey; (5) Continuation of transport evaluation studies to evaluate the relative survival between transported and nontransported fish; (6) Assessment of the condition, health, size, growth and smolt status of hatchery and natural migrants; (7) Investigation of the effects of canal and fishway operations and environmental conditions on fish migration and survival; (8) Documentation of temporal distribution and diversity of resident

  13. Effect of multiple turbine passage on juvenile Snake River salmonid survival

    SciTech Connect

    Ham, K. D.; Anderson, J. J.; Vucellck, J. A.

    2005-09-01

    Juvenile salmonids originating in the Snake River upstream of Lower Granite Dam must pass up to eight hydroelectric projects during their downstream migration to the Pacific Ocean. Fish may pass a project through a turbine or a spillbay or be screened into a bypass system that either collects fish into a barge or releases them downstream of the project. Previous reviews of studies of downstream passage for salmon at hydroelectric projects in the Columbia River basin found higher mean mortality at turbines than for spillways or bypass systems. The potential mechanisms of mortality during turbine passage may include pressure changes, cavitation, shear, turbulence, strike, or grinding. Observing those mechanisms is challenging in the field, but laboratory studies have demonstrated that a single exposure to shear or pressure changes similar to turbine passage conditions can result in injury for some individuals. Because fish pass several dams along their migration, individuals experience a series of passage events. If estimates of surviving the passage of a single project are applied to each passage event, then the underlying assumption is that the mortality at each project is independent of previous exposure. If individuals approaching a project were already sub-lethally stressed, higher than expected mortality rates might occur upon subsequent passage events. Report presents the hypothesis that fish passing more than one turbine will experience a greater than expected rate of mortality. Because measuring an incremental increase in mortality would be challenging in the field, scientists developed an approach to first assess whether such an increment has any potential to influence a fish population. This approach identified populations at risk and will help design laboratory or field experiments to address those risks.

  14. Wild salmonids and sea louse infestations on the west coast of Scotland: sources of infection and implications for the management of marine salmon farms.

    PubMed

    Butler, James R A

    2002-06-01

    The sea louse (Lepeophtheirus salmonis Krøyer) is a major health problem for both farmed and wild salmonids. This paper investigates louse epidemiology and management in the salmon-farming zone of western Scotland. Based on a review of the marine ecology of wild salmon (Salmo salar L) and sea trout (Salmo trutta L), and catch and farm production statistics, best estimates were made for numbers of wild and farm hosts present in coastal waters in March-June 2000. Applying data for ovigerous female louse infections and fecundity, the sources and risks of larval transmission to wild salmon and sea trout were modelled. Farm salmon in the second spring of production were the primary host group (98% of fish), while numbers of wild salmonids (< 1%) and escaped farm salmon (2%) were relatively insignificant. Farm salmon produced 97% of louse eggs at high levels (eight ovigerous lice per fish), and 78% at low levels (one per fish). Wild salmonids produced < 1% of eggs under both scenarios, but escaped farm salmon produced 3% and 21%, respectively. All hosts potentially cross-infect one another, but farm salmon are more likely to infect wild and farm smolts, and also other farm salmon. Monitoring of lice on sea trout in June 1998-2000 by the Association of West Coast Fisheries Trusts corroborated the model's conclusions. Localised epizootics occurred every year and coincided with the presence of ovigerous lice on local farms. In areas of mixed-year class production on farms, epizootics were evident every spring, but occurred every second spring in areas of single-year class production. In 1998-2000 at least 14-40% of sea trout were infected with potentially lethal infestations of lice. Ovigerous louse levels of < 0.005 per fish were required on farm salmon in the spring of 2000 to produce less eggs than those emitted by wild salmonids. With the industry's continued expansion, and thus increased numbers of farm salmon, a target of zero ovigerous lice will be required on farms

  15. System-Wide Significance of Predation on Juvenile Salmonids in the Columbia and Snake River Reservoirs : Annual Report of Research 1991.

    SciTech Connect

    Shively, R.S.

    1991-01-01

    We indexed consumption rates of northern squawfish (Ptychoch oregonensis) preying upon juvenile salmonids in four lower Snake River reservoirs. Stomach contents were also collected from smallmouth bass (Micropterus dolomieui), channel catfish (Ictaluris gunctatus), and walleye (Stizostedion vitreum). Northern squawfish digestive tracts were analyzed and the overall diet (% weight) was dominated by fish and crustaceans. Examination of stomach contents smallmouth bass showed that crustaceans (primarily crayfish) dominated their diets. Overall, the consumption rate of juvenile salmonids by smallmouth bass was low. The northern squawfish consumption index (CI) at Snake River locations ranged from zero at all mid-reservoir locations to 1.2 at Lower Granite forebay. In John Day Reservoir, CI values ranged from 0.5 to 1.9 in May and from 0.9 to 3.0 in July. Consumption index values were highest in forebay and tailrace areas, and were slightly higher in BRZs than in non-restricted zones.

  16. Natural Propagation and Habitat Improvement, Volume I, Oregon, Supplement A: Habitat Enhancement Evaluation of Fish and Wash Creeks, 1983 Annual Report.

    SciTech Connect

    Everest, Fred

    1984-04-01

    Habitat improvements for anadromous salmonids on Fish Creek in the upper Clackamas Basin were evaluated. The primary objectives of the evaluation effort include: (1) evaluate and quantify the changes in salmonid spawning and rearing habitat resulting from a variety of habitat improvements; (2) evaluate and quantify the changes in fish populations and biomass resulting from habitat improvements; and (3) evaluate the cost-effectiveness of habitat improvements developed with BPA and KV funds on Fish Creek. This report integrates data for the evaluation efforts collected in the Fish Creek Basin in 1982 and 1983. 3 references, 34 figures, 23 tables.

  17. Genetic characterization of infectious hematopoietic necrosis virus of coastal salmonid stocks in Washington State

    USGS Publications Warehouse

    Emmenegger, E.J.; Kurath, G.

    2002-01-01

    Infectious hematopoietic necrosis virus (IHNV) is a pathogen that infects many Pacific salmonid stocks from the watersheds of North America. Previous studies have thoroughly characterized the genetic diversity of IHNV isolates from Alaska and the Hagerman Valley in Idaho. To enhance understanding of the evolution and viral transmission patterns of IHNV within the Pacific Northwest geographic range, we analyzed the G gene of IHNV isolates from the coastal watersheds of Washington State by ribonuclease protection assay (RPA) and nucleotide sequencing. The RPA analysis of 23 isolates indicated that the Skagit basin IHNV isolates were relatively homogeneous as a result of the dominance of one G gene haplotype (S). Sequence analysis of 303 bases in the middle of the G gene (midG region) of 61 isolates confirmed the high frequency of a Skagit River basin sequence and identified another sequence commonly found in isolates from the Lake Washington basin. Overall, both the RPA and sequence analysis showed that the Washington coastal IHNV isolates are genetically homogeneous and have little genetic diversity. This is similar to the genetic diversity pattern of IHNV from Alaska and contrasts sharply with the high genetic diversity demonstrated for IHNV isolates from fish farms along the Snake River in Idaho. The high degree of sequence and haplotype similarity between the Washington coastal IHNV isolates and those from Alaska and British Columbia suggests that they have a common viral ancestor. Phylogenetic analyses of the isolates we studied and those from different regions throughout the virus's geographic range confirms a conserved pattern of evolution of the virus in salmonid stocks north of the Columbia River, which forms Washington's southern border.

  18. Intestinal fluid absorption in anadromous salmonids: importance of tight junctions and aquaporins

    PubMed Central

    Sundell, Kristina S.; Sundh, Henrik

    2012-01-01

    The anadromous salmonid life cycle includes both fresh water (FW) and seawater (SW) stages. The parr-smolt transformation (smoltification) pre-adapt the fish to SW while still in FW. The osmoregulatory organs change their mode of action from a role of preventing water inflow in FW, to absorb ions to replace water lost by osmosis in SW. During smoltification, the drinking rate increases, in the intestine the ion and fluid transport increases and is further elevated after SW entry. In SW, the intestine absorbs ions to create an inwardly directed water flow which is accomplished by increased Na+, K+-ATPase (NKA) activity in the basolateral membrane, driving ion absorption via ion channels and/or co-transporters. This review will aim at discussing the expression patterns of the ion transporting proteins involved in intestinal fluid absorption in the FW stage, during smoltification and after SW entry. Of equal importance for intestinal fluid absorption as the active absorption of ions is the permeability of the epithelium to ions and water. During the smoltification the increase in NKA activity and water uptake in SW is accompanied by decreased paracellular permeability suggesting a redirection of the fluid movement from a paracellular route in FW, to a transcellular route in SW. Increased transcellular fluid absorption could be achieved by incorporation of aquaporins (AQPs) into the enterocyte membranes and/or by a change in fatty acid profile of the enterocyte lipid bilayer. An increased incorporation of unsaturated fatty acids into the membrane phospholipids will increase water permeability by enhancing the fluidity of the membrane. A second aim of the present review is therefore to discuss the presence and regulation of expression of AQPs in the enterocyte membrane as well as to discuss the profile of fatty acids present in the membrane phospholipids during different stages of the salmonid lifecycle. PMID:23060812

  19. Annual Review of BPA-Funded Projects in Natural and Artificial Propagation of Salmonids, March 27-29, 1985, Holiday Inn Airport, Portland, Oregon.

    SciTech Connect

    United States. Bonneville Power Administration.

    1985-04-01

    The Fish and Wildlife Division of Bonneville Power Administration (BPA) hosted a meeting for contractors to present the results of fiscal year 1984 research conducted to implement the Northwest Power Planning Council's Fish and Wildlife Program. The meeting focused on those projects specifically related to natural and artificial propagation of salmonids. The presentations were held at the Holiday Inn Airport in Portland, Oregon, on March 27-29, 1985. This document contains abstracts of the presentations from that meeting. Section 1 contains abstracts on artificial propagation, fish health, and downstream migration, and Section 2 contains abstracts on natural propagation and habitat improvement. The abstracts are indexed by BPA Project Number and by Fish and Wildlife Program Measure. The registered attendees at the meeting are listed alphabetically in Appendix A and by affiliation in Appendix B.

  20. Characterization of the live salmonid movement network in Ireland: Implications for disease prevention and control.

    PubMed

    Yatabe, T; More, S J; Geoghegan, F; McManus, C; Hill, A E; Martínez-López, B

    2015-11-01

    Live fish movement is considered as having an important role in the transmission of infectious diseases. For that reason, interventions for cost-effective disease prevention and control rely on a sound understanding of the patterns of live fish movements in a region or country. Here, we characterize the network of live fish movements in the Irish salmonid farming industry during 2013, using social network analysis and spatial epidemiology methods, and identify interventions to limit the risk of disease introduction and spread. In the network there were 62 sites sending and/or receiving fish, with a total of 130 shipments (84 arcs) comprising approx. 17.2 million fish during the year. Atlantic salmon shipments covered longer distances than trout shipments, with some traversing the entire country. The average shipment of Atlantic salmon was 146,186 (SD 194,344) fish, compared to 77,928 (127,009) for trout, however, variability was high. There were 3 periods where shipments peaked (February-April, June-September, and November), which were related to specific stages of fish. The network was disconnected and had two major weak components, the first one with 39 nodes (mostly Atlantic salmon sites), and the second one with 10 nodes (exclusively trout sites). Correlation between in and out-degree at each site and assortativity coefficient were slightly low and non-significant: -0.08 (95% CI: -0.22, 0.06) and -0.13 (95% CI: -0.36, 0.08), respectively, indicating random mixing with regard to node degree. Although competing models also produced a good fit to degree distribution, it is likely that the network possesses both small-world and scale-free topology. This would facilitate the spread and persistence of infection in the salmon production system, but would also facilitate the design of risk-based surveillance strategies by targeting hubs, bridges or cut-points. Using Infomap community detection algorithms, 2 major communities were identified within the giant weak

  1. A standard operating procedure for the surgical implantation of transmitters in juvenile salmonids

    USGS Publications Warehouse

    Liedtke, T.L.; Beeman, J.W.; Gee, L.P.

    2012-01-01

    Biotelemetry is a useful tool to monitor the movements of animals and is widely applied in fisheries research. Radio or acoustic technology can be used, depending on the study design and the environmental conditions in the study area. A broad definition of telemetry also includes the use of Passive Integrated Transponder (PIT) tags, either separately or with a radio or acoustic transmitter. To use telemetry, fish must be equipped with a transmitter. Although there are several attachment procedures available, surgical implantation of transmitters in the abdominal cavity is recognized as the best technique for long-term telemetry studies in general (Stasko and Pincock, 1977; Winter, 1996; Jepsen, 2003), and specifically for juvenile salmonids, Oncorhynchus spp. (Adams and others, 1998a, 1998b; Martinelli and others, 1998; Hall and others, 2009). Studies that use telemetry assume that the processes by which the animals are captured, handled, and tagged, as well as the act of carrying the transmitter, will have minimal effect on their behavior and performance. This assumption, commonly stated as a lack of transmitter effects, must be valid if telemetry studies are to describe accurately the movements and behavior of an entire population of interest, rather than the subset of that population that carries transmitters. This document describes a standard operating procedure (SOP) for surgical implantation of radio or acoustic transmitters in juvenile salmonids. The procedures were developed from a broad base of published information, laboratory experiments, and practical experience in tagging thousands of fish for numerous studies of juvenile salmon movements near Columbia River and Snake River hydroelectric dams. Staff from the Western Fisheries Research Center's Columbia River Research Laboratory (CRRL) frequently have used telemetry studies to evaluate new structures or operations at hydroelectric dams in the Columbia River Basin, and these evaluations typically

  2. Spatial and temporal variations in sea lice (Copepoda: Caligidae) infestations of three salmonid species farmed in net pens in southern Chile.

    PubMed

    Zagmutt-Vergara, Francisco J; Carpenter, Tim E; Farver, Thomas B; Hedrick, Ronald P

    2005-04-18

    Sea lice infestations have become a major health problem for farmed salmonids throughout the world including Chile. In southern Chile, 6 geographical areas, divided into 22 geographical zones with a total of 127 salmon farming centers and 1519 sea pens, were regularly sampled from December 1999 to April 2002. A linear mixed-effects model (LME) approach was used to describe the infestations of adult forms of sea lice on 3 salmonid species farmed in southern Chile. The variables fish species, water temperature, water salinity, fish weight, juvenile parasite count, pen shape, treatment status in previous month and the interaction of previous and current month treatments were found to be statistically significant fixed effects for the population sampled. The most susceptible species to sea lice infestation was rainbow trout Oncorhynchus mykiss, while the least susceptible species was coho salmon O. kisutch. Fishes in pens treated in the previous month with avermectins were associated with the smallest sea lice count compared to fishes in pens not treated or treated with other products. The variability in sea lice infestations in areas and zones within areas was not statistically significant when controlling for the previously mentioned fixed variables. The variability between centers, the within-pen variability, and the interaction between within-pen effect and the date of measurement were statistically significant and not explained by the fixed effects. Potential sources for this variability are discussed. We conclude that the epidemiology of sea lice infestations in farmed salmonids in southern Chile is complex and in need of further study. PMID:15918480

  3. Successive Oral Immunizations Against Piscirickettsia Salmonis and Infectious Salmon Anemia Virus are Required to Maintain a Long-Term Protection in Farmed Salmonids.

    PubMed

    Tobar, Iván; Arancibia, Sergio; Torres, Constanza; Vera, Verónica; Soto, Paola; Carrasco, Claudia; Alvarado, Marcelo; Neira, Eduardo; Arcos, Sandra; Tobar, Jaime A

    2015-01-01

    Currently, there is a growing demand to determine the protective status of vaccinated fish in order to prevent diseases outbreaks. A set of different parameters that include the infectious and immunological status of vaccinated salmonids from 622 Chilean farms were analyzed during 2011-2014. The aim of this study was to optimize the vaccination program of these centers through the determination of the protective state of vaccinated fish using oral immunizations. This state was determined from the association of the concentration of the immunoglobulin M (IgM) in the serum and the mortality rate of vaccinated fish. Salmonids were vaccinated with different commercial mono- or polyvalent vaccines against salmonid rickettsial septicemia (SRS) and infectious salmon anemia (ISA), first by the intraperitoneal injection of oil-adjuvanted antigens and then by the stimulation of mucosal immunity using oral vaccines as a booster vaccination. The results showed that high levels of specific IgM antibodies were observed after injectable vaccination, reaching a maximum concentration at 600-800 degree-days. Similar levels of antibodies were observed when oral immunizations were administrated. The high concentration of antibodies [above 2750 ng/mL for ISA virus (ISAv) and 3500 ng/mL for SRS] was maintained for a period of 800 degree-days after each vaccination procedure. In this regard, oral immunizations maintained a long-term high concentration of anti-SRS and anti-ISAv specific IgM antibodies. When the concentration of antibodies decreased below 2000 pg/mL, a window of susceptibility to SRS infection was observed in the farm, suggesting a close association between antibody levels and fish protective status. These results demonstrated that, in the field, several oral immunizations are essential to uphold a high level of specific anti-pathogens antibodies and, therefore, the protective status during the whole productive cycle. PMID:26074916

  4. Successive Oral Immunizations Against Piscirickettsia Salmonis and Infectious Salmon Anemia Virus are Required to Maintain a Long-Term Protection in Farmed Salmonids

    PubMed Central

    Tobar, Iván; Arancibia, Sergio; Torres, Constanza; Vera, Verónica; Soto, Paola; Carrasco, Claudia; Alvarado, Marcelo; Neira, Eduardo; Arcos, Sandra; Tobar, Jaime A.

    2015-01-01

    Currently, there is a growing demand to determine the protective status of vaccinated fish in order to prevent diseases outbreaks. A set of different parameters that include the infectious and immunological status of vaccinated salmonids from 622 Chilean farms were analyzed during 2011–2014. The aim of this study was to optimize the vaccination program of these centers through the determination of the protective state of vaccinated fish using oral immunizations. This state was determined from the association of the concentration of the immunoglobulin M (IgM) in the serum and the mortality rate of vaccinated fish. Salmonids were vaccinated with different commercial mono- or polyvalent vaccines against salmonid rickettsial septicemia (SRS) and infectious salmon anemia (ISA), first by the intraperitoneal injection of oil-adjuvanted antigens and then by the stimulation of mucosal immunity using oral vaccines as a booster vaccination. The results showed that high levels of specific IgM antibodies were observed after injectable vaccination, reaching a maximum concentration at 600–800 degree-days. Similar levels of antibodies were observed when oral immunizations were administrated. The high concentration of antibodies [above 2750 ng/mL for ISA virus (ISAv) and 3500 ng/mL for SRS] was maintained for a period of 800 degree-days after each vaccination procedure. In this regard, oral immunizations maintained a long-term high concentration of anti-SRS and anti-ISAv specific IgM antibodies. When the concentration of antibodies decreased below 2000 pg/mL, a window of susceptibility to SRS infection was observed in the farm, suggesting a close association between antibody levels and fish protective status. These results demonstrated that, in the field, several oral immunizations are essential to uphold a high level of specific anti-pathogens antibodies and, therefore, the protective status during the whole productive cycle. PMID:26074916

  5. Efficiency of Portable Antennas for Detecting Passive Integrated Transponder Tags in Stream-Dwelling Salmonids

    PubMed Central

    Moyer, Katherine R.

    2016-01-01

    Portable antennas have become an increasingly common technique for tracking fish marked with passive integrated transponder (PIT) tags. We used logistic regression to evaluate how species, fish length, and physical habitat characteristics influence portable antenna detection efficiency in stream-dwelling brown trout (Salmo trutta), bull trout (Salvelinus confluentus), and redband trout (Oncorhynchus mykiss newberrii) marked with 12-mm PIT tags. We redetected 56% (20/36) of brown trout, 34% (68/202) of bull trout, and 33% (20/61) of redband trout after a recovery period of 21 to 46 hours. Models indicate support for length and species and minor support for percent boulder, large woody debris, and percent cobble as parameters important for describing variation in detection efficiency, although 95% confidence intervals for estimates were large. The odds of detecting brown trout (1.5 ± 2.2 [mean ± SE]) are approximately four times as high as bull trout (0.4 ± 1.6) or redband trout (0.3 ± 1.8) and species-specific differences may be related to length. Our reported detection efficiency for brown trout falls within the range of other studies, but is the first reported for bull trout and redband trout. Portable antennas may be a relatively unbiased way of redetecting varying sizes of all three salmonid species. PMID:26901317

  6. Efficiency of Portable Antennas for Detecting Passive Integrated Transponder Tags in Stream-Dwelling Salmonids.

    PubMed

    Banish, Nolan P; Burdick, Summer M; Moyer, Katherine R

    2016-01-01

    Portable antennas have become an increasingly common technique for tracking fish marked with passive integrated transponder (PIT) tags. We used logistic regression to evaluate how species, fish length, and physical habitat characteristics influence portable antenna detection efficiency in stream-dwelling brown trout (Salmo trutta), bull trout (Salvelinus confluentus), and redband trout (Oncorhynchus mykiss newberrii) marked with 12-mm PIT tags. We redetected 56% (20/36) of brown trout, 34% (68/202) of bull trout, and 33% (20/61) of redband trout after a recovery period of 21 to 46 hours. Models indicate support for length and species and minor support for percent boulder, large woody debris, and percent cobble as parameters important for describing variation in detection efficiency, although 95% confidence intervals for estimates were large. The odds of detecting brown trout (1.5 ± 2.2 [mean ± SE]) are approximately four times as high as bull trout (0.4 ± 1.6) or redband trout (0.3 ± 1.8) and species-specific differences may be related to length. Our reported detection efficiency for brown trout falls within the range of other studies, but is the first reported for bull trout and redband trout. Portable antennas may be a relatively unbiased way of redetecting varying sizes of all three salmonid species. PMID:26901317

  7. Efficiency of portable antennas for detecting passive integrated transponder tags in stream-dwelling salmonids

    USGS Publications Warehouse

    Banish, Nolan P.; Burdick, Summer M.; Moyer, Katherine R.

    2016-01-01

    Portable antennas have become an increasingly common technique for tracking fish marked with passive integrated transponder (PIT) tags. We used logistic regression to evaluate how species, fish length, and physical habitat characteristics influence portable antenna detection efficiency in stream-dwelling brown trout (Salmo trutta), bull trout (Salvelinus confluentus), and redband trout (Oncorhynchus mykiss newberrii) marked with 12-mm PIT tags. We redetected 56% (20/36) of brown trout, 34% (68/202) of bull trout, and 33% (20/61) of redband trout after a recovery period of 21 to 46 hours. Models indicate support for length and species and minor support for percent boulder, large woody debris, and percent cobble as parameters important for describing variation in detection efficiency, although 95% confidence intervals for estimates were large. The odds of detecting brown trout (1.5 ± 2.2 [mean ± SE]) are approximately four times as high as bull trout (0.4 ± 1.6) or redband trout (0.3 ± 1.8) and species-specific differences may be related to length. Our reported detection efficiency for brown trout falls within the range of other studies, but is the first reported for bull trout and redband trout. Portable antennas may be a relatively unbiased way of redetecting varying sizes of all three salmonid species.

  8. Evaluation of juvenile salmonid behavior near a prototype weir box at Cowlitz Falls Dam, Washington, 2013

    USGS Publications Warehouse

    Kock, Tobias J.; Liedtke, Theresa L.; Ekstrom, Brian K.; Tomka, Ryan G.; Rondorf, Dennis W.

    2014-01-01

    Collection of juvenile salmonids at Cowlitz Falls Dam is a critical part of the effort to restore salmon in the upper Cowlitz River because the majority of fish that are not collected at the dam pass downstream and enter a large reservoir where they become landlocked and lost to the anadromous fish population. However, the juvenile fish collection system at Cowlitz Falls Dam has failed to achieve annual collection goals since it first began operating in 1996. Since that time, numerous modifications to the fish collection system have been made and several prototype collection structures have been developed and tested, but these efforts have not substantially increased juvenile fish collection. Studies have shown that juvenile steelhead (Oncorhynchus mykiss), coho salmon (Oncorhynchus kisutch), and Chinook salmon (Oncorhynchus tshawytscha) tend to locate the collection entrances effectively, but many of these fish are not collected and eventually pass the dam through turbines or spillways. Tacoma Power developed a prototype weir box in 2009 to increase capture rates of juvenile salmonids at the collection entrances, and this device proved to be successful at retaining those fish that entered the weir. However, because of safety concerns at the dam, the weir box could not be deployed near a spillway gate where the prototype was tested, so the device was altered and re-deployed at a different location, where it was evaluated during 2013. The U.S. Geological Survey conducted an evaluation using radiotelemetry to monitor fish behavior near the weir box and collection flumes. The evaluation was conducted during April–June 2013. Juvenile steelhead and coho salmon (45 per species) were tagged with a radio transmitter and passive integrated transponder (PIT) tag, and released upstream of the dam. All tagged fish moved downstream and entered the forebay of Cowlitz Falls Dam. Median travel times from the release site to the forebay were 0.8 d for steelhead and 1.2 d for coho

  9. Salmonid genomes have a remarkably expanded akirin family, coexpressed with genes from conserved pathways governing skeletal muscle growth and catabolism

    PubMed Central

    Kristjánsson, Bjarni K.; Johnston, Ian A.

    2010-01-01

    Metazoan akirin genes regulate innate immunity, myogenesis, and carcinogenesis. Invertebrates typically have one family member, while most tetrapod and teleost vertebrates have one to three. We demonstrate an expanded repertoire of eight family members in genomes of four salmonid fishes, owing to paralog preservation after three tetraploidization events. Retention of paralogs secondarily lost in other teleosts may be related to functional diversification and posttranslational regulation. We hypothesized that salmonid akirins would be transcriptionally regulated in fast-twitch skeletal muscle during activation of conserved pathways governing catabolism and growth. The in vivo nutritional state of Arctic charr (Salvelinus alpinus L.) was experimentally manipulated, and transcript levels for akirin family members and 26 other genes were measured by quantitative real-time PCR (qPCR), allowing the establishment of a similarity network of expression profiles. In fasted muscle, a class of akirins was upregulated, with one family member showing high coexpression with catabolic genes coding the NF-κB p65 subunit, E2 ubiquitin-conjugating enzymes, E3 ubiquitin ligases, and IGF-I receptors. Another class of akirin was upregulated with subsequent feeding, coexpressed with 14-3-3 protein genes. There was no similarity between expression profiles of akirins with IGF hormones or binding protein genes. The level of phylogenetic relatedness of akirin family members was not a strong predictor of transcriptional responses to nutritional state, or differences in transcript abundance levels, indicating a complex pattern of regulatory evolution. The salmonid akirins epitomize the complexity linking the genome to physiological phenotypes of vertebrates with a history of tetraploidization. PMID:20388840

  10. Development and corroboration of a bioenergetics model for northern pikeminnow (Ptychocheilus oregonensis) feeding on juvenile salmonids in the Columbia River

    USGS Publications Warehouse

    Petersen, J.H.; Ward, D.L.

    1999-01-01

    A bioenergetics model was developed and corroborated for northern pikeminnow Ptychocheilus oregonensis, an important predator on juvenile salmonids in the Pacific Northwest. Predictions of modeled predation rate on salmonids were compared with field data from three areas of John Day Reservoir (Columbia River). To make bioenergetics model estimates of predation rate, three methods were used to approximate the change in mass of average predators during 30-d growth periods: observed change in mass between the first and the second month, predicted change in mass calculated with seasonal growth rates, and predicted change in mass based on an annual growth model. For all reservoir areas combined, bioenergetics model predictions of predation on salmon were 19% lower than field estimates based on observed masses, 45% lower than estimates based on seasonal growth rates, and 15% lower than estimates based on the annual growth model. For each growth approach, the largest differences in field-versus-model predation occurred at the midreservoir area (-84% to -67% difference). Model predictions of the rate of predation on salmonids were examined for sensitivity to parameter variation, swimming speed, sampling bias caused by gear selectivity, and asymmetric size distributions of predators. The specific daily growth rate of northern pikeminnow predicted by the model was highest in July and October and decreased during August. The bioenergetics model for northern pikeminnow performed well compared with models for other fish species that have been tested with field data. This model should be a useful tool for evaluating management actions such as predator removal, examining the influence of temperature on predation rates, and exploring interactions between predators in the Columbia River basin.

  11. Comparative evaluation of molecular diagnostic tests for Nucleospora salmonis and prevalence in migrating juvenile salmonids from the Snake River, USA

    USGS Publications Warehouse

    Badil, Samantha; Elliott, Diane G.; Kurobe, Tomofumi; Hedrick, Ronald P.; Clemens, Kathy; Blair, Marilyn; Purcell, Maureen K.

    2011-01-01

    Nucleospora salmonis is an intranuclear microsporidian that primarily infects lymphoblast cells and contributes to chronic lymphoblastosis and a leukemia-like condition in a range of salmonid species. The primary goal of this study was to evaluate the prevalence of N. salmonis in out-migrating juvenile hatchery and wild Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss from the Snake River in the U.S. Pacific Northwest. To achieve this goal, we first addressed the following concerns about current molecular diagnostic tests for N. salmonis: (1) nonspecific amplification patterns by the published nested polymerase chain reaction (nPCR) test, (2) incomplete validation of the published quantitative PCR (qPCR) test, and (3) whether N. salmonis can be detected reliably from nonlethal samples. Here, we present an optimized nPCR protocol that eliminates nonspecific amplification. During validation of the published qPCR test, our laboratory developed a second qPCR test that targeted a different gene sequence and used different probe chemistry for comparison purposes. We simultaneously evaluated the two different qPCR tests for N. salmonis and found that both assays were highly specific, sensitive, and repeatable. The nPCR and qPCR tests had good overall concordance when DNA samples derived from both apparently healthy and clinically diseased hatchery rainbow trout were tested. Finally, we demonstrated that gill snips were a suitable tissue for nonlethal detection of N. salmonis DNA in juvenile salmonids. Monitoring of juvenile salmonid fish in the Snake River over a 3-year period revealed low prevalence of N. salmonis in hatchery and wild Chinook salmon and wild steelhead but significantly higher prevalence in hatchery-derived steelhead. Routine monitoring of N. salmonis is not performed for all hatchery steelhead populations. At present, the possible contribution of this pathogen to delayed mortality of steelhead has not been determined.

  12. Salmonid genomes have a remarkably expanded akirin family, coexpressed with genes from conserved pathways governing skeletal muscle growth and catabolism.

    PubMed

    Macqueen, Daniel J; Kristjánsson, Bjarni K; Johnston, Ian A

    2010-06-01

    Metazoan akirin genes regulate innate immunity, myogenesis, and carcinogenesis. Invertebrates typically have one family member, while most tetrapod and teleost vertebrates have one to three. We demonstrate an expanded repertoire of eight family members in genomes of four salmonid fishes, owing to paralog preservation after three tetraploidization events. Retention of paralogs secondarily lost in other teleosts may be related to functional diversification and posttranslational regulation. We hypothesized that salmonid akirins would be transcriptionally regulated in fast-twitch skeletal muscle during activation of conserved pathways governing catabolism and growth. The in vivo nutritional state of Arctic charr (Salvelinus alpinus L.) was experimentally manipulated, and transcript levels for akirin family members and 26 other genes were measured by quantitative real-time PCR (qPCR), allowing the establishment of a similarity network of expression profiles. In fasted muscle, a class of akirins was upregulated, with one family member showing high coexpression with catabolic genes coding the NF-kappaB p65 subunit, E2 ubiquitin-conjugating enzymes, E3 ubiquitin ligases, and IGF-I receptors. Another class of akirin was upregulated with subsequent feeding, coexpressed with 14-3-3 protein genes. There was no similarity between expression profiles of akirins with IGF hormones or binding protein genes. The level of phylogenetic relatedness of akirin family members was not a strong predictor of transcriptional responses to nutritional state, or differences in transcript abundance levels, indicating a complex pattern of regulatory evolution. The salmonid akirins epitomize the complexity linking the genome to physiological phenotypes of vertebrates with a history of tetraploidization. PMID:20388840

  13. Understanding the influence of predation on introduced fishes on juvenile salmonids in the Columbia River Basin: Closing some knowledge gaps. Late summer and fall diet and condition of smallmouth bass, walleye, and channel catfish in the middle Columbia River, USA. Interim Report of Research 2011.

    USGS Publications Warehouse

    Rose, Brien P.; Hansen, Gabriel S.; Weaver, Michele; Ayers, David; Van Dyke, Erick S.; Mesa, Matthew G.

    2012-01-01

    American shad Alosa sapidissima in the middle Columbia River (MCR)—a high energy food available in the summer and fall—may be contributing to the increased growth and enhanced condition of nonnative piscivores. To test this hypothesis we quantified the late summer and autumn diets of smallmouth bass Micropterus dolomieu, walleye Sander vitreus, and channel catfish Ictalurus punctatus in the three lowermost reservoirs on the Columbia River (Bonneville [BON], The Dalles [TDA], and John Day [JDA]). The diet of smallmouth bass (SMB) was fairly similar among reservoirs, with crustaceans (52–82%) and fish (13–38%) being the dominant prey groups by percent mass. Cottidae were usually the dominant fish prey in the diet of SMB at all areas and the contribution of juvenile shad ranged from 0–8.2%. Fish (mostly Cyprinidae and Cottidae) were always the dominant prey item for walleye (WAL) at all areas and at all times, ranging from 70–100% of their diet by mass. Juvenile American shad composed from 10–27% (by mass) of the diet of walleye, depending on area and month. For channel catfish (CHC), the most common prey items consumed were crustaceans (20%–80% by mass) and unidentified items (30%–80%). Fish represented a relatively small component (< 4%) of their diet. We also evaluated the condition of SMB and WAL by determining relative weights (Wr) and hepatosomatic indices (HSI). Mean Wr for SMB greater than 300 mm ranged from 0.89 to 0.94 depending on area and month and showed a significant increase from August to September for fish in BON only. Overall, mean Wr of WAL was similar at all areas, ranging from 0.89–0.91, and increased significantly from September to mid-October and November for fish in TDA only. Overall, mean HSI of SMB ranged from 1.18 to 1.48, did not differ between fish in different reservoirs, and increased significantly from September to mid-October and November for fish from the lower JDA only. Mean HSI of WAL was significantly higher in

  14. Genetics and genomics of disease resistance in salmonid species

    PubMed Central

    Yáñez, José M.; Houston, Ross D.; Newman, Scott

    2014-01-01

    Infectious and parasitic diseases generate large economic losses in salmon farming. A feasible and sustainable alternative to prevent disease outbreaks may be represented by genetic improvement for disease resistance. To include disease resistance into the breeding goal, prior knowledge of the levels of genetic variation for these traits is required. Furthermore, the information from the genetic architecture and molecular factors involved in resistance against diseases may be used to accelerate the genetic progress for these traits. In this regard, marker assisted selection and genomic selection are approaches which incorporate molecular information to increase the accuracy when predicting the genetic merit of selection candidates. In this article we review and discuss key aspects related to disease resistance in salmonid species, from both a genetic and genomic perspective, with emphasis in the applicability of disease resistance traits into breeding programs in salmonids. PMID:25505486

  15. Pair-Trawl Detection of PIT-Tagged Juvenile Salmonids Migrating in the Columbia River Estuary, 2008 Report of Research.

    SciTech Connect

    Magie, Robert J.; Morris, Matthew S.; Ledgerwood, Richard D.

    2009-06-03

    In 2008, we sampled migrating juvenile Pacific salmonids Oncorhynchus spp. tagged with passive integrated transponder (PIT) tags using a surface pair trawl in the upper Columbia River estuary (rkm 61-83). The cod-end of the trawl was replaced with a cylindrical PIT-tag detection antenna with an 86-cm-diameter fish-passage opening and two detection coils connected in series. The pair trawl was 105 m long with a 91.5-m opening between the wings and a sample depth of 4.9 m. Also during 2008, we finalized the development of a prototype 'matrix' antenna, which was larger than previous antennas by a considerable magnitude. The matrix antenna consisted of 6 coils: a 3-coil front component and a 3-coil rear component, which were separated by 1.5-m of net mesh. The fish-passage opening was 2.5 m wide by 3.0 m tall and was attached to a standard-size pair trawl net. Intermittent sampling with a single crew began on 7 March and targeted yearling Chinook salmon O. tshawytscha and steelhead O. mykiss. Daily sampling using two crews began on 30 April and continued through 14 June; during this period we detected 2.7% of all juvenile salmonids previously detected at Bonneville Dam--a measure of sample efficiency. Sampling with a single crew continued through 20 August and targeted subyearling Chinook salmon. We detected 7,397 yearling Chinook salmon, 2,735 subyearling Chinook salmon, 291 coho salmon O. kisutch, 5,950 steelhead, and 122 sockeye salmon O. nerka in the upper estuary. We deployed the matrix antenna system and the older, cylindrical antenna system (86-cm-diameter fish-passage opening) simultaneously in mid-May 2008 to test matrix detection efficiency. The cylindrical antenna system had been used successfully in 2007 and early 2008. Because distribution of migrating salmonids in the estuary changes rapidly, we felt that a tandem sampling effort between the two systems was the only way to truly evaluate comparative detection efficiency. We deployed both systems within 1

  16. Is hyporheic flow an indicator for salmonid spawning site selection?

    NASA Astrophysics Data System (ADS)

    Benjankar, R. M.; Tonina, D.; Marzadri, A.; McKean, J. A.; Isaak, D.

    2015-12-01

    Several studies have investigated the role of hydraulic variables in the selection of spawning sites by salmonids. Some recent studies suggest that the intensity of the ambient hyporheic flow, that present without a salmon egg pocket, is a cue for spawning site selection, but others have argued against it. We tested this hypothesis by using a unique dataset of field surveyed spawning site locations and an unprecedented meter-scale resolution bathymetry of a 13.5 km long reach of Bear Valley Creek (Idaho, USA), an important Chinook salmon spawning stream. We used a two-dimensional surface water model to quantify stream hydraulics and a three-dimensional hyporheic model to quantify the hyporheic flows. Our results show that the intensity of ambient hyporheic flows is not a statistically significant variable for spawning site selection. Conversely, the intensity of the water surface curvature and the habitat quality, quantified as a function of stream hydraulics and morphology, are the most important variables for salmonid spawning site selection. KEY WORDS: Salmonid spawning habitat, pool-riffle system, habitat quality, surface water curvature, hyporheic flow

  17. Assessing survival of Mid-Columbia River released juvenile salmonids at McNary Dam, Washington, 2008-09

    USGS Publications Warehouse

    Evans, Scott D.; Walker, Christopher E.; Brewer, Scott J.; Adams, Noah S.

    2010-01-01

    Few studies have evaluated survival of juvenile salmon over long river reaches in the Columbia River and information regarding the survival of sockeye salmon at lower Columbia River dams is lacking. To address these information gaps, the U.S. Geological Survey was contracted by the U.S. Army Corps of Engineers to evaluate the possibility of using tagged fish released in the Mid-Columbia River to assess passage and survival at and downstream of McNary Dam. Using the acoustic telemetry systems already in place for a passage and survival study at McNary Dam, fish released from the tailraces of Wells, Rocky Reach, Rock Island, Wanapum, and Priest Rapids Dams were detected at McNary Dam and at the subsequent downstream arrays. These data were used to generate route-specific survival probabilities using single-release models from fish released in the Mid-Columbia River. We document trends in passage and survival probabilities at McNary Dam for yearling Chinook and sockeye salmon and juvenile steelhead released during studies in the Mid-Columbia River. Trends in the survival and passage of these juvenile salmonid species are presented and discussed. However, comparisons made across years and between study groups are not possible because of differences in the source of the test fish, the type of acoustic tags used, the absence of the use of passive integrated transponder tags in some of the release groups, differences in tagging and release protocols, annual differences in dam operations and configurations, differences in how the survival models were constructed (that is, number of routes that could be estimated given the number of fish detected), and the number and length of reaches included in the analysis (downstream reach length and arrays). Despite these differences, the data we present offer a unique opportunity to examine the migration behavior and survival of a group of fish that otherwise would not be studied. This is particularly true for sockeye salmon because

  18. Developing a Predation Index and Evaluating Ways to Reduce Salmonid Losses to Predation in the Columbia River Basin, Final Report August 1988-September 1990.

    SciTech Connect

    Nigro, Anthony A.

    1990-12-01

    We report our results of studies to develop a predation index and evaluate ways to reduce juvenile salmonid losses to predation in the Columbia River Basin. Study objectives of each were: develop an index to estimate predation losses of juvenile salmonids (Oncorhynchus spp) in reservoirs throughout the Columbia River Basin, describe the relationships among predator-caused mortality of juvenile salmonids and physical and biological variables, examine the feasibility of developing bounty, commercial or recreational fisheries on northern squawfish (Ptychocheilus oregonensis) and develop a plan to evaluate the efficacy of predator control fisheries; determine the economic feasibility of developing bounty and commercial fisheries for northern squawfish, assist ODFW with evaluating the economic feasibility of recreational fisheries for northern squawfish and assess the economic feasibility of utilizing northern squawfish, carp (Cyprinus carpio) and suckers (Castostomus spp) in multispecies fisheries; evaluate commercial technology of various fishing methods for harvesting northern squawfish in Columbia River reservoirs and field test the effectiveness of selected harvesting systems, holding facilities and transportation systems; and modify the existing Columbia River Ecosystem Model (CREM) to include processes necessary to evaluate effects of removing northern squawfish on their population size structure and abundance, document the ecological processes, mathematical equations and computer (FORTRAN) programming of the revised version of CREM and conduct systematic analyses of various predator removal scenarios, using revised CREM to generate the simulations. Individual reports are indexed separately.

  19. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

    USGS Publications Warehouse

    Chase, D.M.; Elliott, D.G.; Pascho, R.J.

    2006-01-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

  20. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis.

    PubMed

    Chase, Dorothy M; Elliott, Diane G; Pascho, Ronald J

    2006-07-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids. PMID:16921877

  1. Acoustic Imaging Evaluation of Juvenile Salmonid Behavior in the Immediate Forebay of the Water Temperature Control Tower at Cougar Dam, 2010

    SciTech Connect

    Khan, Fenton; Johnson, Gary E.; Royer, Ida M.; Phillips, Nathan RJ; Hughes, James S.; Fischer, Eric S.; Ploskey, Gene R.

    2011-10-01

    This report presents the results of an evaluation of juvenile Chinook salmonid (Oncorhynchus tshawytscha) behavior in the immediate forebay of the Water Temperature Control (WTC) tower at Cougar Dam in 2010. The study was conducted by the Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers. The overall goal of the study was to characterize juvenile salmonid behavior and movement patterns in the immediate forebay of the WTC tower for fisheries resource managers to use to make decisions on bioengineering designs for long-term structures and/or operations to facilitate safe downstream passage for juvenile salmonids. We collected acoustic imaging (Dual-Frequency Identification Sonar; DIDSON) data from February 1, 2010 through January 31, 2011 to evaluate juvenile salmonid behavior year-round in the immediate forebay surface layer of the WTC tower (within 20 m, depth 0-5 m). From October 28, 2010 through January 31, 2011 a BlueView acoustic camera was also deployed in an attempt to determine its usefulness for future studies as well as augment the DIDSON data. For the DIDSON data, we processed a total of 35 separate 24-h periods systematically covering every other week in the 12-month study. Two different 24-hour periods were processed for the BlueView data for the feasibility study. Juvenile salmonids were present in the immediate forebay of the WTC tower throughout 2010. The juvenile salmonid abundance index was low in the spring (<200 fish per sample-day), began increasing in late April and peaked in mid-May. Fish abundance index began decreasing in early June and remained low in the summer months. Fish abundance increased again in the fall, starting in October, and peaked on November 8-9. A second peak occurred on December 22. Afterwards, abundance was low for the rest of the study (through January 2011). Average fish length for juvenile salmonids during early spring 2010 was 214 {+-} 86 mm (standard deviation). From May through early November

  2. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin : Evaluating Wetland Restoration Projects in the Columbia River Estuary using Hydroacoustic Telemetry Arrays to Estimate Movement, Survival, and Residence Times of Juvenile Salmonids, Volume XXII (22).

    SciTech Connect

    Perry, Russell W.; Skalski, John R.

    2008-08-01

    Wetlands in the Columbia River estuary are actively being restored by reconnecting these habitats to the estuary, making more wetland habitats available to rearing and migrating juvenile salmon. Concurrently, thousands of acoustically tagged juvenile salmonids are released into the Columbia River to estimate their survival as they migrate through the estuary. Here, we develop a release-recapture model that makes use of these tagged fish to measure the success of wetland restoration projects in terms of their contribution to populations of juvenile salmon. Specifically, our model estimates the fraction of the population that enter the wetland, survival within the wetland, and the mean residence time of fish within the wetland. Furthermore, survival in mainstem Columbia River downstream of the wetland can be compared between fish that remained the mainstem and entered the wetland. These conditional survival estimates provide a means of testing whether the wetland improves the subsequent survival of juvenile salmon by fostering growth or improving their condition. Implementing such a study requires little additional cost because it takes advantage of fish already released to estimate survival through the estuary. Thus, such a study extracts the maximum information at minimum cost from research projects that typically cost millions of dollars annually.

  3. Lake Roosevelt Fisheries Evaluation Program, Part C; Lake Roosevelt Pelagic Fish Study: Washington Department of Fish and Wildlife, 1998 Annual Report.

    SciTech Connect

    Baldwin, Casey; Polacek, Matt; Bonar, Scott

    2002-11-01

    Pelagic fishes, such as kokanee and rainbow trout, provide an important fishery in Lake Roosevelt; however, spawner returns and creel results have been below management goals in recent years. Our objective was to identify factors that potentially limit pelagic fish production in Lake Roosevelt including entrainment, food limitation, piscivory, and other abiotic factors. We estimated the ratio of total fish entrained through Grand Coulee Dam to the pelagic fish abundance for September and October, 1998. If the majority of these fish were pelagic species, then entrainment averaged 10-13% of pelagic fish abundance each month. This rate of entrainment could impose considerable losses to pelagic fish populations on an annual basis. Therefore, estimates of species composition of entrained fish will be important in upcoming years to estimate the proportion of stocked pelagic fish lost through the dam. Food was not limiting for kokanee or rainbow trout populations since growth rates were high and large zooplankton were present in the reservoir. Estimates of survival for kokanee were low (< 0.01 annual) and unknown for rainbow trout. We estimated that the 1997 standing stock biomass of large (>1.1 mm) Daphnia could have supported 0.08 annual survival by kokanee and rainbow trout before fish consumption would have exceeded available biomass during late winter and early spring. Therefore, if recruitment goals are met in the future there may be a bottleneck in food supply for pelagic planktivores. Walleye and northern pikeminnow were the primary piscivores of salmonids in 1996 and 1997. Predation on salmonid prey was rare for rainbow trout and not detected for burbot or smallmouth bass. Northern pikeminnow had the greatest individual potential as a salmonid predator due to their high consumptive demand; however, their overall impact was limited because of their low relative abundance. We modeled the predation impact of 273,524 walleye in 1996, and 39,075 northern pikeminnow in

  4. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho, 2004-2005 Annual Report.

    SciTech Connect

    Meyer, Kevin A.; Lamansky, Jr., James A.

    2005-08-01

    In the western United States, exotic brook trout Salvelinus fontinalis frequently have a deleterious effect on native salmonids, and biologists often attempt to remove brook trout in streams using electrofishing. Although the success of electrofishing removal projects typically is low, few studies have assessed the underlying mechanisms of failure, especially in terms of compensatory responses. We evaluated the effectiveness of a three-year removal project in reducing brook trout and enhancing native salmonids in 7.8 km of an Idaho stream and looked for brook trout compensatory responses such as decreased natural mortality, increased growth, increased fecundity at length, or earlier maturation. Due to underestimates of the distribution of brook trout in the first year and personnel shortages in the third year, the multiagency watershed advisory group that performed the project fully treated the stream (i.e. multipass removals over the entire stream) in only one year. In 1998, 1999, and 2000, a total of 1,401, 1,241, and 890 brook trout were removed, respectively. For 1999 and 2000, an estimated 88 and 79% of the total number of brook trout in the stream were removed. For the section of stream that was treated in all years, the abundance of age-1 and older brook trout decreased by 85% from 1998 to 2003. In the same area, the abundance of age-0 brook trout decreased 86% from 1998 to 1999 but by 2003 had rebounded to near the original abundance. Abundance of native redband trout Oncorhynchus mykiss decreased for age-1 and older fish but did not change significantly for age-0 fish. Despite high rates of removal, total annual survival rate for brook trout increased from 0.08 {+-} 0.02 in 1998 to 0.20 {+-} 0.04 in 1999 and 0.21 {+-} 0.04 in 2000. Growth of age-0 brook trout was significantly higher in 2000 (the year after their abundance was lowest) compared to other years, and growth of age-1 and age-2 brook trout was significantly lower following the initial removal

  5. Routine clinical inspections in Norwegian marine salmonid sites: A key role in surveillance for freedom from pathogenic viral haemorrhagic septicaemia (VHS).

    PubMed

    Lyngstad, Trude Marie; Hellberg, Hege; Viljugrein, Hildegunn; Bang Jensen, Britt; Brun, Edgar; Sergeant, Evan; Tavornpanich, Saraya

    2016-02-01

    Since the mid-1980s, clinical inspections of aquaculture sites carried out on a regular basis by authorized veterinarians and fish health biologists (known as fish health services: FHS) have been an essential part of aquatic animal health surveillance in Norway. The aims of the present study were (1) to evaluate the performance of FHS routine clinical inspections for the detection of VHS and (2) to explore the effectiveness of risk-based prioritisation of FHS inspections for demonstrating freedom from VHS in marine salmonid sites in Norway. A stochastic simulation model was developed to estimate site sensitivity (SeS), population sensitivity (SeP), and probability of freedom (PFree). The estimation of SeS takes into consideration the probability that FHS submit samples if a site is infected, the probability that a sample is tested if submitted, the effective probability of infection in fish with clinical signs, laboratory test sensitivity, and the number of tested samples. SeP and PFree were estimated on a monthly basis over a 12 month period for six alternative surveillance scenarios and included the risk factors: region, species, area production density, and biosecurity level. Model results indicate that the current surveillance system, based on routine inspections by the FHS has a high capability for detecting VHS and that there is a high probability of freedom from VHS in Norwegian marine farmed salmonids (PFree >95%). Sensitivity analysis identified the probabilities that samples are submitted and submitted samples are tested, as the most influential input variables. The model provides a supporting tool for evaluation of potential changes in the surveillance strategy, and can be viewed as a platform for similar exotic viral infectious diseases in marine salmonid farming in Norway, if they share similar risk factors. PMID:26754927

  6. Migration depth and residence time of juvenile salmonids in the forebays of hydropower dams prior to passage through turbines or juvenile bypass systems: implications for turbine-passage survival.

    PubMed

    Li, Xinya; Deng, Zhiqun D; Brown, Richard S; Fu, Tao; Martinez, Jayson J; McMichael, Geoffrey A; Skalski, John R; Townsend, Richard L; Trumbo, Bradly A; Ahmann, Martin L; Renholds, Jon F

    2015-01-01

    Little is known about the three-dimensional depth distributions in rivers of individually marked fish that are in close proximity to hydropower facilities. Knowledge of the depth distributions of fish approaching dams can be used to understand how vulnerable fish are to injuries such as barotrauma as they pass through dams. To predict the possibility of barotrauma injury caused by pressure changes during turbine passage, it is necessary to understand fish behaviour relative to acclimation depth in dam forebays as they approach turbines. A guiding study was conducted using high-resolution three-dimensional tracking results of salmonids implanted with Juvenile Salmon Acoustic Telemetry System transmitters to investigate the depth distributions of subyearling and yearling Chinook salmon (Oncorhynchus tshawytscha) and juvenile steelhead (Oncorhynchus mykiss) passing two dams on the Snake River in Washington State. Multiple approaches were evaluated to describe the depth at which fish were acclimated, and statistical analyses were performed on large data sets extracted from ∼28 000 individually tagged fish during 2012 and 2013. Our study identified patterns of depth distributions of juvenile salmonids in forebays prior to passage through turbines or juvenile bypass systems. This research indicates that the median depth at which juvenile salmonids approached turbines ranged from 2.8 to 12.2 m, with the depths varying by species/life history, year, location (which dam) and diel period (between day and night). One of the most enlightening findings was the difference in dam passage associated with the diel period. The amount of time that turbine-passed fish spent in the immediate forebay prior to entering the powerhouse was much lower during the night than during the day. This research will allow scientists to understand turbine-passage survival better and enable them to assess more accurately the effects of dam passage on juvenile salmon survival. PMID:27293685

  7. Migration depth and residence time of juvenile salmonids in the forebays of hydropower dams prior to passage through turbines or juvenile bypass systems: implications for turbine-passage survival

    PubMed Central

    Li, Xinya; Deng, Zhiqun D.; Brown, Richard S.; Fu, Tao; Martinez, Jayson J.; McMichael, Geoffrey A.; Skalski, John R.; Townsend, Richard L.; Trumbo, Bradly A.; Ahmann, Martin L.; Renholds, Jon F.

    2015-01-01

    Little is known about the three-dimensional depth distributions in rivers of individually marked fish that are in close proximity to hydropower facilities. Knowledge of the depth distributions of fish approaching dams can be used to understand how vulnerable fish are to injuries such as barotrauma as they pass through dams. To predict the possibility of barotrauma injury caused by pressure changes during turbine passage, it is necessary to understand fish behaviour relative to acclimation depth in dam forebays as they approach turbines. A guiding study was conducted using high-resolution three-dimensional tracking results of salmonids implanted with Juvenile Salmon Acoustic Telemetry System transmitters to investigate the depth distributions of subyearling and yearling Chinook salmon (Oncorhynchus tshawytscha) and juvenile steelhead (Oncorhynchus mykiss) passing two dams on the Snake River in Washington State. Multiple approaches were evaluated to describe the depth at which fish were acclimated, and statistical analyses were performed on large data sets extracted from ∼28 000 individually tagged fish during 2012 and 2013. Our study identified patterns of depth distributions of juvenile salmonids in forebays prior to passage through turbines or juvenile bypass systems. This research indicates that the median depth at which juvenile salmonids approached turbines ranged from 2.8 to 12.2 m, with the depths varying by species/life history, year, location (which dam) and diel period (between day and night). One of the most enlightening findings was the difference in dam passage associated with the diel period. The amount of time that turbine-passed fish spent in the immediate forebay prior to entering the powerhouse was much lower during the night than during the day. This research will allow scientists to understand turbine-passage survival better and enable them to assess more accurately the effects of dam passage on juvenile salmon survival. PMID:27293685

  8. Feasibility Study for Evaluating Cumulative Exposure of Downstream Migrant Juvenile Salmonids to Total Dissolved Gas. Final Report 1996.

    SciTech Connect

    Abernethy, C.Scott; Dauble, Dennis D.; Johnson, Robert L.

    1997-11-01

    A feasibility study was initiated to determine if downstream migrant salmonids could be monitored to determine potential relationships between total dissolved gas (TDG) exposure and signs of gas bubble trauma (GBT). The primary objectives were to: (1) establish logistical requirements for in-river monitoring of TDG exposure, including net pen design, deployment, and navigation constraints; (2) resolve uncertainties associated with effects of the net pen on fish behavior; (3) test the accuracy and precision of in-river monitoring equipment used to measure fish distribution and water quality; and (4) determine the application of hydrologic/flow models to predictions of TDG exposure. In-river measurements included water velocity, boat position, and selected water quality parameters (temperature, dissolved oxygen, pH, depth, conductivity). Fish distribution within the net pen was monitored using scanning sonar, and a split-beam echo sounder was used to evaluate vertical distribution of fish m in the river adjacent to the net pen. Three test drifts were conducted from late July through late August. The studies demonstrated that it was feasible to assemble and deploy a large net pen for mobile monitoring of TDG exposure. Accurate monitoring of vertical and lateral distribution of smolts was performed, and diel differences in behavior were documented. Further, the fish sounded in response to researcher activity on the perimeter platform. Thus, in-transit monitoring for GBT or mortality would affect fish depth distribution and exposure to TDG. Principal recommendations for future studies are directed at improving maneuverability of the net pen in adverse weather conditions and applying new acoustics technology to simultaneously collect fish distribution data from within and outside of the pen. 6 refs., 17 figs., 2 tabs.

  9. Characterization of Gatewell Orifice Lighting at the Bonneville Dam Second Powerhouse and Compendium of Research on Light Guidance with Juvenile Salmonids

    SciTech Connect

    Mueller, Robert P.; Simmons, Mary Ann

    2007-12-29

    The goal of the study described in this report is to provide U.S. Army Corps of Engineers (USACE) biologists and engineers with general design guidelines for using artificial lighting to enhance the passage of juvenile salmonids into the collection channel at the Bonneville Dam second powerhouse (B2). During fall 2007, Pacific Northwest National Laboratory (PNNL) researchers measured light levels in the field at one powerhouse orifice through which fish must pass to reach the collection channel. Two light types were evaluated—light-emitting diode (LED) lights and halogen spot lights. Additional measurements with mercury lamps were made at the PNNL Aquatic Research Laboratory to determine baseline intensity of the current lighting. A separate chapter synthesizes the relevant literature related to light and fish guidance for both field and laboratory studies. PNNL will also review the Corps plans for existing lighting protocol at all of the Portland District projects and help develop a uniform lighting scheme which could be implemented. The specific objectives for this study are to 1. Create a synthesis report of existing lighting data for juvenile salmonid attraction and deterrence and how the data are used at fish bypass facilities. 2. Evaluate current B2 orifice lighting conditions with both LED and halogen sources. 3. Make recommendations as to what lighting intensity, source, and configuration would improve passage at the B2 orifices. 4. Review USACE plans for retrofit of existing systems (to be assessed at a later date).

  10. Vaccines for fish in aquaculture.

    PubMed

    Sommerset, Ingunn; Krossøy, Bjørn; Biering, Eirik; Frost, Petter

    2005-02-01

    Vaccination plays an important role in large-scale commercial fish farming and has been a key reason for the success of salmon cultivation. In addition to salmon and trout, commercial vaccines are available for channel catfish, European seabass and seabream, Japanese amberjack and yellowtail, tilapia and Atlantic cod. In general, empirically developed vaccines based on inactivated bacterial pathogens have proven to be very efficacious in fish. Fewer commercially available viral vaccines and no parasite vaccines exist. Substantial efficacy data are available for new fish vaccines and advanced technology has been implemented. However, before such vaccines can be successfully commercialized, several hurdles have to be overcome regarding the production of cheap but effective antigens and adjuvants, while bearing in mind environmental and associated regulatory concerns (e.g., those that limit the use of live vaccines). Pharmaceutical companies have performed a considerable amount of research on fish vaccines, however, limited information is available in scientific publications. In addition, salmonids dominate both the literature and commercial focus, despite their relatively small contribution to the total volume of farmed fish in the world. This review provides an overview of the fish vaccines that are currently commercially available and some viewpoints on how the field is likely to evolve in the near future. PMID:15757476

  11. System-Wide Significance of Predation on Juvenile Salmonids in Columbia and Snake River Reservoirs and Evaluation of Predation Control Measures : Annual Report 1993.

    SciTech Connect

    Gadomski, Dena M.; Petersen, James H.; Poe, Thomas P.

    1993-12-01

    This project had three major goals. The first was to assist the Oregon Department of Fish and Wildlife with predation indexing as part of an effort to estimate the relative magnitude of juvenile salmonid losses to northern squawfish Ptychocheilus oregonensis in reservoirs throughout the Columbia River Basin. The second goal was to evaluate the northern squawfish control program and test critical assumptions about mid-reservoir predation processes. The final goal was to determine mechanisms underlying northern squawfish recruitment and factors affecting year-class strength.

  12. Assess Current and Potential Salmonid Production in Rattlesnake Creek Associated with Restoration Efforts; Yakama Indian Nation, Annual Report 2002-2003.

    SciTech Connect

    Morris, Gregory

    2003-05-01

    This document represents the FY2002 BPA contract Statement of Work for the Yakama Nation (YN) portion of the project entitled 'Assessment of current and potential salmonid production in Rattlesnake Creek associated with restoration efforts'. The purpose of the project is to complete detailed surveys of water quality, fish populations, habitat conditions and riparian health in the Rattlesnake Creek sub-basin of the White Salmon River in south central Washington. Results of the surveys will be used to establish Rattlesnake Creek sub-basin baseline environmental factors prior to anticipated removal of Condit Dam in 2006 and enable cost-effective formulation of future watershed restoration strategies.

  13. A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA

    USGS Publications Warehouse

    Muhlfeld, Clint C.; D'Angelo, Vincent S.; S. T. Kalinowski; Landguth, Erin L.; C. C. Downs; J. Tohtz; Kershner, Jeffrey L.

    2012-01-01

    Biologists are often faced with the difficult decision in managing native salmonids of where and when to install barriers as a conservation action to prevent upstream invasion of nonnative fishes. However, fine-scale approaches to assess long-term persistence of populations within streams and watersheds chosen for isolation management are often lacking. We employed a spatially-explicit approach to evaluate stream habitat conditions, relative abundance, and genetic diversity of native westslope cutthroat trout (Oncorhynchus clarkii lewisi) within the Akokala Creek watershed in Glacier National Park- a population threatened by introgressive hybridization with nonnative rainbow trout (O. mykiss) from nearby sources. The systematic survey of 24 stream reaches showed broad overlap in fish population and suitable habitat characteristics among reaches and no natural barriers to fish migration were found. Analysis of population structure using 16 microsatellite loci showed modest amounts of genetic diversity among reaches, and that fish from Long Bow Creek were the only moderately distinct genetic group. We then used this information to assess the potential impacts of three barrier placement scenarios on long-term population persistence and genetic diversity. The two barrier placement scenarios in headwater areas generally failed to meet general persistence criteria for minimum population size (2,500 individuals, Ne = 500), maintenance of long-term genetic diversity (He), and no population subdivision. Conversely, placing a barrier near the stream mouth and selectively passing non-hybridized, migratory spawners entering Akokala Creek met all persistence criteria and may offer the best option to conserve native trout populations and life history diversity. Systematic, fine-scale stream habitat, fish distribution, and genetic assessments in streams chosen for barrier installation are needed in conjunction with broader scale assessments to understand the potential impacts of

  14. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho; 1998 Annual Report.

    SciTech Connect

    Meyer, Kevin A.

    1999-03-01

    Native resident salmonids in the western United States are in decline throughout much of their range. The purpose of the multi-phased project is to restore native salmonids in the upper Snake River basin to self-sustaining, harvestable levels.

  15. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.

    PubMed

    Pasquier, Jeremy; Cabau, Cédric; Nguyen, Thaovi; Jouanno, Elodie; Severac, Dany; Braasch, Ingo; Journot, Laurent; Pontarotti, Pierre; Klopp, Christophe; Postlethwait, John H; Guiguen, Yann; Bobe, Julien

    2016-01-01

    With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts. PMID:27189481

  16. Evaluation of Juvenile Fish Bypass and Adult Fish Facilities at Water Diversions in the Umatilla River; 1992 Annual Report.

    SciTech Connect

    Knapp, Suzanne M.

    1993-03-01

    We report on our progress from October 1991 through September 1992 in evaluating juvenile fish bypass facilities at Three Mile Falls and Westland dams on the Umatilla River. We also report on our progress from October 1991 through June 1992 in evaluating adult fish passage in the lower Umatilla River and adult fish passage facilities at Three Mile Falls Dam. The study is a cooperative effort by the Oregon Department of Fish and Wildlife (ODFW) and the Confederated Tribes of the Umatilla Indian Reservation (CTUIR). These are the study objectives addressed by ODFW and CTUIR: (1) Report A (ODFW): To evaluate the juvenile fish bypass facility in the West Extension Irrigation District Canal at Three Mile Falls Dam and document juvenile salmonid passage through the juvenile fish bypass facility and east-bank adult fish ladder. To measure velocity and develop trap designs at Westland Dam. (2) Report B (CTUIR): To examine the passage of adult salmonids at Three Mile Falls Dam. The study is part of a program to rehabilitate anadromous fish stocks in the Umatilla River Basin, including restoration of coho salmon (Oncorhynchus kisutch) and chinook salmon (Oncorhynchus tshawytscha), as well as enhancement of summer steelhead (Oncorhynchus mykiss).

  17. Evaluation of Juvenile Fish Bypass and Adult Fish Passage Facilities at Water Diversions in the Umatilla River; 1993 Annual Report.

    SciTech Connect

    Knapp, Suzanne M.

    1994-03-01

    This report presents progress from October 1992 through September 1993 in evaluating juvenile fish bypass facilities at Three Mile Falls, Maxwell, Westland, and Feed Canal dams on the Umatilla River, and in evaluating adult fish passage in the lower Umatilla River. Also reported is an effort to evaluate delayed mortality and stress responses of juvenile salmonids resulting from trapping and transport at high temperatures. These studies are part of a program to rehabilitate anadromous fish stocks in the matilla River Basin, including restoration of coho salmon and chinook salmon, as well as enhancement of summer steelhead.

  18. 75 FR 76400 - Endangered and Threatened Species; Take of Anadromous Fish

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-08

    ... analysis as part of Project 3, in Pescadero Lagoon. Project 1 is a study on the summer ecology of juvenile... salmonids in Tomales Bay, and Pescadero Lagoon and their overall dependence on estuarine resources based on...), and release smolts. In Pescadero Lagoon, a subset of fish will be implanted with PIT tags. Adults...

  19. Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Renibacterium salmoninarum is the causative agent of bacterial kidney disease, a major pathogen of salmonid fish species worldwide. Very low levels of intra-species genetic diversity have hampered efforts to understand the transmission dynamics and recent evolutionary history of this Gram-positive b...

  20. INFLUENCE OF HUMAN ACTIVITIES ON LANDSCAPE AND HABITAT FACTORS CONTROLLING PACIFIC NORTHWEST COASTAL STREAM FISH ASSEMBLAGES

    EPA Science Inventory

    Fish assemblages in the Oregon-Washington coast range consist primarily of coldwater taxa of salmonids, cottids, dace, and Pacific giant salamander. This region has a dynamic natural disturbance regime, where mass failures, debris torrents, fire, and tree-fall are driven by clim...

  1. Timing matters: species-specific interactions between spawning time, substrate quality, and recruitment success in three salmonid species

    PubMed Central

    Sternecker, Katharina; Denic, Marco; Geist, Juergen

    2014-01-01

    Substratum quality and oxygen supply to the interstitial zone are crucial for the reproductive success of salmonid fishes. At present, degradation of spawning grounds due to fine sediment deposition and colmation are recognized as main factors for reproductive failure. In addition, changes in water temperatures due to climate change, damming, and cooling water inlets are predicted to reduce hatching success. We tested the hypothesis that the biological effects of habitat degradation depend strongly on the species-specific spawning seasons and life-history strategies (e.g., fall- vs. spring-spawners, migratory vs. resident species) and assessed temperature as an important species-specific factor for hatching success within river substratum. We studied the species-specific differences in their responses to such disturbances using egg-to-fry survival of Danube Salmon (Hucho hucho), resident brown trout (Salmo trutta fario), and migratory brown trout (Salmo trutta lacustris) as biological endpoint. The egg incubation and hatching success of the salmonids and their dependence on temperature and stream substratum quality were compared. Hatching rates of Danube salmon were lower than of brown trout, probably due to higher oxygen demands and increased interstitial respiration in spring. Increases in maximum water temperature reduced hatching rates of resident and migratory brown trout (both fall-spawners) but were positively correlated with hatching rates of Danube salmon (a spring-spawner). Significantly longer incubation periods of resident and migratory brown trout coincided with relatively low stream substratum quality at the end of the egg incubation. Danube salmon seem to avoid low oxygen concentrations in the hyporheic zone by faster egg development favored by higher water temperatures. Consequently, the prediction of effects of temperature changes and altered stream substratum properties on gravel-spawning fishes and biological communities should consider the

  2. Salmonid Gamete Preservation in the Snake River Basin, 2001 Annual Report.

    SciTech Connect

    Armstrong, Robyn; Kucera, Paul

    2002-06-01

    Steelhead (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) populations in the Northwest are decreasing. Genetic diversity is being lost at an alarming rate. Along with reduced population and genetic variability, the loss of biodiversity means a diminished environmental adaptability. The Nez Perce Tribe (Tribe) strives to ensure availability of genetic samples of the existing male salmonid population by establishing and maintaining a germplasm repository. The sampling strategy, initiated in 1992, has been to collect and preserve male salmon and steelhead genetic diversity across the geographic landscape by sampling within the major river subbasins in the Snake River basin, assuming a metapopulation structure existed historically. Gamete cryopreservation conserves genetic diversity in a germplasm repository, but is not a recovery action for listed fish species. The Tribe was funded in 2001 by the Bonneville Power Administration (BPA) and the U.S. Fish and Wildlife Service Lower Snake River Compensation Plan (LSRCP) to coordinate gene banking of male gametes from Endangered Species Act (ESA) listed steelhead and spring and summer chinook salmon in the Snake River basin. In 2001, a total of 398 viable chinook salmon semen samples from the Lostine River, Catherine Creek, upper Grande Ronde River, Lookingglass Hatchery (Imnaha River stock), Lake Creek, the South Fork Salmon River weir, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi Hatchery, and Sawtooth Hatchery (upper Salmon River stock) were cryopreserved. Also, 295 samples of male steelhead gametes from Dworshak Hatchery, Fish Creek, Grande Ronde River, Little Sheep Creek, Pahsimeroi Hatchery and Oxbow Hatchery were also cryopreserved. The Grande Ronde chinook salmon captive broodstock program stores 680 cryopreserved samples at the University of Idaho as a long-term archive, half of the total samples. A total of 3,206 cryopreserved samples from Snake River basin steelhead and

  3. Hydroacoustic Evaluation of Juvenile Salmonid Passage at The Dalles Dam in 2004

    SciTech Connect

    Johnson, Gary E.; Hanks, Michael E.; Khan, Fenton; Cook, Chris B.; Hedgepeth, J; Mueller, Robert P.; Rakowski, Cynthia L.; Richmond, Marshall C.; Sargeant, Susan L.; Serkowski, John A.; Skalski, John R.

    2005-06-01

    The U.S. Army Corps of Engineers Portland District engaged the Pacific Northwest National Laboratory to evaluate juvenile salmon passage at The Dalles Dam in 2004 to inform decisions about long-term measures and operations to enhance sluiceway and spill passage and reduce turbine passage to improve smolt survival at the dam. PNNL used fixed-location hydroacoustic sampling across the entire project, especially at the sluiceway and spillway, using multiple split-beam transducers at selected locations. At the sluiceway nearfield, we used an acoustic camera to track fish. The fish data were interpreted and integrated with hydraulic data from a CFD model and in-field ADCP measurements. Two sluiceway operations were compared: West only (SL 1) vs. West+East (SL 1 + SL 18). Based on our findings, we concluded that The Dalles Dam sluiceway has the potential to be highly efficient and effective at passing juvenile salmonids. This potential could be tapped with hydraulic and entrance enhancements to the sluiceway. We recommended the following: (1) six rather than three sluice gates should be opened to take advantage of the maximum hydraulic capacity of the sluiceway. (2) The turbine units below open sluice gates should be operated as a standard fish operations procedure. (3) In 2005, the Corps and fisheries agencies should consider operating sluice gates in one or more of the following combinations of six gates: (a) SL 1-1, 1-2, 1-3 and SL 18-1, 18-2, 18-3 (repeat 2004 operation), (b) SL 1-1, 1-2, 1-3 and SL 11-1, 11-2, 11-3, or (c) SL 1-1, 1-2, 1-3 and SL 2-1, 2-2, 2-3. The following elements for surface flow bypasses which should be considered during design of any sluiceway enhancements at The Dalles Dam: (1) form an extensive surface flow bypass flow net (surface bypass discharge greater than {approx}7% of total project discharge), (2) create a gradual increase in water velocity approaching the surface flow bypass (ideally, acceleration < 1 m/s/m), (3) make water

  4. Development of a rapid and efficient microinjection technique for gene insertion into fertilized salmonid eggs

    SciTech Connect

    Chandler, D.P.; Welt, M.; Leung, F.C.

    1990-10-01

    An efficient one-step injection technique for gene insertion into fertilized rainbow trout (Oncorhynchus mykiss) eggs is described, and basic parameters affecting egg survival are reported. Freshly fertilized rainbow trout eggs were injected in the perivitelline space with a recombinant mouse metallothionein-genomic bovine growth hormone (bGH) DNA construct using a 30-gauge hypodermic needle and a standard microinjection system. Relative to control, site of injection and DNA concentration did not affect the egg survival, but injections later than 3--4 hours post fertilization were detrimental. The injection technique permitted treatment of 100 eggs/hr with survivals up to 100%, resulting in a 4% DNA uptake rate as indicated by DNA dot blot analysis. Positive dot blot results also indicated that the injected DNA is able to cross the vitelline membrane and persist for 50--60 days post hatching, obviating the need for direct injection into the germinal disk. Results are consistent with previous transgenic fish work, underscoring the usefulness of the technique for generating transgenic trout and salmonids. 24 refs., 6 figs., 3 tabs.

  5. Low temperature-dependent salmonid alphavirus glycoprotein processing and recombinant virus-like particle formation.

    PubMed

    Metz, Stefan W; Feenstra, Femke; Villoing, Stephane; van Hulten, Marielle C; van Lent, Jan W; Koumans, Joseph; Vlak, Just M; Pijlman, Gorben P

    2011-01-01

    Pancreas disease (PD) and sleeping disease (SD) are important viral scourges in aquaculture of Atlantic salmon and rainbow trout. The etiological agent of PD and SD is salmonid alphavirus (SAV), an unusual member of the Togaviridae (genus Alphavirus). SAV replicates at lower temperatures in fish. Outbreaks of SAV are associated with large economic losses of ~17 to 50 million $/year. Current control strategies rely on vaccination with inactivated virus formulations that are cumbersome to obtain and have intrinsic safety risks. In this research we were able to obtain non-infectious virus-like particles (VLPs) of SAV via expression of recombinant baculoviruses encoding SAV capsid protein and two major immunodominant viral glycoproteins, E1 and E2 in Spodoptera frugiperda Sf9 insect cells. However, this was only achieved when a temperature shift from 27°C to lower temperatures was applied. At 27°C, precursor E2 (PE2) was misfolded and not processed by host furin into mature E2. Hence, E2 was detected neither on the surface of infected cells nor as VLPs in the culture fluid. However, when temperatures during protein expression were lowered, PE2 was processed into mature E2 in a temperature-dependent manner and VLPs were abundantly produced. So, temperature shift-down during synthesis is a prerequisite for correct SAV glycoprotein processing and recombinant VLP production. PMID:21991361

  6. Low Temperature-Dependent Salmonid Alphavirus Glycoprotein Processing and Recombinant Virus-Like Particle Formation

    PubMed Central

    Villoing, Stephane; van Hulten, Marielle C.; van Lent, Jan W.; Koumans, Joseph; Vlak, Just M.; Pijlman, Gorben P.

    2011-01-01

    Pancreas disease (PD) and sleeping disease (SD) are important viral scourges in aquaculture of Atlantic salmon and rainbow trout. The etiological agent of PD and SD is salmonid alphavirus (SAV), an unusual member of the Togaviridae (genus Alphavirus). SAV replicates at lower temperatures in fish. Outbreaks of SAV are associated with large economic losses of ∼17 to 50 million $/year. Current control strategies rely on vaccination with inactivated virus formulations that are cumbersome to obtain and have intrinsic safety risks. In this research we were able to obtain non-infectious virus-like particles (VLPs) of SAV via expression of recombinant baculoviruses encoding SAV capsid protein and two major immunodominant viral glycoproteins, E1 and E2 in Spodoptera frugiperda Sf9 insect cells. However, this was only achieved when a temperature shift from 27°C to lower temperatures was applied. At 27°C, precursor E2 (PE2) was misfolded and not processed by host furin into mature E2. Hence, E2 was detected neither on the surface of infected cells nor as VLPs in the culture fluid. However, when temperatures during protein expression were lowered, PE2 was processed into mature E2 in a temperature-dependent manner and VLPs were abundantly produced. So, temperature shift-down during synthesis is a prerequisite for correct SAV glycoprotein processing and recombinant VLP production. PMID:21991361

  7. Evolutionary effects of alternative artificial propagation programs: implications for viability of endangered anadromous salmonids

    PubMed Central

    McClure, Michelle M; Utter, Fred M; Baldwin, Casey; Carmichael, Richard W; Hassemer, Peter F; Howell, Philip J; Spruell, Paul; Cooney, Thomas D; Schaller, Howard A; Petrosky, Charles E

    2008-01-01

    Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning. PMID:25567637

  8. Diagnostic testing patterns of Renibacterium salmoninarum in spawning salmonid stocks in Michigan.

    PubMed

    Faisal, M; Eissa, A E

    2009-04-01

    Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, is a slowly progressing disease that threatens salmon conservation and restoration programs in North America. The purpose of this study was to track naturally occurring R. salmoninarum infection in representative, Michigan, USA, salmonid stocks using nested polymerase chain reaction (nPCR), quantitative enzyme-linked immunosorbent assay (Q-ELISA), and culture. The Q-ELISA test detected 67.6% infection prevalence, which is lower than culture (77.2%) or nPCR (94.2%), yet it provided semiquantitative data on infection intensity. The disagreement in results among the three assays may reflect the different phases of R. salmoninarum infection at the time of sampling. The testing results demonstrated the presence of six patterns, with each of the patterns representing a probable stage along the course of natural R. salmoninarum infection. Findings also suggest that fish stocks tested in this study were not uniform in the distribution of the diagnostic patterns and that, from studying such patterns, one can determine the course of BKD infection in a particular population. PMID:19395754

  9. Research, Monitoring, and Evaluation of Avian Predation on Salmonid Smolts in the Lower and Mid-Columbia River, 2006 Final Season Summary.

    SciTech Connect

    Roby, Daniel D.; Collis, Ken; Lyons, Donald E.

    2009-06-18

    statistically significant change in the size of the Caspian tern colony on East Sand Island since 2000. Tern nesting success averaged 0.72 fledglings per breeding pair in 2006, significantly higher than in 2005 (0.37 fledglings per breeding pair), a year of poor ocean conditions. Despite the presumably higher availability of marine forage fishes in 2006, the proportion of juvenile salmonids in diets of Caspian terns (32% of prey items) averaged higher than in 2005 (23% of prey items) and 2004 (18% of prey items). Steelhead smolts were particular vulnerable to predation by East Sand Island terns in 2006, with predation rates as high as 20% on particular groups of PIT-tagged fish reaching the estuary. Consumption of juvenile salmonids by terns nesting at the East Sand Island colony in 2006 was approximately 5.3 million smolts (95% c.i. = 4.4-6.2 million), significantly higher than the estimated 3.6 million smolts consumed in 2005, but still roughly 7 million fewer smolts consumed compared to 1998 (when all terns nested on Rice Island in the upper estuary). Caspian terns nesting on East Sand Island continue to rely primarily on marine forage fishes as a food supply, even in 2005 when availability of marine forage fishes declined due to poor ocean conditions. Further management of Caspian terns to reduce losses of juvenile salmonids would be implemented under the Caspian Tern Management Plan for the Columbia River Estuary; the Records of Decision (RODs) authorizing implementation of the plan were signed in November 2006. The ROD lists as the management goal the redistribution of approximately half of the East Sand Island Caspian tern colony to alternative colony sites in interior Oregon and San Francisco Bay, California (USFWS 2006). Implementation of the management plan is stalled, however, because of the lack of appropriated funds.

  10. A Study to Determine the Biological Feasibility of a New Fish Tagging System : Annual Report 1984.

    SciTech Connect

    Prentice, Earl F.; Sims, C.W.; Park, D.L.

    1985-05-01

    The potential of the Passive Integrated Transponder (PIT) tag for marking salmonids was evaluated. In Phase I, sham PIT tags were injected into the body cavity of juvenile salmonids. Tagged fish ranged in weight from 0.8 to 43.9 g. Observations based on six tests, ranging in time from 19 to 99 days, indicated that the test site for injecting the tag was along the mid-ventral line in the area of the pectoral or pelvic fins. Tag retention of 99% (n = 400) and survival of 99% were achieved. Minimal tissue response to the tag was noted in both tag locations. In Phase II, a PIT tag detector system designed to detect and record the passage of juvenile salmonids was evaluated. By restricting the rate at which fish entered the monitoring tunnel to one fish per second, detection averaged 94.3% compared to 86.6% for multiple fish entry. In Phase III, a monitoring system designed to detect and decode adult fish tagged with a PIT tag was evaluated. The average detection and proper decoding of these tagged fish was 94.4% for 211 fish. Improvements in the detection system are recommended.

  11. Approach, passage, and survival of juvenile salmonids at Little Goose Dam, Washington: Post-construction evaluation of a temporary spillway weir, 2009

    USGS Publications Warehouse

    Beeman, J.W.; Braatz, A.C.; Hansel, H.C.; Fielding, S.D.; Haner, P.V.; Hansen, G.S.; Shurtleff, D.J.; Sprando, J.M.; Rondorf, D.W.

    2010-01-01

    This report describes a study of dam passage and survival of radio-tagged juvenile salmonids after installation of a temporary spillway weir (TSW) at Little Goose Dam, Washington, in 2009. The purpose of the study was to document fish passage and survival when the dam was operated with the TSW in place. Spillway weirs are one of several methods used to improve downstream passage of juvenile salmonids. Each spillway weir design is based on the concept of providing an overflow weir with a depth more similar to the natural migration depth of juvenile salmonids than conventional spill bays. Little Goose Dam was the last of the four lower Snake River dams to have a spillway weir installed. This was the first year that some form of surface passage device was operating at all Snake River and Columbia River dams between Lewiston, Idaho, and the Columbia River estuary. The study design stipulated that a total of 30 percent of the river discharge would continuously be passed over the TSW and the conventional spill bays, and this percentage was achieved. The TSW also was to be operated at the 'low crest' elevation during the spring and the 'high crest' elevation during the summer, but the TSW was only operated at the low crest elevation during this study. Behavior, passage, and survival of spring and summer juvenile salmonid migrants passing through Little Goose Dam were examined using radio telemetry. Survival was estimated using the Route Specific Survival Model (RSSM) by releasing tagged fish near Central Ferry State Park 21 kilometers upstream of the dam and in the tailrace approximately 0.5 kilometer downstream of the dam. From April 18 to May 21, 2009, 1,520 yearling Chinook salmon (Oncorhynchus tshawytscha) and 1,517 juvenile steelhead (O. mykiss) were radio tagged and released. From June 6 to July 5, 2009, 4,251 subyearling Chinook salmon (O. tshawytscha) were radio tagged and released. Release dates of subyearling Chinook salmon were selected to avoid 'reservoir

  12. Using bioenergetics modeling to estimate consumption of native juvenile salmonids by nonnative northern pike in the Upper Flathead River System, Montana

    USGS Publications Warehouse

    Muhlfeld, C.C.; Bennett, D.H.; Kirk, Steinhorst R.; Marotz, B.; Boyer, M.

    2008-01-01

    Introductions of nonnative northern pike Esox lucius have created recreational fisheries in many waters in the United States and Canada, yet many studies have shown that introduced northern pike may alter the composition and structure of fish communities through predation. We estimated the abundance of nonnative northern pike (2002-2003) and applied food habits data (1999-2003) to estimate their annual consumption of native bull trout Salvelinus confluentus and westslope cutthroat trout Oncorhynchus clarkii lewisi juveniles in the upper Flathead River system, Montana. Population estimates were generally consistent among years and ranged from 1,200 to 1,300 individuals. Westslope cutthroat trout were present in the diet of younger (???600 mm) and older (>600 mm) northern pike during all seasons and bull trout were found only in larger northern pike during all seasons but summer. Bioenergetics modeling estimated that the northern pike population annually consumed a total of 8.0 metric tons (mt) of fish flesh; the highest biomass was composed of cyprinids (4.95 mt) followed by whitefishes Prosopium spp. (1.02 mt), bull trout (0.80 mt), westslope cutthroat trout (0.68 mt), yellow perch Perca flavescens (0.41 mt),1 and other fishes (centrarchids and cottids; 0.14 mt). Numerically, the northern pike population consumed more than 342,000 fish; cyprinids and catostomids comprised approximately 82% of prey fish (278,925), whereas over 13,000 westslope cutthroat trout and nearly 3,500 bull trout were eaten, comprising about 5% of the prey consumed. Our results suggest that predation by introduced northern pike is contributing to the lower abundance of native salmonids in the system and that a possible benefit might accrue to native salmonids by reducing these predatory interactions. ?? Copyright by the American Fisheries Society 2008.

  13. Changes in Wisconsin's Lake Michigan salmonid sport fishery, 1969-1985

    USGS Publications Warehouse

    Hansen, Michael J.; Schultz, Paul T.; Lasee, Becky A.

    1990-01-01

    The modern sport fishery for salmonids in Wisconsin waters of Lake Michigan was begun during 1963-1969 with the stocking of rainbow trout (Oncorhynchus mykiss), lake trout (Salvelinus namaycush), brook trout (S. fontinalis), brown trout (Salmo trutta), coho salmon (O. kisutch), and chinook salmon (O. tshawytscha). The fishery grew rapidly during 1969-1985 as angler effort increased 10-fold, catch rate doubled, and catch increased 20-fold. The stocking and catch became increasingly dominated by chinook salmon, with coho salmon and lake trout of secondary importance and brown, rainbow, and brook trout of least importance. Trolling dominated the fishery, particularly by launched-boat anglers and, more recently, by moored-boat anglers. Charter boat trolling grew the most continuously and had the highest catch rates. The catch by trollers was dominated by chinook and coho salmon and lake trout. Pier, stream, and shore anglers fished less overall, but had catch rates that were similar to launched-boat anglers. The catch by pier and shore anglers was spread among chinook and coho salmon, and lake, brown and rainbow trout. The catch by stream anglers was dominated by chinook salmon. The percentage of stocked fish that were subsequently caught (catch ratio) was highest for fingerling chinook salmon (12.9%). Yearling brook trout, brown trout, coho salmon, lake trout, and rainbow trout had intermediate catch ratios (5.1-9.8%). Fingerling brook trout, brown trout, and lake trout had the lowest catch ratios (2.5-3.5%). The catch ratio for rainbow trout dropped from 9.8 to 5.1% after stocking with a different strain (the Shasta strain). Fingerling rainbow trout produced the lowest returns (<0.5%). We derived stocking recommendations for each species and life stage based on these catch ratios, and catch objectives based on maintaining catch levels recorded during 1983-1985.

  14. A review of tricaine methanesulfonate for anesthesia of fish

    SciTech Connect

    Carter, Kathleen M.; Woodley, Christa M.; Brown, Richard S.

    2011-01-01

    Tricaine methanesulfonate (TMS) is the only FDA approved anesthetic for use in a select number of fish species, including salmonids. It is used widely in hatcheries and research to immobilize fish for marking or transport and to suppress sensory systems during invasive procedures. Improper use can decrease fish viability and possibly distort physiological data. Since animals may be anesthetized by junior staff or students who may have little experience in fish anesthesia, training in the proper use of TMS may decrease variability in results and increase fish survival. This document acts as a primer on the use of TMS for anesthetizing juvenile salmonids, with an emphasis on its use in surgical applications. Within, we briefly discuss many aspects TMS. We describe the legal uses for TMS, and what is currently known about the proper storage and preparation of the anesthetic. We outline methods and precautions for administration and changes in fish behavior during progressively deeper anesthesia. We also discuss the physiological effects of TMS and its potential for decreasing fish health.

  15. A paleoscience approach to estimating the effects of climatic warming on salmonid fisheries of the Columbia River Basin

    SciTech Connect

    Chatters, J.C.; Butler, V.L.; Scott, M.J.; Anderson, D.M.; Neitzel, D.A.

    1992-10-01

    To understand how climatic warming might affect salmonid populations, we are following a four-step procedure, incorporating paleoenvironmental data at the beginning and ending points, as follows. First, we used geomorphic, paleobotanical, and paleomalacological data to reconstruct stream conditions during the last 8000 years. Second, we estimated the effect on salmon of conditions extant approximately 6000 to 7000 radiocarbon years before present (B.P.), when temperatures were as much as 2{degrees}C warmer than at present. This became an analog of future warmer climate and its effects on spawning, incubation, and rearing parameters of the NPPC`s Tributary Parameter Model (TPM) for estimating salmoned production. Third, we ran the TPM in conjunction with the NPPC System Planning Model (SPM) to calculate the effect of these analog conditions on the population of returning adult fish in selected stream systems. Ultimately, we will run the models for all salmon-accessible subbasins of the Columbia River system. Finally, we are identifying fish remains obtained from archaeological sites along the Columbia River to compare variations in the taxonomic composition of ancient fish assemblages with model predictions.

  16. A paleoscience approach to estimating the effects of climatic warming on salmonid fisheries of the Columbia River Basin

    SciTech Connect

    Chatters, J.C.; Butler, V.L.; Scott, M.J.; Anderson, D.M.; Neitzel, D.A.

    1992-10-01

    To understand how climatic warming might affect salmonid populations, we are following a four-step procedure, incorporating paleoenvironmental data at the beginning and ending points, as follows. First, we used geomorphic, paleobotanical, and paleomalacological data to reconstruct stream conditions during the last 8000 years. Second, we estimated the effect on salmon of conditions extant approximately 6000 to 7000 radiocarbon years before present (B.P.), when temperatures were as much as 2[degrees]C warmer than at present. This became an analog of future warmer climate and its effects on spawning, incubation, and rearing parameters of the NPPC's Tributary Parameter Model (TPM) for estimating salmoned production. Third, we ran the TPM in conjunction with the NPPC System Planning Model (SPM) to calculate the effect of these analog conditions on the population of returning adult fish in selected stream systems. Ultimately, we will run the models for all salmon-accessible subbasins of the Columbia River system. Finally, we are identifying fish remains obtained from archaeological sites along the Columbia River to compare variations in the taxonomic composition of ancient fish assemblages with model predictions.

  17. A global assessment of salmon aquaculture impacts on wild salmonids.

    PubMed

    Ford, Jennifer S; Myers, Ransom A

    2008-02-01

    Since the late 1980s, wild salmon catch and abundance have declined dramatically in the North Atlantic and in much of the northeastern Pacific south of Alaska. In these areas, there has been a concomitant increase in the production of farmed salmon. Previous studies have shown negative impacts on wild salmonids, but these results have been difficult to translate into predictions of change in wild population survival and abundance. We compared marine survival of salmonids in areas with salmon farming to adjacent areas without farms in Scotland, Ireland, Atlantic Canada, and Pacific Canada to estimate changes in marine survival concurrent with the growth of salmon aquaculture. Through a meta-analysis of existing data, we show a reduction in survival or abundance of Atlantic salmon; sea trout; and pink, chum, and coho salmon in association with increased production of farmed salmon. In many cases, these reductions in survival or abundance are greater than 50%. Meta-analytic estimates of the mean effect are significant and negative, suggesting that salmon farming has reduced survival of wild salmon and trout in many populations and countries. PMID:18271629

  18. The fish pathogen Renibacterium salmoninarum: growth in a microaerophilic atmosphere.

    PubMed

    Hirvelä-Koski, Varpu

    2008-02-01

    Renibacterium salmoninarum is the etiologic agent of bacterial kidney disease (BKD) occurring worldwide in salmonid fish. This bacterium has previously been regarded as a strict aerobic species. However, in this study it is shown that R. salmoninarum grows well in microaerophilic atmosphere, the colony size being larger and the colonies being more mucoid than in aerobic conditions. Microaerophilic cultivation might be one possibility to increase the sensitivity of the cultivation method for the detection of this slowly growing pathogen. PMID:17884309

  19. Fish Allergy

    MedlinePlus

    ... Story" 5 Things to Know About Zika & Pregnancy Fish Allergy KidsHealth > For Parents > Fish Allergy Print A ... From Home en español Alergia al pescado About Fish Allergy A fish allergy is not exactly the ...

  20. Fish Movement Ecology in High Gradient Headwater Streams: Its Relevance to Fish Passage Restoration through Stream Culvert Barriers

    USGS Publications Warehouse

    Hoffman, Robert L.; Dunham, Jason B.

    2007-01-01

    Executive Summary Restoration of fish passage through culvert barriers has emerged as a major issue in the Pacific Northwest and nationwide. The problem has many dimensions, including the huge number of potential barriers, uncertainty about which structures are actually barriers, the benefits and risks involved with restoration, and the financial costs and timelines. This report attempts to address what we call 'thinking outside of the pipe' in terms of fish passage information needs. This means understanding the value of each potential passage restoration project in the context of other possible projects, and to view individual restoration projects within a larger landscape of habitats and population processes. In this report we provide a brief review of some essential characteristics of animal movement and examples from a focal group of fishes in Washington State: salmon, trout, and char. While several other fishes and many other species use streams where culvert passage barriers may occur, it is the salmonids that are by far the most widespread and in most cases extending furthest into the headwaters of stream networks in Washington. We begin this report by outlining some basic characteristics of animal movement and then apply that foundation to the case of salmonid fishes. Next we consider the consequences of disrupting fish movement with human-constructed barriers, such as culverts. Finally, this body of evidence is summarized and we propose a short list of what we view as high priority information needs to support more effective restoration of fish passage through culverts.

  1. Acoustics as a tool for the assessment of Great Lakes forage fishes

    USGS Publications Warehouse

    Argyle, Ray L.

    1992-01-01

    Sharp reductions in forage fish populations in Lake Michigan have raised concerns about the continued ability of the forage stocks to support large populations of lake trout and other salmonid predators. There was a need for a more comprehensive and accurate estimate of forage fish abundance and distribution to evaluate these concerns. In response, cooperative diel surveys of the Lake Michigan forage species were conducted in late summer 1987 and spring 1989 with acoustics, midwater and bottom trawls.

  2. Evaluation of Juvenile Salmonid Outmigration and Survival in the Lower Umatilla River Basin, Annual Report 2003-2006.

    SciTech Connect

    White, Tara

    2007-02-01

    This report summarizes activities conducted by the Oregon Department of Fish and Wildlife's Juvenile Outmigration and Survival M&E project in the Umatilla River subbasin between 2004-2006. Information is used to make informed decisions on hatchery effectiveness, natural production success, passage improvement and flow enhancement strategies. Data collected includes annual estimates of smolt abundance, migration timing, and survival, life history characteristics and productivity status and trends for spring and fall Chinook salmon, coho salmon and summer steelhead. Productivity data provided is the key subbasin scale measure of the effectiveness of salmon and steelhead restoration actions in the Umatilla River. Information is also used for regional planning and recovery efforts of Mid-Columbia River (MCR) ESA-listed summer steelhead. Monitoring is conducted via smolt trapping and PIT-tag interrogation at Three Mile Falls Dam. The Umatilla Juvenile Outmigration and Survival Project was established in 1994 to evaluate the success of management actions and fisheries restoration efforts in the Umatilla River Basin. Project objectives for the 2004-2006 period were to: (1) operate the PIT tag detection system at Three Mile Falls Dam (TMFD), (2) enhance provisional PIT-tag interrogation equipment at the east bank adult fish ladder, (3) monitor the migration timing, abundance and survival of naturally-produced juvenile salmonids and trends in natural production, (4) determine migration parameters and survival of hatchery-produced fish representing various rearing, acclimation and release strategies, (5) evaluate the relative survival between transported and non-transported fish, (6) monitor juvenile life history characteristics and evaluate trends over time, (7) investigate the effects of river, canal, fishway operations and environmental conditions on smolt migration and survival, (8) document the temporal distribution and diversity of resident fish species, and (9

  3. One Fish Two Fish.

    ERIC Educational Resources Information Center

    Hoffman, Michele

    1998-01-01

    This activity explains fisheries resource management to seven-year olds. First-grade students learn concepts such as offspring viability, life expectancy, and distribution of species, which help to determine when, where, and how people fish and the importance of fishing responsibly. Lists materials, procedures, and extensions. (SJR)

  4. Enumeration of Juvenile Salmonids in the Okanogan Basin Using Rotary Screw Traps, Performance Period: March 15, 2006 - July 15, 2006.

    SciTech Connect

    Johnson, Peter N.; Rayton, Michael D.

    2007-05-01

    The Colville Tribes identified the need for collecting baseline census data on the timing and abundance of juvenile salmonids in the Okanogan River basin for the purpose of documenting local fish populations, augmenting existing fishery data and assessing natural production trends of salmonids. This report documents and assesses the pilot year of rotary trap capture of salmonid smolts on the Okanogan River. The project is a component of the Colville Tribes Okanogan Basin Monitoring and Evaluation Program (OBMEP) which began in 2004. Trapping for outmigrating fish began on 14 March 2006 and continued through 11 July 2006. Anadromous forms of Oncorhynchus, including summer steelhead (O. mykiss), Chinook (O. tshawytscha), and sockeye (O. nerka), were targeted for this study; all have verified, natural production in the Okanogan basin. Both 8-ft and 5-ft rotary screw traps were deployed on the Okanogan River from the Highway 20 Bridge and typically fished during evening hours or 24 hours per day, depending upon trap position and discharge conditions. Juvenile Chinook salmon were the most abundant species trapped in 2006 (10,682 fry and 2,024 smolts), followed by sockeye (205 parr and 3,291 smolts) and steelhead (1 fry and 333 smolts). Of the trapped Chinook, all fry were wild origin and all but five of the smolts were hatchery-reared. All trapped sockeye were wild origin and 88% of the steelhead smolts were hatchery-reared. Mark-recapture experiments were conducted using Chinook fry and hatchery-reared steelhead smolts (sockeye were not used in 2006 because the peak of the juvenile migration occurred prior to the onset of the mark-recapture experiments). A total of 930 chinook fry were marked and released across eight separate release dates (numbers of marked Chinook fry released per day ranged from 34 to 290 fish). A total of 11 chinook fry were recaptured for an overall trap efficiency of 1.18%. A total of 710 hatchery-reared steelhead were marked and released across

  5. Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta, Lower Columbia River, 2007 Annual Report.

    SciTech Connect

    Sobocinski, Kathryn; Johnson, Gary; Sather, Nichole

    2008-03-17

    This document is the first annual report for the study titled 'Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta in the Lower Columbia River'. Hereafter, we refer to this research as the Tidal Freshwater Monitoring (TFM) Study. The study is part of the research, monitoring, and evaluation effort developed by the Action Agencies (Bonneville Power Administration, U.S. Army Corps of Engineers, U.S. Bureau of Reclamation) in response to obligations arising from the Endangered Species Act as a result of operation of the Federal Columbia River Power System (FCRPS). The project is performed under the auspices of the Northwest Power and Conservation Council's Columbia Basin Fish and Wildlife Program. The goal of the 2007-2009 Tidal Freshwater Monitoring Study is to answer the following questions: In what types of habitats within the tidal freshwater area of the lower Columbia River and estuary (LCRE; Figure 1) are yearling and subyearling salmonids found, when are they present, and under what environmental conditions?1 And, what is the ecological importance2 of shallow (0-5 m) tidal freshwater habitats to the recovery of Upper Columbia River spring Chinook salmon and steelhead and Snake River fall Chinook salmon? Research in 2007 focused mainly on the first question, with fish stock identification data providing some indication of Chinook salmon presence at the variety of habitat types sampled. The objectives and sub-objectives for the 2007 study were as follows: (1) Habitat and Fish Community Characteristics-Provide basic data on habitat and fish community characteristics for yearling and subyearling salmonids at selected sites in the tidal freshwater reach in the vicinity of the Sandy River delta. (1a) Characterize vegetation assemblage percent cover, conventional water quality, substrate composition, and beach slope at each of six sampling sites in various tidal freshwater habitat types. (1b) Determine fish

  6. Surgical implantation techniques for electronic tags in fish

    SciTech Connect

    Wagner, Glenn N.; Cooke, Steven J.; Brown, Richard S.; Deters, Katherine A.

    2011-01-01

    Intracoelomic implantation of transmitters into fish requires making a surgical incision, incision closure, and other surgery related techniques; however, the tools and techniques used in the surgical process vary widely. We review the available literature and focus on tools and techniques used for conducting surgery on juvenile salmonids because of the large amount of research that is conducted on them. The use of sterilized surgical instruments properly selected for a given size of fish will minimize tissue damage and infection rates, and speed the wound healing of fish implanted with transmitters. For the implantation of transmitters into small fish, the optimal surgical methods include making an incision on the ventral midline along the linea alba (for studies under 1 month), protecting the viscera (by lifting the skin with forceps while creating the incision), and using absorbable monofilament suture with a small-swaged-on swaged-on tapered or reverse-cutting needle. Standardizing the implantation techniques to be used in a study involving particular species and age classes of fish will improve survival and transmitter retention while allowing for comparisons to be made among studies and across multiple years. This review should be useful for researchers working on juvenile salmonids and other sizes and species of fish.

  7. Topographic and lithologic controls on occurrence of cobble-boulder channel beds: implications for salmonid over-wintering habitat

    NASA Astrophysics Data System (ADS)

    Donaldson, E. T.; Sklar, L. S.; Marshall, J. A.; Ligon, F. K.; Dietrich, W. E.

    2009-12-01

    Channel beds dominated by cobble- and boulder-sized particles provide over-wintering habitat to Steelhead trout (Oncorhynchus mykiss) and other salmonids because the fish use the interstitial space as refuge from high flows, particularly where large woody debris and off-channel habitat are not present. Methods for predicting the occurrence and quality of cobble-boulder (CoBo) substrate are needed to guide population modeling and landuse management to support salmonid restoration efforts. Here we report results of an ongoing study of the controls on CoBo occurrence in Pescadero Creek, a forested coastal watershed draining the north-western side of the Santa Cruz mountains in central California. Our operational definition of CoBo is a bed material median grain size of 120 mm, with a thickness of at least 150 mm, open interstitial matrix, and low recurrence interval of mobilization (e.g 50 years). CoBo habitat is typically found at channel slopes of 2% and greater, and where drainage area is sufficient to provide perennial flow, however many channels with these slope-area characteristics are too fine-grained to serve as CoBo habitat. We hypothesize that the occurrence of Cobo habitat is controlled by hillslope sediment supply conditions. In particular, production of a sufficient supply of cobbles and boulders requires a durable bedrock lithology and either steep topography capable of producing debris flow-generating landslides or bedrock-walled inner gorges. In larger-drainage-area, lower-slope mainstem channels, coarse sediment plumes associated with tributary junctions may also be common sites of CoBo occurrence. We are using a combination of field reconnaissance and surveying, geologic mapping, and DEM analysis of channel network and hillslope topography to assess sediment supply conditions associated with occurrence of CoBo substrates. We are also assessing the habitat quality of reaches with CoBo substrates, which can be degraded by high supply of gravel and

  8. Salmonid Gamete Preservation in the Snake River Basin : 2000 Annual Report.

    SciTech Connect

    Armstrong, Robyn; Kucera, Paul A.

    2001-06-01

    Steelhead (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) populations in the Northwest are decreasing. Genetic diversity is being lost at an alarming rate. The Nez Perce Tribe (Tribe) strives to ensure availability of genetic samples of the existing male salmonid population by establishing and maintaining a germplasm repository. The sampling strategy, initiated in 1992, has been to collect and preserve male salmon and steelhead genetic diversity across the geographic landscape by sampling within the major river subbasins in the Snake River basin, assuming a metapopulation structure existed historically. Gamete cryopreservation conserves genetic diversity in a germplasm repository, but is not a recovery action for listed fish species. The Tribe was funded in 2000 by the Bonneville Power Administration (BPA) and the U.S. Fish and Wildlife Service Lower Snake River Compensation Plan (LSRCP) to coordinate gene banking of male gametes from Endangered Species Act listed steelhead and spring and summer chinook salmon in the Snake River basin. In 2000, a total of 349 viable chinook salmon semen samples from the Lostine River, Catherine Creek, upper Grande Ronde River, Lookingglass Hatchery (Imnaha River stock), Rapid River Hatchery, Lake Creek, the South Fork Salmon River weir, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi Hatchery, and Sawtooth Hatchery (upper Salmon River stock) were cryopreserved. Also, 283 samples of male steelhead gametes from Dworshak Hatchery, Fish Creek, Grande Ronde River, Imnaha River, Little Sheep Creek, Pahsimeroi Hatchery and Oxbow Hatchery were also cryopreserved. The Tribe acquired 5 frozen steelhead samples from the Selway River collected in 1994 and 15 from Fish Creek sampled in 1993 from the U.S. Geological Survey, for addition into the germplasm repository. Also, 590 cryopreserved samples from the Grande Ronde chinook salmon captive broodstock program are being stored at the University of Idaho as

  9. A Quantitative Polymerase Chain Reaction Assay for the Detection and Quantification of Epizootic Epitheliotropic Disease Virus (EEDV; Salmonid Herpesvirus 3).

    PubMed

    Glenney, Gavin W; Barbash, Patricia A; Coll, John A

    2016-03-01

    Epizootic epitheliotropic disease virus (EEDV; salmonid herpesvirus [SalHV3]; family Alloherpesviridae) causes a systemic disease of juvenile and yearling Lake Trout Salvelinus namaycush. No cell lines are currently available for the culture and propagation of EEDV, so primary diagnosis is limited to PCR and electron microscopy. To better understand the pervasiveness of EEDV (carrier or latent state of infection) in domesticated and wild Lake Trout populations, we developed a sensitive TaqMan quantitative PCR (qPCR) assay to detect the presence of the EEDV terminase gene in Lake Trout tissues. This assay was able to detect a linear standard curve over nine logs of plasmid dilution and was sensitive enough to detect single-digit copies of EEDV. The efficiency of the PCR assay was 99.4 ± 0.06% (mean ± SD), with a 95% confidence limit of 0.0296 (R(2) = 0.994). Methods were successfully applied to collect preliminary data from a number of species and water bodies in the states of Pennsylvania, New York, and Vermont, indicating that EEDV is more common in wild fish than previously known. In addition, through the development of this qPCR assay, we detected EEDV in a new salmonid species, the Cisco Coregonus artedi. The qPCR assay was unexpectedly able to detect two additional herpesviruses, the Atlantic Salmon papillomatosis virus (ASPV; SalHV4) and the Namaycush herpesvirus (NamHV; SalHV5), which both share high sequence identity with the EEDV terminase gene. With these unexpected findings, we subsequently designed three primer sets to confirm initial TaqMan qPCR assay positives and to differentiate among EEDV, ASPV, and NamHV by detecting the glycoprotein genes via SYBR Green qPCR. Received April 20, 2015; accepted November 10, 2015. PMID:26980561

  10. DEVELOPMENT OF FIELD-BASED EMPIRICAL MODELS OF SUITABLE TEMPERATURE REGIMES FOR INTERIOR SALMONIDS

    EPA Science Inventory

    Interior salmonids are species of growing interest and concern in the Pacific Northwest. Evidence of population declines associated with habitat loss and fragmentation have culminate in every species being listed, or proposed or petitioned for listing under he Endangered Species...

  11. Apparent digestibility of possible fish meal replacements in Atlantic Salmon, Salmo salar and Arctic Charr, Salvelinus alpinus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To increase the sustainability of salmonid production, alternative protein sources to fish meal need to be identified. Many studies have examined terrestrial plant meals/protein concentrates as alternatives. Recently the focus has turned to aquatic protists and plants as well as by-products from oth...

  12. Genome sequence of the fish pathogen Renibacterium salmoninarum suggests reductive evolution away from an environmental Arthrobacter ancestor.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Renibacterium salmoninarum (Rs) is the causative agent of bacterial kidney disease and a significant threat to the healthy and sustainable production of salmonid fish worldwide. The pathogen is difficult to culture in vitro, genetic manipulation is challenging, and current therapies and preventative...

  13. Evaluation of family growth response to fish meal and plant protein-based diets of rainbow trout (Oncorhynchus mykiss)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Both environmental and economic concerns have led to the development of fish-meal free diets for salmonids. The ability of rainbow trout to efficiently utilize plant-based diets for growth and reproduction, and the genetic variation within populations for these traits, has not been thoroughly examin...

  14. Salmonid Gamete Preservation in the Snake River Basin, Annual Report 2002.

    SciTech Connect

    Young, William; Kucera, Paul

    2003-07-01

    In spite of an intensive management effort, chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) populations in the Northwest have not recovered and are currently listed as threatened species under the Endangered Species Act. In addition to the loss of diversity from stocks that have already gone extinct, decreased genetic diversity resulting from genetic drift and inbreeding is a major concern. Reduced population and genetic variability diminishes the environmental adaptability of individual species and entire ecological communities. The Nez Perce Tribe (NPT), in cooperation with Washington State University and the University of Idaho, established a germplasm repository in 1992 in order to preserve the remaining salmonid diversity in the region. The germplasm repository provides long-term storage for cryopreserved gametes. Although only male gametes can be cryopreserved, conserving the male component of genetic diversity will maintain future management options for species recovery. NPT efforts have focused on preserving salmon and steelhead gametes from the major river subbasins in the Snake River basin. However, the repository is available for all management agencies to contribute gamete samples from other regions and species. In 2002 a total of 570 viable semen samples were added to the germplasm repository. This included the gametes of 287 chinook salmon from the Lostine River, Catherine Creek, upper Grande Ronde River, Imnaha River (Lookingglass Hatchery), Lake Creek, South Fork Salmon River, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi River (Pahsimeroi Hatchery), and upper Salmon River (Sawtooth Hatchery) and the gametes of 280 steelhead from the North Fork Clearwater River (Dworshak Hatchery), Fish Creek, Little Sheep Creek, Pahsimeroi River (Pahsimeroi Hatchery) and Snake River (Oxbow Hatchery). In addition, gametes from 60 Yakima River spring chinook and 34 Wenatchee River coho salmon were added to the

  15. Protective immunity in fish against protozoan diseases.

    PubMed

    Woo, P T K

    2007-09-01

    The demand for and costs of producing land-based animal protein continues to escalate as the world population increases. Fish is an excellent protein, but the catch-fishery is stagnant or in decline. Intensive cage culture of fish is a viable option especially in countries with lakes/rivers and/or a long coastline; however, disease outbreaks will likely occur more frequently with cage culture. Hence protective strategies are needed, and one approach is to exploit the piscine immune system. This discussion highlights immunity (innate/natural and adaptive/acquired) in fish against three pathogenic protozoa (Amyloodinium ocellatum, Ichthyophthirius multifiliis and Cryptobia salmositica). Histone-like proteins in the mucus and skin of naturally resistant fish kill trophonts of A. ocellatum, and also may cause abnormal development of tomonts. Breeding of Cryptobia-resistant brook charrs is possible as resistance is controlled by a dominant Mendelian locus, and the parasite is lysed via the Alternative Pathway of Complement Activation. Production of transgenic Cryptobia-tolerant salmon is an option. Recovered fish are protected from the three diseases (acquired immunity). Live I. multifiliis theronts injected intraperitoneally into fish elicit protection. Also, a recombinant immoblizing-antigen vaccine against ichthyophthirosis has been developed but further evaluations are necessary. The live Cryptobia vaccine protects salmonids from infections while the DNA-vaccine stimulates production of antibodies to neutralize the disease causing factor (metalloprotease) in cryptobiosis; hence infected fish recover more rapidly. PMID:18410078

  16. The life cycle of Ceratomyxa shasta, a myxosporean parasite of salmonids, requires a freshwater polychaete as an alternate host.

    PubMed

    Bartholomew, J L; Whipple, M J; Stevens, D G; Fryer, J L

    1997-10-01

    The actinosporean life stage of Ceratomyxa shasta, a myxozoan parasite of salmonids, and the annelid worm that serves as its alternate host were identified in laboratory transmission experiments and their roles were confirmed using molecular techniques. Infection by the parasite occurred in susceptible fish that were either exposed to or force fed the freshwater polychaete, Manayunkia speciosa, infected with the actinosporean. These observations were confirmed using the polymerase chain reaction with primers designed from the C. shasta 18S rDNA sequence. DNA was amplified from polychaetes harboring the actinosporean that caused infection in the fish but not from uninfected polychaetes. Amplified DNA from an infected polychaete was sequenced and its homology with the 18S rDNA sequence of C. shasta spores verified the proposed life cycle. Ultrastructural examination of the actinosporean in the polychaete showed developmental stages in the epidermis rather than within the intestinal epithelium as described for other myxozoans. The methods described will be useful in identifying alternate hosts and morphologically diverse life stages in the complex life cycles of other myxosporea and in understanding the relationships between these parasites and their hosts. PMID:9379291

  17. Occurrence of salmonid alphavirus (SAV) and piscine orthoreovirus (PRV) infections in wild sea trout Salmo trutta in Norway.

    PubMed

    Madhun, Abdullah Sami; Isachsen, Cecilie Helen; Omdal, Linn Maren; Bårdsgjære Einen, Ann Cathrine; Bjørn, Pål Arne; Nilsen, Rune; Karlsbakk, Egil

    2016-07-01

    Viral diseases represent a serious problem in Atlantic salmon (Salmo salar L.) farming in Norway. Pancreas disease (PD) caused by salmonid alphavirus (SAV) and heart and skeletal muscle inflammation (HSMI) caused by piscine orthoreovirus (PRV) are among the most frequently diagnosed viral diseases in recent years. The possible spread of viruses from salmon farms to wild fish is a major public concern. Sea trout S. trutta collected from the major farming areas along the Norwegian coast are likely to have been exposed to SAV and PRV from farms with disease outbreaks. We examined 843 sea trout from 4 counties in Norway for SAV and PRV infections. We did not detect SAV in any of the tested fish, although significant numbers of the trout were caught in areas with frequent PD outbreaks. Low levels of PRV were detected in 1.3% of the sea trout. PRV-infected sea trout were caught in both salmon farming and non-farming areas, so the occurrence of infections was not associated with farming intensity or HSMI cases. Our results suggest that SAV and PRV infections are uncommon in wild sea trout. Hence, we found no evidence that sea trout are at risk from SAV or PRV released from salmon farms. PMID:27409234

  18. Using Satellite Tracking and Isotopic Information to Characterize the Impact of South American Sea Lions on Salmonid Aquaculture in Southern Chile

    PubMed Central

    Sepúlveda, Maritza; Newsome, Seth D.; Pavez, Guido; Oliva, Doris; Costa, Daniel P.; Hückstädt, Luis A.

    2015-01-01

    Apex marine predators alter their foraging behavior in response to spatial and/or seasonal changes in natural prey distribution and abundance. However, few studies have identified the impacts of aquaculture that represents a spatially and temporally predictable and abundant resource on their foraging behavior. Using satellite telemetry and stable isotope analysis we examined the degree of spatial overlap between the South American sea lion (SASL) and salmon farms, and quantify the amount of native prey versus farmed salmonids in SASL diets. We instrumented eight SASL individuals with SRDL-GPS tags. Vibrissae, hair and skin samples were collected for δ13C and δ15N analyses from five of the tagged individuals and from four males captured in a haul-out located adjacent to salmon farms. Tracking results showed that almost all the foraging areas of SASL are within close proximity to salmon farms. The most important prey for the individuals analyzed was farmed salmonids, with an estimated median (±SD) contribution of 19.7 ± 13.5‰ and 15.3 ± 9.6‰ for hair and skin, respectively. Using vibrissae as a temporal record of diet for each individual, we observed a remarkable switch in diet composition in two SASL, from farmed salmonids to pelagic fishes, which coincided with the decrease of salmon production due to the infectious salmon anemia virus that affected salmon farms in Chile at the end of 2008. Our study demonstrates the usefulness of integrating stable isotope derived dietary data with movement patterns to characterize the impacts of a non-native prey on the foraging ecology of an apex marine predator, providing important applied implications in situations where interactions between aquaculture and wildlife are common. PMID:26309046

  19. Using Satellite Tracking and Isotopic Information to Characterize the Impact of South American Sea Lions on Salmonid Aquaculture in Southern Chile.

    PubMed

    Sepúlveda, Maritza; Newsome, Seth D; Pavez, Guido; Oliva, Doris; Costa, Daniel P; Hückstädt, Luis A

    2015-01-01

    Apex marine predators alter their foraging behavior in response to spatial and/or seasonal changes in natural prey distribution and abundance. However, few studies have identified the impacts of aquaculture that represents a spatially and temporally predictable and abundant resource on their foraging behavior. Using satellite telemetry and stable isotope analysis we examined the degree of spatial overlap between the South American sea lion (SASL) and salmon farms, and quantify the amount of native prey versus farmed salmonids in SASL diets. We instrumented eight SASL individuals with SRDL-GPS tags. Vibrissae, hair and skin samples were collected for δ13C and δ15N analyses from five of the tagged individuals and from four males captured in a haul-out located adjacent to salmon farms. Tracking results showed that almost all the foraging areas of SASL are within close proximity to salmon farms. The most important prey for the individuals analyzed was farmed salmonids, with an estimated median (±SD) contribution of 19.7 ± 13.5‰ and 15.3 ± 9.6‰ for hair and skin, respectively. Using vibrissae as a temporal record of diet for each individual, we observed a remarkable switch in diet composition in two SASL, from farmed salmonids to pelagic fishes, which coincided with the decrease of salmon production due to the infectious salmon anemia virus that affected salmon farms in Chile at the end of 2008. Our study demonstrates the usefulness of integrating stable isotope derived dietary data with movement patterns to characterize the impacts of a non-native prey on the foraging ecology of an apex marine predator, providing important applied implications in situations where interactions between aquaculture and wildlife are common. PMID:26309046

  20. Sub-lethal plasma ammonia accumulation and the exercise performance of salmonids.

    PubMed

    McKenzie, D J; Shingles, A; Taylor, E W

    2003-08-01

    The proposal that plasma ammonia accumulation might impair the swimming performance of fish was first made over a decade ago, and has now proven to be the case for a number of salmonid species. The first experimental evidence was indirect, when a negative linear relationship between plasma ammonia concentrations and maximum sustainable swimming speed (U(crit)) was found following the exposure of brown trout (Salmo trutta) to sub-lethal concentrations of copper in soft acidic water. Since then, negative linear relationships between plasma ammonia concentration and U(crit) have been demonstrated following exposure of brown trout, rainbow trout (Oncorhynchus mykiss) and coho salmon (Oncorhynchus kisutch) to elevated water ammonia. For brown trout, the relationships between plasma ammonia and U(crit) were remarkably similar following either exposure to elevated water ammonia or to sub-lethal copper. This indicates that the impairment of swimming performance resulting from exposure to sub-lethal concentrations of heavy metals may be attributable in large part to an accumulation of endogenous ammonia. The negative relationship between plasma ammonia concentration and U(crit) was similar in size-matched rainbow and brown trout but, under similar regimes of ammonia exposure, rainbow trout were able to maintain a significantly lower plasma ammonia concentration, revealing inter-specific differences in ammonia permeability and/or transport. One primary mechanism by which ammonia accumulation may impair exercise performance is a partial depolarisation of membrane potential in tissues such as the brain and white muscle. This may prejudice the co-ordination of swimming movements and reduce or abolish the development of muscle tension, thus, compromising swimming efficiency and performance at the top end of the range. PMID:12890542

  1. Assessment of Native Salmonids Above Hells Canyon Dam, Idaho, 2002-2003 Annual Report.

    SciTech Connect

    Meyer, Kevin A.; Lamansky, Jr., James A.

    2004-03-01

    We assessed the relationships between specific stream attributes and Yellowstone cutthroat trout Oncorhynchus clarki bouvieri distribution and biomass at 773 stream reaches (averaging 100 m in length) throughout the Upper Snake River Basin in Idaho, in an effort to identify possible limiting factors. Because limiting factors were expected to vary across the range of cutthroat trout distribution in Idaho, separate logistic and multiple regression models were developed for each of the nine major river drainages to relate stream conditions to occurrence and biomass of cutthroat trout. Adequate stream flow to measure fish and habitat existed at 566 sites, and of those, Yellowstone cutthroat trout were present at 322 sites, while rainbow trout O. mykiss (or rainbow x cutthroat hybrids) and brook trout Salvelinus fontinalis occurred at 108 and 181 sites, respectively. In general, cutthroat trout presence at a specific site within a drainage was associated with a higher percentage of public property, higher elevation, more gravel and less fine substrate, and more upright riparian vegetation. However, there was much variation between drainages in the direction and magnitude of the relationships between stream characteristics and Yellowstone cutthroat trout occurrence and biomass, and in model strength. This was especially true for biomass models, in which we were able to develop models for only five drainages that explained more than 50% of the variation in cutthroat trout biomass. Sample size appeared to affect the strength of the biomass models, with a higher explanation of biomass variation in drainages with lower sample sizes. The occurrence of nonnative salmonids was not strongly related to cutthroat trout occurrence, but their widespread distribution and apparent ability to displace native cutthroat trout suggest they may nevertheless pose the largest threat to long-term cutthroat trout persistence in the Upper Snake River Basin.

  2. Rainbow trout (Oncorhynchus mykiss) muscle satellite cells are targets of salmonid alphavirus infection.

    PubMed

    Biacchesi, Stéphane; Jouvion, Grégory; Mérour, Emilie; Boukadiri, Abdelhak; Desdouits, Marion; Ozden, Simona; Huerre, Michel; Ceccaldi, Pierre-Emmanuel; Brémont, Michel

    2016-01-01

    Sleeping disease in rainbow trout is characterized by an abnormal swimming behaviour of the fish which stay on their side at the bottom of the tanks. This sign is due to extensive necrosis and atrophy of red skeletal muscle induced by the sleeping disease virus (SDV), also called salmonid alphavirus 2. Infections of humans with arthritogenic alphaviruses, such as Chikungunya virus (CHIKV), are global causes of debilitating musculoskeletal diseases. The mechanisms by which the virus causes these pathologies are poorly understood due to the restrictive availability of animal models capable of reproducing the full spectrum of the disease. Nevertheless, it has been shown that CHIKV exhibits a particular tropism for muscle stem cells also known as satellite cells. Thus, SDV and its host constitute a relevant model to study in details the virus-induced muscle atrophy, the pathophysiological consequences of the infection of a particular cell-type in the skeletal muscle, and the regeneration of the muscle tissue in survivors together with the possible virus persistence. To study a putative SDV tropism for that particular cell type, we established an in vivo and ex vivo rainbow trout model of SDV-induced atrophy of the skeletal muscle. This experimental model allows reproducing the full panel of clinical signs observed during a natural infection since the transmission of the virus is arthropod-borne independent. The virus tropism in the muscle tissue was studied by immunohistochemistry together with the kinetics of the muscle atrophy, and the muscle regeneration post-infection was observed. In parallel, an ex vivo model of SDV infection of rainbow trout satellite cells was developed and virus replication and persistence in that particular cell type was followed up to 73 days post-infection. These results constitute the first observation of a specific SDV tropism for the muscle satellite cells. PMID:26743565

  3. Fish Hearing.

    ERIC Educational Resources Information Center

    Blaxter, J. H. S.

    1980-01-01

    Provides related information about hearing in fish, including the sensory stimulus of sound in the underwater environment, mechanoreceptors in fish, pressure perception and the swimbladder, specializations in sound conduction peculiar to certain fish families. Includes numerous figures. (CS)

  4. City Fishing.

    ERIC Educational Resources Information Center

    Lange, Robert E.

    1979-01-01

    A program of supplying opportunities for fishing at locations within and near urban areas was developed. This effort included stocking, management of bodies of water for fishing, and presentation of fishing clinics for urban fishermen. (RE)

  5. John Day Fish Passage and Screening; 2001 Annual Report.

    SciTech Connect

    Allen, Steve

    2002-03-26

    The accomplishments of the John Day, Umatilla, and Walla Walla Fish Passage and Screening Programs include the following: Operation and maintenance of 364 existing fish screening devices (see Table 4), replacement of 18 outdated fish screening devices that totaled 31 rotary drums (some were multiple drum systems), 4 new screens at unscreened diversions, 26 pump intake fish screens, fabrication of components for 16 additional fish screens for the Rogue basin, construction of two fish passage structures, and participation in other activities. After the replacement or construction of 22 fish screening devices during 2001, we now have 108 screening devices that meet NMFS criteria. Funding for these projects was attained from BPA, NMFS and OWEB. The John Day Fish Passage and Screening Program focused construction efforts into new and replacement fish screening devices for these various programs throughout the state of Oregon. The program also continued to develop and implement innovative designs to meet the diverse and expanding needs for the state of Oregon. Projects completed during this report period meet the current National Marine Fisheries Service (NMFS) criteria. Fish species targeted for protection include ESA Listed Mid-Columbia steelhead, Columbia basin bull trout, anadromous and resident salmonids, and numerous non-game fish species. Priority project locations have been identified as the upper reaches of the Middle Fork, North Fork, South Fork and the Mainstem of the John Day River and their tributaries. These upper reaches contain critical salmon and steelhead spawning and rearing habitat.

  6. Annual Review of BPA-Funded Anadromous Fish Projects, March 18-20, 1986, Holiday Inn Airport, Portland, Oregon.

    SciTech Connect

    United States. Bonneville Power Administration.

    1986-02-01

    This report contains descriptions of projects specifically related to anadromous salmonids. They include projects in the following categories: (1) fish and wildlife projects in western Montana; (2) fish health and physiology; (3) habitat enhancement and passage improvement - Oregon I; (4) passage improvement and natural propagation - Washington; (5) habitat enhancement and passage improvements - Oregon II; (6) future hydroelectric assessments; (7) habitat enhancement and passage improvement - Idaho; (8) downstream migration: flows and monitoring; (9) downstream migration: reservoir impacts; and (10) habitat evaluation and monitoring. (ACR)

  7. Protection against Cryptobia (Trypanoplasma) salmositica and Salmonid Cryptobiosis.

    PubMed

    Woo, P T

    1998-07-01

    Cryptobia (Trypanoplasma) salmositica is a haemoflagellate that causes morbidity and mortality in salmon, Oncorhynchus spp, on the Pacific coast of North America. In this review, Patrick Woo briefly describes the pathogen, its transmissions (either indirectly via its leech vector, Piscicola salmositica, or directly between fish) and the clinical signs of the disease. He then outlines strategies that have been developed to protect fish against the pathogen, and the mechanism of innate resistance to disease in Cryptobia-tolerant fish. Protective strategies include the breeding of fish that are resistant to infection, and the use of an attenuated C. salmositica strain to protect susceptible fish from disease for at least two years. He ends the review with suggestions for further research that include the use of the leech vector to deliver the vaccine and the development of more novel protective strategies (eg. immunochemotherapy, anti-idiotype vaccine) against cryptobiosis. PMID:17040782

  8. Acoustic Imaging Evaluation of Juvenile Salmonid Behavior in the Immediate Forebay of the Water Temperature Control Tower at Cougar Dam, 2010

    SciTech Connect

    Khan, Fenton; Johnson, Gary E.; Royer, Ida M.; Phillips, Nathan RJ; Hughes, James S.; Fischer, Eric S.; Ham, Kenneth D.; Ploskey, Gene R.

    2012-04-01

    This report presents the results of an evaluation of juvenile Chinook salmon (Oncorhynchus tshawytscha) behavior at Cougar Dam on the south fork of the McKenzie River in Oregon in 2010. The study was conducted by the Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers (USACE). The overall goal of the study was to characterize juvenile salmonid behavior and movement patterns in the immediate forebay of the Water Temperature Control (WTC) tower of the dam for USACE and fisheries resource managers use in making decisions about bioengineering designs for long-term structures and/or operations to facilitate safe downstream passage for juvenile salmonids. We collected acoustic imaging (Dual-Frequency Identification Sonar; DIDSON) data from March 1, 2010, through January 31, 2011. Juvenile salmonids (hereafter, called 'fish') were present in the immediate forebay of the WTC tower throughout the study. Fish abundance index was low in early spring (<200 fish per sample-day), increased in late April, and peaked on May 19 (6,039 fish). A second peak was observed on June 6 (2904 fish). Fish abundance index decreased in early June and remained low in the summer months (<100 fish per sample-day). During the fall and winter, fish numbers varied with a peak on November 10 (1881 fish) and a minimum on December 7 (12 fish). A second, smaller, peak occurred on December 22 (607 fish). A univariate statistical analysis indicated fish abundance index (log10-transformed) was significantly (P<0.05) positively correlated with forebay elevation, velocity over the WTC tower intake gate weirs, and river flows into the reservoir. A subsequent multiple regression analysis resulted in a model (R2=0.70) predicting fish abundance (log-transformed index values) using two independent variables of mean forebay elevation and the log10 of the forebay elevation range. From the approximate fish length measurements made using the DIDSON imaging software, the average fish length

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

    USGS Publications Warehouse

    Harr, C. Albert; Novitzki, R.P.

    1979-01-01

    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).

  10. Islands in the ice stream: were spawning habitats for native salmonids in the Great Lakes created by paleo-ice streams?

    USGS Publications Warehouse

    Riley, Stephen; Binder, Thomas R.; Tucker, Taaja R.; Menzies, John; Eyles, Nick; Janssen, John; Muir, Andrew M.; Esselman, Peter C.; Wattrus, Nigel J.; Krueger, Charles C.

    2016-01-01

    Lake trout Salvelinus namaycush, lake whitefish Coregonus clupeaformis and cisco Coregonus artedi are salmonid fishes native to the Laurentian Great Lakes that spawn on rocky substrates in the fall and early winter. After comparing the locations of spawning habitat for these species in the main basin of Lake Huron with surficial substrates and the hypothesized locations of fast-flowing Late Wisconsinan paleo-ice streams, we hypothesize that much of the spawning habitat for these species in Lake Huron is the result of deposition and erosion by paleo-ice streams. This hypothesis may represent a new framework for the identification and protection of spawning habitat for these native species, some of which are currently rare or extirpated in some of the Great Lakes. We further suggest that paleo-ice streams may have been responsible for the creation of native salmonid spawning habitat elsewhere in the Great Lakes and in other glaciated landscapes.

  11. Salmonids have an extraordinary complex type I IFN system: characterization of the IFN locus in rainbow trout oncorhynchus mykiss reveals two novel IFN subgroups.

    PubMed

    Zou, Jun; Gorgoglione, Bartolomeo; Taylor, Nicholas G H; Summathed, Thitiya; Lee, Po-Tsang; Panigrahi, Akshaya; Genet, Carine; Chen, Young-Mao; Chen, Tzong-Yueh; Ul Hassan, Mahmood; Mughal, Sharif M; Boudinot, Pierre; Secombes, Christopher J

    2014-09-01

    Fish type I IFNs are classified into two groups with two (group I) or four (group II) cysteines in the mature peptide and can be further divided into four subgroups, termed IFN-a, -b, -c, and -d. Salmonids possess all four subgroups, whereas other teleost species have one or more but not all groups. In this study, we have discovered two further subgroups (IFN-e and -f) in rainbow trout Oncorhynchus mykiss and analyzed the expression of all six subgroups in rainbow trout and brown trout Salmo trutta. In rainbow trout RTG-2 and RTS-11 cells, polyinosinic-polycytidylic acid stimulation resulted in early activation of IFN-d, whereas the IFN-e subgroup containing the highest number of members showed weak induction. In contrast with the cell lines, remarkable induction of IFN-a, -b, and -c was detected in primary head kidney leukocytes after polyinosinic-polycytidylic acid treatment, whereas a moderate increase of IFNs was observed after stimulation with resiquimod. Infection of brown trout with hemorrhagic septicemia virus resulted in early induction of IFN-d, -e, and -f and a marked increase of IFN-b and IFN-c expression in kidney and spleen. IFN transcripts were found to be strongly correlated with the viral burden and with marker genes of the IFN antiviral cascade. The results demonstrate that the IFN system of salmonids is far more complex than previously realized, and in-depth research is required to fully understand its regulation and function. PMID:25080482

  12. Effects of habitat alteration on the epizootiology of Myxobolus cerebralis, the causative agent of salmonid whirling disease.

    PubMed

    Granath, Willard O

    2014-04-01

    Whirling disease, caused by the myxozoan parasite Myxobolus cerebralis , is a serious health threat to salmonid fish and its control remains problematic. The parasite has a 2-host life cycle involving a salmonid and the aquatic oligochaete Tubifex tubifex . A commonly used strategy to control parasites that requires an obligatory invertebrate host is to eliminate or reduce the host population size to a point where parasite transmission can no longer occur. Large numbers of T. tubifex are frequently found in degraded habitats that are characterized by an abundance of fine sediments, organic matter, and a lack of aquatic invertebrate diversity. If such environments are rehabilitated, then the normal flora and fauna should re-establish and the numbers of T. tubifex should decline due to their inability to compete with the re-established invertebrates. During an epizootiological study on Rock Creek, located in west-central Montana, 2 opportunities were available to examine the effects of habitat restoration on the transmission of M. cerebralis . The Puyear Ranch re-establishment project was a major endeavor conducted on the main channel of Rock Creek, a little more than midway upstream. Another significant restoration was conducted on Upper Willow Creek, a tributary of Rock Creek, located closer to the headwaters. Sentinel trout studies, along with examining T. tubifex for the parasite and measuring various water-quality parameters, revealed that the restoration of the Puyear Ranch locality had no significant effect on reducing the intensity of M. cerebralis in trout. This was likely due to the restored area being located mid-river, just downstream from a "hot spot" of infected T. tubifex . In comparison, there was a significant reduction in the intensity of M. cerebralis in sentinel fish after the Upper Willow Creek restoration project was completed. Unlike the Puyear Ranch locality, there was no hot spot of infected T. tubifex above the area rehabilitated on Upper

  13. Fish behavior in relation to modeling fish passage through hydropower turbines: A review

    SciTech Connect

    Coutant, C.C.; Whitney, R.R.

    1997-06-01

    We evaluated the literature on fish behavior as it relates to passage of fish near or through hydropower turbines. The goal was to foster compatibility of engineered systems with the normal behavior patterns of fish species and life stages such that entrainment into turbines and injury in passage are minimized. We focused on aspects of fish behavior that could be used for computational fluid dynamics (CFD) modeling of fish trajectories through turbine systems. Downstream-migrating salmon smolts are generally surface oriented and follow flow. Smolts orient to the ceilings of turbine intakes but are horizontally distributed more evenly, except as affected by intake-specific turbulence and vortices. Smolts often enter intakes oriented head-upstream. Non-salmonids are entrained episodically, suggesting accidental capture of schools (often of juveniles or in cold water) and little behavioral control during turbine passage. Models of fish trajectories should not assume neutral buoyancy throughout the time a fish passes through a turbine, largely because of pressure effects on swim bladders. Fish use their lateral line system to sense obstacles and change their orientation, but this sensory-response system may not be effective in the rapid passage times of turbine systems. A Effects of pre-existing stress levels on fish performance in turbine passage are not well known but may be important. There are practical limits of observation and measurement of fish and flows in the proximity of turbine runners that may inhibit development of information germane to developing a more fish-friendly turbine. We provide recommendations for CFD modelers of fish passage and for additional research. 20 refs., 2 figs.

  14. Transgenic Fish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fish into which foreign DNA is artificially introduced and integrated into their genome are called transgenic fish. Since the development of the first transgenic fish in 1985, techniques to produce transgenic fish have improved tremendously, resulting in the production of genetically modified (GM) ...

  15. Coregonid fishes of the Great Lakes

    USGS Publications Warehouse

    Koelz, Walter N.

    1929-01-01

    Wherever they occur, the coregonids, like the salmonids, are important food fishes; but probably nowhere do they attain so much importance in the fisheries as in the region of the Great Lakes. This investigation has as its object the determination of the forms of coregonid fishes that occur in these lakes and the collection of data on their natural history. In addition to its economic significance, the problem is one of scientific interest. It concerns not merely the ecology of the Great Lakes species but it involves also the ultimate consideration of their origin and evolution and of their relationships with one another and with the coregonids of Asia and Europe, as well as with those of other parts of America.

  16. Research, Monitoring, and Evaluation of Avian Predation on Salmonid Smolts in the Lower and Mid-Columbia River, 2008 Draft Season Summary.

    SciTech Connect

    Roby, Daniel D.; Collis, Ken; Lyons, Donald E.

    2009-07-08

    This report describes investigations into predation by piscivorous colonial waterbirds on juvenile salmonids (Oncorhynchus spp.) from throughout the Columbia River basin during 2008. East Sand Island in the Columbia River estuary again supported the largest known breeding colony of Caspian terns (Hydroprogne caspia) in the world (approximately 10,700 breeding pairs) and the largest breeding colony of double-crested cormorants (Phalacrocorax auritus) in western North America (approximately 10,950 breeding pairs). The Caspian tern colony increased from 2007, but not significantly so, while the double-crested cormorant colony experienced a significant decline (20%) from 2007. Average cormorant nesting success in 2008, however, was down only slightly from 2007, suggesting that food supply during the 2008 nesting season was not the principal cause of the decline in cormorant colony size. Total consumption of juvenile salmonids by East Sand Island Caspian terns in 2008 was approximately 6.7 million smolts (95% c.i. = 5.8-7.5 million). Caspian terns nesting on East Sand Island continued to rely primarily on marine forage fishes as a food supply. Based on smolt PIT tag recoveries on the East Sand Island Caspian tern colony, predation rates were highest on steelhead in 2008; minimum predation rates on steelhead smolts detected passing Bonneville Dam averaged 8.3% for wild smolts and 10.7% for hatchery-raised smolts. In 2007, total smolt consumption by East Sand Island double-crested cormorants was about 9.2 million juvenile salmonids (95% c.i. = 4.4-14.0 million), similar to or greater than that of East Sand Island Caspian terns during that year (5.5 million juvenile salmonids; 95% c.i. = 4.8-6.2 million). The numbers of smolt PIT tags recovered on the cormorant colony in 2008 were roughly proportional to the relative availability of PIT-tagged salmonids released in the Basin, suggesting that cormorant predation on salmonid smolts in the estuary was less selective than tern

  17. Acoustic Camera Evaluation of Juvenile Salmonid Approach and Fate at Surface Flow Outlets of Two Hydropower Dams

    SciTech Connect

    Ploskey, Gene R.; Johnson, Gary E.; Weiland, Mark A.; Khan, Fenton; Mueller, Robert P.; Serkowski, John A.; Rakowski, Cynthia L.; Hedgepeth, J.; Skalski, John R.; Ebberts, Blaine D.; Klatte, Bernard A.

    2006-08-04

    The objective of this study was to estimate and compare fate probabilities for juvenile salmon approaching two surface flow outlets (SFOs) to identify effective design characteristics. The SFOs differed principally in forebay location, depth, discharge, and water velocity over a sharp-crested weir. Both outlets were about 20 ft wide. The 22-ft deep Bonneville Powerhouse 2 Corner Collector (B2CC) was located in the southwest corner of the forebay and passed 5,000 ft3/s of water at normal-pool elevation. In contrast, The Dalles Dam ice and trash sluiceway outlet above Main Unit 1-3 (TDITC) was not located in a forebay corner, was only 7-ft deep, and discharged about 933 ft3/s at normal-pool elevation. The linear velocity of water over the weir was about 15 ft/s at the B2CC and 5 ft/s at the TDITC. We used a Dual-Frequency Identification Sonar (DIDSON) to record movements of fish within about 65 ft of the B2CC and within 35 ft of the TDITC. We actively tracked fish by manually adjusting pan and tilt rotator angles to keep targets in view. Contrary to expectations, active tracking did not provide a predominance of long tracks that clearly indicated fish fate because most tracks were incomplete. Active tracking did increase error in fish-position estimation, which complicated data processing, so we plan to sample multiple fixed zones in the future. The probability of fish entering each SFO was estimated by a Markov chain analysis, which did not require complete fish tracks. At the B2CC, we tracked 7,943 juvenile salmonids and most of them entered the B2CC. Fish moving south 40 to 60 ft upstream of the dam face were more likely to enter the eddy at the south end of the powerhouse than to enter the B2CC. At the TDITC, we tracked 2,821 smolts. Fish movement was complex with active swimming toward and away from the entrance. The high entrance probability zone (EPZ), where over 90% of tracked fish entered the SFO, extended 32 ft out at the B2CC and only 8 ft out at the TDITC

  18. Latent Toxicity of Endothall to Anadromous Salmonids During Seawater Challenge.

    PubMed

    Courter, Lauren A; Garrison, Thomas M; Courter, Ian I

    2016-05-01

    Limited evidence exists on the latent effects of toxicant exposure on the seawater adaptability of anadromous salmon and steelhead. It is unclear whether such an effect exists for the widely used and relatively non-toxic herbicide endothall. Coho salmon, Oncorhynchus kisutch (coho), Chinook salmon, O. tshawytscha (Chinook), and anadromous rainbow trout, O. mykiss (steelhead) were subjected to a 10-day seawater challenge following freshwater treatments [0-12 mg acid equivalent (a.e)./L at 96 h]. Mean survival resulted in 82 % (n = 225), 84 % (n = 133), 90 % (n = 73) and 59 % (n = 147) survival for 0, 3-5, 6-8, and 9-12 mg a.e./L, respectively. Our results indicate a lower toxicity threshold compared with previously reported acute toxicity results, but higher compared with previous seawater challenge studies. We demonstrate the utility of the seawater challenge assay to accurately define toxic effects of pesticides on salmonids with complex life-histories. PMID:27000379

  19. Assess Current and Potential Salmonid Production in Rattlesnake Creek in Association with Restoration Effors; US Geological Survey Reports, 2003-2004 Annual Report.

    SciTech Connect

    Allen, M. Brady; Connolly, Patrick J.; Munz, Carrie S.

    2006-02-01

    This project was designed to document existing habitat conditions and fish populations within the Rattlesnake Creek watershed (White Salmon River subbasin, Washington) before major habitat restoration activities are implemented and prior to the reintroduction of salmon and steelhead above Condit Dam. Returning adult salmon Oncorhynchus spp. and steelhead O. mykiss have not had access to Rattlesnake Creek since 1913. An assessment of resident trout populations should serve as a good surrogate for evaluation of factors that would limit salmon and steelhead production in the watershed. Personnel from United States Geological Survey's Columbia River Research Laboratory (USGS-CRRL) attend to three main objectives of the Rattlesnake Creek project. The first is to characterize stream and riparian habitat conditions. This effort includes measures of water quality, water quantity, stream habitat, and riparian conditions. The second objective is to determine the status of fish populations in the Rattlesnake Creek drainage. To accomplish this, we derived estimates of salmonid population abundance, determined fish species composition, assessed distribution and life history attributes, obtained tissue samples for genetic analysis, and assessed fish diseases in the watershed. The third objective was to use the collected habitat and fisheries information to help identify and prioritize areas in need of restoration. As this report covers the third year of at least a five-year study, it is largely restricted to describing our efforts and findings for the first two objectives.

  20. Assess Current and Potential Salmonid Production in Rattlesnake Creek Associated with Restoration Efforts; Underwood Conservation District, Annual Report 2002-2003.

    SciTech Connect

    White, Jim

    2004-02-01

    This project addresses existing habitat conditions, fish population status, and restoration priority sites within the Rattlesnake Creek watershed, a sub-basin of the White Salmon River. Our partners in this project are the United States Geological Service (USGS), and the Yakama Indian Nation (YIN). Underwood Conservation District (UCD) is involved in the project via accomplishment of water quality monitoring, sampling for stable isotopes, and characterization of the watershed geomorphology. These work items are part of an effort to characterize the stream and riparian habitat conditions in Rattlesnake Creek, to help guide habitat and fish restoration work. Water chemistry and temperature information is being collected both on Rattlesnake Creek, and on other tributaries and the main stem of the White Salmon River. Information on the entire system enables us to compare results obtained from Rattlesnake Creek with the rest of the White Salmon system. Water chemistry and temperature data have been collected in a manner that is comparable with data gathered in previous years. The results from data gathered in the 2001-2002 performance period are reported in appendix A at the end of this 2002-2003 report. Additional work being conducted as part of this study includes; an estimate of salmonid population abundance (YIN and USGS); a determination of fish species composition, distribution, and life history (YIN and USGS), and a determination of existing kinds, distribution, and severity of fish diseases (YIN and USGS). The overall objective is to utilize the above information to prioritize restoration efforts in Rattlesnake Creek.

  1. Assess Current and Potential Salmonid Production in Rattlesnake Creek Associated with Restoration Efforts; US Geological Survey Reports, 2002-2003 Annual Report.

    SciTech Connect

    Connolly, Patrick J.

    2003-12-01

    This project was designed to document existing habitat conditions and fish populations within the Rattlesnake Creek watershed (White Salmon River subbasin, Washington) before major habitat restoration activities are implemented and prior to the reintroduction of salmon and steelhead above Condit Dam. Returning adult salmon Oncorhynchus spp. and steelhead O. mykiss have not had access to Rattlesnake Creek since 1913. An assessment of resident trout populations should serve as a good surrogate for evaluation of factors that would limit salmon and steelhead production in the watershed. Personnel from United States Geological Survey's Columbia River Research Laboratory (USGS-CRRL) attend to three main objectives of the Rattlesnake Creek project. The first is to characterize stream and riparian habitat conditions. This effort includes measures of water quality, water quantity, stream habitat, and riparian conditions. The second objective is to determine the status of fish populations in the Rattlesnake Creek drainage. To accomplish this, we derived estimates of salmonid population abundance, determined fish species composition, assessed distribution and life history attributes, obtained tissue samples for genetic analysis, and assessed fish diseases in the watershed. The third objective is to use the collected habitat and fisheries information to help identify and prioritize areas in need of restoration. As this report covers the second year of at least a three-year study, it is largely restricted to describing our efforts and findings for the first two objectives.

  2. Assess Current and Potential Salmonid Production in Rattlesnake Creek Associated with Restoration Efforts; US Geological Survey Reports, 2001-2002 Annual Report.

    SciTech Connect

    Connolly, Patrick J.

    2003-01-01

    This project was designed to document existing habitat conditions and fish populations within the Rattlesnake Creek watershed (White Salmon River subbasin, Washington) before major habitat restoration activities are implemented and prior to the reintroduction of salmon and steelhead above Condit Dam. Returning adult salmon Oncorhynchus spp. and steelhead O. mykiss have not had access to Rattlesnake Creek since 1914. An assessment of resident trout populations should serve as a good surrogate for evaluation of factors that would limit salmon and steelhead production in the watershed. Personnel from United States Geological Survey's Columbia River Research Laboratory (USGS-CRRL) attend to three main objectives of the Rattlesnake Creek project. The first is to characterize stream and riparian habitat conditions. This effort includes measures of water quality, water quantity, stream habitat, and riparian conditions. The second objective is to determine the status of fish populations in the Rattlesnake Creek drainage. To accomplish this, we derived estimates of salmonid population abundance, determined fish species composition, assessed distribution and life history attributes, obtained tissue samples for future genetic analysis, and assessed fish diseases in the watershed. The third objective is to use the collected habitat and fisheries information to help identify and prioritize areas in need of restoration. As this report covers the first year of a three-year study, this report is restricted to describing our work on the first two objectives only.

  3. Assess Current and Potential Salmonid Production in Rattlesnake Creek in Association with Restoration Efforts, US Geological Survey Report, 2004-2005 Annual Report.

    SciTech Connect

    Allen, M. Brady; Connolly, Patrick J.; Jezorek, Ian G.

    2006-06-01

    This project was designed to document existing habitat conditions and fish populations within the Rattlesnake Creek watershed (White Salmon River subbasin, Washington) before major habitat restoration activities are implemented and prior to the reintroduction of salmon and steelhead above Condit Dam. Returning adult salmon Oncorhynchus spp. and steelhead O. mykiss have not had access to Rattlesnake Creek since 1913. An assessment of resident trout populations should serve as a good surrogate for evaluation of factors that would limit salmon and steelhead production in the watershed. Personnel from United States Geological Survey's Columbia River Research Laboratory (USGS-CRRL) attended to three main objectives of the Rattlesnake Creek project. The first objective was to characterize stream and riparian habitat conditions. This effort included measures of water quality, water quantity, stream habitat, and riparian conditions. The second objective was to determine the status of fish populations in the Rattlesnake Creek drainage. To accomplish this, we derived estimates of salmonid population abundance, determined fish species composition, assessed distribution and life history attributes, obtained tissue samples for genetic analysis, and assessed fish diseases in the watershed. The third objective was to use the collected habitat and fisheries information to help identify and prioritize areas in need of restoration. As this report covers the fourth year of a five-year study, it is largely restricted to describing our efforts and findings for the first two objectives.

  4. PCB's in fish from selected waters of New York State.

    PubMed

    Spagnoli, J J; Skinner, L C

    1977-09-01

    PCB residues in fish from 41 stations throughout New York State were monitored in 1975. Nearly all fish contained PCB's in detectable amounts although the levels of contamination and specific Aroclor varied. The Hudson River contained the highest known PCB concentrations within the United States; levels often exceeded 100 ppm. Other waters and fish which were significantly contaminated include Lake Ontario salmonids and Cayuga Lake lake trout. Onondaga Lake, previously closed to fishing because of mercury contamination, also appears to have abnormally high levels of PCB's approaching in some instances the action level of the Food and Drug Administration, U.S. Department of Health, Education, and Welfare. Samples from marine waters generally have contaminant levels substantially below 5.0 ppm. PMID:414199

  5. Assessment of harbor seal predation on adult salmonids in a Pacific Northwest estuary.

    PubMed

    Wright, Bryan E; Riemer, Susan D; Brown, Robin F; Ougzin, Aicha M; Bucklin, Katherine A

    2007-03-01

    The populations of many native species have increased or expanded in distribution in recent decades, sometimes with negative consequences to sympatric native species that are rarer or less adaptable to anthropogenic changes to the environment. An example of this phenomenon from the Pacific Northwest is predation by locally abundant pinnipeds (seals and sea lions) on threatened, endangered, or otherwise depleted salmonid (Oncorhynchus spp.) populations. We used survey sampling methodology, acoustic telemetry, and molecular genetics to quantify the amount of harbor seal (Phoca vitulina) predation on a depressed run of coho salmon (O. kisutch) and to determine whether some seals consumed a disproportionately higher number of salmonids than others. Based on a probability sample totaling 759.5 h of observation, we estimated that seals consumed 1161 adult salmonids (95% CI = 503-1818 salmonids) during daylight hours over an 18.9-km estuarine study area in Oregon during an 84-d period in fall 2002. Simultaneous tracking of 56 seals via an acoustic telemetry array indicated that a small proportion of marked seals (12.5%) exhibited behavior that was consistent with specialization on salmonids. These seals spent the majority of their time in the riverine portion of the study area and did so disproportionately more at night than day. Genetic analysis of 116 salmonid structures recovered from 11 seal fecal samples suggested that coho salmon accounted for approximately one-half of total salmonid consumption. Though subject to considerable uncertainty, the combined results lead us to infer that seals consumed 21% (range = 3-63%) of the estimated prespawning population of coho salmon. We speculate that the majority of the predation occurred upriver, at night, and was done by a relatively small proportion of the local seal population. Understanding the extent and nature of pinniped predation can provide important inputs into risk assessments and other modeling efforts designed to

  6. Spatial hierarchical geomorphic controls on salmonid spawning habitat: using geomorphic parameters to set ecological status targets

    NASA Astrophysics Data System (ADS)

    Moir, H. J.

    2009-12-01

    To set river restoration targets or identifying ‘reference condition’ benchmarks, the ‘ecological status’ of river systems is often subjectively based on how humans perceive a non-impacted river should look. Rarely are these objectives based on an explicit understanding of how physical conditions provide the habitats required by instream biota to optimally complete their life cycles. Furthermore, although much research acknowledges the spatial hierarchical physical controls on instream habitats, there is little attempt to integrate across scales while explicitly linking key aspects of instream ecology to geomorphic form and process. This paper describes the physical controls on salmon (Atlantic and Chinook) spawning habitat across a range of spatial scales (basin - reach - meso - micro). Over the past five decades much work has been conducted describing the micro-habitat (typically depth, velocity and substrate) of spawning salmonids. However, this not accounted for the implicit inter-relationships between these basic habitat variables in rivers. It is demonstrated that the specific micro-scale physical conditions selected by salmonids reflect the intersection of biotic requirements with geomorphic processes that produce specific joint hydraulic-sedimentary patterns. At the next, meso-scale, different morphological units (e.g. pools, riffles) provide contrasting joint hydraulic and sedimentary relationships that intersect to varying degrees with micro-habitat requirements, producing unit types that are used more or less frequently. Morphology also exerts a strong control on the distribution of hydraulics across a meso-scale unit under varying flow. Thus, some morphologies provide more ‘stable’ habitat conditions as discharge changes. Furthermore, the proximity of spawning units to other units that provide adult holding/ resting habitat (e.g. pools) is also shown to be an important meso-scale control. Over longer time scales, prevailing fluvial forces

  7. Windrow composting as an effective method to dispose of large numbers of fish

    USGS Publications Warehouse

    Tabb, L.C.I.; Starliper, C.E.; Shotts, E.B., Jr.; Everson, J.; Palmisano, A.W.

    1998-01-01

    During July 1998, at the USGS Leetown Science Center, Kearneysville, West Virginia, an epizootic occurred in 16-month-old Atlantic salmon (Salmo salar). The cause ofmortality was diagnosed as furunculosis, a serious disease in salmonid fishes caused by the bacterium Aeromonas salmonicida. The fish were being maintained as part ofongoing research and were held in uncovered 30-m-Iong concrete raceways, each supplied with about 757 L per minute of 12 ?C pathogen-free spring water. The means by which the fish became infected could not be determined, and there was no recent history offurunculosis in the hatchery system.

  8. AN INTEGRATED WATERSHED APPROACH LINKING SALMONID PRODUCTIVITY TO FRESHWATER HABITAT

    EPA Science Inventory

    EPA's Western Ecology Division is undertaking research addressing catchment-scale dynamics of freshwater habitat productivity for native fishes. Through partnerships with state and federal agencies and private landowners, current field efforts focus on linkages among stream chemi...

  9. DOWNSTREAM MIGRATION OF SALMONID SMOLTS IN OREGON RIVERS AND ESTUARIES

    EPA Science Inventory

    Migratory fish passage is an important designated use for many Oregon estuaries. Acoustic transmitters were implanted in coho smolts in 2004 and 2006 to evaluate how estuarine habitat, and habitat loss, might affect population health. Acoustic receivers that identified individu...

  10. Augmented Fish Health Monitoring, 1992 Annual Report.

    SciTech Connect

    Warren, James W.

    1992-08-01

    The Augmented Fish Health Monitoring Project (Project) had its origin, in the mid-1980's, in perceived differences or inconsistencies in fish disease detection, diagnosis and control capabilities between the five conservation agencies rearing and releasing anadromous salmonids for fishery resource management and mitigation purposes in the Columbia River basin. Agency fish health programs varied greatly. Some agencies had personnel, equipment and funding to frequently monitor the health status of both juvenile production fish and adult salmon or steelhead trout at the time of spawning. Other agencies had much smaller programs and limited resources. These differences became better understood when the Pacific Northwest Fish Health Protection Committee developed its Model Fish Health Protection Program including recommendations for standard fish disease detection procedures. Even though some agencies could not immediately attain the goals set by the Model Program it was unanimously adopted as a desirable objective. Shortly thereafter, a multi-party planning group was assembled to help the Bonneville Power Administration (BPA) find ways to improve agency fish health programs and implement measures under the Fish and Wildlife Program of the Northwest Power Planning Council. The planning group assessed existing agency fish health monitoring capabilities, agreed upon satisfactory levels of capability to detect and identify important fish pathogens, and designed a five-year project establishing comparable fish health monitoring capability in each agency. It was strongly believed that such a project would improve the health and quality of the millions of hatchery fish released annually in the Columbia River basin and improve interagency communications and disease control coordination. During 1986 and 1987 BPA individually negotiated five separate contracts with the fishery agencies to standardize fish health monitoring, develop a common data collection and reporting format

  11. Columbia River Fishes of the Lewis and Clark Expedition

    SciTech Connect

    Dauble, Dennis D.

    2007-06-21

    The Lewis and Clark expedition crossed the Continental Divide in 1805 on the way west to the Pacific Ocean. Based on journal entries, members of the expedition probably encountered two species of resident salmonids and four of the six species of anadromous salmonids and steelhead (Family Salmonidae, genus Oncorhynchus). The salmonid species were called common salmon (now known as Chinook salmon O. tshawytscha), red char (sockeye salmon O.nerka) white salmon trout (coho salmon [also known as silver salmon] O. kisutch), salmon trout (steelhead O. mykiss), and spotted trout (cutthroat trout O. clarkii). There was no evidence of the expedition encountering pink salmon O. gorbuscha, chum salmon O. keta, or species of true char Salvelinus spp. Common fishes procured from Indian tribes living along the lower Columbia River included eulachon Thaleichthys pacificus and white sturgeon Acipenser transmontanus. The identity of three additional resident freshwater species is questionable. Available descriptions suggest that what they called mullet were largescale sucker Catastomus macrocheilus, and that chubb were peamouth Mylocheilus caurinus. The third questionable fish, which they called bottlenose, was probably mountain whitefish Prosopium williamsoni, although there is no evidence that the species was observed in the Columbia River drainage. Missing from the species list were more than 20 other fishes known to Sahaptin-speaking people from the mid-Columbia region. More complete documentation of the icthyofauna of the Pacific Northwest region did not occur until the latter half of the 19th century. However, journals from the Lewis and Clark expedition provide the first documentation of Columbia River fishes.

  12. Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production and used as a model species to gain knowledge of many aspects of fish biology. As a salmonid, the species experienced recent whole genome duplication, making it a model for studying the evolution of t...

  13. Development of an Index to Bird Predation of Juvenile Salmonids within the Yakima River, 1999 Annual Report.

    SciTech Connect

    Gassley, James M.; Grue, Christian E.

    2001-10-01

    interpolate gull and Common Merganser abundance on days when surveys were not conducted. Seasonal patterns of avian piscivore abundance were identified, diurnal patterns of gull abundance at hotspots were identified, predation indices were calculated for hotspots and summer river reaches, and the efficacy of aerial surveys for estimating bird abundance within river reaches was evaluated. Primary avian predators were California and Ring-billed Gulls at hotspots and Common Mergansers within upper river reaches. Estimated take (presumed to be salmonids) by gulls at hotspots (22 April-30 May) was 4,084 fish at the Chandler Bypass Outfall and 12,636 fish at Horn Rapids Dam. Combined take was 2.65% of the salmonids passing over Chandler Dam or 0.89 % of all smolts estimated passing or being released from the Chandler Dam area during the 1999 smolt migration season. Estimated take by Common Mergansers within upper river reaches in summer was 4,092 kg between 7 May and 18 August 1999.

  14. Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta, Lower Columbia River, 2007

    SciTech Connect

    Sobocinski, Kathryn L.; Johnson, Gary E.; Sather, Nichole K.; Storch, Adam; Jones, Tucker A.; Mallette, Christine; Dawley, Earl M.; Skalski, John R.; Teel, David; Moran, Paul

    2008-03-18

    This document is the first annual report for the study titled “Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Vicinity of the Sandy River Delta in the Lower Columbia River.” Hereafter, we refer to this research as the Tidal Freshwater Monitoring (TFM) Study. The study is part of the research, monitoring, and evaluation effort developed by the Action Agencies (Bonneville Power Administration, U.S. Army Corps of Engineers, U.S. Bureau of Reclamation) in response to obligations arising from the Endangered Species Act as a result of operation of the Federal Columbia River Power System (FCRPS). The project is performed under the auspices of the Northwest Power and Conservation Council’s Columbia Basin Fish and Wildlife Program.

  15. Marine effect of introduced salmonids: Prey consumption by exotic steelhead and anadromous brown trout in the Patagonian Continental Shelf

    USGS Publications Warehouse

    Ciancio, J.; Beauchamp, D.A.; Pascual, M.

    2010-01-01

    On the basis of stable isotope analysis, we estimated the marine diet of the most abundant anadromous salmonid species in Patagonian Atlantic basins. The results were coupled with bioenergetic and population models to estimate the consumption of food by salmonids and was compared with that by seabirds, the most abundant top predators in the area. Amphipods were the main salmonid prey, followed by sprat, silversides, squid, and euphausiids. The total consumption, even assuming large anadromous salmonid populations, represented <5% of the total consumption by seabirds. We also identified the particular seabird colonies and artisanal fisheries with which salmonid trophic interactions at a more local scale could be significant. ?? 2010, by the American Society of Limnology and Oceanography, Inc.

  16. Year-Round Monitoring of Contaminants in Neal and Rogers Creeks, Hood River Basin, Oregon, 2011-12, and Assessment of Risks to Salmonids

    PubMed Central

    Hapke, Whitney B.; Morace, Jennifer L.; Nilsen, Elena B.; Alvarez, David A.; Masterson, Kevin

    2016-01-01

    Pesticide presence in streams is a potential threat to Endangered Species Act listed salmonids in the Hood River basin, Oregon, a primarily forested and agricultural basin. Two types of passive samplers, polar organic chemical integrative samplers (POCIS) and semipermeable membrane devices (SPMDs), were simultaneously deployed at four sites in the basin during Mar. 2011–Mar. 2012 to measure the presence of pesticides, polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs). The year-round use of passive samplers is a novel approach and offers several new insights. Currently used pesticides and legacy contaminants, including many chlorinated pesticides and PBDEs, were present throughout the year in the basin’s streams. PCBs were not detected. Time-weighted average water concentrations for the 2-month deployment periods were estimated from concentrations of chemicals measured in the passive samplers. Currently used pesticide concentrations peaked during spring and were detected beyond their seasons of expected use. Summed concentrations of legacy contaminants in Neal Creek were highest during July–Sept., the period with the lowest streamflows. Endosulfan was the only pesticide detected in passive samplers at concentrations exceeding Oregon or U.S. Environmental Protection Agency water-quality thresholds. A Sensitive Pesticide Toxicity Index (SPTI) was used to estimate the relative acute potential toxicity among sample mixtures. The acute potential toxicity of the detected mixtures was likely greater for invertebrates than for fish and for all samples in Neal Creek compared to Rogers Creek, but the indices appear to be low overall (<0.1). Endosulfans and pyrethroid insecticides were the largest contributors to the SPTIs for both sites. SPTIs of some discrete (grab) samples from the basin that were used for comparison exceeded 0.1 when some insecticides (azinphos methyl, chlorpyrifos, malathion) were detected at concentrations near or

  17. Year-round monitoring of contaminants in Neal and Rogers Creeks, Hood River Basin, Oregon, 2011-12, and assessment of risks to salmonids

    USGS Publications Warehouse

    Temple, Whitney B.; Morace, Jennifer L.; Nilsen, Elena B.; Alvarez, David; Masterson, Kevin

    2016-01-01

    Pesticide presence in streams is a potential threat to Endangered Species Act listed salmonids in the Hood River basin, Oregon, a primarily forested and agricultural basin. Two types of passive samplers, polar organic chemical integrative samplers (POCIS) and semipermeable membrane devices (SPMDs), were simultaneously deployed at four sites in the basin during Mar. 2011–Mar. 2012 to measure the presence of pesticides, polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs). The year-round use of passive samplers is a novel approach and offers several new insights. Currently used pesticides and legacy contaminants, including many chlorinated pesticides and PBDEs, were present throughout the year in the basin’s streams. PCBs were not detected. Time-weighted average water concentrations for the 2-month deployment periods were estimated from concentrations of chemicals measured in the passive samplers. Currently used pesticide concentrations peaked during spring and were detected beyond their seasons of expected use. Summed concentrations of legacy contaminants in Neal Creek were highest during July–Sept., the period with the lowest streamflows. Endosulfan was the only pesticide detected in passive samplers at concentrations exceeding Oregon or U.S. Environmental Protection Agency water-quality thresholds. A Sensitive Pesticide Toxicity Index (SPTI) was used to estimate the relative acute potential toxicity among sample mixtures. The acute potential toxicity of the detected mixtures was likely greater for invertebrates than for fish and for all samples in Neal Creek compared to Rogers Creek, but the indices appear to be low overall (<0.1). Endosulfans and pyrethroid insecticides were the largest contributors to the SPTIs for both sites. SPTIs of some discrete (grab) samples from the basin that were used for comparison exceeded 0.1 when some insecticides (azinphos methyl, chlorpyrifos, malathion) were detected at concentrations near or

  18. Year-Round Monitoring of Contaminants in Neal and Rogers Creeks, Hood River Basin, Oregon, 2011-12, and Assessment of Risks to Salmonids.

    PubMed

    Hapke, Whitney B; Morace, Jennifer L; Nilsen, Elena B; Alvarez, David A; Masterson, Kevin

    2016-01-01

    Pesticide presence in streams is a potential threat to Endangered Species Act listed salmonids in the Hood River basin, Oregon, a primarily forested and agricultural basin. Two types of passive samplers, polar organic chemical integrative samplers (POCIS) and semipermeable membrane devices (SPMDs), were simultaneously deployed at four sites in the basin during Mar. 2011-Mar. 2012 to measure the presence of pesticides, polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs). The year-round use of passive samplers is a novel approach and offers several new insights. Currently used pesticides and legacy contaminants, including many chlorinated pesticides and PBDEs, were present throughout the year in the basin's streams. PCBs were not detected. Time-weighted average water concentrations for the 2-month deployment periods were estimated from concentrations of chemicals measured in the passive samplers. Currently used pesticide concentrations peaked during spring and were detected beyond their seasons of expected use. Summed concentrations of legacy contaminants in Neal Creek were highest during July-Sept., the period with the lowest streamflows. Endosulfan was the only pesticide detected in passive samplers at concentrations exceeding Oregon or U.S. Environmental Protection Agency water-quality thresholds. A Sensitive Pesticide Toxicity Index (SPTI) was used to estimate the relative acute potential toxicity among sample mixtures. The acute potential toxicity of the detected mixtures was likely greater for invertebrates than for fish and for all samples in Neal Creek compared to Rogers Creek, but the indices appear to be low overall (<0.1). Endosulfans and pyrethroid insecticides were the largest contributors to the SPTIs for both sites. SPTIs of some discrete (grab) samples from the basin that were used for comparison exceeded 0.1 when some insecticides (azinphos methyl, chlorpyrifos, malathion) were detected at concentrations near or exceeding

  19. Steepness and Concavity Controls on the Expression of Reach-Scale Channel Morphology, Debris Flow Deposition, and the Spatial Distribution of Salmonids in the Pacific Northwest

    NASA Astrophysics Data System (ADS)

    May, C. L.; Dietrich, W. E.

    2004-12-01

    Steepness and concavity indexes derived from the power function relationship between drainage area and channel slope provide a first-order control on (1) the expression of reach-scale channel morphology, (2) runout potential of debris flows, and (3) the spatial distribution of anadromous fish in the Pacific Northwest. Channels steeper than about 10% are typically dominated by the effects of periodic debris flow scour and subsequent accumulation of coarse sediment. Downstream of this area, channels with slopes between 3 to 10% represent a transition from debris flow to fluvial process dominance. In this transitional region of the network, debris flow deposits often form fill deposits that are subsequently incised by fluvial re-working that leads to the formation of step-pool sequences. Such reaches have restricted salmonid access, generally being most favorable to steelhead and cutthroat trout. The stronger the concavity of a channel profile, the shorter the length of this transitional reach. In the Oregon Coast Range, steepness and concavity values are high and the spatial extent of transitional channels is greatly restricted (typically only occurring in reaches with draining areas between 0.5 and 1.5 km2). The abrupt change in slope from steep debris flow prone channels to low-gradient pool-riffle and bedrock channels promotes debris flow deposition and fan formation at tributary junctions. In these highly concave basins, a relatively large proportion of the fluvial channel network have gradients below 3% and are accessible to salmonids, resulting in a broad spatial distribution. This broad distribution allows for a spreading of risk that may enhance a population's ability to persist during severe disturbance. In contrast, many catchments in the Klamath Mountains of northern California have high steepness values but low concavity. In this region, the portion of the network occupied by transitional reaches is greatly expanded. Step-pool channels dominate the

  20. Evaluation of Fish Passage Sites in the Walla Walla River Basin, 2008

    SciTech Connect

    Chamness, Mickie A.

    2008-08-29

    In 2008, Pacific Northwest National Laboratory evaluated the Hofer Dam fish screen and provided technical assistance at two other fish passage sites as requested by the Bonneville Power Administration, the Walla Walla Watershed Council, or the Confederated Tribes of the Umatilla Indian Reservation. Evaluation of new sites such as Hofer Dam focuses on their design, construction, operation, and maintenance to determine if they effectively provide juvenile salmonids with safe passage through irrigation diversions. There were two requests for technical assistance in 2008. In the first, the Confederated Tribes of the Umatilla Indian Reservation requested an evaluation of the Nursery Bridge fish screens associated with the fish ladder on the east side of the Walla Walla River. One set of brushes that clean the screens was broken for an extended period. Underwater videography and water velocity measurements were used to determine there were no potential adverse effects on juvenile salmonids when the west set of screens was clean enough to pass water normally. A second request, received from the National Marine Fisheries Service and the Walla Walla Watershed Council, asked for evaluation of water velocities through relatively new head gates above and adjacent to the Eastside Ditch fish screens on the Walla Walla River. Water moving through the head gates and not taken for irrigation is diverted to provide water for the Nursery Bridge fish ladder on the east side of the river. Elevations used in the design of the head gates were incorrect, causing excessive flow through the head gates that closely approached or exceeded the maximum swimming burst speed of juvenile salmonids. Hofer Dam was evaluated in June 2008. PNNL researchers found that conditions at Hofer Dam will not cause impingement or entrainment of juvenile salmonids but may provide habitat for predators and lack strong sweeping flows to encourage juvenile salmonid passage downstream. Further evaluation of

  1. Sources of variability and comparability between salmonid stomach contents and isotopic analyses: study design lessons and recommendations

    USGS Publications Warehouse

    Vinson, M.R.; Budy, P.

    2011-01-01

    We compared sources of variability and cost in paired stomach content and stable isotope samples from three salmonid species collected in September 2001–2005 and describe the relative information provided by each method in terms of measuring diet overlap and food web study design. Based on diet analyses, diet overlap among brown trout, rainbow trout, and mountain whitefish was high, and we observed little variation in diets among years. In contrast, for sample sizes n ≥ 25, 95% confidence interval (CI) around mean δ15Ν and δ13C for the three target species did not overlap, and species, year, and fish size effects were significantly different, implying that these species likely consumed similar prey but in different proportions. Stable isotope processing costs were US$12 per sample, while stomach content analysis costs averaged US$25.49 ± $2.91 (95% CI) and ranged from US$1.50 for an empty stomach to US$291.50 for a sample with 2330 items. Precision in both δ15Ν and δ13C and mean diet overlap values based on stomach contents increased considerably up to a sample size of n = 10 and plateaued around n = 25, with little further increase in precision.

  2. A Novel Liquid Medium for the Efficient Growth of the Salmonid Pathogen Piscirickettsia salmonis and Optimization of Culture Conditions

    PubMed Central

    Marshall, Sergio H.; Henríquez, Vitalia; Gómez, Fernando A.; Martínez, Irene; Altamirano, Claudia

    2013-01-01

    Piscirickettsia salmonis is the bacterium that causes Piscirickettsiosis, a systemic disease of salmonid fish responsible for significant economic losses within the aquaculture industry worldwide. The growth of the bacterium for vaccine formulation has been traditionally accomplished by infecting eukaryotic cell lines, a process that involves high production costs and is time-consuming. Recent research has demonstrated that it is possible to culture pure P. salmonis in a blood containing (cell-free) medium. In the present work we demonstrate the growth of P. salmonis in a liquid medium free from blood and serum components, thus establishing a novel and simplified bacteriological medium. Additionally, the new media reported provides improved growth conditions for P. salmonis, where biomass concentrations of approximately 800 mg cell dry weight L−1 were obtained, about eight times higher than those reported for the blood containing medium. A 2- level full factorial design was employed to evaluate the significance of the main medium components on cell growth and an optimal temperature range of 23–27°C was determined for the microorganism to grow in the novel liquid media. Therefore, these results represent a breakthrough regarding P. salmonis research in order to optimize pure P. salmonis growth in liquid blood and serum free medium. PMID:24039723

  3. A Polyprotein-Expressing Salmonid Alphavirus Replicon Induces Modest Protection in Atlantic Salmon (Salmo Salar) Against Infectious Pancreatic Necrosis

    PubMed Central

    Abdullah, Azila; Olsen, Christel M.; Hodneland, Kjartan; Rimstad, Espen

    2015-01-01

    Vaccination is an important strategy for the control and prevention of infectious pancreatic necrosis (IPN) in farmed Atlantic salmon (Salmo salar) in the post-smolt stage in sea-water. In this study, a heterologous gene expression system, based on a replicon construct of salmonid alphavirus (SAV), was used for in vitro and in vivo expression of IPN virus proteins. The large open reading frame of segment A, encoding the polyprotein NH2-pVP2-VP4-VP3-COOH, as well as pVP2, were cloned and expressed by the SAV replicon in Chinook salmon embryo cells (CHSE-214) and epithelioma papulosum cyprini (EPC) cells. The replicon constructs pSAV/polyprotein (pSAV/PP) and pSAV/pVP2 were used to immunize Atlantic salmon (Salmo salar) by a single intramuscular injection and tested in a subsequent IPN virus (IPNV) challenge trial. A low to moderate protection against IPN was observed in fish immunized with the replicon vaccine that encoded the pSAV/PP, while the pSAV/pVP2 construct was not found to induce protection. PMID:25606973

  4. The emergence of epitheliocystis in the upper Rhone region: evidence for Chlamydiae in wild and farmed salmonid populations.

    PubMed

    Guevara Soto, Maricruz; Vidondo, Beatriz; Vaughan, Lloyd; Seth-Smith, Helena M B; Nufer, Lisbeth; Segner, Helmut; Rubin, Jean-Francois; Schmidt-Posthaus, Heike

    2016-05-01

    We present the first study comparing epitheliocystis in a wild and farmed salmonid in Europe. Sampling three tributaries to the Lake Geneva, including one from headwaters to river mouth, revealed an unequal distribution of epitheliocystis in brown trout (Salmo trutta). When evaluated histologically and comparing sites grouped as wild versus farm, the probability of finding infected trout is higher on farms. In contrast, the infection intensities, as estimated by the number of cysts per gill arch, were higher on average and showed maximum values in the wild trout. Sequence analysis showed the most common epitheliocystis agents were Candidatus Piscichlamydia salmonis, all clustering into a single clade, whereas Candidatus Clavichlamydia salmonicola sequences cluster in two closely related subspecies, of which one was mostly found in farmed fish and the other exclusively in wild brown trout, indicating that farms are unlikely to be the source of infections in wild trout. A detailed morphological analysis of cysts using transmission electron microscopy revealed unique features illustrating the wide divergence existing between Ca. P. salmonis and Ca. C. salmonicola within the phylum Chlamydiae. PMID:26802008

  5. Salmonid alphavirus glycoprotein E2 requires low temperature and E1 for virion formation and induction of protective immunity.

    PubMed

    Hikke, Mia C; Braaen, Stine; Villoing, Stephane; Hodneland, Kjartan; Geertsema, Corinne; Verhagen, Lisa; Frost, Petter; Vlak, Just M; Rimstad, Espen; Pijlman, Gorben P

    2014-10-29

    Salmonid alphavirus (SAV; also known as Salmon pancreas disease virus; family Togaviridae) causes pancreas disease and sleeping disease in Atlantic salmon and rainbow trout, respectively, and poses a major burden to the aquaculture industry. SAV infection in vivo is temperature-restricted and progeny virus is only produced at low temperatures (10-15 °C). Using engineered SAV replicons we show that viral RNA replication is not temperature-restricted suggesting that the viral structural proteins determine low-temperature dependency. The processing/trafficking of SAV glycoproteins E1 and E2 as a function of temperature was investigated via baculovirus vectors in Sf9 insect cells and by transfection of CHSE-214 fish cells with DNA constructs expressing E1 and E2. We identified SAV E2 as the temperature determinant by demonstrating that membrane trafficking and surface expression of E2 occurs only at low temperature and only in the presence of E1. Finally, a vaccination-challenge model in Atlantic salmon demonstrates the biological significance of our findings and shows that SAV replicon DNA vaccines encoding E2 elicit protective immunity only when E1 is co-expressed. This is the first study that identifies E2 as the critical determinant of SAV low-temperature dependent virion formation and defines the prerequisites for induction of a potent immune response in Atlantic salmon by DNA vaccination. PMID:25269093

  6. Genetic relatedness of infectious hematopoietic necrosis virus (IHNV) from cultured salmonids in Korea.

    PubMed

    Kim, Kwang Il; Cha, Seung Joo; Lee, Chu; Baek, Harim; Hwang, Seong Don; Cho, Mi Young; Jee, Bo Young; Park, Myoung-Ae

    2016-08-01

    Infectious hematopoietic necrosis virus (IHNV; n = 18) was identified in the Korean national surveillance program between February 2013 and April 2015, suggesting that IHNV is a major viral pathogen in cultured salmonids. By phylogeny analysis, we found that the JRt-Nagano and JRt-Shizuoka groups could each be further subdivided into three distinct subtypes. The Korean strains were genetically similar to Japanese isolates, suggesting introduction from Japan. Interestingly, the amino acid sequences of the middle glycoprotein gene show that distinct Korean subtypes have circulated, indicating that the settled IHNVs might be evolved stably in cultured salmonid farm environments. PMID:27255747

  7. Effect of acclimation temperature on the upper thermal tolerance of Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus: thermal limits of a North American salmonid.

    PubMed

    Underwood, Z E; Myrick, C A; Rogers, K B

    2012-06-01

    In an effort to explore the thermal limitations of Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus, the critical thermal maxima (T(cmax) ) of 1+ year Lake Nanita strain O. c. pleuriticus were evaluated when acclimated to 10, 15 and 20° C. The mean ±s.d.T(cmax) for O. c. pleuriticus acclimated to 10° C was 24·6 ± 2·0°C (n = 30), for 15° C-acclimated fish was 26·9 ± 1·5° C (n = 23) and for 20° C-acclimated fish was 29·4 ± 1·1° C (n = 28); these results showed a marked thermal acclimation effect (Q₁₀ = 1·20). Interestingly, there was a size effect within treatments, wherein the T(cmax) of larger fish was significantly lower than that of smaller fish acclimated to the same temperature. The critical thermal tolerances of age 0 year O. c. pleuriticus were also evaluated from three separate populations: Lake Nanita, Trapper Creek and Carr Creek reared under 'common-garden' conditions prior to thermal acclimation. The Trapper Creek population had significantly warmer T(cmax) than the Lake Nanita population, but that of the Carr Creek fish had T(cmax) similar to both Trapper Creek and Lake Nanita fish. A comparison of these O. c. pleuriticus T(cmax) results with those of other stream-dwelling salmonids suggested that O. c. pleuriticus are less resistant to rapid thermal fluctuations when acclimated to cold temperatures, but can tolerate similar temperatures when acclimated to warmer temperatures. PMID:22650425

  8. Can fisheries management make substantial progress towards further reductions in sport fish PCB concentrations?

    SciTech Connect

    Jackson, L.J.

    1995-12-31

    Great Lakes managers continue to be concerned by PCB concentrations in Great Lakes sport fish. A reduction in sport fish consumption advisory levels would heighten public concern and increase pressure on managers to reduce contaminant levels in sport fish. PCB concentrations in Great Lakes sediments remain high and exchange with the water column is significant. Atmospheric inputs help maintain PCB availability in the Great Lakes. However, it is not technically feasible to control sediment and atmospheric inputs. Here the author uses a detailed age-structured simulation model of chinook salmon, alewife and rainbow smelt to examine the potential for fish management actions to make progress towards reducing PCB concentrations of sport fish consumed by humans. Chinook salmon PCB concentrations were found to be more affected by prey PCB concentrations than chinook salmon growth rates. Salmonid predators selectively attack the largest prey, but these prey are likely the oldest and most contaminated. The interaction between size selective predation by chinook salmon and their growth rates suggests that there is an ideal stocking level of sport fish that should keep the average prey fish small, and therefore have relatively low PCE concentrations, but not reduce the age structure of the alewife population to include few reproductive individuals. These results are applicable to other stocked salmonids too, (e.g., lake trout, brown trout, coho salmon, steelhead) because they also exhibit size selective predation and their recruitment is primarily by stocking.

  9. Summary of juvenile salmonid passage and survival at McNary Dam-Acoustic survival studies, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Evans, Scott D.

    2011-01-01

    Passage and survival data were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Given the importance of these annual studies, the primary objectives of this report were to summarize the findings of these annual studies to ensure that passage and survival metrics are consistently calculated and reported across all years and to consolidate this information in a single document, thereby making it easier to reference. It is worth noting that this report does not contain all the information from all the annual reports. The intent of this report was to summarize the key findings from multiple years of research. The reader is encouraged to reference the annual reports if more detailed information is needed. Chapter 1 summarizes existing behavior, passage, and survival results for fish released 10 rkm upstream of McNary Dam and from the McNary Dam tailrace during 2006-09. Chapter 2 summarizes existing behavior, passage, and survival results for fish released in the mid-Columbia River and detected at McNary Dam during 2006-09. Results from 2006 indicated that higher spill discharge generally resulted in higher fish passage through spill, and in turn, higher fish survival through the entire dam. Within the spillway, passage effectiveness was highest for the south spill bays, adjacent to the powerhouse. Increased passage in this area, combined with detailed 3-dimensional approach paths, aided in the design and location of the temporary spillway weirs (TSWs) at McNary Dam prior to the 2007 migration of juvenile salmonids. During the 2007 study, the TSWs were tested under two spill treatments during the spring and summer: a "2006 Modified spill," and a "2007 test spill." In the spring, slightly higher discharge through spill bays 14-17 was the primary difference between the spill

  10. Fish Dishes.

    ERIC Educational Resources Information Center

    Derby, Marie

    2003-01-01

    Describes an art project that was inspired by Greek pottery, specifically dishes shaped as fish. Explains that fourth-grade students drew a fish shape that was later used to create their clay version of the fish. Discusses how the students examined the pottery to make decisions about color and design. (CMK)

  11. Progression and severity of gas bubble trauma in juvenile salmonids

    USGS Publications Warehouse

    Mesa, M.G.; Weiland, L.K.; Maule, A.G.

    2000-01-01

    We conducted laboratory experiments to assess the progression and to quantify the severity of signs of gas bubble trauma (GBT) in juvenile chinook salmon Oncorhynchus tshawytscha and steelhead Oncorhynchus mykiss exposed to different levels of total dissolved gas (TDG), and we attempted to relate these signs to the likelihood of mortality. When fish were exposed to 110% TDG for up to 22 d, no fish died, and there were few signs of GBT in the lateral line or gills. Bubbles in the fins, however, were relatively common, and they progressively worsened over the experimental period. When fish were exposed to 120% TDG for up to 140 h, chinook salmon had an LT20 (time necessary to kill 20% of the fish) ranging from 40 to 120 h, whereas steelhead had LT20s ranging from 20 to 35 h. In steelhead, bubbles in the lateral line, fins, and gills displayed poor trends of worsening over time, showed substantial interindividual variability, and were poorly related to mortality. In chinook salmon, only bubbles in the lateral line showed a distinct worsening over time, and the severity of bubbles in the lateral line was highly correlated with mortality. When fish were exposed to 130% TDG for up to 11 h, LT20s for chinook salmon ranged from 3 to 6 h, whereas those for steelhead ranged from 5 to 7 h. In chinook salmon, bubbles in the lateral line and fins, but not those in the gills, showed distinct trends of worsening over time. In steelhead, bubbles in the lateral line displayed the most significant trend of progressive severity. In both species at 130% TDG, the severity of all GBT signs was highly correlated with mortality. The progressive nature of GBT and the methods we developed to examine fish for GBT may be useful for monitoring programs that aim to assess the severity of dissolved gas supersaturation exposures experienced by fish in the wild. However, the efficacy of such programs seems substantially hindered by problems associated with (1) the variable persistence of GBT signs

  12. Incorporating Geomorphological and Biological Processes Into Recovery Planning Strategies for Listed Salmonids in the Pacific Northwest

    NASA Astrophysics Data System (ADS)

    Ruckelshaus, M.; Beechie, T.; Lagueux, K.; Haas, A.

    2005-05-01

    A number of species of Pacific salmonids are listed under the U.S. Endangered Species Act due to a combination of habitat loss and degradation, hatchery programs, and harvest practices. Efforts are underway throughout the geographic ranges of the listed salmon to develop recovery plans describing the necessary conditions for delisting. Habitat restoration strategies in some watershed recovery plans address the functioning of landscape processes that create and sustain stream habitats, in addition to the traditional focus on instream habitat conditions and their effects on salmon populations. Including restoration approaches that aim to improve habitat-forming processes is a step forward in addressing the root causes of habitat problems for salmon. In this talk, we illustrate how GIS-based analyses indicating the degree of impairment to sediment supply, stream flows, and riparian functions were used to help identify restoration strategies for Chinook salmon populations in a watershed in Puget Sound, WA. We first developed empirical relationships between landscape attributes (i.e., land cover, geology and forest road density) and processes or conditions (stream flows, riparian zone condition, large wood recruitment, and sediment supply rates). Then we summarized those landscape attributes in all sub-basins within the watershed to indicate the likely current condition of peak flow hydrology, riparian function, and sediment supply. Finally, we quantified the degree of impairment in these 3 processes relative to their likely historical rates or conditions, and classified sub-basins into groupings of common restoration strategies. Specific habitat restoration actions aimed at redressing the riparian, sediment, and flow problems at their sources were identified separately for each sub-basin strategy group. We explored the potential effects of 3 alternative restoration approaches on the status of Chinook salmon populations at the watershed scale using a fish

  13. Local habitat conditions explain the variation in the strength of self-thinning in a stream salmonid

    PubMed Central

    Myrvold, Knut Marius; Kennedy, Brian P

    2015-01-01

    Self-thinning patterns are frequently used to describe density dependence in populations on timescales shorter than the organism's life span and have been used to infer carrying capacity of the environment. Among mobile animals, this concept has been used to document density dependence in stream salmonids, which compete over access to food and space. The carrying capacity, growth conditions, and initial cohort sizes often vary between streams and stream sections, which would influence the onset and strength of the density dependence. Despite much effort in describing habitat relationships in stream fishes, few studies have explicitly tested how the physical environment affects the slope of the thinning curves. Here, we investigate the prevalence and strength of self-thinning in juvenile stages of a steelhead (Oncorhynchus mykiss) population in Idaho, USA. Further, we investigate the roles of local physical habitat and metabolic constraints in explaining the variation in thinning curves among study sites in the watershed. Only yearling steelhead exhibited an overall significant thinning trend, but the slope of the mass–density relationship (−0.53) was shallower than predicted by theory and reported from empirical studies. There was no detectable relationship in subyearling steelhead. Certain abiotic factors explained a relatively large portion of the variation in the strength of the self-thinning among the study reaches. For subyearling steelhead, the slopes were negatively associated with the average water depth and flow velocity in the study sites, whereas slopes in yearlings were steeper in sites that incurred a higher metabolic cost. Our results show that the prevalence and strength of density dependence in natural fish populations can vary across heterogeneous watersheds and can be more pronounced during certain stages of a species' life history, and that environmental factors can mediate the extent to which density dependence is manifested in predictable

  14. Assessing barotrauma in neutrally and negatively bouyant juvenile salmonids exposed to simulated hydro-turbine passage using a mobile aquatic barotrauma laboratory

    SciTech Connect

    Stephenson, John R.; Gingerich, Andrew J.; Brown, Richard S.; Pflugrath, Brett D.; Deng, Zhiqun; Carlson, Thomas J.; Langeslay, Mike; Ahmann, Martin L.; Johnson, Robert L.; Seaburg, Adam

    2010-10-01

    Barotrauma, injuries sustained following rapid decompression, occurs in many different fisheries applications. Previous attempts to quantify barotrauma in fish have been limited by hyper/hypobaric system function. Further, field studies are often confounded by covariates. The Mobile Aquatic Barotrauma Laboratory (MABL) was designed to address these limitations. Specifically, this testing facility allows the user to evaluate similar complex pressure scenarios that migrating juvenile salmonids are exposed to following turbine or spillway passage. In addition, factors including total dissolved gas, temperature, and acclimation pressure are controlled automatically with this mobile lab. In this paper we also present a case study where negative and neutrally buoyant juvenile Chinook salmon were exposed to simulated hydro-turbine passage (STP). Gill emboli, swim bladder rupture, mortality, and internal haemorrhaging were used as end points. The severity of the decompression profile and the fish’s ability to gain neutral buoyancy were used as predictor variables. We determined that fish that achieved neutral buoyancy during a 16 hour acclimation period had a greater risk of injury following STP than negatively buoyant conspecifics. This research solidifies the need to allow fish to become neutrally buoyant when assessing barotrauma and mortality in field and laboratory applications. Finally, MABL can be configured to examine a variety of different species and pressure profiles, and physical parameters in a controlled environment.

  15. Enumeration of Salmonids in the Okanogan Basin Using Underwater Video, Performance Period: October 2005 (Project Inception) - 31 December 2006.

    SciTech Connect

    Johnson, Peter N.; Rayton, Michael D.; Nass, Bryan L.; Arterburn, John E.

    2007-06-01

    The Confederated Tribes of the Colville Reservation (Colville Tribes) identified the need for collecting baseline census data on the timing and abundance of adult salmonids in the Okanogan River Basin in order to determine basin and tributary-specific spawner distributions, evaluate the status and trends of natural salmonid production in the basin, document local fish populations, and augment existing fishery data. This report documents the design, installation, operation and evaluation of mainstem and tributary video systems in the Okanogan River Basin. The species-specific data collected by these fish enumeration systems are presented along with an evaluation of the operation of a facility that provides a count of fish using an automated method. Information collected by the Colville Tribes Fish & Wildlife Department, specifically the Okanogan Basin Monitoring and Evaluation Program (OBMEP), is intended to provide a relative abundance indicator for anadromous fish runs migrating past Zosel Dam and is not intended as an absolute census count. Okanogan Basin Monitoring and Evaluation Program collected fish passage data between October 2005 and December 2006. Video counting stations were deployed and data were collected at two locations in the basin: on the mainstem Okanogan River at Zosel Dam near Oroville, Washington, and on Bonaparte Creek, a tributary to the Okanogan River, in the town of Tonasket, Washington. Counts at Zosel Dam between 10 October 2005 and 28 February 2006 are considered partial, pilot year data as they were obtained from the operation of a single video array on the west bank fishway, and covered only a portion of the steelhead migration. A complete description of the apparatus and methodology can be found in 'Fish Enumeration Using Underwater Video Imagery - Operational Protocol' (Nass 2007). At Zosel Dam, totals of 57 and 481 adult Chinook salmon were observed with the video monitoring system in 2005 and 2006, respectively. Run timing for

  16. Evaluation of Juvenile Fish Bypass and Adult Fish Passage Facilities at Three-Mile Falls Dam; Umatilla River, Oregon, 1989 Annual Report.

    SciTech Connect

    Nigro, Anthony A.

    1990-09-01

    We report on our progress from October 1989 through September 1990 on evaluating juvenile fish bypass and adult fish passage facilities at Three Mile Falls Dam on the Umatilla River. The study is a cooperative effort by the Oregon Department of Fish and Wildlife (ODFW) and the Confederated Tribes of the Umatilla Indian Reservation (CTUIR). Study objectives addressed by ODFW and CTUIR are: (1) ODFW (Report A): Operate and evaluate the juvenile fish bypass system in the West Extension Irrigation District canal at Three Mile Falls Dam; and (2) CTUIR (Report 8): Examine the passage of adult salmonids at Three Mile Falls Dam. The study is part of a program to rehabilitate anadromous fish stocks in the Umatilla River Basin that includes restorations of coho salmon Oncorhynchus Wsutch and chinook salmon 0. tshawytscha and enhancement of summer steelhead 0. mytiss.

  17. Off-flavors in salmonids raised in recirculating aquaculture systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Producers of aquaculture products will typically verify the flavor quality of their product by sensory evaluation (flavor testing) before harvesting the crop for market. “Off-flavors” detected in the product may require holding the fish in a purging system containing fresh, clean water to depurate ...

  18. Emerging trends in salmonid RAS - Part II. System enhancements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dozens of land-based, closed containment systems are coming on line to produce salmon. New projects are bringing new principles into the salmon industry. Depuration systems maximize the removal of earthy and musty flavors in harvested fish. An emerging trend has been to apply technologies that incre...

  19. Kalispel Resident Fish Project : Annual Report, 1995.

    SciTech Connect

    Maroney, Joseph; Donley, Christopher; Scott, Jason; Lockwood, Jr., Neil

    1997-06-01

    In 1995 the Kalispel Natural Resource Department (KNRD) in conjunction with the Washington Department of Fish and Wildlife (WDFW) initiated the implementation of a habitat and population enhancement project for bull trout (Salvelinus confluentus), westslope cutthroat trout (Oncorhynchus clarki lewisi) and largemouth bass (Micropterus salmoides). Habitat and population assessments were conducted in seven tributaries of the Box Canyon reach of the Pend Oreille River. Assessments were used to determine the types and quality of habitat that were limiting to native bull trout and cutthroat trout populations. Assessments were also used to determine the effects of interspecific competition within these streams. A bull trout and brook trout (Salvelinus fontinalis) hybridization assessment was conducted to determine the degree of hybridization between these two species. Analysis of the habitat data indicated high rates of sediment and lack of wintering habitat. The factors that contribute to these conditions have the greatest impact on habitat quality for the tributaries of concern. Population data suggested that brook trout have less stringent habitat requirements; therefore, they have the potential to outcompete the native salmonids in areas of lower quality habitat. No hybrids were found among the samples, which is most likely attributable to the limited number of bull trout. Data collected from these assessments were compiled to develop recommendations for enhancement measures. Recommendations for restoration include riparian planting and fencing, instream structures, as well as, removal of non-native brook trout to reduce interspecific competition with native salmonids in an isolated reach of Cee Cee Ah Creek.

  20. John Day Fish Passage and Screening; 2002 Annual Report.

    SciTech Connect

    Hartlerode, Ray; Dabashinsky, Annette; Allen, Steve

    2003-01-28

    This project is necessary to insure that replacement of fish screening devices and fishways meet current NMFS design criteria for the protection of all salmonid life stages. The mission of the fish passage program in Northeast Oregon is to protect and enhance fish populations by assisting private landowners, public landowners, irrigation districts and others by maintaining fish screening devices and fishways. These facilities reduce or eliminate fish loss associated with irrigation withdrawals, and as a result insure fish populations are maintained for enjoyment by present and future generations. Assistance is provided through state and federal programs. This can range from basic technical advice to detailed construction, fabrication and maintenance of screening and passage facilities. John Day screens personnel identified 50 sites for fish screen replacement, and one fish passage project. These sites are located in critical spawning, rearing and migration areas for spring chinook, summer steelhead and bull trout. All projects were designed and implemented to meet current NMFS criteria. It is necessary to have a large number of sites identified due to changes in weather, landowner cooperation and access issues that come up as we try and implement our goal of 21 completed projects.

  1. Detection of the causative agent of furunculusis, Aeromonas salmonicida in salmonids of the Krka River.

    PubMed

    Kapetanović, D; Vardić, I; Kurtović, B; Valić, D; Teskeredzić, E

    2008-02-01

    In this paper we describe the bacterial community associated with salmonids from the Krka River. Diversity analysis demonstrated that majority of the recovered bacteria were related to Aeromonadaceae group. Bacterial analysis also revealed the presence of Shigella spp. and Pseudomonas fluorescens. Isolation of Aeromonas salmonicida from trout, presents first isolation of this bacteria Croatian rivers. PMID:17624808

  2. Low summer water temperatures influence occurrence of naturalized salmonids across a mountain watershed

    USGS Publications Warehouse

    Mullner, S.A.; Hubert, W.A.

    2005-01-01

    We investigated relationships between the absence of salmonids and low summer water temperatures across a 150-km2 Rocky Mountain watershed. A model predicting maximum July water temperature (MJT) from measurements of perennial stream length, wetted width, and midrange basin elevation was developed from temperature data obtained at 20 sites across the watershed. The model was used to predict MJT in 75 reaches across the watershed where salmonids were sampled. The lowest predicted MJT in reaches where age-0 and juvenile-adult brook trout Salvelinus fontinalis were observed was 9??C. The lowest predicted MJT in reaches where age-0 progeny of the genus Oncorhynchus spp. (i.e., rainbow trout O. mykiss or cutthroat trout O. clarkii) were observed was 13??C and where Oncorhynchus spp. adults where observed was 12??C. The probability of occurrence of both age-0 and adult brook trout and Oncorhynchus spp. increased as MJT increased above these thresholds. Our results indicate that low MJT in some portions of a mountain watershed can be related to the absence of salmonids. Consequently, data on MJT may provide managers with a means of assessing where summer water temperatures are not suitable for establishment of naturalized salmonid populations. ?? Copyright by the American Fisheries Society 2005.

  3. Genome Sequence of a Lactococcus lactis Strain Isolated from Salmonid Intestinal Microbiota

    PubMed Central

    Opazo, Rafael; Gajardo, Felipe; Ruiz, Mauricio

    2016-01-01

    Lactococcus lactis is a common inhabitant of the intestinal microbiota of salmonids, especially those in aquaculture systems. Here, we present a genome sequence of a Lactococcus lactis strain isolated from the intestinal contents of rainbow trout reared in Chile. PMID:27563049

  4. Comparison of growth and metabolic regulation between wild, domesticated and transgenic salmonids.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To gain a better understanding of the aspects underlying normal and growth hormone enhanced growth in salmonids, quantitative expression analysis was performed for a number of genes related to muscle growth, metabolism, immunology and energy regulation. This analysis was performed in liver and musc...

  5. Genome Sequence of a Lactococcus lactis Strain Isolated from Salmonid Intestinal Microbiota.

    PubMed

    Opazo, Rafael; Gajardo, Felipe; Ruiz, Mauricio; Romero, Jaime

    2016-01-01

    Lactococcus lactis is a common inhabitant of the intestinal microbiota of salmonids, especially those in aquaculture systems. Here, we present a genome sequence of a Lactococcus lactis strain isolated from the intestinal contents of rainbow trout reared in Chile. PMID:27563049

  6. Influence of intermittent stream connectivity on water quality and salmonid survivorship.

    NASA Astrophysics Data System (ADS)

    Hildebrand, J.; Woelfle-Erskine, C. A.; Larsen, L.

    2014-12-01

    Anthropogenic stress and climate change are causing an increasing number of California streams to become intermittent and are driving earlier and more severe summertime drying. The extent to which emerging water conservation alternatives impact flows or habitat quality (e.g. temperature, DO) for salmonids remains poorly understood. Here, we investigate the proximal drivers of salmonid mortality over a range of connectivity conditions during summertime intermittency in Salmon Creek watershed, Sonoma County, CA. Through extensive sampling in paired subwatersheds over a period of two years, we tested the hypothesis that accumulation of readily bioavailable DOC in poorly flushed pools drives DO decline associated with loss of salmonids. We then traced the origin and flow pathways of DOC throughout the watershed using Parallel Factor Analysis (PARAFAC). We obtained samples for DOC and stable isotope analyses at monthly intervals from 20 piezometers and surface water in the study reaches and from private wells and springs distributed throughout the watersheds. We also obtained in situ DO, conductivity and pH readings within stream study reaches. We determined DOC quality by SUVA (specific UV absorbance) and fluorescence index. We calculated stream metabolism rates using the single station method. In pools instrumented with DO sensors, we compared changing DOC quality during the summer months to changes in DO concentrations and stream metabolism. Our results show that the duration of complete disconnection of pools during the summer months and stream metabolic rates are positively correlated with salmonid mortality. Furthermore, our results indicate that salmonid mortality is greatest in disconnected pools with low DOC fluorescence indices and high SUVA values, indicative of terrestrially derived DOC and little or no groundwater inflow. Conversely low salmonid mortality was found in disconnected pools with high fluorescence index and low SUVA, indicative of microbially

  7. Fish oil replacement in current aquaculture feed: is cholesterol a hidden treasure for fish nutrition?

    PubMed

    Norambuena, Fernando; Lewis, Michael; Hamid, Noor Khalidah Abdul; Hermon, Karen; Donald, John A; Turchini, Giovanni M

    2013-01-01

    Teleost fish, as with all vertebrates, are capable of synthesizing cholesterol and as such have no dietary requirement for it. Thus, limited research has addressed the potential effects of dietary cholesterol in fish, even if fish meal and fish oil are increasingly replaced by vegetable alternatives in modern aquafeeds, resulting in progressively reduced dietary cholesterol content. The objective of this study was to determine if dietary cholesterol fortification in a vegetable oil-based diet can manifest any effects on growth and feed utilization performance in the salmonid fish, the rainbow trout. In addition, given a series of studies in mammals have shown that dietary cholesterol can directly affect the fatty acid metabolism, the apparent in vivo fatty acid metabolism of fish fed the experimental diets was assessed. Triplicate groups of juvenile fish were fed one of two identical vegetable oil-based diets, with additional cholesterol fortification (high cholesterol; H-Chol) or without (low cholesterol; L-Chol), for 12 weeks. No effects were observed on growth and feed efficiency, however, in fish fed H-Col no biosynthesis of cholesterol, and a remarkably decreased apparent in vivo fatty acid β-oxidation were recorded, whilst in L-Chol fed fish, cholesterol was abundantly biosynthesised and an increased apparent in vivo fatty acid β-oxidation was observed. Only minor effects were observed on the activity of stearyl-CoA desaturase, but a significant increase was observed for both the transcription rate in liver and the apparent in vivo activity of the fatty acid Δ-6 desaturase and elongase, with increasing dietary cholesterol. This study showed that the possible effects of reduced dietary cholesterol in current aquafeeds can be significant and warrant future investigations. PMID:24324720

  8. Fish Oil Replacement in Current Aquaculture Feed: Is Cholesterol a Hidden Treasure for Fish Nutrition?

    PubMed Central

    Norambuena, Fernando; Lewis, Michael; Hamid, Noor Khalidah Abdul; Hermon, Karen; Donald, John A.; Turchini, Giovanni M.

    2013-01-01

    Teleost fish, as with all vertebrates, are capable of synthesizing cholesterol and as such have no dietary requirement for it. Thus, limited research has addressed the potential effects of dietary cholesterol in fish, even if fish meal and fish oil are increasingly replaced by vegetable alternatives in modern aquafeeds, resulting in progressively reduced dietary cholesterol content. The objective of this study was to determine if dietary cholesterol fortification in a vegetable oil-based diet can manifest any effects on growth and feed utilization performance in the salmonid fish, the rainbow trout. In addition, given a series of studies in mammals have shown that dietary cholesterol can directly affect the fatty acid metabolism, the apparent in vivo fatty acid metabolism of fish fed the experimental diets was assessed. Triplicate groups of juvenile fish were fed one of two identical vegetable oil-based diets, with additional cholesterol fortification (high cholesterol; H-Chol) or without (low cholesterol; L-Chol), for 12 weeks. No effects were observed on growth and feed efficiency, however, in fish fed H-Col no biosynthesis of cholesterol, and a remarkably decreased apparent in vivo fatty acid β-oxidation were recorded, whilst in L-Chol fed fish, cholesterol was abundantly biosynthesised and an increased apparent in vivo fatty acid β-oxidation was observed. Only minor effects were observed on the activity of stearyl-CoA desaturase, but a significant increase was observed for both the transcription rate in liver and the apparent in vivo activity of the fatty acid Δ-6 desaturase and elongase, with increasing dietary cholesterol. This study showed that the possible effects of reduced dietary cholesterol in current aquafeeds can be significant and warrant future investigations. PMID:24324720

  9. Fish Rhabdoviruses

    USGS Publications Warehouse

    Kurath, G.; Winton, J.

    2008-01-01

    Many important viral pathogens of fish are members of the family Rhabdoviridae. The viruses in this large group cause significant losses in populations of wild fish as well as among fish reared in aquaculture. Fish rhabdoviruses often have a wide host and geographic range, and infect aquatic animals in both freshwater and seawater. The fish rhabdoviruses comprise a diverse collection of isolates that can be placed in one of two quite different groups: isolates that are members of the established genusNovirhabdovirus, and those that are most similar to members of the genus Vesiculovirus. Because the diseases caused by fish rhabdoviruses are important to aquaculture, diagnostic methods for their detection and identification are well established. In addition to regulations designed to reduce the spread of fish viruses, a significant body of research has addressed methods for the control or prevention of diseases caused by fish rhabdoviruses, including vaccination. The number of reported fish rhabdoviruses continues to grow as a result of the expansion of aquaculture, the increase in global trade, the development of improved diagnostic methods, and heightened surveillance activities. Fish rhabdoviruses serve as useful components of model systems to study vertebrate virus disease, epidemiology, and immunology.

  10. Fish flavor.

    PubMed

    Kawai, T

    1996-02-01

    This article reviews features of flavor in three groups of fishes and summarizes them as follows: (1) fresh saltwater fish are nearly odorless because they contain a small quantity of volatiles; (2 freshwater fish give off pyrrolidine and earthy-odor compounds, which are responsible for their maturity and surrounding water pollution, and (3) euryhaline fish exhibit a variety of unsaturated carbonyls and alcohols derived from enzymatic and nonenzymatic oxidation of polyunsaturated fatty acids (PAs). These features are discussed, as are the effects of different enzymatic activities on PA oxidation and the effects of pH on mechanisms of formation of the volatiles. The monotonous volatile constitution of saltwater fish is likely caused by an unknown antioxidation system restraining the fish from oxidizing. The variety of constitution of euryhaline fish, especially that of anadromous fish under spawning conditions, could result from the loss of that system. The thermal environments of heated foods are also reviewed. The basic environment of fish, which allows the formation of flavor compounds, is discussed to confirm the volatiles found in unheated fish. PMID:8744606

  11. Forestry practices and aquatic biodiversity: Fish

    USGS Publications Warehouse

    Gresswell, Robert E.

    2005-01-01

    example, the salmonids in the coastal rivers and streams, and the larger interconnected streams, rivers, and lakes of the interior exhibit a variety of ecotypes and migratory life histories (Healey 1986; Trotter 1989; Larson and McIntire 1993; Northcote 1997). This life-history variation appears to be associated with adaptation to spatial and temporal variation in environment (e.g., Schaffer and Elson 1975; Carl and Healey 1984; Beacham and Murray 1987), and there is some evidence of the genetic heritability of life-history traits (Carl and Healey 1984; Gharrett and Smoker 1993; Hankin, Nicholas, and Downey 1993). Persistence of any level of biological organization (e.g., life-history type, population, metapopulation, subspecies, species, community) is related to the interaction of environmental and biological components, and intraspecific diversity is a means of spreading risk (sensu den Boer 1968) of extirpation in dynamic environments (Gresswell 1999). Unfortunately, despite the broad distribution and extensive intraspecific diversity, persistence of native fishes is uncertain in the Pacific Northwest. Many populations of anadromous salmonids, once synonymous with vigorous biological communities throughout the region, are threatened with extinction (Nehlsen, Williams, and Lichatowich 1991; Frissell 1993; Thurow, Lee, and Rieman 1997). Furthermore, over half of the native taxa in the Columbia River Basin are either listed under the Endangered Species Act, are being considered for listing, or are deemed sensitive by the management agencies (Lee et al. 1997; Thurow, Lee, and Rieman 1997). Potamodromous species like bull trout Salvelinus confluentus are estimated to occur as strong populations in less than 5% of their potential range (Rieman, Lee, and Thurow 1997). Although not currently listed under the endangered species list, the coastal cutthroat trout Oncorhynchus clarki is managed as a sensitive species in Oregon and California (Hall, Bisson, and Gresswell 1997

  12. Laboratory studies on the effects of shear on fish: Final report

    SciTech Connect

    Neitzel, Duane A.; Richmond, M. C.; Dauble, D. D.; Mueller, R. P.; Moursund, R. A.; Abernethy, C. S.; Guensch, G. R.; Cada, G. F.

    2000-09-01

    The overall objective of these studies was to specify an index describing the hydraulic force that fish experience when subjected to a shear environment. Fluid shear is a phenomenon that is important to fish. However, elevated levels of shear may result in strain rates that injure or kill fish. At hydroelectric generating facilities, concerns have been expressed that strain rates associated with passage through turbines, spillways, and fish bypass systems may adversely affect migrating fish. Development of fish-friendly hydroelectric turbines requires knowledge of the physical forces (injury mechanisms) that impact entrained fish and the fish’s tolerance to these forces. It requires up-front, pre-design specifications for the environmental conditions that occur within the turbine system; in other words, determining or assuming conditions known to injure fish will assist engineers in the design of a fish-friendly turbine system. To address the development of biological specifications, this experiment designed and built a test facility where juvenile fish could be subjected to a range of shear environments and quantified their biological response. The test data reported here provide quantified strain rates and the relationship of these forces to direct and indirect biological effects on fish. The study concludes that juvenile salmonids and American shad should survive shear environments where strain rates do not exceed 500 cm/s/cm at a Dy of 1.8 cm. Additional studies are planned with a sensor fish to better link hydraulic conditions found within the laboratory and field environments.

  13. Total Dissolved Gas Effects on Fishes of the Lower Columbia River

    SciTech Connect

    McGrath, Kathy E.; Dawley, Earl; Geist, David R.

    2006-03-31

    Gas supersaturation problems generated by spill from dams on the Columbia River were first identified in the 1960s. Since that time, considerable research has been conducted on effects of gas supersaturation on aquatic life, primarily juvenile salmonids. Also since that time, modifications to dam structures and operations have reduced supersaturated gas levels produced by the dams. The limit for total dissolved gas saturation (TDGS) as mandated by current Environmental Protection Agency water quality standards is 110%. State management agencies issue limited waivers to water quality, allowing production of levels of up to 120% TDGS to facilitate the downstream migration of juvenile salmonids. Recently, gas supersaturation as a water quality issue has resurfaced as concerns have grown regarding chronic effects of spill-related total dissolved gas on salmonids, including incubating embryos and larvae, resident fish species, and other aquatic organisms. Because of current concerns, and because the last comprehensive review of research on supersaturation effects on fishes was conducted in 1997, we reviewed recent supersaturation literature to identify new or ongoing issues that may not be adequately addressed by the current 110% TDGS limit and the 120% TDGS water quality waiver. We found that recent work supports older research indicating that short-term exposure to levels up to 120% TDGS does not produce acute effects on migratory juvenile or adult salmonids when compensating depths are available. Monitoring programs at Snake and Columbia river dams from 1995 to the early 2000s documented a low incidence of significant gas bubble disease or mortality in Columbia River salmonids, resident fishes, or other taxa. We did, however, identify five areas of concern in which total dissolved gas levels lower than water quality limits may produce sublethal effects on fishes of the Columbia River. These areas of concern are 1) sensitive and vulnerable species or life stages, 2

  14. The antiviral innate immune response in fish: evolution and conservation of the IFN system.

    PubMed

    Langevin, Christelle; Aleksejeva, Elina; Passoni, Gabriella; Palha, Nuno; Levraud, Jean-Pierre; Boudinot, Pierre

    2013-12-13

    Innate immunity constitutes the first line of the host defense after pathogen invasion. Viruses trigger the expression of interferons (IFNs). These master antiviral cytokines induce in turn a large number of interferon-stimulated genes, which possess diverse effector and regulatory functions. The IFN system is conserved in all tetrapods as well as in fishes, but not in tunicates or in the lancelet, suggesting that it originated in early vertebrates. Viral diseases are an important concern of fish aquaculture, which is why fish viruses and antiviral responses have been studied mostly in species of commercial value, such as salmonids. More recently, there has been an interest in the use of more tractable model fish species, notably the zebrafish. Progress in genomics now makes it possible to get a relatively complete image of the genes involved in innate antiviral responses in fish. In this review, by comparing the IFN system between teleosts and mammals, we will focus on its evolution in vertebrates. PMID:24075867

  15. Stream flow, salmon and beaver dams: roles in the structuring of stream fish communities within an anadromous salmon dominated stream.

    PubMed

    Mitchell, Sean C; Cunjak, Richard A

    2007-11-01

    The current paradigm of fish community distribution is one of a downstream increase in species richness by addition, but this concept is based on a small number of streams from the mid-west and southern United States, which are dominated by cyprinids. Further, the measure of species richness traditionally used, without including evenness, may not be providing an accurate reflection of the fish community. We hypothesize that in streams dominated by anadromous salmonids, fish community diversity will be affected by the presence of the anadromous species, and therefore be influenced by those factors affecting the salmonid population. Catamaran Brook, New Brunswick, Canada, provides a long-term data set to evaluate fish community diversity upstream and downstream of an obstruction (North American beaver Castor canadensis dam complex), which affects distribution of Atlantic salmon Salmo salar. The Shannon Weiner diversity index and community evenness were calculated for sample sites distributed throughout the brook and over 15 years. Fish community diversity was greatest upstream of the beaver dams and in the absence of Atlantic salmon. The salmon appear to depress the evenness of the community but do not affect species richness. The community upstream of the beaver dams changes due to replacement of slimy sculpin Cottus cognatus by salmon, rather than addition, when access is provided. Within Catamaran Brook, location of beaver dams and autumn streamflow interact to govern adult Atlantic salmon spawner distribution, which then dictates juvenile production and effects on fish community. These communities in an anadromous Atlantic salmon dominated stream do not follow the species richness gradient pattern shown in cyprinid-dominated streams and an alternative model for stream fish community distribution in streams dominated by anadromous salmonids is presented. This alternative model suggests that community distribution may be a function of semipermeable obstructions

  16. Development of an Index to Bird Predation of Juvenile Salmonids within the Yakima River, 2001 Annual Report.

    SciTech Connect

    Major, III, Walter; Grue, Christian E.; Ryding, Kristen E.

    2002-08-01

    Avian predation of fish is suspected to contribute to the loss of out-migrating juvenile salmonids in the Yakima Basin, potentially constraining natural and artificial production. In 1997 and 1998, the Yakima/ Klickitat Fisheries Project (YKFP)--whose goal is increasing natural production within the Yakima River--initiated investigations to assess the feasibility of developing an index to avian predation of juvenile salmon within the river. This research confirmed that Ring-billed Gulls and Common Mergansers were the primary avian predators of juvenile salmon (Phinney et al. 1998), and that under certain conditions could significantly impact migrating smolt populations. Beginning in 1999, the Washington Cooperative Fish and Wildlife Research Unit (WACFWRU) was asked by the YKFP to continue development of avian consumption indices. Monitoring methods developed by Phinney et al. (1998) were adopted (with modifications) and monitoring of impacts to juvenile salmon along river reaches and at areas of high predator/prey concentrations (colloquially referred to as ''hotspots'') has continued each year through 2001. In 2001, piscivorous birds were counted from river banks at hotspots and from a raft or drift boat along river reaches. Consumption by gulls at hotspots was based on direct observations of foraging success and modeled abundance; consumption by all other piscivorous birds was estimated using published dietary requirements and modeled abundance. Seasonal patterns of avian piscivore abundance were identified, diurnal patterns of gull abundance at hotspots were identified, and predation indices were calculated for hotspots and river reaches (for both spring and summer). Changes in survey methods in 2001 included the addition of surveys in the ''Canyon'' reach during spring and altering the method of directly measuring gull feeding rates at hotspots. Primary avian predators in 2001 were ''gulls'' (California and Ring-billed) at hotspots and Common Mergansers within

  17. Changes in Gas Bubble Disease Signs for Migrating Juvenile Salmonids Experimentally Exposed to Supersaturated Gasses, 1996-1997 Progress Report.

    SciTech Connect

    Absolon, Randall F.

    1999-03-01

    This study was designed to answer the question of whether gas bubble disease (GBD) signs change as a result of the hydrostatic conditions juvenile salmonids encounter when they enter the turbine intake of hydroelectric projects during their downstream migration.

  18. Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2008.

    SciTech Connect

    Faulkner, James R.; Smith, Steven G.; Muir, William D.

    2009-06-23

    In 2008, the National Marine Fisheries Service completed the sixteenth year of a study to estimate survival and travel time of juvenile salmonids Oncorhynchus spp. passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder (PIT) tags. We PIT tagged and released a total of 18,565 hatchery steelhead O. mykiss, 15,991 wild steelhead, and 9,714 wild yearling Chinook salmon O. tshawytscha at Lower Granite Dam in the Snake River. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and at sites within the hydropower system in both the Snake and Columbia Rivers. These included 122,061 yearling Chinook salmon tagged at Lower Granite Dam for evaluation of latent mortality related to passage through Snake River dams. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, Ice Harbor, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the single-release model). Primary research objectives in 2008 were to: (1) estimate reach survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling Chinook salmon and steelhead, (2) evaluate relationships between survival estimates and migration conditions, and (3) evaluate the survival estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2008 for PIT-tagged yearling Chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Additional details on the methodology and statistical models used are provided in previous reports cited here. Survival

  19. Texture Fish

    ERIC Educational Resources Information Center

    Stone, Julie

    2007-01-01

    In an effort to provide an opportunity for her first graders to explore texture through an engaging subject, the author developed a three-part lesson that features fish in a mixed-media artwork: (1) Exploring Textured Paint; (2) Creating the Fish; and (3) Role Playing. In this lesson, students effectively explore texture through painting, drawing,…

  20. How Will Climate Change Affect Channel Morphology and Salmonid Habitat in Mountain Basins?

    NASA Astrophysics Data System (ADS)

    Buffington, J. M.; Goode, J.

    2010-12-01

    Riverine habitat for salmonids is intimately linked to channel morphology and fluvial processes (channel hydraulics, sediment transport and scour regime) which are, in turn, controlled by watershed hydrology and erosional processes that input sediment to the fluvial system. Climate change has the potential to alter the timing, magnitude, and style of sediment and water inputs to mountain rivers. Channel response to these changes may range from small-scale adjustments of channel characteristics (e.g., width, depth, grain size, scour depth) to larger-scale changes in channel type (e.g., metamorphosis from a pool-riffle channel to a plane-bed morphology). Identifying which parts of the river network will remain relatively stable in response to climate change, and which are likely to cross critical morphologic and scour thresholds is important for predicting effects on salmonid populations. Toward this end, a regime framework is presented for predicting the relative degree of morphologic stability and scour potential in different physiographic settings (different water and sediment regimes). Digital elevation models are used to explore the spatial distribution of these conditions and potential consequences for salmonid habitat across the landscape. Results suggest that the potential for scour and morphologic variability are strongly influenced by hydroclimate; snowmelt channels are relatively stable across floods of different magnitude, while rainfall-dominated channels are more variable and less stable. Transitional changes in hydrologic regime (mixed rain and snow) have the greatest potential for altering geomorphic conditions and salmonid habitat. However, the vulnerability of salmonids to climate-driven changes in scour regime depend on the species and its life history (i.e., depth to which eggs are buried and timing of incubation relative to scouring flows). Overall, the regime approach provides a useful first-order assessment of channel condition and response

  1. Abundances of northwestern salamander larvae in montane lakes with and without fish, Mount Rainier National Park, Washington

    USGS Publications Warehouse

    Larson, Gary L.; Hoffman, Robert L.

    2002-01-01

    In Mount Rainier National Park, the northwestern salamander usually inhabits relatively large and deep lakes and ponds (average size = 0.3 ha; average depth > 2 m) that contain flocculent, organic bottom sediments and abundant coarse wood. Prior to 1970, salmonids were introduced into many of the park's lakes and ponds that were typical habitat of the northwestern salamander. The objective of this study was to compare, in lakes and ponds with suitable habitat characteristics for northwestern salamanders, the observed abundances of larvae in takes and ponds with and without these introduced salmonids. Day surveys of 61 lakes were conducted between 1993 and 1999. Fish were limited to takes and ponds deeper than 2 in. For the 48 lakes and ponds deeper than 2 in (i.e., 25 fishless lakes and 23 fish lakes), the mean and median observed abundances of northwestern salamander larvae in fishless lakes and ponds was significantly greater than the mean and median observed abundances of larvae in lakes and ponds with fish. Northwestern salamander larvae were not observed in 11 fish lakes. These lakes were similar in median elevation, surface area, and maximum depth to the fishless lakes. The 12 fish lakes with observed larvae were significantly lower in median elevation, larger in median surface area, and deeper in median maximum depth than the fishless lakes. Low to null observed abundances of northwestern salamander larvae in lakes and ponds with fish were attributed to a combination of fish predation of larvae and changes in larval behavior.

  2. Variability in triactinomyxon production from Tubifex tubifex populations from the same mitochondrial DNA lineage infected with Myxobolus cerebralis, the causative agent of whirling disease in salmonids.

    PubMed

    Rasmussen, Charlotte; Zickovich, Julie; Winton, James R; Kerans, Billie L

    2008-06-01

    Myxobolus cerebralis, the causative agent of whirling disease, infects both salmonid fish and an aquatic oligochaete, Tubifex tubifex. Although M. cerebralis has been detected in river drainages throughout the United States, disease severity among wild fish populations has been highly variable. Tubifex tubifex populations have been genetically characterized using sequences from the 16S mitochondrial DNA (mtDNA) gene, the 18S ribosomal RNA gene, the internal transcribed spacer region 1 (ITS1), and randomly amplified polymorphic DNA (RAPD). Our earlier work indicated that large differences in compatibility between the parasite and populations of T. tubifex may play a substantial role in the distribution of whirling disease and resulting mortality in different watersheds. In the present study, we examined 4 laboratory populations of T. tubifex belonging to 16S mtDNA lineage III and 1 population belonging to 16S mtDNA lineage I for triactinomyxon (TAM) production after infection with M. cerebralis myxospores. All 4 16S mtDNA lineage III populations produced TAMs, but statistically significant differences in TAM production were observed. Most individuals in the 16S mtDNA lineage III-infected populations produced TAMs. The 16S mtDNA lineage I population produced few TAMs. Further genetic characterization of the 16S mtDNA lineage III populations with RAPD markers indicated that populations producing similar levels of TAMs had more genetic similarity. PMID:18605778

  3. Variability in triactinomyxon production from Tubifex tubifex populations from the same mitochondrial DNA lineage infected with Myxobolus cerebralis, the causative agent of whirling disease in salmonids

    USGS Publications Warehouse

    Rasmussen, C.; Zickovich, J.; Winton, J.R.; Kerans, B.L.

    2008-01-01

    Myxobolus cerebralis, the causative agent of whirling disease, infects both salmonid fish and an aquatic oligochaete, Tubifex tubifex. Although M. cerebralis has been detected in river drainages throughout the United States, disease severity among wild fish populations has been highly variable. Tubifex tubifex populations have been genetically characterized using sequences from the 16S mitochondrial DNA (mtDNA) gene, the 18S ribosomal RNA gene, the internal transcribed spacer region 1 (ITS1), and randomly amplified polymorphic DNA (RAPD). Our earlier work indicated that large differences in compatibility between the parasite and populations of T. tubifex may play a substantial role in the distribution of whirling disease and resulting mortality in different watersheds. In the present study, we examined 4 laboratory populations of T. tubifex belonging to 16S mtDNA lineage III and 1 population belonging to 16S mtDNA lineage I for triactinomyxon (TAM) production after infection with M. cerebralis myxospores. All 4 16S mtDNA lineage III populations produced TAMs, but statistically significant differences in TAM production were observed. Most individuals in the 16S mtDNA lineage III-infected populations produced TAMs. The 16S mtDNA lineage I population produced few TAMs. Further genetic characterization of the 16S mtDNA lineage III populations with RAPD markers indicated that populations producing similar levels of TAMs had more genetic similarity. ?? American Society of Parasitologists 2008.

  4. Migrational Characteristics, Biological Observations, and Relative Survival of Juvenile Salmonids Entering the Columbia River Estuary, 1966-1983, 1985 Final Report of Research.

    SciTech Connect

    Dawley, Earl M.

    1986-04-01

    Natural runs of salmonids in the Columbia River basin have decreased as a result of hydroelectric-dam development, poor land- and forest-management, and over-fishing. This has necessitated increased salmon culture to assure adequate numbers of returning adults. Hatchery procedures and facilities are continually being modified to improve both the efficiency of production and the quality of juveniles produced. Initial efforts to evaluate changes in hatchery procedures were dependent upon adult contributions to the fishery and returns to the hatchery. Procedures were developed for sampling juvenile salmon and steelhead entering the Columbia River estuary and ocean plume. The sampling of hatchery fish at the terminus of their freshwater migration assisted in evaluating hatchery production techniques and identifying migrational or behavioral characteristics that influence survival to and through the estuary. The sampling program attempted to estimate survival of different stocks and define various aspects of migratory behavior in a large river, with flows during the spring freshet from 4 to 17 thousand cubic meters per second (m/sup 3//second).

  5. A Markov chain analysis of the movements of juvenile salmonids in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the information collected at McNary Dam was in the form of three-dimensional tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and test configurations of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting three-dimensional results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we investigated the feasibility of using a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis is one way that can be used to summarize numerically the behavior of fish in the forebay. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, proportions of yearling and subyearling Chinook salmon passing the three powerhouse areas was often greater in the southern and middle areas, compared to the northern area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to confirm and quantify the extent of milling behavior that had been observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the

  6. Forecasting survival and passage of migratory juvenile salmonids

    USGS Publications Warehouse

    Connor, William P.; Steinhorst, R. Kirk; Burge, Howard L.

    2000-01-01

    We developed methods to forecast survival and cumulative percent passage for subyearling chinook salmon Oncorhynchus tshawytscha at a dam to help managers effectively time the release of reservoir water to mitigate for passage delays and reduced survival. We tagged Snake River subyearling chinook salmon upstream of a dam from 1993 to 1998 and determined when a subsample of the tagged fish passed the dam. We randomly selected data (1993, 1994, 1996, and 1998) to develop a quadratic discriminant function for predicting which fish would survive to the dam and to develop a multiple-regression equation to predict the date survivors would pass the dam. We used the predicted passage dates within a year to calculate a daily cumulative percent passage forecast and then calculated a 90% forecast interval that varied by year, depending on the number of predicted survivors. We validated the forecast method using data for 1995 and 1997. The 1995 forecasted passage curve differed from the observed passage curve for 25 d of the 168-d emigration season. The 1997 forecasted and observed passage curves were similar for the entire 168-d emigration season. The 90% forecast interval was ±18.8% in 1995 and ±22.4% in 1997. We conclude that our method is a valid tool for in-season water management but acknowledge the potential for interannual variability in forecast performance.

  7. A Study to Determine the Biological Feasibility of a New Fish Tagging System: Annual Report, 1985-1986.

    SciTech Connect

    Prentice, Earl F.; Park, D.L.; Flagg, T.A.; McCutcheon, S.

    1986-12-01

    An ongoing cooperative project between the Bonneville Power Administration and the National Marine Fisheries Service was initiated in 1983 to evaluate the technical and biological feasibility of adapting a new identification system to salmonids. The system is based upon the passive integrated transponder (PIT) tag. This report discusses the work completed in 1985 and is divided into laboratory and field studies. All studies were conducted with the tag implanted into the body cavity of the test fish via a 12-gauge hypodermic needle.

  8. A fisheries evaluation of the Westside Ditch and Wapato Canal fish screening facilities, Spring 1989

    SciTech Connect

    Neitzel, D.A.; Abernethy, C.S.; Lusty, E.W.

    1990-06-01

    The Bonneville Power Administration, the United States Bureau of Reclamation, and the Washington State Department of Ecology are funding the construction and evaluation of fish passage and protection facilities at irrigation and hydroelectric diversions in the Yakima River Basin, Washington State. The programs provide offsite enhancement to compensate for fish and wildlife losses caused by hydroelectric development throughout the Columbia River Basin, and they address natural propagation of salmon to help mitigate the impact of irrigation in the Yakima River Basin. The Westside Ditch and Wapato Screens are two of the juvenile screening facilities. This report evaluates the effectiveness of the screens facilities for intercepting and returning juvenile salmonids unharmed to the Yakima River from which they were diverted. We evaluated the effectiveness of new fish screening facilities in the Westside Ditch and Wapato Canal in south-central Washington State. The screen integrity tests indicated that test fish released in front of the screens could enter the canal behind the screens. The study emphasized salmonids. Test fish were steelhead Oncorhynchus mykiss smolts, spring chinook salmon O. tshawytscha smolts, and rainbow trout O. mykiss fry. Evaluations were conducted during typical spring flows in the diversion. 13 refs., 10 figs., 6 tabs.

  9. Factors Controlling Dissolved Oxygen Concentration in the Hyporheic Zone Induced by Fish Egg Nests

    NASA Astrophysics Data System (ADS)

    Ford, A.; Cardenas, M. B.; Kaufman, M.; Zheng, L.; Kessler, A. J.

    2014-12-01

    There is currently limited research on the effects of bed depressions, such as those associated with fish nests, on hyporheic flow and biogeochemistry. A series of flume experiments are in progress, with the aim of understanding the effects of bed depressions on the hyporheic flow of oxygenated water. This study focuses on fish nests, also called redds, which represent a typical depression or scour feature. Previous research has shown that redd topography induces hyporheic circulation, but experiments regarding the oxygen concentration in and around the redds have not been conducted. We are determining the ways in which redds affect dissolved oxygen distribution and how this is controlled by hyporheic flow. The oxygen concentration across the cross-sectional plane of a fish nest is measured using a planar optode and microsensors. Hydraulic measurements include pressure measurements along the sediment-water interface and dye visualization. The redd design is based on a salmonid redd, which consists of a scour feature and a tailspin. The salmonid eggs are found in the tailspin. We hypothesize that the oxygen concentration will be greatest in close proximity to the gravel base of the redd and concentration will decrease with increasing depth and distance from the redd. Higher oxygen concentrations in the tailspin supports the placement of fish eggs within that area as opposed to a less oxygenated area of the streambed. Thus, fish nests are likely bio-engineered to optimize hyporheic flow and biogeochemistry to improve egg viability.

  10. The Influence of Salmonid Spawning on Grain Architecture, Critical Bed Shear Stress, and Bed Load Transport in Streams

    NASA Astrophysics Data System (ADS)

    Buxton, T.; Buffington, J. M.; Yager, E. M.; Fremier, A. K.; Hassan, M. A.

    2012-12-01

    Salmonid spawning occurs in many high to mid-order streams in North America and Europe, but the detailed mechanics of this disturbance on stream bed mobility is not well studied. We calculated and measured spawning effects on incipient bed mobility and sediment transport in a laboratory flume and found that the tailspill portion of simulated spawning nests ("redds") are less stable than unspawned beds. This result agrees with field research by others, but counters prior calculations of tailspill stability that used grain architecture relationships derived from unspawned beds. Redds have coarser and better sorted surfaces, which reduce grain exposure and protrusion compared to unspawned beds, but load cell measurements of the total resistance to movement of grains on redds were lower despite deeper grain pockets and larger pivot angles. This is because the redd-building process flushed fine sediment that had previously cemented bed material, resulting in a looser bed structure and more mobile grains. These observations are supported by force balance calculations of critical shear stress on redds being lower on average than on unspawned beds. Computational results are supported by visual observations and measurements of bed load transport from redds and unspawned beds in the flume, where redds mobilized sooner and exhibited a higher sediment transport rate than unspawned beds. Redds were observed to erode by translating, then dispersing and evacuating downstream, before grains on the unspawned bed mobilized. Further increase in discharge mobilized greater proportions of the unspawned bed but did not scour the deeper portion of redds where spawners deposit their eggs. Our results suggest both an evolutionary trade-off and advantage to large spawning populations. Namely, the structurally loose tailspill likely increases intragravel flow to eggs at the expense of tailspill instability, which may sufficiently elevate sediment yields in streams with high spawner densities

  11. The intercellular organization of the two muscular systems in the adult salmonid heart, the compact and the spongy myocardium.

    PubMed

    Pieperhoff, Sebastian; Bennett, William; Farrell, Anthony Peter

    2009-11-01

    The ventricle of the salmonid heart consists of an outer compact layer of circumferentially arranged cardiomyocytes encasing a spongy myocardium that spans the lumen of the ventricle with a fine arrangement of muscular trabeculae. While many studies have detailed the anatomical structure of fish hearts, few have considered how these two cardiac muscle architectures are attached to form a functional working unit. The present study considers how the spindle-like cardiomyocytes, unlike the more rectangular structure of adult mammalian cardiomyocytes, form perpendicular connections between the two muscle layers that withstand the mechanical forces generated during cardiac systole and permit a simultaneous, coordinated contraction of both ventricular components. Therefore, hearts of rainbow trout (Oncorhynchus mykiss) and sockeye salmon (Oncorhynchus nerka) were investigated in detail using scanning electron microscopy (SEM) and various light microscopic techniques. In contrast to earlier suggestions, we found no evidence for a distinct connective tissue layer between the two muscle architectures that might 'glue' together the compact and the spongy myocardium. Instead, the contact layer between the compact and the spongy myocardium was characterized by a significantly higher amount of desmosome-like (D) and fascia adhaerens-like (FA) adhering junctions compared with either region alone. In addition, we observed that the trabeculae form muscular sheets of fairly uniform thickness and variable width rather than thick cylinders of variable diameter. This sheet-like trabecular anatomy would minimize diffusion distance while maximizing the area of contact between the trabecular muscle and the venous blood as well as the muscle tension generated by a single trabecular sheet. PMID:19627390

  12. A simple method for in situ monitoring of water temperature in substrates used by spawning salmonids

    USGS Publications Warehouse

    Zimmerman, Christian E.; Finn, James E.

    2012-01-01

    Interstitial water temperature within spawning habitats of salmonids may differ from surface-water temperature depending on intragravel flow paths, geomorphic setting, or presence of groundwater. Because survival and developmental timing of salmon are partly controlled by temperature, monitoring temperature within gravels used by spawning salmonids is required to adequately describe the environment experienced by incubating eggs and embryos. Here we describe a simple method of deploying electronic data loggers within gravel substrates with minimal alteration of the natural gravel structure and composition. Using data collected in spawning sites used by summer and fall chum salmon Oncorhynchus keta from two streams within the Yukon River watershed, we compare contrasting thermal regimes to demonstrate the utility of this method.

  13. Interspecific habitat associations of juvenile salmonids in Lake Ontario tributaries: implications for Atlantic salmon restoration

    USGS Publications Warehouse

    Johnson, James H.; Chalupnicki, Marc

    2014-01-01

    Diel variation in habitat use of subyearling Chinook salmon (Oncorhynchus tshawytscha), subyearling coho salmon (O. kisutch), yearling steelhead (O. mykiss), and yearling Atlantic salmon (Salmo salar) was examined during the spring in two tributaries of Lake Ontario. A total of 1318 habitat observations were made on juvenile salmonids including 367 on steelhead, 351 on Chinook salmon, 333 on Atlantic salmon, and 261 on coho salmon. Steelhead exhibited the most diel variation in habitat use and Chinook the least. Juvenile salmonids were generally associated with more cover and larger substrate during the day in both streams. Interspecific differences in habitat use in both streams occurred with Atlantic salmon (fast velocities) and coho salmon (pools) using the least similar habitat. Chinook salmon and Atlantic salmon used similar habitat in both streams. These findings should help guide future management actions specific to habitat protection and restoration of Atlantic salmon in Lake Ontario tributaries.

  14. Gill (Na+ +K+)-ATPase involvement and regulation during salmonid adaptation to salt water.

    PubMed

    Borgatti, A R; Pagliarani, A; Ventrella, V

    1992-08-01

    1. The involvement of gill (Na+ +K+)-ATPase in salmonid adaptation to salt water (SW) is discussed. 2. Gill (Na+ +K+)-ATPase increase during SW adaptation is mainly related to the increased number and complexity of chloride cells deputed to salt extrusion. 3. The temporal relationships between serum peaks of thyroid hormones, cortisol, growth hormone, prolactin and gill (Na+ +K+)-ATPase rise during salmonid smoltification, suggest a hormonal involvement in the enzyme stimulation and thus in the acquirement of SW tolerance. 4. Literature on gill (Na+ +K+)-ATPase response to hormonal treatment is reviewed. The effects produced on gill (Na+ +K+)-ATPase and chloride cells by exogenous hormones point out a complex inter-relationship between the hormones considered. The mechanisms involved in hormonal regulation of the enzyme remain a matter of debate. PMID:1355028

  15. Acoustic Telemetry Evaluation of Juvenile Salmonid Passage and Survival at John Day Dam with Emphasis on the Prototype Surface Flow Outlet, 2008

    SciTech Connect

    Weiland, Mark A.; Ploskey, Gene R.; Hughes, James S.; Deng, Zhiqun; Fu, Tao; Monter, Tyrell J.; Johnson, Gary E.; Khan, Fenton; Wilberding, Matthew C.; Cushing, Aaron W.; Zimmerman, Shon A.; Faber, Derrek M.; Durham, Robin E.; Townsend, Richard L.; Skalski, John R.; Kim, Jina; Fischer, Eric S.; Meyer, Matthew M.

    2009-12-01

    The main purpose of the study was to evaluate the performance of Top Spill Weirs installed at two spillbays at John Day Dam and evaluate the effectiveness of these surface flow outlets at attracting juvenile salmon away from the powerhouse and reducing turbine passage. The Juvenile Salmonid Acoustic Telemetry System (JSATS) was used to estimate survival of juvenile salmonids passing the dam and also for calculating performance metrics used to evaluate the efficiency and effectiveness of the dam at passing juvenile salmonids.

  16. Liquid chromatographic determination of oxytetracycline in edible fish fillets from six species of fish

    USGS Publications Warehouse

    Meinertz, J.R.; Stehly, G.R.; Gingerich, W.H.

    1998-01-01

    The approved use of oxytetracycline (OTC) in U.S. Aquaculture is limited to specific diseases in salmonids and channel catfish. OTC may also be effective in controlling diseases in other fish species important to public aquaculture, but before approved use of OTC can be augmented, an analytical method for determining OTC in fillet tissue from multiple species of fish will be required to support residue depletion studies. The objective of this study was to develop and validate a liquid chromatographic (LC) method that is accurate, precise, and sensitive for OTC in edible fillets from multiple species of fish. Homogenized fillet tissues from walleye, Atlantic salmon, striped bass, white sturgeon, rainbow trout, and channel catfish were fortified with OTC at nominal concentrations of 10, 20, 100, 1000, and 5000 ng/g. In tissues fortified with OTC at 100, 1000, and 5000 ng/g, mean recoveries ranged from 83 to 90%, and relative standard deviations (RSDs) ranged from 0.9 to 5.8%. In all other tissues, mean recoveries ranged from 59 to 98%, and RSDs ranged from 3.3 to 20%. Method quantitation limits ranged from 6 to 22 ng/g for the 6 species. The LC parameters produced easily integratable OTC peaks without coelution of endogenous compounds. The method is accurate, precise, and sensitive for OTC in fillet tissue from 6 species of fish from 5 phylogenetically diverse groups.

  17. One Fish, Two Fish, Redfish, You Fish!

    ERIC Educational Resources Information Center

    White, Katherine; Timmons, Maryellen; Medders, Paul

    2011-01-01

    The recreational fishing activity presented in this article provides a hands-on, problem-based experience for students; it unites biology, math, economics, environmental policy, and population dynamics concepts. In addition, the activity allows students to shape environmental policy in a realistic setting and evaluate their peers' work. By…

  18. Fish Rhabdovirus Cell Entry Is Mediated by Fibronectin

    PubMed Central

    Bearzotti, Monique; Delmas, Bernard; Lamoureux, Annie; Loustau, Anne-Marie; Chilmonczyk, Stefan; Bremont, Michel

    1999-01-01

    Three monoclonal antibodies (MAbs) generated against rainbow trout gonad cells (RTG-2) have been selected for their ability to protect cells from the viral hemorrhagic septicemia virus (VHSV) infection, a salmonid rhabdovirus. Protection from infection was restricted to the salmonid-derived cell lines indicating species specificity of the blocking MAbs. Surprisingly, the blocking activity of these MAbs was also effective against other nonantigenically related fish rhabdoviruses. Indirect immunofluorescence and immunoelectron microscopy observations demonstrated that the three MAbs were all directed against an abundant cell plasma membrane component, and immunoprecipitation studies indicated that the target consisted of a heterodimeric complex with molecular masses of 200 and 44 kDa. Biochemical data provided the following evidence that fibronectin is part of this complex and that it could represent the main receptor for fish rhabdoviruses. (i) An antiserum generated against the 200-kDa protein reacted against the recombinant rainbow trout fibronectin expressed in Escherichia coli. (ii) The purified rainbow trout fibronectin was able to bind specifically to VHSV. To our knowledge, this is the first identification of a cellular component acting as a primary receptor for a virus replicating in lower vertebrates and, more interestingly, for viruses belonging to the Rhabdoviridae family. PMID:10438860

  19. Fishing Forecasts

    NASA Technical Reports Server (NTRS)

    1988-01-01

    ROFFS stands for Roffer's Ocean Fishing Forecasting Service, Inc. Roffer combines satellite and computer technology with oceanographic information from several sources to produce frequently updated charts sometimes as often as 30 times a day showing clues to the location of marlin, sailfish, tuna, swordfish and a variety of other types. Also provides customized forecasts for racing boats and the shipping industry along with seasonal forecasts that allow the marine industry to formulate fishing strategies based on foreknowledge of the arrival and departure times of different fish. Roffs service exemplifies the potential for benefits to marine industries from satellite observations. Most notable results are reduced search time and substantial fuel savings.

  20. Cle Elum Lake Restoration Feasibility Study: Fish Husbandry Research, 1988-1991 Progress Report.

    SciTech Connect

    Flagg, Thomas A.

    1991-09-01

    The National Marine Fisheries Service (NMFS) and the Bonneville Power Administration (BPA) are involved in a project to evaluate the feasibility of re-establishing anadromous salmon runs to Cle Elum Lake in the Yakima River Basin of Washington state. Historically, the Yakima River system supported large runs of anadromous salmonids that contributed significantly to the Columbia River harvest. Habitat destruction and overfishing drastically reduced run abundance prior to the early 1900s. Salmon runs were eliminated from upper reaches of the Yakima River Basin with development of irrigation storage reservoirs without fishways in the early 1900s. The goal of the NMFS/BPA project is to determine if it is feasible for anadromous salmonids to recolonize the habitat above Cle Elum Dam under the present format of irrigation water withdrawal from the reservoir. The primary concern is whether anadromous fish can successfully exit Cle Elum Lake and survive downstream passage through the Yakima and Columbia Rivers to the ocean.

  1. Seasonal Juvenile Salmonid Presence and Migratory Behavior in the Lower Columbia River

    SciTech Connect

    Carter, Jessica A.; McMichael, Geoffrey A.; Welch, Ian D.; Harnish, Ryan A.; Bellgraph, Brian J.

    2009-04-30

    To facilitate preparing Biological Assessments of proposed channel maintenance projects, the Portland District of the U.S. Army Corps of Engineers contracted the Pacific Northwest National Laboratory to consolidate and synthesize available information about the use of the lower Columbia River and estuary by juvenile anadromous salmonids. The information to be synthesized included existing published documents as well as data from five years (2004-2008) of acoustic telemetry studies conducted in the Columbia River estuary using the Juvenile Salmon Acoustic Telemetry System. For this synthesis, the Columbia River estuary includes the section of the Columbia River from Bonneville Dam at river kilometer (Rkm) 235 downstream to the mouth where it enters the Pacific Ocean. In this report, we summarize the seasonal salmonid presence and migration patterns in the Columbia River estuary based on information from published studies as well as relevant data from acoustic telemetry studies conducted by NOAA Fisheries and the Pacific Northwest National Laboratory (PNNL) between 2004 and 2008. Recent acoustic telemetry studies, conducted using the Juvenile Salmon Acoustic Telemetry System (JSATS; developed by the Portland District of the U.S. Army Corps of Engineers), provided information on the migratory behavior of juvenile steelhead (O. mykiss) and Chinook salmon in the Columbia River from Bonneville Dam to the Pacific Ocean. In this report, Section 2 provides a summary of information from published literature on the seasonal presence and migratory behavior of juvenile salmonids in the Columbia River estuary and plume. Section 3 presents a detailed synthesis of juvenile Chinook salmon and steelhead migratory behavior based on use of the JSATS between 2004 and 2008. Section 4 provides a discussion of the information summarized in the report as well as information drawn from literature reviews on potential effects of channel maintenance activities to juvenile salmonids rearing in

  2. Multispectral Imaging for Determination of Astaxanthin Concentration in Salmonids

    PubMed Central

    Dissing, Bjørn S.; Nielsen, Michael E.; Ersbøll, Bjarne K.; Frosch, Stina

    2011-01-01

    Multispectral imaging has been evaluated for characterization of the concentration of a specific cartenoid pigment; astaxanthin. 59 fillets of rainbow trout, Oncorhynchus mykiss, were filleted and imaged using a rapid multispectral imaging device for quantitative analysis. The multispectral imaging device captures reflection properties in 19 distinct wavelength bands, prior to determination of the true concentration of astaxanthin. The samples ranged from 0.20 to 4.34 g per g fish. A PLSR model was calibrated to predict astaxanthin concentration from novel images, and showed good results with a RMSEP of 0.27. For comparison a similar model were built for normal color images, which yielded a RMSEP of 0.45. The acquisition speed of the multispectral imaging system and the accuracy of the PLSR model obtained suggest this method as a promising technique for rapid in-line estimation of astaxanthin concentration in rainbow trout fillets. PMID:21573000

  3. Saprolegniosis in salmonids and their eggs in Japan.

    PubMed

    Hussein, M M; Hatai, K; Nomura, T

    2001-01-01

    An epizootic of the fungal infection saprolegniosis that occurred in freshwater-cultured salmons and their eggs at some hatcheries in Hokkaido (Japan) was investigated. In almost all cases, the initial clinical sign was characterized by the growth of cotton-like mycelia on the fishs' body surface, especially the head, adipose fin, and caudal fin, but the mycelia were not visible to the naked eye in the internal organs. Thirty-three strains isolated from lesions were classified in the genus Saprolegnia according to their morphological and biological characteristics on hemp seed cultures at various temperatures. Fifteen of the strains were identified as Saprolegnia parasitica, 16 were identified as S. salmonis, and two were identified as S. australis. PMID:11272500

  4. Smallmouth bass and largemouth bass predation on juvenile Chinook salmon and other salmonids in the Lake Washington basin

    USGS Publications Warehouse

    Tabor, R.A.; Footen, B.A.; Fresh, K.L.; Celedonia, M.T.; Mejia, F.; Low, D.L.; Park, L.

    2007-01-01

    We assessed the impact of predation by smallmouth bass Micropterus dolomieu and largemouth bass M. salmoides on juveniles of federally listed Chinook salmon Oncorhynchus tshawytscha and other anadromous salmonid populations in the Lake Washington system. Bass were collected with boat electrofishing equipment in the south end of Lake Washington (February-June) and the Lake Washington Ship Canal (LWSC; April-July), a narrow waterway that smolts must migrate through to reach the marine environment. Genetic analysis was used to identify ingested salmonids to obtain a more precise species-specific consumption estimate. Overall, we examined the stomachs of 783 smallmouth bass and 310 largemouth bass greater than 100 mm fork length (FL). Rates of predation on salmonids in the south end of Lake Washington were generally low for both black bass species. In the LWSC, juvenile salmonids made up a substantial part of bass diets; consumption of salmonids was lower for largemouth bass than for smallmouth bass. Smallmouth bass predation on juvenile salmonids was greatest in June, when salmonids made up approximately 50% of their diet. In the LWSC, overall black bass consumption of salmonids was approximately 36,000 (bioenergetics model) to 46,000 (meal turnover consumption model) juveniles, of which about one-third was juvenile Chinook salmon, one-third was coho salmon O. kisutch, and one-third was sockeye salmon O. nerka. We estimated that about 2,460,000 juvenile Chinook salmon (hatchery and wild sources combined) were produced in the Lake Washington basin in 1999; thus, the mortality estimates in the LWSC range from 0.5% (bioenergetics) to 0.6% (meal turnover). Black bass prey mostly on subyearlings of each salmonid species. The vulnerability of subyearlings to predation can be attributed to their relatively small size; their tendency to migrate when water temperatures exceed 15??C, coinciding with greater black bass activity; and their use of nearshore areas, where overlap

  5. Differential invasion success of salmonids in southern Chile: patterns and hypotheses

    USGS Publications Warehouse

    Arismendi, Ivan; Penaluna, Brooke E.; Dunham, Jason B.; García de Leaniz, Carlos; Soto, Doris; Fleming, Ian A.; Gomez-Uchidam, Daniel; Gajardo, Gonzalo; Vargas, Pamela V.; León-Muñoz, Jorge

    2014-01-01

    Biological invasions create complex ecological and societal issues worldwide. Most of the knowledge about invasions comes only from successful invaders, but less is known about which processes determine the differential success of invasions. In this review, we develop a framework to identify the main dimensions driving the success and failure of invaders, including human influences, characteristics of the invader, and biotic interactions. We apply this framework by contrasting hypotheses and available evidence to explain variability in invasion success for 12 salmonids introduced to Chile. The success of Oncorhynchus mykiss and Salmo trutta seems to be influenced by a context-specific combination of their phenotypic plasticity, low ecosystem resistance, and propagule pressure. These well-established invaders may limit the success of subsequently introduced salmonids, with the possible exception of O. tshawytscha, which has a short freshwater residency and limited spatial overlap with trout. Although propagule pressure is high for O. kisutch and S. salar due to their intensive use in aquaculture, their lack of success in Chile may be explained by environmental resistance, including earlier spawning times than in their native ranges, and interactions with previously established and resident Rainbow Trout. Other salmonids have also failed to establish, and they exhibit a suite of ecological traits, environmental resistance, and limited propagule pressure that are variably associated with their lack of success. Collectively, understanding how the various drivers of invasion success interact may explain the differential success of invaders and provide key guidance for managing both positive and negative outcomes associated with their presence.

  6. Epidemiology and Control of Infectious Diseases of Salmonids in the Columbia River Basin, 1984 Annual Report.

    SciTech Connect

    Fryer, John L.

    1985-11-01

    The Department of Microbiology at Oregon State University with funding from the Bonneville Power Administration has conducted a study since 1983 relating to the epidemiology and control of three diseases of salmonids in the Columbia River Basin. These diseases are ceratomyxosis, caused by the protozoan parasite Ceratomyxa Shasta, bacterial kidney disease, the etiological agent of which is Renibacterium salmoninarum and infectious hematopoietic necrosis which is caused by a rhabdovirus. Each of these diseases is difficult or impossible to treat with antimicrobial agents. The presence of the infectious stage of C. shasta was again detected at Little Goose Dam on the Snake River. The prevalence of ceratomyxosis increased from 1.1% in 1984 to 10% in 1985. None of the susceptible rainbow trout exposed in the Yakima and Umatilla Rivers died of this disease. Ceratomyxosis in resistant chinook salmon smolts seined from the Columbia River just above the estuary seems dependent on whether or not they are held after capture in fresh or salt water. In fresh water the disease incidence ranged from 7--19%, whereas in salt water it ranged from 0--3%. These results which suggest that recovery from ceratomyxosis may occur after the smolts enter salt water are different from those obtained with susceptible Alsea steelhead trout where experimental groups in salt water have died at the same rate as those in fresh water. Comparing data from groups of Columbia River chinook smolts held after capture in either fresh or salt water, R. salmoninarum is a much more effective pathogen in the salt water environment. After four years of sampling smolts in the open ocean, numbers of this microorganism sufficient to cause death have been detected in chinook (7%) and, coho salmon (2%) and steelhead trout (1%). Results from three years of sampling have consistently indicated that additional fish infected with R. salmoninarum will be detected if egg washings are included in the procedures for

  7. The Design and Analysis of Salmonid Tagging Studies in the Columbia Basin : Volume II: Experiment Salmonid Survival with Combined PIT-CWT Tagging.

    SciTech Connect

    Newman, Ken

    1997-06-01

    Experiment designs to estimate the effect of transportation on survival and return rates of Columbia River system salmonids are discussed along with statistical modeling techniques. Besides transportation, river flow and dam spill are necessary components in the design and analysis otherwise questions as to the effects of reservoir drawdowns and increased dam spill may never be satisfactorily answered. Four criteria for comparing different experiment designs are: (1) feasibility, (2) clarity of results, (3) scope of inference, and (4) time to learn. In this report, alternative designs for conducting experimental manipulations of smolt tagging studies to study effects of river operations such as flow levels, spill fractions, and transporting outmigrating salmonids around dams in the Columbia River system are presented. The principles of study design discussed in this report have broad implications for the many studies proposed to investigate both smolt and adult survival relationships. The concepts are illustrated for the case of the design and analysis of smolt transportation experiments. The merits of proposed transportation studies should be measured relative to these principles of proper statistical design and analysis.

  8. Fish Facts

    MedlinePlus

    ... not eat any fish because they worry about mercury in seafood. Mercury is a metal that, at high levels, can ... many types of seafood have little or no mercury at all. So your risk of mercury exposure ...

  9. Designer Fish.

    ERIC Educational Resources Information Center

    Hall, William R., Jr.

    1990-01-01

    Described is an activity in which students are asked to design a fish that would survive in a natural system. A project to computerize the activity is discussed. The development of this artificial intelligence software is detailed. (CW)

  10. Fish Allergy

    MedlinePlus

    ... specific fish used on the label. Read all product labels carefully before purchasing and consuming any item. Ingredients ... Getting Started Newly Diagnosed Emergency Care Plan Food Labels Mislabeled Products Tips for Managing Food Allergies Resources For... Most ...

  11. Revisiting the paradigm of myostatin in vertebrates: insights from fishes.

    PubMed

    Gabillard, Jean-Charles; Biga, Peggy R; Rescan, Pierre-Yves; Seiliez, Iban

    2013-12-01

    In the last decade, myostatin (MSTN), a member of the TGFβ superfamily, has emerged as a strong inhibitor of muscle growth in mammals. In fish many studies reveal a strong conservation of mstn gene organization, sequence, and protein structures. Because of ancient genome duplication, teleostei may have retained two copies of mstn genes and even up to four copies in salmonids due to additional genome duplication event. In sharp contrast to mammals, the different fish mstn orthologs are widely expressed with a tissue-specific expression pattern. Quantification of mstn mRNA in fish under different physiological conditions, demonstrates that endogenous expression of mstn paralogs is rarely related to fish muscle growth rate. In addition, attempts to inhibit MSTN activity did not consistently enhance muscle growth as in mammals. In vitro, MSTN stimulates myotube atrophy and inhibits proliferation but not differentiation of myogenic cells as in mammals. In conclusion, given the strong mstn expression non-muscle tissues of fish, we propose a new hypothesis stating that fish MSTN functions as a general inhibitors of cell proliferation and cell growth to control tissue mass but is not specialized into a strong muscle regulator. PMID:24018114

  12. Behavioral factors influencing spatial distributions of fish in contaminated environments

    SciTech Connect

    Little, E.E.; DeLonay, A.J.; Lipton, J.

    1994-12-31

    In addition to contaminant preference/avoidance responses, contaminant-induced behavioral factors can also influence the spatial distribution of fish. The seaward migrations of smolting anadromous salmonids, can be disrupted by a variety of contaminants, including metals such as copper. This disruption can be reflected in a delay in this normal loss of positive rheotaxis, as fish orient down stream. In estuaries, the fish may fail to show preferences for salt water as well as inhibited physiological adaptations to saltwater. Competitive interactions can also be responsible for the loss of population. Brown trout, for example, appear to be more tolerant of exposure to many contaminants than native fishes, and may also be more aggressive in their interaction with native species. Thus, native fishes in marginal habitats may be driven out by brown trout. Finally predator-prey interactions may play a role in the diminishing native fish populations through increased predation-induced mortality caused by impaired anti-predator defenses. Uniform tests or protocols are required to provide reliable, reproducible results, necessary for regulatory action. Discussion will focus on issues related to generation and establishment of consensus guidelines to encourage the application of behavior in contaminant assessment and application in measures of environmental injury.

  13. A summary of 22 Years of Fish Screen Evaluation in the Yakima River Basin, Summary Report 1985-2007.

    SciTech Connect

    Chamness, Mickie A.

    2007-12-03

    Sixty fish screen facilities were constructed in the Yakima River basin between 1985 and 2006 as part of the Northwest Power and Conservation Council plan to mitigate the effects of federal hydroelectric projects on fish and wildlife populations. This report summarizes evaluations of some of those and other fish screen facilities conducted by Pacific Northwest National Laboratory (PNNL) from 1985 through 2006. The objective of these studies was to determine if the newly designed and constructed fish screens were effective at providing juvenile salmonids safe passage past irrigation diversions. To answer that question, PNNL conducted release-and-catch studies at eight Phase I sites in the Yakima River basin. Increasing concerns about the impacts of hatchery fish releases on the wild fish population, as well as the cost and time necessary to perform these kinds of biological studies at more than 60 planned Phase II sites, required development of techniques to evaluate the effectiveness of the sites without releasing fish. The new techniques involved collecting information on screen design, operation, and effectiveness at guiding fish safely through the fish screen facility. Performance measures including water velocities and passage conditions provide a good alternative to biological studies at significantly lower cost and time. Physical techniques were used at all 10 Phase I and 28 Phase II sites evaluated by PNNL over the following 19 years. Results of these studies indicate the Phase I and II fish screen facilities are designed and capable of providing safe passage for juvenile salmonids so long as construction, maintenance, and operations meet the criteria used in the design of each site and the National Marine Fisheries Service criteria for juvenile fish screen design.

  14. Using real-time PCR and Bayesian analysis to distinguish susceptible tubificid taxa important in the transmission of Myxobolus cerebralis, the cause of salmonid whirling disease.

    PubMed

    Fytilis, Nikolaos; Rizzo, Donna M; Lamb, Ryan D; Kerans, Billie L; Stevens, Lori

    2013-05-01

    Aquatic oligochaetes have long been appreciated for their value in assessing habitat quality because they are ubiquitous sediment-dwelling filter feeders. Many oligochaete taxa are also important in the transmission of fish diseases. Distinguishing resistant and susceptible taxa is important for managing fish disease, yet challenging in practice. Tubifex tubifex (Oligochaeta: Tubificidae) is the definitive host for the complex life-cycle parasite, Myxobolus cerebralis, the causative agent of salmonid whirling disease. We developed two hydrolysis probe-based qualitative real-time PCR (qPCR) multiplex assays that distinguish among tubificid taxa collected from the Madison River, Montana, USA. The first assay distinguishes T. tubifex from Rhyacodrilus spp.; while the second classifies T. tubifex identified by the first assay into two genetic lineages (I and III). Specificity and sensitivity were optimized for each assay; the two assays showed specificity of 94.3% and 98.6% for the target oligochaetes, respectively. DNA sequencing verified the results. The development of these assays allowed us to more fully describe tubificid community composition (the taxa and their abundance at a site) and estimate the relative abundances of host taxa. To relate tubificid relative abundance to fish disease risk, we determined M. cerebralis infection prevalence in samples identified as T. tubifex using similar molecular techniques. Given prior information (i.e., morphological identification of sexually mature worms), Bayesian analysis inferred that the first qPCR assay improved taxonomic identification. Bayesian inference of the relative abundance of T. tubifex, combined with infection assay results, identified sites with a high prevalence of infected T. tubifex. To our knowledge, this study represents both the first assessment of oligochaete community composition using a qPCR assay based on fluorescent probes and the first use of Bayesian analysis to fully characterize the dominant

  15. Anadromous salmonids in the Delta: New science 2006–2016

    USGS Publications Warehouse

    Perry, Russell W.; Buchanan, Rebecca A.; Brandes, Patricia L.; Burau, Jon R.; Israel, Joshua A

    2016-01-01

    As juvenile salmon enter the Sacramento–SanJoaquin River Delta (“the Delta”) they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this complex channel network were limited.Fortunately, thanks to technological advances such as acoustic telemetry and chemical and structural otolith analysis, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. Here, we review new science between 2006and 2016 that sheds light on how different life stages and runs of juvenile salmon grow, move, and survive in the complex channel network of the Delta. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis of otoliths has provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use the Delta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

  16. Muscle metabolic remodeling in response to endurance exercise in salmonids

    PubMed Central

    Morash, Andrea J.; Vanderveken, Mark; McClelland, Grant B.

    2014-01-01

    Phenotypic plasticity of skeletal muscle is relevant to swimming performance and metabolism in fishes, especially those that undergo extreme locomotory feats, such as seasonal migration. However, the influence of endurance exercise and the molecular mechanisms coordinating this remodeling are not well understood. The present study examines muscle metabolic remodeling associated with endurance exercise in fed rainbow trout as compared to migrating salmon. Trout were swum for 4 weeks at 1.5 BL/s, a speed similar to that of migrating salmon and red and white muscles were sampled after each week. We quantified changes in key enzymes in aerobic and carbohydrate metabolism [citrate synthase (CS), β-hydroxyacyl-CoA dehydrogenase (HOAD), hexokinase (HK)] and changes in mRNA expression of major regulators of metabolic phenotype (AMPK, PPARs) and lipid (carnitine palmitoyltransferase, CPT I), protein (aspartate aminotransferase, AST) and carbohydrate (HK) oxidation pathways. After 1 week of swimming substantial increases were seen in AMPK and PPARα mRNA expression and of their downstream target genes, CPTI and HK in red muscle. However, significant changes in CS and HK activity occurred only after 4 weeks. In contrast, there were few changes in mRNA expression and enzyme activities in white muscle over the 4-weeks. Red muscle results mimic those found in migrating salmon suggesting a strong influence of exercise on red muscle phenotype. In white muscle, only changes in AMPK and PPAR expression were similar to that seen with migrating salmon. However, in contrast to exercise alone, in natural migration HK decreased while AST increased suggesting that white muscle plays a role in supplying fuel and intermediates possibly through tissue breakdown during prolonged fasting. Dissecting individual and potentially synergistic effects of multiple stressors will enable us to determine major drivers of the metabolic phenotype and their impacts on whole animal performance. PMID

  17. System-Wide Significance of Predation on Juvenile Salmonids in Columbia and Snake River Reservoirs : Annual Report of Research 1990.

    SciTech Connect

    Petersen, C.J.

    1991-03-01

    The consumption rates of northern squawfish (Ptychocheilus oregonensis) preying upon juvenile salmonids were indexed in four reservoirs (Bonneville, The Dalles, John Day and McNary) of the lower Columbia River. During the spring and summer of 1990, over 2000 northern squawfish were collected from dam forebays, dam tailraces and mid-reservoir locations. Gut content data, predator weight and water temperature were used to compute a consumption index (CI) for northern squawfish. Juvenile salmonids were found in 435 of 1598 northern squawfish guts analyzed. Besides salmonids and other preyfish, crustaceans formed a significant portion of the diet. The CI of northern squawfish varied by season and location. At most locations, summer CI's of northern squawfish were higher than in the spring. Efforts to match sample collection with times of highest juvenile salmonid passage were successful except during July at The Dalles and Bonneville Reservoirs. Consumption indices were moderate to high at several locations even when passage was relatively low, suggesting salmonid predation rate by northern squawfish was not always a function of prey density. 19 refs., 5 figs., 12 tabs.

  18. Kalispel Non-Native Fish Suppression Project 2007 Annual Report.

    SciTech Connect

    Wingert, Michele; Andersen, Todd

    2008-11-18

    Non-native salmonids are impacting native salmonid populations throughout the Pend Oreille Subbasin. Competition, hybridization, and predation by non-native fish have been identified as primary factors in the decline of some native bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarki lewisi) populations. In 2007, the Kalispel Natural Resource Department (KNRD) initiated the Kalispel Nonnative Fish Suppression Project. The goal of this project is to implement actions to suppress or eradicate non-native fish in areas where native populations are declining or have been extirpated. These projects have previously been identified as critical to recovering native bull trout and westslope cutthroat trout (WCT). Lower Graham Creek was invaded by non-native rainbow (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis) after a small dam failed in 1991. By 2003, no genetically pure WCT remained in the lower 700 m of Graham Creek. Further invasion upstream is currently precluded by a relatively short section of steep, cascade-pool stepped channel section that will likely be breached in the near future. In 2008, a fish management structure (barrier) was constructed at the mouth of Graham Creek to preclude further invasion of non-native fish into Graham Creek. The construction of the barrier was preceded by intensive electrofishing in the lower 700 m to remove and relocate all captured fish. Westslope cutthroat trout have recently been extirpated in Cee Cee Ah Creek due to displacement by brook trout. We propose treating Cee Cee Ah Creek with a piscicide to eradicate brook trout. Once eradication is complete, cutthroat trout will be translocated from nearby watersheds. In 2004, the Washington Department of Fish and Wildlife (WDFW) proposed an antimycin treatment within the subbasin; the project encountered significant public opposition and was eventually abandoned. However, over the course of planning this 2004 project, little public

  19. Analyses of potential factors affecting survival of juvenile salmonids volitionally passing through turbines at McNary and John Day Dams, Columbia River

    USGS Publications Warehouse

    Beeman, John; Hansel, Hal; Perry, Russell; Hockersmith, Eric; Sandford, Ben

    2011-01-01

    This report describes analyses of data from radio- or acoustic-tagged juvenile salmonids passing through hydro-dam turbines to determine factors affecting fish survival. The data were collected during a series of studies designed to estimate passage and survival probabilities at McNary (2002-09) and John Day (2002-03) Dams on the Columbia River during controlled experiments of structures or operations at spillways. Relatively few tagged fish passed turbines in any single study, but sample sizes generally were adequate for our analyses when data were combined from studies using common methods over a series of years. We used information-theoretic methods to evaluate biological, operational, and group covariates by creating models fitting linear (all covariates) or curvilinear (operational covariates only) functions to the data. Biological covariates included tag burden, weight, and water temperature; operational covariates included spill percentage, total discharge, hydraulic head, and turbine unit discharge; and group covariates included year, treatment, and photoperiod. Several interactions between the variables also were considered. Support of covariates by the data was assessed by comparing the Akaike Information Criterion of competing models. The analyses were conducted because there was a lack of information about factors affecting survival of fish passing turbines volitionally and the data were available from past studies. The depth of acclimation, tag size relative to fish size (tag burden), turbine unit discharge, and area of entry into the turbine intake have been shown to affect turbine passage survival of juvenile salmonids in other studies. This study indicates that turbine passage survival of the study fish was primarily affected by biological covariates rather than operational covariates. A negative effect of tag burden was strongly supported in data from yearling Chinook salmon at John Day and McNary dams, but not for subyearling Chinook salmon or

  20. Changes in Gas Bubble Disease Signs and Survival of Migrating Juvenile Salmonids Experimentally Exposed to Supersaturated Gasses, 1995-1996 Progress Report.

    SciTech Connect

    Absolon, Randall F.

    1997-11-01

    Research conducted in 1996 to evaluate (1) changes in GBD signs in juvenile salmonids resulting from passage through turbine intakes and bypass systems, and (2) relative survival during migration through the lower Snake River for juvenile salmonids experimentally exposed to supersaturation of dissolved gas.

  1. Hydroacoustic Evaluation of Fish Passage Through Bonneville Dam in 2002

    SciTech Connect

    Ploskey, Gene R. ); Schilt, Carl R.; Kim, J; Escher, Charles; Skalski, John R.

    2003-08-15

    The Portland District of the U.S. Army Corps of Engineers requested that the Pacific Northwest National Laboratory (PNNL) and the U.S. Army Engineer Research and Development Center (ERDC) conduct fish-passage studies at Bonneville Dam in 2002. The ERDC contracted with MEVATEC Corporation to provide staff ranging from scientists to technicians to help conduct the study. This study supports the Portland-District goal of maximizing fish-passage efficiency (FPE) and obtaining 95% survival for juvenile salmon passing Bonneville Dam. In this report, we present results of two studies of juvenile salmonid passage at Bonneville Dam that we carried out in the 2002 downstream passage season April 20 through July 15, 2002. The first study of Project-wide FPE provides hourly estimates of fish passage and associated variances for all operating turbine units, spill bays, and the two sluiceway entrances at Powerhouse 1 (B1), as well as estimates of a variety of fish-passage efficiency and effectiveness measures. This was the third consecutive year of full-project hydroacoustic sampling and passage estimation. The second study was more narrowly focused on B2 turbines and had two components: (1) to sample the FGE at two modified turbine intakes and compare them with efficiencies of other B2 units that were sampled in the first study, and (2) to evaluate proportions of fish passing up into gatewell slots versus through screen gaps at a few B2 turbine intakes.

  2. Effective Climate Refugia for Cold-water Fishes

    NASA Astrophysics Data System (ADS)

    Ebersole, J. L.; Morelli, T. L.; Torgersen, C.; Isaak, D.; Keenan, D.; Labiosa, R.; Fullerton, A.; Massie, J.

    2015-12-01

    Climate change threatens to create fundamental shifts in in the distributions and abundances of endothermic organisms such as cold-water salmon and trout species (salmonids). Recently published projected declines in mid-latitude salmonid distributions under future climates range from modest to severe, depending on modeling approaches, assumptions, and spatial context of analyses. Given these projected losses, increased emphasis on management for ecosystem resilience to help buffer cold-water fish populations and their habitats against climate change is emerging. Using terms such as "climate-proofing", "climate-ready", and "climate refugia", such efforts stake a claim for an adaptive, anticipatory planning response to the climate change threat. To be effective, such approaches will need to address critical uncertainties in both the physical basis for projected landscape changes in water temperature and streamflow, as well as the biological responses of organisms. Recent efforts define future potential climate refugia based on projected streamflows, air temperatures, and associated water temperature changes. These efforts reflect the relatively strong conceptual foundation for linkages between regional climate change and local hydrological responses and thermal dynamics. Yet important questions remain. Drawing on case studies throughout the Pacific Northwest, we illustrate some key uncertainties in the responses of salmonids and their habitats to altered hydro-climatic regimes currently not well addressed by physical or ecological models. Key uncertainties include biotic interactions, organismal adaptive capacity, local climate decoupling due to groundwater-surface water interactions, the influence of human engineering responses, and synergies between climatic and other stressors. These uncertainties need not delay anticipatory planning, but rather highlight the need for identification and communication of actions with high probabilities of success, and targeted

  3. Umatilla River Fish Passage Operations Program, 2003-2004 Annual Report.

    SciTech Connect

    Bronson, James P.; Duke, Bill B.

    2005-08-01

    Threemile Falls Dam (Threemile Dam), located near the town of Umatilla, is the major collection and counting point for adult salmonids returning to the Umatilla River. Returning salmon and steelhead were enumerated at Threemile Dam from August 19, 2003 to July 8, 2004. A total of 3,388 summer steelhead (Oncorhynchus mykiss); 1,482 adult, 638 jack, and 2,150 subjack fall chinook (O. tshawytscha); 8,319 adult and 667 jack coho (O. kisutch); and 2,965 adult and 270 jack spring chinook (O. tshawytscha) were counted. All fish were enumerated at the east bank facility. Of the fish counted, 34 summer steelhead and 31 adult and 9 jack spring chinook were hauled upstream from Threemile Dam. There were 3,166 summer steelhead; 1,076 adult, 554 jack and 2,026 subjack fall chinook; 8,213 adult and 647 jack coho; and 2,152 adult and 174 jack spring chinook either released at, or allowed to volitionally migrate past, Threemile Dam. Also, 121 summer steelhead; 388 adult and 19 jack fall chinook; and 561 adult and 29 jack spring chinook were collected for brood. In addition, 239 spring chinook were collected for the outplanting efforts in the Walla Walla Basin. There were also 25 pair hatchery steelhead adults collected for the progeny maker study. The Westland Canal juvenile facility (Westland), located near the town of Echo at rivermile (RM) 27, is the major collection point for outmigrating juvenile salmonids and steelhead kelts. The canal was open for 184 days between January 12 and July 6, 2004. During that period, fish were bypassed back to the river 173 days and were trapped 10 days. An estimated 44 pounds of juvenile fish were transported from Westland to the Umatilla River boat ramp (RM 0.5). Approximately 84% of the juveniles transported were salmonids. No steelhead kelts were hauled from Westland this year. The Threemile Dam west bank juvenile bypass was opened on February 10, 2004 for outmigration sampling and continued until July 7, 2004 when sampling was discontinued

  4. Commercial Fishing.

    ERIC Educational Resources Information Center

    Florida State Dept. of Education, Tallahassee. Div. of Vocational Education.

    This document is a curriculum framework for a program in commercial fishing to be taught in Florida secondary and postsecondary institutions. This outline covers the major concepts/content of the program, which is designed to prepare students for employment in occupations with titles such as net fishers, pot fishers, line fishers, shrimp boat…

  5. Gone Fishing.

    ERIC Educational Resources Information Center

    Olson-Demme, Hillary; Kisiel, Jim

    2003-01-01

    Presents a hands-on activity in which students create a model of an ocean ecosystem to gain an understanding of how humans can alter biodiversity through their actions. Uses differing levels of fishing technology to explore the concepts of sustainability and overfishing. (Author/SOE)

  6. Froude Number is the Single Most Important Hydraulic Parameter for Salmonid Spawning Habitat.

    NASA Astrophysics Data System (ADS)

    Gillies, E.; Moir, H. J.

    2015-12-01

    Many gravel-bed rivers exhibit historic straightening or embanking, reducing river complexity and the available habitat for key species such as salmon. A defensible method for predicting salmonid spawning habitat is an important tool for anyone engaged in assessing a river restoration. Most empirical methods to predict spawning habitat use lookup tables of depth, velocity and substrate. However, natural site selection is different: salmon must pick a location where they can successfully build a redd, and where eggs have a sufficient survival rate. Also, using dimensional variables, such as depth and velocity, is problematic: spawning occurs in rivers of differing size, depth and velocity range. Non-dimensional variables have proven useful in other branches of fluid dynamics, and instream habitat is no different. Empirical river data has a high correlation between observed salmon redds and Froude number, without insight into why. Here we present a physics based model of spawning and bedform evolution, which shows that Froude number is indeed a rational choice for characterizing the bedform, substrate, and flow necessary for spawning. It is familiar for Froude to characterize surface waves, but Froude also characterizes longitudinal bedform in a mobile bed river. We postulate that these bedforms and their hydraulics perform two roles in salmonid spawning: allowing transport of clasts during redd building, and oxygenating eggs. We present an example of this Froude number and substrate based habitat characterization on a Scottish river for which we have detailed topography at several stages during river restoration and subsequent evolution of natural processes. We show changes to the channel Froude regime as a result of natural process and validate habitat predictions against redds observed during 2014 and 2015 spawning seasons, also relating this data to the Froude regime in other, nearby, rivers. We discuss the use of the Froude spectrum in providing an indicator of

  7. Risk factors for outbreaks of infectious pancreatic necrosis (IPN) and associated mortality in Norwegian salmonid farming.

    PubMed

    Bang Jensen, Britt; Kristoffersen, Anja B

    2015-06-01

    Infectious pancreatic necrosis (IPN) has for many years been considered one of the most important restraints to the production of salmonids in European aquaculture. In Norway, the disease is responsible for high losses in post-smolts in the first few weeks after sea transfer. Despite the importance of IPN, there are few epidemiological studies on risk factors and mitigation strategies. In this paper, we present analyses of data from all cohorts put to sea in 2009 to 2012 on Norwegian marine salmonid farms. The data used were obtained from national registers on salmonid production and disease outbreaks. The results showed that the risk of IPN outbreak was higher for spring versus autumn cohorts, Atlantic salmon versus rainbow trout and for cohorts on farms with previous history of IPN. The risk increased with increasing cohort size and infection pressure, whereas increasing temperature and weight at sea transfer decreased the risk. Estimations from a model of cumulative mortality within the first 6 mo after sea transfer showed that mortality in cohorts with IPN increased to approximately 7.2% as compared to a 'baseline' cohort with a mortality of 3.4%. If the cohort had both IPN and pancreas disease (PD), the estimated mortality increased to 12.9%, and cohorts with both IPN, PD and heart and skeletal muscle inflammation (HSMI) had an estimated mortality of 16.6%, when all other significant factors were kept constant (these were cohort type, year, temperature at sea transfer and weight at sea transfer). Our results provide valuable inputs for mitigation strategies and for economic modelling of consequences of disease. PMID:26036825

  8. Flavobacterium psychrophilum Infections in Salmonid Broodstock and Hatchery-Propagated Stocks of the Great Lakes Basin.

    PubMed

    Van Vliet, Danielle; Loch, Thomas P; Faisal, Mohamed

    2015-12-01

    Bacterial coldwater disease (BCWD), caused by Flavobacterium psychrophilum, threatens wild and propagated salmonids worldwide and leads to substantial economic losses. In addition to being horizontally transmitted, F. psychrophilum can be passed from infected parents to their progeny, furthering the negative impacts of this pathogen. In Michigan, both feral and captive salmonid broodstocks are the gamete sources used in fishery propagation efforts. A 5-year study was initiated to follow the prevalence of systemic F. psychrophilum infections in feral broodstocks of four species (steelhead Oncorhynchus mykiss [potadromous Rainbow Trout]; Coho Salmon O. kisutch; Chinook Salmon O. tshawytscha; and Atlantic Salmon Salmo salar) residing in three Great Lakes watersheds. Additionally, captive broodstocks of four species (Rainbow Trout, Brown Trout Salmo trutta, Lake Trout Salvelinus namaycush, and Brook Trout Salvelinus fontinalis) maintained at two facilities were assessed for the presence of F. psychrophilum. The resultant offspring from each broodstock population were sampled for F. psychrophilum infections multiple times throughout hatchery residency. Using selective flavobacterial culture and PCR confirmation, F. psychrophilum was detected in all broodstocks except the captive Lake Trout and Brook Trout. Logistic regression analysis demonstrated that among the infected feral broodstocks, Chinook Salmon from the Lake Michigan watershed had the highest prevalence of systemic F. psychrophilum infection (mean = 63.2%). Among the captive broodstocks, the Gilchrist Creek strain of Brown Trout had the highest infection prevalence (mean = 5%). Collectively, the captive broodstocks were found to have significantly lower infection prevalence than the feral broodstocks. Despite the high prevalence of systemic F. psychrophilum infections in many broodstock populations, the bacterium was rarely detected in their progeny during hatchery rearing. However, heavy losses associated

  9. A Study to Determine the Biological Feasability of a New Fish Tagging System : Annual Report, 1986-1987.

    SciTech Connect

    Prentice, Earl F.; Flagg, T.A.

    1987-12-01

    In 1983, a multi-year project to evaluate the technical and biological feasibility of adapting a new identification system to salmonids was established. The system is based upon a miniaturized passive integrated transponder (PIT) tag. This report discusses the work completed and is divided into laboratory studies, field studies, and systems development. All studies were conducted using a glass-encapsulated tag implanted into the body cavity of test fish via a 12-gauge hypodermic needle. Laboratory studies with juvenile chinook salmon, Oncorhynchus tshawytscha, showed that retention of glass-encapsulated PIT tags was 99-100% in fish weighing 3 g (mean weight) or larger. No adverse tissue response to the tag was noted. The survival of fish 5 g (mean weight) or larger was usually greater than 99%. However, fish ranging in weight from 2 to 4 g, or fish undergoing a physiological change such as smoltification may have a low mortality (usually less than 5.0%) after tagging. The mortality rate in the smaller fish was dependent upon tagging skill whereas mortality in smolting fish seemed dependent upon the level of stress. Growth comparisons between tagged and control fish indicated PIT-tagged fish had a slightly depressed growth rate at some measurement periods. The operational life of glass-encapsulated PIT tags implanted in fish was good, with 100% of the tags operating after 401 days. No tags were rejected from the fish during the observation period.

  10. Mathematical modeling in biological populations through branching processes. Application to salmonid populations.

    PubMed

    Molina, Manuel; Mota, Manuel; Ramos, Alfonso

    2015-01-01

    This work deals with mathematical modeling through branching processes. We consider sexually reproducing animal populations where, in each generation, the number of progenitor couples is determined in a non-predictable environment. By using a class of two-sex branching processes, we describe their demographic dynamics and provide several probabilistic and inferential contributions. They include results about the extinction of the population and the estimation of the offspring distribution and its main moments. We also present an application to salmonid populations. PMID:24526259

  11. Analysis of Historic Data for Juvenile and Adult Salmonid Production. Phase 1, Final Report.

    SciTech Connect

    Hilborn, Ray; Pascual, Miguel; Donnelly, Robert; Coronado-Hernadez, Claribel

    1993-11-01

    Survival of hatchery reared Columbia River chinook (Oncorhynchus tshawytscha) salmon from release to return is highly variable and thought to be related to river flow during juvenile outmigration in the spring. The purpose of this project is to examine the relationship between survival of coded-wire-tagged (CWT) Columbia River salmonids and in-river flow and other freshwater factors. This report covers Phase 1, in which two methods to estimate survival were developed and evaluated, and criteria for data selection were established.

  12. Epizootiology of Myxobolus cerebralis, the causative agent of salmonid whirling disease in the Rock Creek drainage of west-central Montana: 2004-2008.

    PubMed

    Granath, Willard O; Vincent, E Richard

    2010-04-01

    Whirling disease, caused by the myxozoan parasite Myxobolus cerebralis , remains a serious health threat to salmonid fish in the western United States. A previously published study on the epizootiology of whirling disease in the Rock Creek watershed of west-central Montana, conducted from 1998 to 2003, showed that the intensity of M. cerebralis infections in sentinel trout increased significantly throughout the drainage and that the range of M. cerebralis had expanded considerably. In addition, the parasite had apparently caused a dramatic decline in rainbow trout densities, but the brown trout population numbers had increased. This earlier study was continued from 2004 to 2008 and the results are reported here. It now appears that the disease intensity may have peaked in 2006 and is on the decline in this watershed. The decline cannot be directly attributed to a change in the prevalence of M. cerebralis-infected Tubifex tubifex, as these numbers remained statistically the same from 1998 to 2008. Similarly, changes in water temperature and water flow do not account for the decrease in disease intensity. However, it is possible that wild rainbow trout are developing resistance to the parasite, a phenomenon recently documented to be occurring in the Willow Creek Reservoir of southwest Montana. PMID:19891515

  13. Unique arylalkylamine N-acetyltransferase-2 polymorphism in salmonids and profound variations in thermal stability and catalytic efficiency conferred by two residues.

    PubMed

    Cazaméa-Catalan, D; Magnanou, E; Helland, R; Besseau, L; Boeuf, G; Falcón, J; Jørgensen, E H

    2013-05-15

    Melatonin contributes to synchronizing major biological and behavioral functions with cyclic changes in the environment. Arylalkylamine N-acetyltransferase (AANAT) is responsible for a daily rhythm in melatonin secretion. Teleost possess two enzyme forms, AANAT1 and AANAT2, preferentially expressed in the retina and the pineal gland, respectively. The concomitant action of light and temperature shapes the daily and seasonal changes in melatonin secretion: the former controls duration while the latter modulates amplitude. Investigating the respective roles of light and temperature is particularly relevant in the context of global warming, which is likely to affect the way fish decode and anticipate seasonal changes, with dramatic consequences on their physiology and behavior. Here we investigated the impact of temperature on pineal melatonin secretion of a migratory species, the Arctic charr (Salvelinus alpinus), the northernmost living and cold-adapted salmonid. We show that temperature directly impacts melatonin production in cultured pineal glands. We also show that one organ expresses two AANAT2 transcripts displaying high similarity between them and with trout Oncorhynchus mykiss AANAT2, differing by only two amino acid sites. We compared the kinetics and 3D models of these enzymes as well as of a chimeric construct, particularly with regard to their response to temperature. Our study brings interesting and new information on the evolutionary diversity of AANAT enzymes in teleosts and the role played by specific residues in the catalytic properties of the enzymes. PMID:23393284

  14. A sensitive loop-mediated isothermal amplification (LAMP) method for detection of Renibacterium salmoninarum, causative agent of bacterial kidney disease in salmonids.

    PubMed

    Gahlawat, S K; Ellis, A E; Collet, B

    2009-06-01

    Loop-mediated isothermal amplification (LAMP) is a novel technique for nucleic acid amplification with high specificity, sensitivity and rapidity and does not require expensive equipment or reagents. In the present study, we developed and evaluated a LAMP method for the rapid detection of Renibacterium salmoninarum causing the bacterial kidney disease in salmonids. This method was more sensitive than quantitative real-time polymerase chain reaction (qPCR). Using DNA template extracted from cultured R. salmoninarum, the LAMP method gave an amplification signal from template diluted to 10(-8) while the limit of detection of qPCR was10(-7). The LAMP method was also highly specific and did not amplify DNA purified from five other Gram-positive and -negative bacterial fish pathogens. The method also worked well using extracts of macrophages infected with R. salmoninarum and kidney material from rainbow trout, which were positive for R. salmoninarum by qPCR and crude R. salmoninarum culture. There was some evidence for inhibitors of the LAMP reaction in the kidney samples, which was overcome by diluting the sample. PMID:19538642

  15. Fish assemblages and environmental variables associated with hard-rock mining in the Coeur d'Alene River basin, Idaho

    USGS Publications Warehouse

    Maret, Terry R.; MacCoy, Dorene E.

    2002-01-01

    As part of the U.S. Geological Survey's National Water Quality Assessment Program, fish assemblages, environmental variables, and associated mine densities were evaluated at 18 test and reference sites during the summer of 2000 in the Coeur d'Alene and St. Regis river basins in Idaho and Montana. Multimetric and multivariate analyses were used to examine patterns in fish assemblages and the associated environmental variables representing a gradient of mining intensity. The concentrations of cadmium (Cd), lead (Pb), and zinc (Zn) in water and streambed sediment found at test sites in watersheds where production mine densities were at least 0.2 mines/km2 (in a 500-m stream buffer) were significantly higher than the concentrations found at reference sites. Many of these metal concentrations exceeded Ambient Water Quality Criteria (AWQC) and the Canadian Probable Effect Level guidelines for streambed sediment. Regression analysis identified significant relationships between the production mine densities and the sum of Cd, Pb, and Zn concentrations in water and streambed sediment (r2 = 0.69 and 0.66, respectively; P < 0.01). Zinc was identified as the primary metal contaminant in both water and streambed sediment. Eighteen fish species in the families Salmonidae, Cottidae, Cyprinidae, Catostomidae, Centrarchidae, and Ictaluridae were collected. Principal components analysis of 11 fish metrics identified two distinct groups of sites corresponding to the reference and test sites, predominantly on the basis of the inverse relationship between percent cottids and percent salmonids (r = -0.64; P < 0.05). Streams located downstream from the areas of intensive hard-rock mining in the Coeur d'Alene River basin contained fewer native fish and lower abundances as a result of metal enrichment, not physical habitat degradation. Typically, salmonids were the predominant species at test sites where Zn concentrations exceeded the acute AWQC. Cottids were absent at these sites, which

  16. A Markov chain analysis of the movements of juvenile salmonids, including sockeye salmon, in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the valuable information collected at McNary Dam was in the form of three-dimensional (hereafter referred to as 3-D) tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and testing of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting 3-D results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we used a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis allowed us to numerically summarize the behavior of fish in the forebay. This report is the second report published in 2012 that uses this analytical method. The first report included only fish released as part of the annual studies conducted at McNary Dam. This second report includes sockeye salmon that were released as part of studies conducted by the Chelan and Grant County Public Utility Districts at mid-Columbia River dams. The studies conducted in the mid-Columbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width was different between studies. Additionally, no passive integrated transponder tags were implanted in sockeye salmon. Differences in transmitter pulse width resulted in lower detection probabilities for sockeye salmon at McNary Dam. The absence of passive integrated transponder tags prevented us from determining if fish passed the powerhouse through the juvenile bypass system (JBS) or turbines. To

  17. Development of a Natural Rearing System to Improve Supplemental Fish Quality, 1999-2003 Progress Report.

    SciTech Connect

    Maynard, Desmond J.

    2003-02-25

    The National Marine Fisheries Service (NMFS) has been conducting Natural Rearing Enhancement System (NATURES) research since the early 1990s. NATURES studies have looked at a variety of mechanisms to enhance production of wild-like salmonids from hatcheries. The goal of NATURES research is to develop fish culture techniques that enable hatcheries to produce salmon with more wild-like characteristics and increased postrelease survival. The development of such techniques is called for in the Columbia Basin Fish and Wildlife Program. This document is the draft report for the Supplemental Fish Quality Contract DE-AI79-91BP20651 Over the history of the project, the effects of seminatural raceway habitats, automated underwater feeders, exercise current velocities, live food diets, and predator avoidance training have been investigated. The findings of these studies are reported in an earlier contract report (Maynard et al. 1996a). The current report focuses on research that has been conducted between 1999 and 2002. This includes studies on the effect of exercise on salmon and steelhead trout, effects of predator avoid training, integration of NATUES protocols into production hatcheries, and the study of social behavior of steelhead grown in enriched and conventional environments. Traditionally, salmon (Oncorhynchus spp.) are reared in barren concrete raceways that lack natural substrate, in-stream structure, or overhead cover. The fish are fed in an unnatural manner with artificial feeds mechanically or hand broadcast across the water surface. This traditional approach has increased the egg-to-smolt survival of hatchery-reared fish by an order of magnitude over that experienced by wild-reared salmon. However, once hatchery-reared fish are released into the wild their smolt-to-adult survival is usually much lower than wild-reared salmon. The reduced postrelease survival of hatchery-reared fish may stem from differences in their behavior and morphology compared to wild

  18. Evidence for competitive dominance of Pink salmon (Oncorhynchus gorbuscha) over other Salmonids in the North Pacific Ocean

    USGS Publications Warehouse

    Ruggerone, G.T.; Nielsen, J.L.

    2004-01-01

    Relatively little is known about fish species interactions in offshore areas of the world's oceans because adequate experimental controls are typically unavailable in such vast areas. However, pink salmon (Oncorhynchus gorbuscha) are numerous and have an alternating-year pattern of abundance that provides a natural experimental control to test for interspecific competition in the North Pacific Ocean and Bering Sea. Since a number of studies have recently examined pink salmon interactions with other salmon, we reviewed them in an effort to describe patterns of interaction over broad regions of the ocean. Research consistently indicated that pink salmon significantly altered prey abundance of other salmon species (e.g., zooplankton, squid), leading to altered diet, reduced total prey consumption and growth, delayed maturation, and reduced survival, depending on species and locale. Reduced survival was observed in chum salmon (O. keta) and Chinook salmon (O. tshawytscha) originating from Puget Sound and in Bristol Bay sockeye salmon (O. nerka). Growth of pink salmon was not measurably affected by other salmon species, but their growth was sometimes inversely related to their own abundance. In all marine studies, pink salmon affected other species through exploitation of prey resources rather than interference. Interspecific competition was observed in nearshore and offshore waters of the North Pacific Ocean and Bering Sea, and one study documented competition between species originating from different continents. Climate change had variable effects on competition. In the North Pacific Ocean, competition was observed before and after the ocean regime shift in 1977 that significantly altered abundances of many marine species, whereas a study in the Pacific Northwest reported a shift from predation- to competition-based mortality in response to the 1982/1983 El Nino. Key traits of pink salmon that influenced competition with other salmonids included great abundance, high

  19. Characterization of manures from fish cage farming in Chile.

    PubMed

    Salazar, F J; Saldana, R C

    2007-12-01

    This study aims to characterize salmonid manures and to determine their potential use in agricultural soils. Sampling was carried out below salmon and trout cages in farms located in lakes and in the sea in the South of Chile during 2002-2003. Manure was analyzed for macronutrients, micronutrients and heavy metals. Results showed a high variability between samples and differences between sea and lake manure. Dry matter contents were low averaging c. 12-15%. Manures showed low OM contents with values Salmonid manure had low nutrients and heavy metal contents and a potential use in agricultural soils, which could reduce the risks of water pollution on water from fish farming. PMID:16962324

  20. Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2001-2002 Annual Report.

    SciTech Connect

    Zabel, Richard; Williams, John G.; Smith, Steven G.

    2002-06-01

    In 2001, the National Marine Fisheries Service and the University of Washington completed the ninth year of a study to estimate survival and travel time of juvenile salmonids (Oncorhynchus spp.) passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from passive integrated transponder (PIT)-tagged fish. We PIT tagged and released at Lower Granite Dam a total of 17,028 hatchery and 3,550 wild steelhead. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream of the hydropower system and sites within the hydropower system. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using the Single-Release Model. Primary research objectives in 2001 were to: (1) estimate reach and project survival and travel time in the Snake and Columbia Rivers throughout the yearling chinook salmon and steelhead migrations; (2) evaluate relationships between survival estimates and migration conditions; and (3) evaluate the survival-estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2001 for PIT-tagged yearling chinook salmon and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Results are reported primarily in the form of tables and figures with a minimum of text. More details on methodology and statistical models used are provided in previous reports cited in the text. Results for summer-migrating chinook salmon will be reported separately.

  1. Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2005-2006 Annual Report.

    SciTech Connect

    Smith, Steven G.; Muir, William D.; Marsh, Douglas M.

    2006-05-01

    In 2005, the National Marine Fisheries Service and the University of Washington completed the thirteenth year of a study to estimate survival and travel time of juvenile salmonids Oncorhynchus spp. passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder tags (PIT tags). We PIT tagged and released a total of 18,439 hatchery steelhead, 5,315 wild steelhead, and 6,964 wild yearling Chinook salmon at Lower Granite Dam in the Snake River. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and at sites within the hydropower system in both the Snake and Columbia Rivers. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, Ice Harbor, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the ''single-release model''). Primary research objectives in 2005 were: (1) Estimate reach survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling Chinook salmon O. tshawytscha and steelhead O. mykiss. (2) Evaluate relationships between survival estimates and migration conditions. (3) Evaluate the survival estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2005 for PIT-tagged yearling Chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Additional details on the methodology and statistical models used are provided in previous reports cited here.

  2. Survival Estimates for the Passage of Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2002-2003 Annual Report.

    SciTech Connect

    Muir, William D.; Smith, Steven G.; Zabel, Richard W.

    2003-07-01

    In 2002, the National Marine Fisheries Service and the University of Washington completed the tenth year of a study to estimate survival and travel time of juvenile salmonids (Oncorhynchus spp.) passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder tags (PIT tags). We PIT tagged and released a total of 19,891 hatchery steelhead at Lower Granite Dam. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and sites within the hydropower system. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the ''Single-Release Model''). Primary research objectives in 2002 were to (1) estimate reach and project survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling chinook salmon O. tshawytscha and steelhead O. mykiss; (2) evaluate relationships between survival estimates and migration conditions; and (3) evaluate the survival-estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2002 for PIT-tagged yearling chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Results are reported primarily in the form of tables and figures; details on methodology and statistical models used are provided in previous reports cited here. Results for summer-migrating chinook salmon will be reported separately.

  3. Characterization of Fish Passage Conditions through a Francis Turbine, Spillway, and Regulating Outlet at Detroit Dam, Oregon, Using Sensor Fish, 2009

    SciTech Connect

    Duncan, Joanne P.; Carlson, Thomas J.

    2011-05-06

    Fish passage conditions through two spillways, a Francis turbine, and a regulating outlet (RO) at Detroit Dam on the North Santiam River in Oregon were evaluated by Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers (USACE), Portland District, using Sensor Fish devices. The objective of the study was to describe and compare passage exposure conditions, identifying potential fish injury regions within the routes. The study was performed in July, October, and December 2009 concurrent with HI-Z balloon-tag studies by Normandeau Associates, Inc. Sensor Fish data were analyzed to estimate 1) exposure conditions, particularly exposure to severe strike, collision, and shear events by passage route sub-regions; 2) differences in passage conditions between passage routes; and 3) relationships to live-fish injury and mortality data estimates. Comparison of the three passage routes evaluated at Detroit Dam indicates that the RO passage route through the 5-ft gate opening was relatively the safest route for fish passage under the operating conditions tested; turbine passage was the most deleterious. These observations were supported also by the survival and malady estimates obtained from live-fish testing. Injury rates were highest for turbine and spillway passage. However, none of the passage routes tested is safe for juvenile salmonid passage.

  4. Characterization of Fish Passage Conditions through a Francis Turbine and Regulating Outlet at Cougar Dam, Oregon, Using Sensor Fish, 2009–2010

    SciTech Connect

    Duncan, Joanne P.

    2011-05-23

    Fish passage conditions through a Francis turbine and a regulating outlet (RO) at Cougar Dam on the south fork of the McKenzie River in Oregon were evaluated by Pacific Northwest National Laboratory for the U.S. Army Corps of Engineers, Portland District, using Sensor Fish devices. The objective of the study was to describe and compare passage exposure conditions, identifying potential fish injury regions encountered during passage via specific routes. The RO investigation was performed in December 2009 and the turbine evaluation in January 2010, concurrent with HI-Z balloon-tag studies by Normandeau Associates, Inc. Sensor Fish data were analyzed to estimate 1) exposure conditions, particularly exposure to severe collision, strike, and shear events by passage route sub-regions; 2) differences in passage conditions between passage routes; and 3) relationships to live-fish injury and mortality data estimates. Comparison of the three passage routes evaluated at Cougar Dam indicates that the RO passage route through the 3.7-ft gate opening was relatively the safest route for fish passage under the operating conditions tested; turbine passage was the most deleterious. These observations were supported also by the survival and malady estimates obtained from live-fish testing. Injury rates were highest for turbine passage. Compared to mainstem Columbia River passage routes, none of the Cougar Dam passage routes as tested are safe for juvenile salmonid passage.

  5. Augmented Fish Health Monitoring in Oregon, 1987-1988 Annual Report.

    SciTech Connect

    Bauer, Jerry

    1988-05-01

    Diminished natural fish production in the Columbia River Basin has prompted increased artificial propagation to compensate both for losses of anadromous salmonids related to hydroelectric facilities and for other causes. The health and quality of artificially propagated smolts probably is a major influence on survival. Smolt survival varies greatly from one location to another, among different species and from one year to the next. Fish health monitoring is necessary to identify cause of mortality, assist in producing a healthy smolt, and provide a means for improving hatchery effectiveness. The Bonneville Power Administration (BPA) conducted a series of meetings to define the minimum ''needed'' level of fish health monitoring, determine what was presently being done and what additional effort was needed in the Basin's 54 anadromous fish hatcheries. Funding for the additional effort in Oregon began June 2, 1987. The goal of this project is to increase smolt-to-adult survival by accomplishing the following: (1) increase monitoring for specific fish pathogens and fish health parameters; (2) measure hatchery water supply quality; (3) identify facility impediments to fish health; (4) create a database of hatchery and fish health information; (5) establish a technical steering committee to evaluate and refine the project annually; and (6) increase communication and technology application among personnel in hatcheries, research, management, other agencies and the public. 4 refs., 3 figs., 10 tabs.

  6. Relationship of otolith strontium-to-calcium ratios and salinity: Experimental validation for juvenile salmonids

    USGS Publications Warehouse

    Zimmerman, C.E.

    2005-01-01

    Analysis of otolith strontium (Sr) or strontium-to-calcium (Sr:Ca) ratios provides a powerful tool to reconstruct the chronology of migration among salinity environments for diadromous salmonids. Although use of this method has been validated by examination of known individuals and translocation experiments, it has never been validated under controlled experimental conditions. In this study, incorporation of otolith Sr was tested across a range of salinities and resulting levels of ambient Sr and Ca concentrations in juvenile chinook salmon (Oncorhynchus tshawytscha), coho salmon (Oncorhynchus kisutch), sockeye salmon (Oncorhynchus nerka), rainbow trout (Oncorhynchus rnykiss), and Arctic char (Salvelinus alpinus). Experimental water was mixed, using stream water and seawater as end members, to create experimental salinities of 0.1, 6.3, 12.7, 18.6, 25.5, and 33.0 psu. Otolith Sr and Sr:Ca ratios were significantly related to salinity for all species (r2 range: 0.80-0.91) but provide only enough predictive resolution to discriminate among fresh water, brackish water, and saltwater residency. These results validate the use of otolith Sr:Ca ratios to broadly discriminate salinity histories encountered by salmonids but highlight the need for further research concerning the influence of osmoregulation and physiological changes associated with smoking on otolith microchemistry.

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

    USGS Publications Warehouse

    Dibble, Kimberly L.; Yackulic, Charles B.; Kennedy, Theodore A.; Budy, Phaedra E.

    2015-01-01

    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.

  8. Genetic improvement of disease resistance in salmonid fish using selective breeding: Overview of concepts, considerations and limitations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In aquaculture, endemic infectious diseases constitute a considerable economic burden due to direct losses as well as indirect impacts on growth and animal welfare. In response to infectious disease, it is well documented that host genetic variation is present in most animal populations, especially ...

  9. The introduction of nonnative fish into wilderness lakes: good intentions, conflicting mandates, and unintended consequences