Ocean distribution and habitat associations of yearling coho (Oncorhynchus kisutch) and Chinook (O. tshawytscha) salmon in the northern California Current

Yearling juvenile coho and Chinook salmon were sampled on 28 cruises in June and September 1981–85 and 1998–07 in continental shelf and oceanic waters off the Pacific Northwest. Oceanographic variables measured included temperature, salinity, water depth, and chlorophyll concentration (all cruises) and copepod biomass during the cruises from 1998–07. Juvenile salmonids were found almost exclusively in continental shelf waters, and showed a patchy distribution: half were collected in ～5% of the collections and none were collected in ～40% of the collections. Variance‐to‐mean ratios of the catches were high, also indicating patchy spatial distributions for both species. The salmon were most abundant in the vicinity of the Columbia River and the Washington coast in June; by September, both were less abundant, although still found mainly off Washington. In June, the geographic center‐of‐mass of the distribution for each species was located off Grays Harbor, WA, near the northern end of our sampling grid, but in September, it shifted southward and inshore. Coho salmon ranged further offshore than Chinook salmon: in June, the average median depth where they were caught was 85.6 and 55.0 m, respectively, and in September it was 65.5 and 43.7 m, respectively. Abundances of both species were significantly correlated with water depth (negatively), chlorophyll (positively) and copepod biomass (positively). Abundances of yearling Chinook salmon, but not of yearling coho salmon, were correlated with temperature (negatively). We discuss the potential role of coastal upwelling, submarine canyons and krill in determining the spatial distributions of the salmon.     

Life‐history differences of juvenile Chinook salmon Oncorhynchus tshawytscha across rearing locations in the Shasta River,California

Salmon from different locations in a watershed can have different life histories. It is often unclear to what extent this variation is a response to the current environmental conditions an individual experiences as opposed to local‐scale genetic adaptation or the environment experienced early in development. We used a mark–recapture transplant experiment in the Shasta River, CA, to test whether life‐history traits of juvenile Chinook salmon Oncorhynchus tshawytscha varied among locations, and whether individuals could adopt a new life history upon encountering new habitat type. The Shasta River, a Klamath River tributary, has two Chinook salmon spawning and juvenile rearing areas, a lower basin canyon (river km 0–12) and upper basin spring complex (river km 40–56), characterised by dramatically different in‐stream habitats. In 2012 and 2013, we created three experimental groups: (i) fish caught, tagged and released in the upper basin; (ii) fish caught at the river mouth (confluence with the Klamath River, river km 0), tagged and released in the upper basin; and (iii) fish caught at the river mouth, tagged and released in the lower basin. Fish released in the upper basin outmigrated later and at a larger size than those released in the lower basin. The traits of fish transplanted to the upper basin were similar to fish originating in the upper basin. Chinook salmon juvenile life‐history traits reflected habitat conditions fish experienced rather than those where they originated, indicating that habitat modification or transportation to new habitats can rapidly alter the life‐history composition of populations.     

Spatial distribution of ocean habitat of yearling Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon off Washington and Oregon,USA

We determined the habitat usage and habitat connectivity of juvenile Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon in continental shelf waters off Washington and Oregon, based on samples collected every June for 9 yr (1998–2006). Habitat usage and connectivity were evaluated using SeaWiFS satellite‐derived chlorophyll a data and water depth. Logistic regression models were developed for both species, and habitats were first classified using a threshold value estimated from a receiver operating characteristic curve. A Bernoulli random process using catch probabilities from observed data, i.e. the frequency of occurrence of a fish divided by the number of times a station was surveyed, was applied to reclassify stations. Zero‐catch probabilities of yearling Chinook and yearling coho salmon decreased with increases in chlorophyll a concentration, and with decreases in water depth. From 1998 to 2006, ～ 47% of stations surveyed were classified as unfavorable habitat for yearling Chinook salmon and ～ 53% for yearling coho salmon. Potentially favorable habitat varied among years and ranged from 9 856 to 15 120 km² (Chinook) and from 14 800 to 16 736 km² (coho). For both species, the smallest habitat area occurred in 1998, an El Niño year. Favorable habitats for yearling Chinook salmon were more isolated in 1998 and 2005 than in other years. Both species had larger and more continuous favorable habitat areas along the Washington coast than along the Oregon coast. The favorable habitats were also larger and more continuous nearshore than offshore for both species. Further investigations on large‐scale transport, mesoscale physical features, and prey and predator availability in the study area are necessary to explain the spatial arrangement of juvenile salmon habitats in continental shelf waters.     

The external phenotype–skeleton link in post‐hatch farmed Chinook salmon (Oncorhynchus tshawytscha)

Skeletal deformities in farmed fish are a recurrent problem. External malformations are easily recognized, but there is little information on how external malformations relate to malformations of the axial skeleton: the external phenotype–skeleton link. Here, this link is studied in post‐hatch to first‐feed life stages of Chinook salmon (Oncorhynchus tshawytscha) raised at 4, 8 and 12°C. Specimens were whole‐mount‐stained for cartilage and bone, and analysed by histology. In all temperature groups, externally normal specimens can have internal malformations, predominantly fused vertebral centra. Conversely, externally malformed fish usually display internal malformations. Externally curled animals typically have malformed haemal and neural arches. External malformations affecting a single region (tail malformation and bent neck) relate to malformed notochords and early fusion of fused vertebral centra. The frequencies of internal malformations in both externally normal and malformed specimens show a U‐shaped response, with lowest frequency in 8°C specimens. The fused vertebral centra that occur in externally normal specimens represent a malformation that can be contained and could be carried through into harvest size animals. This study highlights the relationship between external phenotype and axial skeleton and may help to set the framework for the early identification of skeletal malformations on fish farms.     

Landscape‐level constraints on recruitment of chinook salmon (Oncorhynchus tshawytscha) in the Columbia River basin,USA

• 1. The decline of salmonid populations in the Pacific Northwest has been well‐documented. It is unclear, however, which threats to salmonid persistence are the most serious, and how best to prioritize recovery efforts intended to ameliorate these threats.
• 2. It has been argued previously that one possible cause of salmon endangerment is degradation of spawning grounds. In order to explore this hypothesis, this study examines the relationships between chinook salmon (Oncorhynchus tshawytscha) productivity and landscape‐level characteristics of spawning grounds in the interior Columbia River Basin.
• 3. Population productivity is expressed as the mean and maximum recruitment rates for different stocks, measured from 1980 to 1990; habitat conditions are calculated using sub‐watershed scale data on land cover, land use, water quality and watershed hydrology.
• 4. Significant linear regression results were obtained for three environmental variables: percentage of land classified as urban, proportion of stream length failing to meet water quality standards, and an index of the ability of streams to recover from sediment flow events. A multiple regression with all three variables accounts for over 60% of the variation in mean salmon recruitment.
• 5. It further appears that these landscape attributes may limit the maximum recruitment rates of salmon, with a magnitude of difference in productivity large enough to be relevant to recovery planners. Additional study will be necessary to identify cause‐and‐effect linkages between habitat quality and salmon recruitment success, and to determine the ultimate impact of changes in recruitment rates on short‐ and long‐term salmon population trajectories.

Copyright © 2002 John Wiley & Sons, Ltd.     

In vivo growth and genomic characterization of rickettsia‐like organisms isolated from farmed Chinook salmon (Oncorhynchus tshawytscha) in New Zealand

A rickettsia‐like organism, designated NZ‐RLO2, was isolated from Chinook salmon (Oncorhynchus tshawytscha) farmed in the South Island, New Zealand. In vivo growth showed NZ‐RLO2 was able to grow in CHSE‐214, EPC, BHK‐21, C6/36 and Sf21 cell lines, while Piscirickettsia salmonis LF‐89^T grew in all but BHK‐21 and Sf21. NZ‐RLO2 grew optimally in EPC at 15°C, CHSE‐214 and EPC at 18°C. The growth of LF‐89 ^T was optimal at 15°C, 18°C and 22°C in CHSE‐24, but appeared less efficient in EPC cells at all temperatures. Pan‐genome comparison of predicted proteomes shows that available Chilean strains of P. salmonis grouped into two clusters (p‐value = 94%). NZ‐RLO2 was genetically different from previously described NZ‐RLO1, and both strains grouped separately from the Chilean strains in one of the two clusters (p‐value = 88%), but were closely related to each other. TaqMan and Sybr Green real‐time PCR targeting RNA polymerase (rpoB) and DNA primase (dnaG), respectively, were developed to detect NZ‐RLO2. This study indicates that the New Zealand strains showed a closer genetic relationship to one of the Chilean P. salmonis clusters; however, more Piscirickettsia genomes from wider geographical regions and diverse hosts are needed to better understand the classification within this genus.     

New Zealand rickettsia‐like organism (NZ‐RLO) and Tenacibaculum maritimum: Distribution and phylogeny in farmed Chinook salmon (Oncorhynchus tshawytscha)

A total of 777 fish from three growing regions of New Zealand Chinook salmon farms comprising of five sites were tested. Quantitative PCR was used to determine the distribution of New Zealand rickettsia‐like organism and Tenacibaculum maritimum. Genetic information from these bacteria were then compared with strains reported worldwide. Using this information, suggested associations of pathogens with clinically affected fish were made. NZ‐RLO was detected in two of the three regions, and T. maritimum was detected in all regions. Three strains of NZ‐RLO were identified during this study. Based on analysis of the ITS rRNA gene, NZ‐RLO1 appears to be part of an Australasian grouping sharing high similarity with the Tasmanian RLO, NZ‐RLO2 was shown to be the same as an Irish strain, and NZ‐RLO3 was shown be closely related to two strains from Chile. Based on multi‐locus sequence typing, the New Zealand T. maritimum was the same as Australian strains. NZ‐RLOs were detected more frequently in fish with skin ulcers than fish without skin ulcers. While additional research is required to investigate the pathogenicity of these organisms, this is the first time that NZ‐RLOs have been associated with the development of clinical infections in farmed Chinook salmon.     

Pacific hake (Merluccius productus Ayres, 1855) hydrolysates as feed attractants for juvenile Chinook salmon (Oncorhynchus tshawytscha Walbaum, 1792)

Soybean meal (SBM) inclusion in salmonid diets can lower feed cost, but dramatically reduces growth and feed utilization, and increases mortality in juvenile chinook salmon Oncorhynchus tshawytscha, due to diminished diet palatability and/or other adverse physiological effects exerted by antinutritional factors in SBM. The objective of this study was to investigate whether commercial Antarctic krill meal Euphausia superba or hydrolysates enzymatically produced from Pacific hake Merluccius productus could reverse the negative palatability effects of SBM inclusion in juvenile chinook salmon diets. Diets without SBM or with SBM and no added feed attractant were used as positive and negative control diets respectively. Incorporation of 2% krill meal or Alcalase^®‐produced hydrolysates into SBM‐containing diets (20% of dry matter by isonitrogenous replacement of fishmeal) significantly (P < 0.05) increased feed intake, feed utilization, fish weight gain and thermal growth coefficient during a 5‐week trial. Nevertheless, the negative effects on fish performance incurred by dietary inclusion of 20% SBM could not be fully reversed, indicating that most of those effects were likely unrelated to palatability. This study demonstrates the potential for using Pacific hake hydrolysates as a dietary feed attractant for salmonid diets, and supports the need for further research to optimize its application for ideal fish performance.     

Freshwater habitat associations between pink (Oncorhynchus gorbuscha), chum (O. keta) and Chinook salmon (O. tshawytscha) in a watershed dominated by sockeye salmon (O. nerka) abundance

To understand the interplay between habitat use and contemporary anadromous Pacific salmon, Oncorhynchus spp., distributions we explored the habitat associations of three species, pink (O. gorbuscha), chum (O. keta) and Chinook salmon (O. tshawytscha) in streams of the Wood River system of Bristol Bay, Alaska, where sockeye salmon (O. nerka) are numerically dominant. We developed models to investigate the occurrence of nondominant salmon in relation to habitat characteristics and sockeye salmon density, using four decades of salmon presence and abundance data. The frequency of occurrence and abundance of nondominant species increased with watershed drainage area and stream depth and decreased with sockeye salmon density. The range of occurrence varied from nonexistent to perennial for the other species in sockeye‐dominated streams. Increasing watershed area resulted in larger stream habitat area and deeper habitats, allowing for the sympatric occurrence and persistence of all salmon species. The relationships between habitat and the presence of these Pacific salmon help define their requirements but also remind us that the patterns of presence and absence, within the overall ranges of salmon species, have yet to be fully understood.     

Seasonal growth and diet of juvenile chinook salmon (Oncorhynchus tshawytscha) in demonstration channels and the main channel of the Waitaki River, New Zealand, 1982–1983

Abstract– Juvenile chinook salmon in the Waitaki River, New Zealand and demonstration channels, living at about 16°C, increased in length by 0.32 mm day⁻¹ between 4 November and 4 March. They gained weight quickly, accumulated large visceral fat deposits and had high conditions factors. At 1600 h, stomachs averaged half full. The number of prey tended to decline as the fish grew and consumed larger items. Initially the diet was based mainly on chironomid larvae, but by December it included a diversity of prey in more equal proportions. These included Deleatidium in the Waitaki; amphipods in the demonstration channels; various trichopterans, hemipterans, elmid beetles, zooplankton. terrestrial dipterans and a variety of other prey. There were significant differences between sites in numbers of prey consumed and these probably reflected differences in the benthos. Diets in the Waitaki differ from those in the Rakaia River and the food of juvenile salmon appears closely linked to the availability of a diverse range of possible prey.     

Application of a Fourier transform—near infrared reflectance spectroscopy method for the rapid proximate analysis of the greenshell mussel (Perna canaliculus) and king (Chinook) salmon (Oncorhynchus tshawytscha)

Greenshell? mussel (GSM, Perna canaliculus) and king (Chinook) salmon (Oncorhynchus tshawytscha) are New Zealand's two major aquaculture species generating $380 million NZD in exports during the 2017–18 financial year. This study addresses the development and validation of a method based on Fourier transform—near infrared reflectance spectroscopy (FT‐NIRs) to determine proximate composition for both species to aid breeding‐, production‐ and consumer decisions. Rapid measurements of GSM (n = 176) were taken by FT‐NIRs and analysed by traditional wet chemistry ‘reference methods’ to develop calibration models for proximate composition (protein, moisture, fat, ash and carbohydrate). The predictive models for moisture (r² = 0.98, root mean square error of cross validation (RMSECV) = 0.314, residual prediction deviation (RPD = 6.47), protein (r² = 0.91, RMSECV = 0.295, RPD = 3.01)) and carbohydrate (r² = 0.87, RMSECV = 0.440, RPD = 2.78) in GSM performed well. Additional models based on 90 portions of salmon were developed to predict moisture (r² = 0.98, RMSECV = 1.02, RPD = 7), protein (r² = 0.96, RMSECV = 0.347, RPD = 5.08), fat (r² = 0.99, RMSECV = 1.09, RPD = 5.98) and ash (r² = 0.72, RMSECV = 0.05, RPD = 1.9). The predictive FT‐NIRs and reference methods were tested for short‐term and intermediate precision, which demonstrated that the repeatability of the predictive models was comparable to the reference methods. Proximate analysis of GSM and king salmon using FT‐NIRs was quick (minutes for sample preparation and analysis rather than days) and all components were assessed simultaneously. This provides a low‐cost short turn‐around method suitable for industry and research applications.