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.     

Vertebral fusions in farmed Chinook salmon (Oncorhynchus tshawytscha) in New Zealand

Vertebral fusions are an established economic concern in farmed Atlantic salmon, but have not been studied in detail in farmed Chinook salmon. Two radiographic studies of vertebral fusions were performed in farmed Chinook salmon. Sixteen of 1,301 (1.2%) smolt and 201 of 2,636 (7.6%) harvest fish had fusions. There were no significant differences in the number of fused vertebrae/fusion in smolt compared with harvest fish. Secondly, tagged fish were repeatedly radiographed to determine the progression of the fusions. Nineteen (4.4%), 23 (5.3%) and 39 (9.0%) fish had fusions as smolt, after 129 days in sea water, and at harvest, respectively. There were no significant differences in the average number of vertebra/fusion between the three time points. Of the fusions that were observed in smolt, additional vertebra did not become fused in 81% of the lesions. Within the rare fusions that did progress due to the involvement of adjacent vertebra, an average of 1.6 vertebrae were added per year. Fish with fusions were significantly lighter than non‐affected fish at harvest. Fusions are common in farmed Chinook salmon; however, they are typically stable after development. As fish with fusions were lighter at harvest, reducing fusions may have an economic benefit.     

Climate effects on size‐at‐age and growth rate of Chinook Salmon (Oncorhynchus tshawytscha) in the Fraser River,Canada

Decline in size‐at‐age of Chinook Salmon (Oncorhynchus tshawytscha) has been observed for many populations across the entire Northeast Pacific Ocean, and identifying external drivers of this decline is important for sustainable management of these ecologically, economically, and culturally valuable resources. We assessed size‐at‐age of 96,939 Chinook Salmon sampled in the Fraser River watershed (Canada) from 1969 to 2017. A broad decline in size‐at‐age was confirmed across all population aggregates of Fraser River Chinook Salmon, in particular since year 2000. By developing a novel probability‐based approach to calculate age‐ and year‐specific growth rates for Fraser River Chinook Salmon and relating growth rates to environmental conditions in specific years through a machine learning method (boosted regression trees), we were able to disentangle multi‐year effects on size‐at‐age and thus identify environmental factors that were most related to the observed size‐at‐age of Chinook Salmon. Among 10 selected environmental variables, ocean salinity at Entrance Island in spring, the Aleutian Low Pressure Index and the North Pacific Current Bifurcation Index were consistently identified as important contributors for four of the seven age and population aggregate combinations. These top environmental contributors could be incorporated into future stock assessment and forecast models to improve Chinook Salmon fisheries management under climate change.     

Comparative evaluation of experimental challenge by intraperitoneal injection and cohabitation of Atlantic salmon (Salmo salar L) after vaccination against Piscirickettsia salmonis (EM90‐like)

The Chilean aquaculture has been challenged for years by piscirickettsiosis. A common prophylactic measurement to try to reduce the impact from this disease is vaccination, but the development of vaccines that induce satisfactory protection of the fish in the field has so far not been successful. Experimental challenge models are used to test vaccine efficacy. The aim of this study was to evaluate the performance of experimental vaccines after challenge by the two most widely used challenge routes, intraperitoneal injection and cohabitation. A total of 1,120 Atlantic salmon were vaccinated with non‐commercial experimental vaccines with increasing amounts of an inactivated Piscirickettsia salmonis EM90‐like isolate. Differences in mortality, macroscopic and microscopic pathological changes, bacterial load and immune gene expression were compared after challenge by different routes. The results revealed a similar progression of the diseases after challenge by both routes and no gross differences reflecting the efficacy of the vaccines could be identified. The analysis of the immune genes suggests a possible suppression of the cellular immunity by CD8 T cell and with this stimulation of bacterial survival and replication. Comparative studies of experimental challenge models are valuable with regard to identifying the best model to mimic real‐life conditions and vaccines’ performance.     

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.     

Relationships between oceanic conditions and growth of Chinook salmon (Oncorhynchus tshawytscha) from California, Washington, and Alaska, USA

We model age‐specific growth rates of Chinook salmon (Oncorhynchus tshawytscha) with two life‐history behaviors from Alaska (i. Situk and ii.Taku Rivers), Puget Sound, Washington (iii., iv. Skagit River), and California (v. Smith River) relative to oceanic conditions in those regions. By analyzing over 20 yr of biological and physical data from the NE Pacific downwelling, upwelling, and transition zones, we are able to determine the factors affecting growth across much of the species’ range and between life‐history behaviors. With scale increment data from returning fish, we use path analysis and partial least squares regression to quantify the relationships between growth and regional‐ and large‐scale oceanic conditions (e.g., sea level height, sea surface temperature, upwelling). Alaskan fish with both ocean‐ and stream‐type behaviors were fit best by the environmental data from the winter in Alaska waters. Specifically, coastal and gyre factors such as sea surface temperature, river flow, and Ekman pumping positively correlated to growth, indicating a productive and strong Alaska Current promoted growth. Growth of fish from California was fit by local factors such as increased upwelling, lower coastal sea surface temperature, and wind stresses during summer and spring, indicating a productive and strong California Current promoted growth. For Puget Sound, Washington, growth of fish that migrate to sea in their first year was generally negatively correlated to a strong California Current. Puget Sound fish that spend a year in freshwater before migrating to sea were modeled well with environmental data from their source region for the first 2 yr at sea and by data from Alaska waters in their third year at sea. Results suggest that conditions in which the transition zone is dominated by neither the Alaska nor California Currents are best for increased growth of Puget Sound fish.     

Flavobacteria colonizing the early life stages of hatchery‐incubated Chinook salmon Oncorhynchus tshawytscha (Walbaum 1792) are markedly diverse

Flavobacterial diseases are significant impediments to hatchery‐based fishery conservation and aquaculture productivity worldwide. Recent studies revealed a multitude of novel flavobacteria within the reproductive fluids and unfertilized eggs of feral Chinook salmon Oncorhynchus tshawytscha broodstock, some of which were associated with systemic disease. Herein, embryonated eggs/fry from these broodstock were assayed for flavobacteria while in incubator stacks in three hatcheries over 2 years, as was the water entering hatchery incubators. Overall, >65% of sampled eggs and 38% of fry were colonized by flavobacteria. One hundred and ninety‐one egg and fry‐associated flavobacterial isolates were characterized phenotypically and via 16S rRNA gene sequencing and phylogenetic analyses, revealing that the majority fell into 22 clades (i.e., 15 Flavobacterium spp. groups and seven Chryseobacterium spp. groups) that varied in presence by facility. Although some matched previously described fish‐pathogenic species, the majority were distinct from all described flavobacteria and likely represent novel species. Of concern, iodophor disinfection at the commonly utilized dose/duration for egg‐surface disinfection did not eliminate flavobacteria. Results also implicated maternal routes of infection and source water for some flavobacteria. In total, study findings underscore the complexity of flavobacterial ecology within hatchery environments and highlight the need for improved hatchery biosecurity practices.     

Development of piscirickettsiosis in Atlantic salmon (Salmo salar L.) smolts after intraperitoneal and cohabitant challenge using an EM90‐like isolate: A comparative study

Piscirickettsiosis, caused by the intracellular Gram‐negative bacteria Piscirickettsia salmonis, is at present the most devastating disease in the Chilean salmon industry. The aim of this study was to analyse disease development after challenge with a P. salmonis strain (EM90‐like) under a controlled environment by comparing intraperitoneal challenge with cohabitation challenge. The P. salmonis EM90‐like isolate was cultured in a liquid medium for the challenge of 400 Atlantic salmon (Salmo salar) smolts. Cumulative mortality was registered, necropsy was performed, and bacterial distribution in the tissues and histopathological changes were analysed. The results revealed a similar progression of the disease for the two different challenge models. Pathological and histopathological changes became more visible during the development of the clinical phase of the disease. Bacterial DNA was identified in all the analysed tissues indicating a systemic infection. Bacterial tropism to visceral organs was demonstrated by real‐time quantitative PCR and immunohistochemistry. Better knowledge of disease development during P. salmonis infection may contribute to further development of challenge models that mimic the field situation during piscirickettsiosis outbreaks. The models can be used to develop and test future preventive measures against the disease.     

Effects of temperature on Renibacterium salmoninarum infection and transmission potential in Chinook salmon,Oncorhynchus tshawytscha (Walbaum)

Renibacterium salmoninarum is a significant pathogen of salmonids and the causative agent of bacterial kidney disease (BKD). Water temperature affects the replication rate of pathogens and the function of the fish immune system to influence the progression of disease. In addition, rapid shifts in temperature may serve as stressors that reduce host resistance. This study evaluated the effect of shifts in water temperature on established R. salmoninarum infections. We challenged Chinook salmon with R. salmoninarum at 12 °C for 2 weeks and then divided the fish into three temperature groups (8, 12 and 15 °C). Fish in the 8 °C group had significantly higher R. salmoninarum‐specific mortality, kidney R. salmoninarum loads and bacterial shedding rates relative to the fish held at 12 or 15 °C. There was a trend towards suppressed bacterial load and shedding in the 15 °C group, but the results were not significant. Bacterial load was a significant predictor of shedding for the 8 and 12 °C groups but not for the 15 °C group. Overall, our results showed little effect of temperature stress on the progress of infection, but do support the conclusion that cooler water temperatures contribute to infection progression and increased transmission potential in Chinook salmon infected with R. salmoninarum.     

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.     

Quantifying the effects of wind, upwelling, curl, sea surface temperature and sea level height on growth and maturation of a California Chinook salmon (Oncorhynchus tshawytscha) population

We used retrospective scale growth chronologies and return size and age of female Chinook salmon (Oncorhynchus tshawytscha) from a northern California, USA, population collected over 22 run years and encompassing 18 complete cohorts to model the effects of oceanographic conditions on growth during ocean residence. Using path analyses and partial least squares regressive approaches, we related growth rate and maturation to seven environmental variables (sea level height, sea surface temperature, upwelling, curl, scalar wind, northerly pseudo‐wind stress and easterly pseudo‐wind stress). During the first year of life, growth was negatively related to summer sea surface temperature, curl and scalar winds, and was positively related to summer upwelling. During the second, third and fourth growth years growth rate was negatively related to sea level height and sea surface temperature, and was positively related to upwelling and curl. The age at maturation and the fork length at which three ocean‐winter fish returned were related to the environment experienced during the spring before the third winter at sea (the year prior return). Faster growth during the year before return led to earlier maturation and larger return size.     

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.     

Recombinant expression and comparative bioactivity of tongue sole insulin‐like growth factor (IGF)‐1 and IGF‐2 in Pichia pastoris

Insulin‐like growth factor (IGF) plays a key role in the complex system that regulates bony fish growth, differentiation, and reproduction. In the current study, recombinant tongue sole IGF‐1 and IGF‐2 were obtained using the Pichia pastoris expression system and their comparative bioactivities were investigated. Tricine–SDS–PAGE and western blot analysis showed that the recombinant tongue sole IGFs were secreted into the culture medium and had a molecular weight of 8.7 kDa. The optimal incubation time and pH for recombinant expression of IGFs were 36 hr and 5.0 respectively. Functional analysis demonstrated that both recombinant tongue sole IGF‐1 and IGF‐2 significantly promoted cell proliferation of MFC‐7 in vitro. In addition, the recombinant tongue sole IGF‐1 and IGF‐2 proteins could suppress hepatic mRNA levels of igf‐1 and igf‐2 in vitro, which showed that they have similar physiological functions. Taken together, the biologically active recombinant tongue sole IGF‐I and IGF‐II proteins will allow us to further investigate their physiological roles in growth regulation of this species. Furthermore, the present results also hinted at the potential application of these two recombinant IGF‐I and IGF‐II proteins into the tongue sole farming industry.     

The use of a real-time PCR primer/probe set to observe infectivity of Yersinia ruckeri in Chinook salmon, Oncorhynchus tshawytscha (Walbaum), and steelhead trout, Oncorhynchus mykiss (Walbaum)

Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a common pathogen affecting aquaculture facilities and implicated in large losses of cultured fish. Fisheries scientists continue to gain a greater understanding of the disease and the pathogen by investigating methods of identification and pre- and post-infection treatment. In this study, a real-time PCR probe set for Y. ruckeri was developed to detect daily changes in the bacterial load during pathogen challenges. Two species of fish, Chinook salmon, Oncorhynchus tshawytscha, and steelhead trout, Oncorhynchus mykiss, were exposed to two strains of Y. ruckeri (Hag and SC) during bath challenges. A subset of fish was killed daily for 14 days, and the kidney tissue was biopsied to enumerate copies of pathogen DNA per gram of tissue. While Chinook exposed to either the Hag or SC strains exhibited similar pathogen loads, those exposed to the Hag strain displayed higher mortality (～66%) than fish exposed to the SC strain (～24% mortality). Steelhead exposed to the Hag strain exhibited a greater pathogen load and higher mortality (～42%) than those exposed to the SC strain (<1% mortality). Steelhead challenged with either strain showed lower pathogen loads than Chinook. The study illustrates the efficacy of the probe set to enumerate Y. ruckeri bacterial growth in the kidneys of fish. Also, strains of Y. ruckeri display species-specific growth patterns that result in differential mortality and pathogen load.