The close proximity of net-pen salmon farms and wild Pacific salmon stocks in British Columbia (BC) is an incentive for precautionary management of the environmentally and economically damaging parasites known as sea lice. Bivalves cultured as part of an integrated multi-trophic aquaculture (IMTA) system may contribute natural, preventative louse control through the ingestion of planktonic sea lice larvae. A field trial was conducted to test sea lice mitigation by bivalves at a commercial Atlantic salmon (Salmo salar) farm in BC using Pacific oysters (Crassostrea gigas). Oysters were cultured in trays around one end of the farm and at a reference site approximately 150 m away from August 2013 until August 2014. Parasitic and planktonic sea lice (Lepeophtheirus salmonis and Caligus clemensi) were monitored before and during oyster deployment, beginning in December 2012. Parasite abundance peaked in January 2013 (6.5 lice/fish, >85% C. clemensi), and the following year in February 2014 (3.3 lice/fish, >80% L. salmonis). Larval density within cages peaked in January, both in 2013 (1.28 larvae/m3) and 2014 (0.96 larvae/m3). Parasite abundance was significantly correlated with both surface salinity (r2= 0.28, p=0.04) and sea lice larval density (r2= 0.65, p=0.01). Observed densities were significantly lower (t=3.41, p=0.009) than those calculated for the site based on water temperature and salinity, the number of adult female lice present, and the approximate number of fish. Sea lice mitigation by oysters was assessed by comparing monthly sea lice larval densities inside bivalve and non-bivalve fish cages, and by analyzing preserved oyster digestive tracts from January 2014 (when larval densities were highest) for presence of L. salmonis DNA using PCR. Using these methods, no significant evidence of sea lice mitigation was detected. Oyster growth was monitored by measuring whole wet weight, soft tissue wet, dry, and ash-free dry weight, and shell length, width, and height approximately every four months. Oysters were sampled equally across different sides of the farm and at the reference site (~150 m away from the farm) at three depths: 1, 3, and 6 m. All seven measurements increased significantly over time. Effects of side and depth varied by growth parameter; in general, oysters at 1 and 3 m were significantly larger than those at 6 m, and oysters cultured at the reference site were either significantly smaller or the same size as those cultured around the farm. Oysters from select sides were consistently, significantly larger than those from other sides and from the reference site. Overall, the findings suggest that sea lice larvae quickly dispersed away from the farm after hatching and were not significantly impacted by bivalve presence around the fish cages. Bivalves grew significantly larger over time and size was significantly impacted by both depth and side of the fish cage. While no evidence of larval sea lice reduction/ingestion by cultured bivalves was detected, this study provides information on all sea lice stages present throughout an Atlantic salmon production cycle, as well as the first detailed growth analysis of Pacific oysters cultured alongside farmed Atlantic salmon in BC. / Graduate / 0792 / byrneaa@gmail.com

Stream living salmonids are generally regarded as drift feeders that rely upon their vision when foraging. It has been shown that salmonids become nocturnal at low water temperatures, but have a low foraging efficiency as light intensity is low, due to their dependence upon vision. Shifting from drift feeding to benthic feeding, has been suggested, and analyses of gut contents during winter have shown that the diet of salmonids mainly consists of benthic invertebrates. Most experimental studies of salmonid foraging have only offered the fish drifting prey or only given the fish access to benthic prey in total darkness. Such conditions rarely occur in nature and the importance of benthic foraging to salmonids may therefore have been underestimated. In this study I conducted a stream laboratory experiment to test if low light intensity caused juvenile Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) (age 0+) to forage more on benthic than drifting prey. The salmon foraged on both drifting and benthic prey during high light but consumed only benthic prey during low light (by one of six fish). Trout foraged on both drifting and benthic prey during both high and low light, but foraging efficiency was lower during low than high light and foraging efficiency was lower for benthic prey than for drifting prey. These results indicate that both species forage more opportunistically than previously thought. / Strömlevande laxfiskar anses generellt vara driftätare som förlitar sig på synen när de födosöker. Det har visats att laxfiskar blir nattaktiva vid låga vattentemperaturer, men har en låg födosökseffektivitet då ljusintensiteten är låg, på grund av sitt beroende av synen. Skifte från driftätande till att äta bentiska byten, har föreslagits, och analyser av maginnehåll under vintern har visat att laxfiskars diet huvudsakligen består av bentiska evertebrater. De flesta experimentella studier av laxfiskars födosök har endast erbjudit fisken driftande byten eller endast gett fisken tillgång till bentiska byten vid totalt mörker. Sådana förhållanden förekommer sällan i naturen och betydelsen av bentiskt födosök för laxfiskar kan därför ha underskattats. I den här studien utförde jag ett experiment i en laboratorieström för att testa om låg ljusintensitet fick juvenil Atlantlax (Salmo salar) och öring (Salmo trutta) (ålder 0+) att födosöka mer på bentiska än driftande byten. Laxen födosökte på både driftande och bentiska byten vid högt ljus men bara bentiska byten åts vid lågt ljus (av en av sex fiskar). Öringen födosökte på både driftande och bentiska byten vid både hög och låg ljusintensitet, men födosökseffektiviteten var lägre vid låg än hög ljusintensitet och födosökseffektiviteten var lägre för bentiska än förbiflytande byten. Dessa resultat indikerar att båda arterna födosöker mer opportunistiskt än vad man tidigare ansett.

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Marine pollution resulting from oil spillage has received much attention mostly due to the damaging effects it has on fisheries and aquacultures. One component of oil that is widely studied due to its toxic and carcinogenic properties is the polycyclic aromatic hydrocarbons. The physical and chemical properties of these compounds control their distribution into the various phases of the environment. The rates of elimination of these compounds from impacted organisms were investigated in laboratory and field experiments using selected marine organisms (Mytilus edulis and Salmo salar). The elimination of individual PAH compounds followed first order kinetics. Elimination rate varied among compounds and generally decreased with increase in molecular weight and degree of alkylation. Elimination rate constants (k2) and biological half-lives (t1/2) evaluated from chronically exposed mussels (collected from Aberdeen harbour) in separate laboratory and field studies were comparable but differed from those evaluated from acutely exposed mussels. Shorter t1/2 were obtained from acutely exposed mussels. The t1/2 ranged between 0.5- 22 d (acute exposure) and 3.8- 31.5 d (chronic exposure).The longer apparent t1/2 calculated for the chronically impacted mussels was attributed to the retention of the compounds in a stable compartment due to long period of exposure that limited exchange with the surrounding water. Contrary to expectation, t1/2 for similar compounds was higher in salmon than in mussels. The reason for this was unknown but attributed to the route of elimination. A good correlation (r2 > 0.72) was found between PAHs tissue concentration and taint intensity in salmon. Comparison of the results from this study with literature data showed that tank water replacement time and exposure duration affects rate of PAHs elimination. The data generated in this study and some of the reviewed studies will find application in different oil spill scenarios. The usefulness and limitations of the n-alkanes profile, PAH distribution and concentration ratios, and specific biomarker ratios from organisms in oil spill source identification was also demonstrated.

The efficacy of a range of anti-parasitic chemotherapeutic agents against the salmon louse Lepeophtheirus salmonis following topical application was studied in vitro and in vivo. In general, adult and preadult lice were susceptible to a wide range of compounds with dose rates, following 1 hour exposures, ranging several orders of magnitude (10.0 - 0.001 mg/L). Overall the pyrethroid compounds which were tested were found to have the widest therapeutic ratios, indicating the potential of this group of chemotherapeutants for sea lice control. Resistance to the organophosphorus (OP) compounds dichlorvos and azamethiphos was detected in isolated populations of lice. Field trials with azamethiphos indicated that the compound was highly efficacious against sensitive lice (@ 0.1 mg/L; however, where resistance was present, efficacy (@ 0.2 mg/L) was highly variable. When used at the above dose rates, azamethiphos was found to be well tolerated by fish as indicated by a lack of significant brain acetylcholinesterase inhibition. Results on cross resistance (between pyrethroids and OPs) were inconclusive which was believed to be, primarily, due to the overall high toxicity of the group; but also to the variable responses from exposed lice. In a series of preliminary trials, one of the pyrethroid compounds, PHRDL-D, was found to effectively remove lice when administered orally to infected salmon, indicating the potential of pyrethroids as oral chemotherapeutants. A comparison of the relative toxicity of azamethiphos (OP), resmethrin (pyrethroid), ivermectin (avermectin) and the structurally similar compound SKB7 (milbemycin), indicated that chalimus stages were only susceptible to ivermectin and SKB7 following topical and intra-peritoneal injection to lice infected fish. In contrast, azamethiphos and resmethrin were found to be non toxic to chalimus larvae at dose rates which were highly toxic to both adult lice and treated fish. Preliminary studies on the uptake of r4C]azamethiphos in adult lice indicated that uptake was both concentration and time dependant, reaching a plateau at the onset of toxicity. Uptake appeared to be primarily associated with frontal plates, 1st antennae and anus. The fmdings indicated that several compounds/compound classes are highly active against lice and, given the limited number of compounds available for sea lice control and the development of resistance to OPs, might be considered as alternatives. In light of these findings, the potential of chemotherapy for the future control of sea lice is discussed.

Growth retardation in King salmon Oncorhynchus tshawytscha (Walbaum) is a common and significant problem affecting marine farming operations in New Zealand. While the basic marine culture requirements for the King salmon species are well understood, the etiology of seawater adaptation and growth retardation remains understudied. Consequently, this study was established to investigate the physiological state and causative factors of growth retardation in collaboration with a leading New Zealand aquaculture company, New Zealand King Salmon Ltd (NZKS). Hypoosmoregulatory indicators are not currently used by marine farmers in New Zealand due to the belief that King salmon are more adaptable to seawater than their more highly cultured counterparts, Coho and Atlantic, and can be transferred to seawater anytime after a critical weight is achieved. This study sought to investigate changes in hypoosmoregulatory ability and its relation to water temperatures commonly used in the hatchery environment. This was determined by changes in the activity of the predominating seawater-adapting gill enzyme Na+/K+-ATPase, as an indirect measure of its abundance during smoltification. Changes in plasma ion profiles and the ability to regulate ions after abrupt transfer were also measured and compared with enzymatic activity throughout the austral springtime smoltification period in commercial strains of under-yearling King salmon. It was found that King salmon do undergo a distinct austral spring-time temporal increase in hypoosmoregulatory processes. This was characterised by a 2-fold increase Na+/K+-ATPase activity which was concomitant with reduced plasma Na+ in freshwater and following a seawater challenge in fish between fork lengths of 140-160 mm. Despite no consistent reduction in Na±/K+-ATPase activity during desmoltification, it was shown that the percent of ATP dependent activity specific to Na+/K+-ATPase diminished over time. Increased residual ATP dependent activity is hypothesised to be a result of apical H+-VATPase activity as a compensatory mechanism to rapidly normalise plasma Na+ during desmoltification concomitant with elevated basolateral Na+/K+-ATPase. Water temperature has been linked with the advancement and shortening of the smoltification period in several species. Gill Na+/K+-ATPase activity and hypoosmoregulatory ability in King salmon were negatively affected by increasing water temperatures above 12°C in contrast to a constant 12°C. The level of growth retardation was dependent on the time of transfer to seawater and was found to increase during a period of reducing hypoosmoregulatory ability. The transfer of growth retarded King salmon back to freshwater resulted in a complete reversal of the growth retarded state, comparable to that observed in Coho and Atlantic salmon. Growth retarded fish were able to readapt back to freshwater with higher survival and growth rates compared to the transfer of normal growing sub-adult King salmon, strongly demonstrating that growth retarded fish are more adapted to freshwater. Osmoregulatory physiology, and endocrinology during the transfer of growth retarded and normal growing fish were investigated. Overall, these results have fundamental implications for the aquaculture of King salmon that are able to be applied by industry to improve current husbandry practices.

Three new NILT genes were successfully cloned and characterized from rainbow trout, with one NILT alternatively spliced into a long isoform containing two Ig domains and a short isoform containing one Ig domain.  The expression of NILTs was studied in six different tissues and two different cell lines, with expression apparent in immunologically important tissues.  Furthermore, phylogenetic analysis showed that NILTs are more closely related to triggering receptor expressed on myeloid (TREM) cells and Nkp44 from humans than to NITRs from rainbow trout. The genomic organisation and structure of the multigene family of NILTs in Atlantic salmon was investigated using a BAC sequencing approach.  This revealed the presence of six novel NILT genes, which either contained one or two Ig domains and several immunoreceptors tyrosine-based inhibitory motifs (ITIMs) in the cytoplasmic region. By homology search two NILT-like genes in zebrafish (<i>Danio rerio</i>) located on chromosome 1 have been obtained. Chromosome 1 in zebrafish also contains the <i>Dare</i>-ZE genes, which are equivalent to the human MHC class I genes located on chromosome 6.  The distance between the later and the TREM genes on chromosome 6 is similar to the distance between the NILT-like genes and <i>Dare</i>-ZE genes on zebrafish chromosome 1.  In addition, two NILT-like Ig domains were obtained from the green spotted pufferfish (<i>Tetraodon nigroviridis</i>), putatively part of the same receptor. The results will contribute to our knowledge of the immune system in fish and provide useful information for the control of inflammatory processes in salmonids.

In the northeast Pacific, salmon are an integral part of ecology, economics and culture. Nearshore areas, where juvenile salmon reside upon leaving their natal streams, are important habitat during a critical time where growth can determine overall survivorship. With the rise in human development in coastal areas, these valuable habitats are becoming increasingly modified, however, the ecological ramifications are not fully understood. This study focuses on two types of anthropogenic influence including shellfish aquaculture, which modifies intertidal areas by adding structures such as intertidal fencing and anti-predator nets, and plastic marine pollution in the form of microplastics. We beach seined at sites within an area extensively modified for shellfish aquaculture (Baynes Sound) to examine juvenile salmon abundance, condition, feeding intensity and prey at aquaculture and non-aquaculture areas. In addition, we also beach seined, and along the east coast of Vancouver Island to determine the incidence of microplastics in juvenile Chinook salmon and their nearshore environments. No significant differences were found between areas in the abundance, diets, condition or feeding intensity of juvenile Coho and Chinook. Chum had different prey and a higher condition and feeding intensity at aquaculture sites, suggesting that species such as Chum feeding on more benthic prey items have a higher probability of being impacted by shellfish aquaculture modifications and in this case we observed positive effects. Microplastic analysis showed juvenile Chinook salmon contained 1.15 1.41 (SD) microplastics per individual while water and sediment samples had 659.88 520.87 microplastics m-3 and 60.2 63.4 microplastics kg-1 dry weight, respectively. We found no differences in microplastic concentrations in juvenile Chinook and water samples among sites but observed significantly higher concentrations in sediment at our Deep Bay site compared to Nanaimo and Cowichan Bay. These differences may be due to site bathymetry and oceanographic differences facilitating settlement at the Deep Bay site and/or may be a result of differential plastic sources in the area including shellfish farming and a marina. Shellfish aquaculture had negligible or positive effects on juvenile salmon abundance, diet, condition and feeding intensity and Chinook microplastic concentrations were relatively low compared to literature values. Although fitness consequences and ecosystem-wide implications must be addressed in the future, it appears shellfish aquaculture and microplastics are not immediate threats to juvenile Pacific salmon along the east coast of Vancouver Island at this time. However, continued monitoring programs and larger-scale studies should be implemented as shoreline modification and plastic use continues to increase. / Graduate / 2017-08-14

Few data are available on distribution, abundance, and ecology of scyphozoans in the Northern California Current (NCC). This thesis is divided into four chapters, each of which contributes to our understanding of a different stage of the scyphozoan life history. The first study describes the settlement preferences of Chrysaora fuscescens planulae in the laboratory. Planulae were found to respond to the interaction of substrate and orientation. Artificial substrates were identified as viable habitat for C. fuscescens. In the second chapter, a population of scyphistomae in Charleston, Oregon were identified to species-level using DNA barcoding techniques. The third and fourth chapters focus on the medusa stage of the life history. Using surveys mailed to fishers in the Pacific Region, this study provides baseline data on the types and magnitudes of economic damages caused by jellyfish on different fisheries and helps assess fishers' perceptions of jellyfish population trends in the NCC. This thesis includes previously unpublished co-authored material.

Sterile triploid Atlantic salmon represent a solution to the issues of pre-harvest sexual maturation and mature escapees from open aquaculture systems. Although the initial problems of reduced performance and increased deformities in triploids have been thoroughly researched, there is a continued lack of information on their susceptibility and response to disease and routine on-farm treatments compared to diploids. Thus, the main aim of this thesis was to enhance the current understanding of triploid health and immunity through experimental disease challenges and treatments, and aid in determining their robustness and, therefore, suitability for aquaculture. A commercial furunculosis vaccine equally protected diploids and triploids against challenge with Aeromonas salmonicida, and adhesion scores were similar between ploidy (Chapter 2). Interestingly, triploids had lower white blood cell counts but increased cellular activity, e.g. respiratory burst, compared to diploids. Following experimental cohabitation infection with Neoparamoeba perurans, causative agent of Amoebic Gill Disease (AGD), ploidy did not affect the manifestation or severity of AGD-associated gill pathology, or the serum innate immune response (Chapter 3). Hydrogen peroxide, used to treat against parasitic diseases, elicited similar primary and secondary stress responses in both ploidy, but led to differences in the expression of stress (cat, gpx1, gr, hsp70, sod1, sod2) and immune (saa5, crp/sap1a, crp/sap1b, il1β) genes (Chapter 4). Finally, vaccination with different vaccine treatments (4 commercial vaccines, 6 different vaccine combinations and a sham-vaccinated control) showed no ploidy differences in adhesion score or antibody response, although vertebral deformities remained higher in triploids (Chapter 5). Increasing severity of vaccine treatments negatively affected weight, length and thermal growth coefficient in both ploidy. Triploids were heavier than diploids at smolt (+ 14 %) and post smolt (+ 32 %). Overall, this research shows that triploid Atlantic salmon respond as well as diploids to disease and treatment challenges, and supports their application into full-scale commercial aquaculture.