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.

We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3′ sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C. clupeaformis putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids.

Since 1996, some populations of Fraser River sockeye salmon ( Oncorhynchus nerka Walbaum in Artedi, 1792) have begun spawning migrations weeks earlier than normal, and most perish en route as a result. We suspect that a high midsummer river temperature is the principal cause of mortality. We intercepted 100 sockeye during normal migration near a spawning stream and measured somatic energy and aspects of plasma biochemistry. Fish were then held at either 10 or 18 °C for 24 days. Before release, fish were biopsied again and implanted with acoustic transmitters. A group of biopsied but untreated control salmon were released at the same time. Sixty-two percent (8 of 13) of control salmon and 68% (21 of 31) of 10 °C salmon reached spawning areas. The 18 °C-treated fish were half as successful (35%; 6 of 17). During the holding period, mortality was 2 times higher and levels of Parvicapsula minibicornis (Kent, Whitaker and Dawe, 1997) infection were higher in the 18 °C-treated group than in the 10 °C-treated group. The only physiological difference between treatments was a change in gill Na⁺,K⁺-ATPase activity. This drop correlated negatively with travel times for the 18 °C-treated males. Reproductive-hormone levels and stress measures did not differ between treatments but showed significant correlations with individual travel times.

Since 1995, several stocks of Fraser River sockeye salmon (Oncorhynchus nerka) have begun upriver spawning migrations significantly earlier than previously observed. In some years, the timing of peak migration has shifted more than 6 weeks. Coincident with this early migration are high levels of en route and pre-spawning mortality, occasionally exceeding 90%. These phenomena pose risks to the perpetuation of these fisheries resources. At present, although there are many competing hypotheses (e.g., energetics, osmoregulatory dysfunction, oceanic conditions, parasites) that may account for early migration and high mortality, there are no definitive answers, nor any causal evidence that link these issues. With poor predictive ability in the face of uncertainty, fisheries managers have been unable to effectively allocate harvest quotas, while ensuring that sufficient fish are able to not only reach the spawning sites, but also successfully reproduce. If trends in mortality rates continue, several imp...

Piscirickettsia salmonis is the intracellular bacterium that causes salmonid rickettsial septicemia, an infectious disease that kills millions of farmed fish each year. The mechanisms used by P. salmonis to survive and replicate within host cells are not known. Piscirickettsiosis causes severe necrosis of hematopoietic kidney. Microarray-based experiments with QPCR validation were used to identify Atlantic salmon macrophage and hematopoietic kidney genes differentially transcribed in response to P. salmonis infection. Infections were confirmed by microscopy and RT-PCR with pathogen-specific primers. In infected salmon macrophages, 71 different transcripts were upregulated and 31 different transcripts were downregulated. In infected hematopoietic kidney, 30 different transcripts were upregulated and 39 different transcripts were downregulated. Ten antioxidant genes, including glutathione S-transferase, glutathione reductase, glutathione peroxidase, and cytochrome b558 α- and β-subunits, were upregulated in infected macrophages but not in infected hematopoietic kidney. Changes in redox status of infected macrophages may allow these cells to tolerate P. salmonis infection, raising the possibility that treatment with antioxidants may reduce hematopoietic tissue damage caused by this rickettsial infection. The downregulation of transcripts involved in adaptive immune responses (e.g., T cell receptor α-chain and C-C chemokine receptor 7) in infected hematopoietic kidney but not in infected macrophages may contribute to infection-induced kidney tissue damage. Molecular biomarkers of P. salmonis infection, characterized by immune-relevant functional annotations and high fold differences in expression between infected and noninfected samples, may aid in the development of anti-piscirickettsial vaccines and therapeutics.