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The type of Atlantic salmon immune response to amoebic gill disease was investigated by analysis of cytokine genes possibly related to the TH1, TH17 and Treg pathways, which were significantly down regulated, while il-4/13 isoforms, possibly related to the TH2 pathway, were found to be significantly up regulated. Moreover, the injection of Atlantic salmon with rIfn-γ, which might initiate the TH1 immune pathway, did not reduce infection load of Paramoeba perurans or severity of gill pathology in challenged fish. Different arginase isoforms present in salmonids were also characterised and the data supported the concept that arginase type II may be a more relevant marker of alterantive activate macrophages in teleost fish induced by rIl-4/13. Regarding the biology of P. perurans, the susceptibility of amoebae to different environmental conditions showed that amoebae exposed to salinities lower than 3 ppt were disrupted or did not recover after 16 days, while all amoebae cultures showed a significant difference between the two temperatures (10°C and 15°C) studied over time. Significant differences were also found in relative abundance of the 30 most prevalent bacterial genera present in the isolated P. perurans cultures (16S rRNA). The impact of stress on the host response to AGD was tested for the presence of an association between temperature (10°C and 15°C) and variation in severity of AGD in Atlantic salmon. This association was demonstrated for the histopathology and P. perurans load analysis, reflecting an earlier and stronger AGD infection at the higher temperature (15°C) treatment. No significant difference between the two temperature treatments was shown in hormonal and molecular responses. Therefore, temperature might not act as a chronic stressor but its effect could be linked to the higher amoebae attachment seen at higher temperatures in the in vitro experiment reported.

In this thesis, we improved our understanding of the effects of hydrology, stream hydraulics, and temperature on juvenile Atlantic salmon (Salmo salar L.) habitat. We demonstrated the key role played by stream morphology and flow regime on in-channel hydraulics and consequently on salmonid habitat. Additionally, we showed how riparian afforestation has potential to moderate climate change effects on stream temperature preserving freshwater ecosystems. The Girnock Burn is an upland Scottish river that has been intensively studied to investigate flow generation processes and stream temperature, and has served as a long-term monitoring site for Atlantic salmon population dynamics since 1966. The general approach applied consisted of combining different types of models including: hydraulic, fish habitat, hydrological and heat transfer models with long-term hydrological and climatic data sets, and digital terrain models (DTMs) at different spatio-temporal scales. Our results showed that the extensive presence of roughness elements (e.g. boulders and cobbles) is capable to provide some refuge areas for juvenile salmon fry for a wide range of flows. However, under extreme flow conditions, in-channel hydraulics might represent a limiting factor. Significant inter-site differences occurred and were consistent throughout the years. Evidence of long-term trend in fry habitat quality could be identified only in summer. Since more extreme flow regimes are expected in the future as a result of climate change, we also proposed a novel analytical approach that allowed us to assess the effects of hydroclimatic variation on fish populations outside the range of observations. Finally, we showed the potential of afforestation to reduce daily stream temperature range, moderating both low and high peaks of more than 2 ○C. This makes riparian shading a valuable mitigation strategy to contrast global warming effects on stream temperatures that should be considered for a sustainable catchment management.

Electrofishing is a sampling tool commonly used by fisheries researchers. While much is known about the effects of electroshock on fish physiology, consequences to the immune system and disease progression have not received attention. To understand the effects of electroshock on immune function we undertook a comparison of electroshock and handling stress in regards to selected immune functions and disease progression in juvenile spring chinook salmon (Oncorhynchus tshawytscha). The handling stress treatment was included to insure the responsiveness of the fish. Our objectives were to determine the effects of electroshock on immune function, determine the mechanism of any observed alteration, and to determine the effects of electroshock on disease progression. Skin mucous lysozyme concentrations were not affected by exposure to electroshock. Respiratory burst activity may be enhanced in leukocytes immediately after an in vitro electroshock. Any effect in vivo, however, appears to be brief given the lack of differences observed 3 h after exposure. The specific immune response, measured as the ability of anterior kidney leukocytes to generate antibody producing cells (APC), was suppressed 3 h after electroshock, but recovered within 24 h. This response was similar in timing and magnitude to that of fish subjected to an acute handling stress. The mechanism of suppression is hypothesized to be via elevation of plasma cortisol concentrations. The ability to generate APC may be suppressed 7 d after electroshock, but it is not evident what mechanism is responsible for this suppression. There was some evidence that the progression of a Renibacterium salmoninarum (RS) infection was altered after exposure to an electroshock. Exposure to electroshock did not have a clear affect on the severity of infection or the number of mortalities, but may have accelerated the time to death in infected fish that died. The limited duration of specific immune suppression and lack of effect on mortality in RS infected fish lead us to conclude that electrofishing under the conditions we tested is a safe procedure in regards to immunity and disease. / Graduation date: 2000

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2004. / Thesis documentation sheet inserted. Appendix reprints five manuscripts and papers co-authored with others. Includes bibliographical references. Also issued electronically via World Wide Web in PDF format; online version lacks appendix.

Determining the physical and biological habitat variables that influence the abundance of juvenile salmonids in British Columbia streams will improve management practices. Habitat models are tools that provide insight into organisms’ habitat needs and provide a more efficient mechanism for estimating population abundance than direct measurement. Models have been developed for salmonids in other jurisdictions, but very few have included invertebrate drift (a primary food source for juvenile salmonids) as a predictive variable. This is because temporal and spatial variation of drift abundance are widely assumed to be so high that drift cannot be reliably estimated without unreasonable effort. This thesis investigates the temporal and spatial variability of invertebrate drift and the impact of its inclusion in habitat models for juvenile salmonid abundance in two chapters. The first objective of the first chapter was to evaluate the temporal variability of invertebrate drift by comparing the seasonal and day-to-day variation in drift abundance to spatial variation within and between sites. The second objective was to develop predictive models for invertebrate drift abundance. Aquatic, terrestrial and total invertebrate drift abundances varied primarily between sites and very little between days or months at the same site, indicating that a single day of sampling is sufficient to assess drift abundance for comparison among sites. The abundance of invertebrate drift was related to productivity- and flow-related habitat variables. The objectives of the second chapter were to develop predictive models for juvenile salmonid abundance in southwestern BC using physical and biological habitat variables, to determine whether habitat variables differ between the Coast and Interior regions of BC, to determine the contribution of invertebrate drift to the relative predictive ability of the models, and to determine cost:benefit ratios for the predictive models and their component variables. The final models for predicting abundance of all young-of-year salmonids combined, and rainbow trout (Oncorhynchus mykiss) and coho salmon (O. kisutch) individually, included variables related to stream structure and productivity, and the models for rainbow and coho showed regional differences. Invertebrate drift did not improve model fit.

As part of a hierarchical approach to classifying watersheds and stream habitats based on geomorphic and geologic criteria, we defined ten classes of fluvial and lacustrine habitats at the scale of valley segments. Valley segments are landscape units which encompass surface waters and the adjacent floodplains and hillslopes with which they interact over time frames of thousands of years. They form a large-scale template that constrains the character of aquatic habitat, controls the effects of disturbances in riparian areas, and mediates responses of streams to upland and upstream events. The regional distribution of valley segment types in southwest Oregon reflects bedrock geology and tectonic history of the landscape. Fluvial segment types differ in stream adjacent landforms, slope erosion processes, floodplain and valley morphology, channel slope, riparian vegetation, streambank texture, gravel bar morphology, and pool-forming features. Studies that do not carefully account for inherent differences between valley segment types could fail to detect critical changes in stream habitat caused by human disturbance. Alluvial valley and alluviated canyon segment types, which have extensive floodplains, low channel slopes, abundant woody debris, and ample gravel beds, are of greatest direct importance for salmon and other native fishes. Virtually all alluvial valleys in the study area have been heavily disturbed by logging, agriculture, and residential development. Alluviated canyon segments located in the few drainage basins where human activity has been limited probably serve as habitat refugia for the last diverse assemblages and productive populations of salmon in the region. Alluviated canyons in extensively-fogged basins exhibit increased abundance of large woody debris, fewer cross-channel debris jams, more extensive bank erosion, reduced pool area and increased riffle area, shallower riffles, and increased surface concentration of fine sediments in pools and other habitats, compared to similar segments in lesser-disturbed basins. These changes in channel morphology and stability appear to be driven by increased sediment load, caused by logging-related landslides and other erosion sources. Field studies in Sixes River basin indicated that abundance and diversity of salmonid fishes declines as maximum stream temperature increases. Changes in summer distribution of juvenile chinook and coho salmon since 1970 are related to changes In water temperature. Although some tributaries have cooled, a decline in rearing distribution in mainstem areas could be caused by long-term loss of channel complexity and associated coolwater refugia. Analysis of fish habitat structures constructed by federal and state agencies indicated that failure rates are high. Recovery of anadromous fish runs in southwest Oregon will require protection of remaining habitat refugia and reduction of sediment yield from disturbed watersheds. / Graduation date: 1992

A hierarchical classification system of Iceland's watersheds and rivers is presented. The classification is based on Iceland's substrate, climate, water, biota, and human cultural influences. The geological formations of Iceland are very different in character depending on their age and formation history. Three major types of formations occur: Tertiary, Plio-Pleistocene, and Pleistocene. These formations have different hydrological characters and different landscapes. There are also large differences in the climate within Iceland. Four major river types are found in Iceland: spring-fed rivers in Pleistocene areas, direct runoff rivers in Plio-Pleistocene areas, direct runoff rivers in Tertiary areas and wetland heath rivers in Tertiary areas. Eleven biogeoclimatic regions occur in Iceland, each having a different watershed type. The classification together with life history theory can explain the distributions, abundances, and life history strategies of Icelandic salmonids. Oceanic conditions must also be considered to explain the life history patterns of anadromous populations. When the freshwater and marine habitat is stable, the life history patterns of individuals in a population tend to be uniform, one life history form being most common. In an unstable environment many life history forms occur and the life span of one generation is long. The properties of the habitat can further explain which life history types are present. In the most stable and favorable rivers of Iceland resident life history forms are more common. Such a classification of a river habitat greatly aids the understanding of the habitat and how it enables and constrains the salmonid populations within it. Consequently adaptations in life histories are better understood and conservation, utilization, and management of these valuable natural resources are made more coherent and efficient. / Graduation date: 1991

Climate is emerging as a primary determinant of marine survival and migratory behaviour for Pacific salmon. For example, a regime shift in the mid-1990s was correlated to a major change in the migratory behaviour of coho salmon (Oncorhynchus kisutch) in the Strait of Georgia, BC. The details of this new behaviour pattern remain relatively unknown. Furthermore, many coho stocks have been declining during the past three decades. Mitigative strategies –such as hatchery programs— have done little to reverse the trend, and little is known about how hatchery fish are affecting wild populations. The objective of this dissertation was to identify key mortality areas and provide the first look at the migratory behaviour of juvenile wild and hatchery coho in southwestern British Columbia using new telemetry technologies. As coho pre-smolts are relatively small compared with other salmonid species that are typically studied using acoustic telemetry, the identification of the appropriate sizes of fish and tags to use was critical. The first study tested the effects of surgically implanting the three smallest sizes of acoustic tags available on the growth, survival, performance and condition of coho pre-smolts. The first of three field studies to follow investigated the early migratory behaviour and survival of an endangered coho population. The second field study examined differences in physiology, survival and migratory behaviour between wild and hatchery-reared coho smolts. Finally, the third study analysed the altered marine migratory behaviour of juvenile coho in the Strait of Georgia. This dissertation provides the first evidence of high freshwater mortality rates in the endangered coho population, which has implications for the management and conservation of this and other at-risk stocks. I found differences in migratory behaviour and physiology between wild and hatchery-reared coho, suggesting that mitigative strategies need further evaluation. Finally, the timing of the anomalous coho migration out of the Strait of Georgia confirmed that population changes in the strait are a consequence of ecosystem-related impacts. These findings demonstrate how new technologies could be used to fill major information gaps and improve the management and conservation of Pacific salmon.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2000. / Bibliography: 92-95.