This research investigated the ecological significance of GW-SW interactions in the hyporheic zone of two Scottish mountain rivers (the Girnock Burn and the River Feshie).  The research comprised three components: (i) an assessment of the influence of GW-SW interactions on the spatio-temporal variability of hyporheic hydrochemistry and macroinvertebrate community structure, (ii) an evaluation of the influence of GW-SW dynamics on small-scale spatio-temporal variability in hyporheic thermal regimes, and (iii) an investigation of the spatial relationship between Atlantic salmon <i>Salmo salar </i>(L.) spawning distributions and patterns of GW-SW exchange in a braided river reach. In the Girnock, marked inter- and intra-reach differences in hyporheic water quality were found and linked to spatio-temporal variability in GW-SW exchange.  Up to 25% of the spatial variability in invertebrate community structure could be accounted for by differences in hyporheic water quality.  Community composition varied markedly between winter, spring and summer seasons, with the relative importance of individual water quality variables differing between seasons. There was much heterogeneity in streambed temperature regimes across the study reaches, with data suggesting that long-residence groundwater contributed significantly to hyporheic exchange.  However, at small (cm to m) scales thermal variability was most likely explained by the interaction of reach-scale GW-SW exchanges with smaller-scale, current-bed form induced hyporheic exchange. In a braided section of the River Feshie, spatially complex and temporally dynamic GW-SW exchange patterns occurred.  Salmon spawning was concentrated in locations characterised by upwelling groundwater at depth, with up to 66% of spawning sites recorded in groundwater dominated channels.

Thesis advisor: Noah P. Snyder / Substrate size and mobility are important to Atlantic salmon (Salmo salar) spawning and rearing success. Channel geometry is a control on bedload mobility in streams. It is believed that channel morphology in many Maine rivers has been altered by land use practices, creating wider and shallower channels, and lowering stream competence. If correct, these changes may be partially responsible for the limited number of returning salmon currently observed in Maine coastal rivers. To evaluate the magnitude of these changes, I performed a statistical comparison of channel morphology between two Atlantic coastal streams: the Narraguagus River in Downeast Maine and the Jacquet River in northern New Brunswick, Canada. Compared to the Narraguagus River, the Jacquet River has relatively healthy returns of adult salmon. Both watersheds have similar drainage areas (Narraguagus 588 km²; Jacquet 510 km²;) and mean annual precipitation (1244 mm; 1200 mm), but differing average channel gradients (0.16%; 0.51%) and longitudinal profiles. During the summer of 2007, I surveyed a 13.6-km section of the Narraguagus with a drainage area range of 129-247 km², and a 10.4-km section of the Jacquet with a drainage area range of 94-265 km². I made measurements of active and bankfull width and depth, and channel gradient at 100-m intervals, and performed grain-size counts at 200-m intervals. I also measured gradient and width in a GIS-based analysis. Results of my analysis show that channel gradient is likely the most influential factor on Atlantic salmon habitat as it relates to sediment size. The two rivers exhibit no significant difference in width-to-depth ratio, when low-gradient outliers in the Narraguagus River are removed. Predicted median riverbed grain sizes were calculated using two methods: (1) from the empirical relationship between basal shear stress and measured grain size; and (2) using the Shields parameter and remote sensing data only. Measured and predicted grain sizes reveal finer river-bed sediments on the Narraguagus River, however, Shields parameter calculations show that sediment should be mobile in both streams. I compare these predictions to field-based habitat mapping on the Narraguagus River. Based on predicted grain sizes, I expect nearly continuous Atlantic salmon spawning (28-95%) and rearing (95-100%) habitat on the Jacquet, and much less spawning (47-62%) and rearing (57-68%) habitat on the Narraguagus. This is likely because the Narraguagus River is segmented into reaches of steeper gradient (S < 0.002) with potentially good habitat, and flatter reaches (S < 0.0005) of poor habitat. The long flat reaches (several km) likely act as sediment sinks, preventing the continuity of downstream sediment transport and causing sediment to be sourced from localized glacial deposits. / Thesis (MS) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Geology and Geophysics.

Thesis advisor: Noah P. Snyder / Dam-influenced streambank morphology has not been studied extensively in rivers in deglaciated landscapes with high densities of colonial-era milldams. Fluvial restoration in the eastern U.S. often focuses on understanding pre-Colonial floodplain processes. Recent work by Walter and Merritts (2008a) in the Piedmont of the U.S. mid-Atlantic region suggests milldams significantly impact sedimentation by creating surfaces composed of post-dam legacy sediment that are often abandoned by the river and function as fill terraces. I analyze channel morphology and sedimentation patterns upstream of two breached dams on the Sheepscot River in mid-coastal Maine using lidar digital elevation models, historical aerial photographs, radiocarbon dating, and hydraulic modeling. In the past several decades, observable channel morphologic changes occurred at the two study sites: Maxcy's Mills dam (built in 1809, it was 2-m high and breached in the late 1950s), and at Head Tide dam (built in the 1760s, it is 4-m high and was partially breached in 1952). The Sheepscot River has a native population of Atlantic salmon, which is a federally listed endangered species. Understanding the existence and transport of legacy sediment has become an important component of habitat restoration efforts in the region. The goal of this investigation is to determine the extent and morphologic function of legacy sediment in order to better understand how historical dam sites affect channel morphology and sediment transport in a post-glacial, low-gradient river system. Field and remote sensing analyses indicate that surfaces (up to 2.65 m high) composed of mud and sand function as floodplains 1 km upstream from Head Tide dam and surfaces 90 cm high continue 2.5 km upstream from Maxcy's Mills. Analysis of seven radiocarbon dates from pieces of tree bark sampled from the stratigraphy (58-187 cm below the surface) of the two study sites suggest up to 1.8 m of sediment upstream of the two study sites was deposited within the past 300 years and is therefore a legacy of the dams. Quantification of the total volume of stored legacy sediment is on the same scale as volumes observed in the mid-Atlantic Piedmont region, leading to the conclusion that post-glacial rivers in northern New England store milldam sediment in similar fashion to streams analyzed in the Walter and Merritts (2008a) study. / Thesis (MS) — Boston College, 2013. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Earth and Environmental Sciences.

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.

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.

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

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

Thesis (M.S.) in Zoology--University of Maine, 2009. / Includes vita. Includes bibliographical references (leaves 60-73).

The Atlantic salmon (Salmo salar) has two developmental processes which are clearly seasonal; smoltification is restricted to the spring and maturation to late autumn. In the farming industry the seasonality of juvenile production is primarily responsible for the seasonal production in market-sized fish. Both smoltification and maturation appear to be controlled by mechanisms timed by photoperiod. This thesis investigates the effects of photoperiod on smoltification and maturation. The performance of both out-of-season eggs and particularly smolts are closely examined and the possible application of photoperiod techniques in the industry discussed. Both potential SI and S2 parr were subjected to natural photoperiods or a range of artificial photoperiods under constant and ambient temperature conditions. S I and S2 smolts reared under natural photoperiods were transferred to sea water during April and May. A 2-3 month period of short days followed by a period of long days was observed to advance smoltification; 0+ and 1+ smolts were transferred to sea during December (4 month advance) and October (6 month advance), respectively. A 12 month seasonal photocycle delayed by 3 months delayed smoltification by 2 months. Out-of-season smolts were produced in January, March, April, May, June, July, October, November and December. All groups of out-of-season smolts exhibited the same growth potential as natural smolts. The different transfer date of out-of-season smolts therefore resulted in different harvest periods compared to natural smolts. The age at maturity of out-of-season smolts was positively related to the length of the seawater growing period prior to the completion of maturation. Out-of-season smolts exhibited increased maturation in association with an increased size (compared to natural smolts) for a particular time of year. These large maturing fish were generally harvested as superior salmon prior to flesh deterioration. Mortality during the first month in sea water was significantly higher in a number of out-of-season smolt groups compared to natural smolts. This was considered to be related to site-specfic environmental conditions rather than the smoltification process. Smoltification was also examined under constant photoperiods and a 4 week period of short daylengths. Dissociation and suppression of certain aspects of smoltification were observed. The different aspects of smoltification: the development of bimodality, hypoosmoregulatory ability, decrease in condition and smolt coloration appeared to be controlled by different independent mechanisms. The development of bimodality, hypoosmoregulatory ability and possibly coloration appeared to be controlled by independent endogenous rhythms. The decrease in condition factor, associated with the parr-smolt transformation required a period of short day length greater than 2 months followed by a period of long daylength. Smoltification and maturation were examined in salmon retained in constant 1DOC borehole water. Smolts held in fresh water grew steadily and matured producing eggs and sperm both in- and out-of-season. There was, however, a period of increased mortality after smoltification and egg quality was reduced especially in fish subjected to photoperiod manipulation. The salmon responded to photoperiodic manipulation. Abrupt changes in photoperiod advanced spawning by 12 weeks and a reciprocal seasonal photoperiod (6 month out of phase with a natural photoperiod) advanced spawning by 22 weeks. The maturation process in the Atlantic salmon would appear to be controlled by similar mechanisms to those described for the rainbow trout. Freshwater holding conditions appeared to decrease the age at maturity and reduce egg quality. The progeny of freshwater broodstock (FI generation) successfully completed smoltification and seawater transfer. Photoperiodic manipulation can be used to produce out-of-season smolts and eggs. Through the use of photoperiod, farms could increase and target production. This could remove the seasonality from the production cycle and help stabilise the pricing structure for market salmon.