The nature and extent of microbial biodiversity remain controversial with persistent debates over patterns of distributions (i.e. cosmopolitanism vs. endemism) and the processes that structure these patterns (neutrality vs. selection). I used culture-independent approaches to address these issues focusing on two groups of ciliates, the Oligotrichia (Spirotrichea) and Choreotrichea (Spirotrichea). To assess the diversity of these ciliates, I designed primers specific to SSU rDNA of ciliates within these clades, and investigated (1) geographic and temporal distributions along three coastal sites in the Northwest Atlantic; (2) the relationship between ciliate communities in the benthos and the plankton along the New England coast; and (3) diversity in ciliate communities across an environmental gradient at six stations in Long Island Sound spanning the frontal region that separates the fresher Connecticut River outflow plume from the open Sound. Each collection had its own distinct assemblage of rare and abundant ciliate haplotypes, and genealogical analyses of my samples combined with published sequences from identified morphospecies reveal that haplotype diversity at these sites is greatest within the genus Strombidium, in the Oligotrichia. Clustering of phylogenetic types indicates that benthic assemblages of oligotrichs and choreotrichs appear to be more like those from spatially distinct benthic communities than the ciliate communities sampled in the water above them. Neither ciliate diversity nor species composition showed any clear relationship to measured environmental parameters (temperature, salinity, accessory pigment composition, and chorophyll), although I observed that diversity decreased moving from nearshore to offshore. I find no strong fit of my communities to log series, geometric, or log normal distributions, though one of the 3 clusters is most consistent with a log series distribution. These analyses suggest that Oligotrich and Choreotrich communities in coastal environments may be distributed in a neutral manner. I investigated the effectiveness of molecular approaches in characterizing ciliate diversity in my samples. Estimates of diversity based on molecular markers are similar to estimates from morphological observations for Choreotrich ciliates, but much greater for Oligotrich ciliates. Sediment and plankton subsamples differed in their robustness to repeated subsampling. Sediment gave variable estimates of diversity while plankton subsamples produced consistent results.

This dissertation research aims to show that there are deterministic microbial distribution patterns based on quantifiable environmental thresholds by determining and rationalizing the relative abundances of hyperthermophilic methanogens, autotrophic iron(III) oxide reducers, and heterotrophic sulfur reducers within deep-sea hydrothermal vents. Organisms of these metabolisms are predicted to be relatively more abundant in different regions depending on environmental conditions such as reduction potential, organic carbon, and hydrogen availability. The relative abundances of these metabolic groups within samples from the Endeavour Segment and Axial Volcano in the northeastern Pacific Ocean were determined. Iron(III) oxide reducers were detected in nearly all samples while methanogens were generally not present or present in concentrations lower than those of the iron(III) reducers. To determine growth constraints and the effect of hydrogen concentration on hyperthermophilic methanogen growth kinetics, Methanocaldococcus jannaschii and two new Methanocaldococcus field isolates were grown at varying hydrogen concentrations. The hydrogen-dependent growth kinetics for all three strains were statistically indistinguishable, exhibiting longer doubling times and lower maximum cell concentrations with decreasing hydrogen concentrations until growth ceased below 17–23 µM. This minimum hydrogen concentration for hyperthermophilic methanogenesis was correlated with field microbiology and fluid geochemistry data from the Endeavour Segment and Axial Volcano. Anomalously high methane concentrations and thermophilic methanogens were only observed in fluid samples where hydrogen concentrations were above this predicted threshold. Aside from anomalous sites, methanogens are predicted to be hydrogen limited, and may rely on hydrogen produced by heterotrophs as suggested by in situ sampling and co-culture experiments. Models and kinetic experiments suggest that iron(III) oxide reducers are not hydrogen limited under the same conditions. A Methanocaldococcus strain that we isolated from Axial Volcano and used in our hydrogen threshold experiments was bioenergetically modeled over its range of growth temperatures, pH, NaCl concentrations, and NH4Cl concentrations. Its methane production rates and growth energies were largely constant but increased at superoptimal temperatures and when nitrogen was limiting. The results of this research demonstrate that the rates of and constraints on metabolic processes can be used to predict the distribution and biogeochemical impact of hyperthermophiles in deep-sea hydrothermal vent systems.

This dissertation investigates the role of climate and ocean conditions on the marine survival of Atlantic salmon. The overall objective was to identify the relevant environmental variables controlling salmon marine survival, in order to establish predictive models of marine recruitment. These models are required to improve the management process of the Irish and European salmon resources. I first explored the levels of synchrony in the marine survival of European salmon, in order to assemble evidence on the spatial scale of the processes controlling survival. I demonstrate that these levels of synchrony are low and I conclude that large scale events are not directly exerting a control on the rates of salmon survival, perhaps indicating the presence of several intermediary processes. Using information from a scale analysis of a monitored Irish population, I then explore the hypothesis that marine survival is linked to marine growth. I present evidence that the level of marine recruitment of 1 SW salmon is linked to growth during the marine residency, and that decreasing growth over the last 30 years explains the observed decrease in salmon recruitment. Finally, I explore the role of several environmental variables on salmon marine survival, by constructing semi-parametric models (GAMs) of marine survival for wild and hatchery Irish populations. These models explain an important part of the inter-annual variability in survival and provide a capability to forecast survival. These models also help to identify the role of specific variables, more specifically the North Atlantic Oscillation, sea surface temperatures, and the abundance of zooplankton, to explain the variations in survival. I conclude that the changes in climate in the northeast Atlantic have affected the salmon via bottom-up effect, by affecting the abundance, distribution and phenology of key zooplankton species in the northern North Sea and southern Norwegian Sea.

This dissertation is the first critical analysis of patterns of species diversity in a deep-sea taxon (the Gastropoda) on a global scale. My analysis is based on 85 epibenthic sled samples collected from soft sediments in ten deep-sea regions of the Norwegian Sea and Atlantic Ocean. Over 21,000 gastropod individuals were sorted to species and their mode of larval development was documented. The basins from which the samples were taken represent a broad range of ecological circumstances that may affect species diversity and taxonomic composition. Bathymetric patterns of species diversity were shown to vary significantly among deep-sea basins. Unusually high or low values of diversity appear to be associated with environmental disturbance or rates of nutrient input. The most important and unexpected finding was that on a global scale there are latitudinal gradients in deep-sea species diversity similar to those in shallow-water and terrestrial environments. Gastropods show a clear and highly significant latitudinal decrease in diversity from the equator to 77$\sp\circ$N in the North Atlantic and a significant decrease from the equator to 37$\sp\circ$S in the South Atlantic. Depressed diversity at higher latitudes in the deep-sea, in part, may be related to seasonal nutrient loading and frequent physical disturbance from bottom currents. At lower latitudes, these same ecological factors may become less intense and variable. A multiple regression analysis showed that the North Atlantic local (sample) diversity is highly correlated with regional (basin) diversity suggesting that evolutionary-historical processes play a role in the development of deep-sea diversity through the mechanism of regional species enrichment. The percentage of species with planktotrophic development in the regional species pool was also correlated with local diversity. For the South Atlantic, the pattern of latitudinal diversity is less clear. On global scales, diversity gradients may be shaped by the interplay between the ecological potential and the history of evolutionary diversification at different latitudes. Underlying evolutionary processes that influence local diversity are difficult to recognize on a local scale, but may be revealed through large-scale patterns of species diversity. (Abstract shortened with permission of author.)

<p> Oysters are important to estuarine ecosystems because of the functions they provide. Thus, oyster restoration projects are undertaken in areas where natural populations have declined. However, restoration techniques can impact sediment organic matter and benthic invertebrates that provide trophic support for important species. This study assesses the impacts of a constructed shell bed on associated sediment and invertebrate communities in a southern California bay. Within the bed site, organic matter, invertebrate abundance, and invertebrate species richness are lower only under the oyster bed. The alteration in the community under the shell is driven by a reduction in species. Tubificidae were the only remaining species under the shell. These results may be explained by the shells&rsquo; action as a barrier to the mud-water interface. While significant, impacts of oyster bed construction are spatially restricted to just under the bed. Longer-term studies should be conducted to address effects of the oysters themselves.</p>

No description available.

<p> The purpose of this dissertation was to examine the influence of environmental variability on the distribution of prey, and the influence of prey spatial structure and habitat variability may have on the distributions of bottlenose dolphins (<i>Tursiops truncatus</i>). Additionally I examined how sociological differences (behavior type and the changes in a foraging behavior specific to Cedar Key Florida) influences the relative roles of bottlenose dolphins within the population. </p><p> The Gowans et al. scheme assumes that small groups form small communities and that foraging groups are small and rare as there are few foraging benefits to promote grouping. Using network analysis, I found that foraging occurs in small groups or alone, but there were preferential associations between individuals in Overall, Socialize, and Travel networks. </p><p> I examined driver-barrier foraging behavior over several field seasons to assess the prediction that there are few foraging benefits to promote grouping. The driver dolphin does have greater catch success than the barrier dolphins regardless of group size. There is also evidence that barrier dolphins may have a role in increasing foraging efficiency by decreasing the number of incomplete bouts. Both the driver and barrier dolphins do better in larger groups when incomplete bouts are factored in. Therefore there are some foraging benefits that can promote grouping. </p><p> In bottlenose dolphin foraging research, it is often assumed that habitat use is related to prey availability, though this is rarely directly tested. From my collaborative work using a database collected by the Florida Fish and Wildlife Commission&rsquo;s Fisheries-Independent Monitoring (FIM) program, I evaluated the abundance of potential prey and their relationship to habitat and other biological and physical variables. I used MULTISPATI, which uses principal components analysis to partition and display patterns of spatial variation. The results show that there are correlations between fish-site scores and environmental variables. Spatial analysis of fish produced clear results, however neither PCA nor MULTISPATI could explain dolphin distribution. This is likely because the spatial scales are not the same grain for the comparisons; dolphins are highly mobile large marine predators (the scale is fine grained), and their prey are significantly smaller and habitat-specific (the scale is coarser).</p>

Fish larvae in Australian waters have been studied progressively in the last 2-3 decades including the distribution and abundance of taxa, growth and age, their prey and predators. However, the effect of nutrient limitation on ichthyoplankton is unstudied, particularly in the oligotrophic Australian waters. My study was aimed to examine the effect of natural or anthropogenic nutrients on the abundance, distribution, growth and condition of fish larvae along-shore of the NSW coast (latitude 30-34S), where the East Australian Current departs the NSW coast and generates local upwelling of cool nutrient-rich water. This study shows no significant difference in the total abundance or diversity of either larval fishes amongst the 112 taxa (111 families and 1 order), among regions within or upstream of the upwelling. However in both months, there were distinctive ichthyoplankton assemblages at the family level. The Carangidae, Labridae, Lutjanidae, Microcanthidae, Myctophidae and Scombridae were more abundant in the EAC or oceanic water masses, while the Callionymidae, Clupeidae, Platycephalidae, Sillaginidae and Terapontidae were mostly found in the surface or deep upwelled/uplifted water masses. This pattern is observed in other ichthyoplankton studies and may be a general and useful method to determine mixing of water masses. Larvae of silver trevally (Pseudocaranx dentex) and yellowtail scad (Trachurus novaezelandiae) were generally larger and less abundant in the topographically induced upwelling region, than north of the region in pre-upwelled conditions of the East Australian Current. Both species were mostly at the preflexion stage (less than 4.3 mm in body length and less than 10 days old) in the pre-upwelled conditions, particularly during November, and proportionally more larger and older larvae in the upwelled waters (mostly post-flexion, greater than 4.3 mm in body length and greater than 10 days old). Ages from sagittal otoliths ranged from 2-25 increments (~days) and exhibited linear growth for both species and months over the size range (3-15 mm standard length). The otolith radius-length relationship and the growth rates were similar between species and months, despite the 3-4C difference between months. Overall growth rates of the younger larvae were uniform throughout the entire sampling area (0.5-0.6 mm.d-1), while older larvae grew significantly faster in the upwelled water (0.41 mm.d-1) compared to the non-upwelled conditions (0.34 mm.d-1). Both species tended to be depleted in 13C in the upwelling region (from ???18.5 to ???19.0), consistent with expected ratios from deeper water, whereas the 15N composition tended to increase in Pseudocaranx, but decrease in Trachurus indicating different diets and possibly trophic level. The early life history of both species indicates spawning in pre-upwelled waters, but larval transport into upwelled waters is necessary for faster growth in the post-flexion stage. The assemblage of larval fishes did differ between the upwelled region and a region south of Sydney???s deepwater outfalls, but the difference was ascribed to a latitudinal effect and the EAC. Both larval carangids were enriched in 15N, possibly due to the enriched dissolved organic matter of primary treated sewage. In summary, this study found that the larval fish community can provide a biological means to trace water masses, and estimate their degree of mixing. Remarkably there was no significant effect of upwelling or sewage addition to the abundance or diversity of larval fish, in the nutrient poor waters of the East Australian Current. Larval carangids and pilchards were abundant in late spring off northern NSW, and their early life histories were inferred. Both larval carangid species seem to be spawned in the EAC waters, but as post-flexion larvae grew faster in the upwelled zone. Pre-flexion (less than 10 day old) larval carangids of both genera indicated spawning in the EAC, and the rarer post-flexion (greater than 10 days old) carangids grew faster in the upwelled waters. Here, both genera had stable isotope signatures characteristic of upwelled waters for carbon, but had different nitrogen signatures, indicative of different diets and trophic level status. Larval pilchards actually grew more slowly in the upwelling region, as observed in coastal waters off Japan, and their nursery grounds may be further offshore in the Tasman Front, analogous to their early life history in the Kuroshio Extension.

Fish larvae in Australian waters have been studied progressively in the last 2-3 decades including the distribution and abundance of taxa, growth and age, their prey and predators. However, the effect of nutrient limitation on ichthyoplankton is unstudied, particularly in the oligotrophic Australian waters. My study was aimed to examine the effect of natural or anthropogenic nutrients on the abundance, distribution, growth and condition of fish larvae along-shore of the NSW coast (latitude 30-34S), where the East Australian Current departs the NSW coast and generates local upwelling of cool nutrient-rich water. This study shows no significant difference in the total abundance or diversity of either larval fishes amongst the 112 taxa (111 families and 1 order), among regions within or upstream of the upwelling. However in both months, there were distinctive ichthyoplankton assemblages at the family level. The Carangidae, Labridae, Lutjanidae, Microcanthidae, Myctophidae and Scombridae were more abundant in the EAC or oceanic water masses, while the Callionymidae, Clupeidae, Platycephalidae, Sillaginidae and Terapontidae were mostly found in the surface or deep upwelled/uplifted water masses. This pattern is observed in other ichthyoplankton studies and may be a general and useful method to determine mixing of water masses. Larvae of silver trevally (Pseudocaranx dentex) and yellowtail scad (Trachurus novaezelandiae) were generally larger and less abundant in the topographically induced upwelling region, than north of the region in pre-upwelled conditions of the East Australian Current. Both species were mostly at the preflexion stage (less than 4.3 mm in body length and less than 10 days old) in the pre-upwelled conditions, particularly during November, and proportionally more larger and older larvae in the upwelled waters (mostly post-flexion, greater than 4.3 mm in body length and greater than 10 days old). Ages from sagittal otoliths ranged from 2-25 increments (~days) and exhibited linear growth for both species and months over the size range (3-15 mm standard length). The otolith radius-length relationship and the growth rates were similar between species and months, despite the 3-4C difference between months. Overall growth rates of the younger larvae were uniform throughout the entire sampling area (0.5-0.6 mm.d-1), while older larvae grew significantly faster in the upwelled water (0.41 mm.d-1) compared to the non-upwelled conditions (0.34 mm.d-1). Both species tended to be depleted in 13C in the upwelling region (from ???18.5 to ???19.0), consistent with expected ratios from deeper water, whereas the 15N composition tended to increase in Pseudocaranx, but decrease in Trachurus indicating different diets and possibly trophic level. The early life history of both species indicates spawning in pre-upwelled waters, but larval transport into upwelled waters is necessary for faster growth in the post-flexion stage. The assemblage of larval fishes did differ between the upwelled region and a region south of Sydney???s deepwater outfalls, but the difference was ascribed to a latitudinal effect and the EAC. Both larval carangids were enriched in 15N, possibly due to the enriched dissolved organic matter of primary treated sewage. In summary, this study found that the larval fish community can provide a biological means to trace water masses, and estimate their degree of mixing. Remarkably there was no significant effect of upwelling or sewage addition to the abundance or diversity of larval fish, in the nutrient poor waters of the East Australian Current. Larval carangids and pilchards were abundant in late spring off northern NSW, and their early life histories were inferred. Both larval carangid species seem to be spawned in the EAC waters, but as post-flexion larvae grew faster in the upwelled zone. Pre-flexion (less than 10 day old) larval carangids of both genera indicated spawning in the EAC, and the rarer post-flexion (greater than 10 days old) carangids grew faster in the upwelled waters. Here, both genera had stable isotope signatures characteristic of upwelled waters for carbon, but had different nitrogen signatures, indicative of different diets and trophic level status. Larval pilchards actually grew more slowly in the upwelling region, as observed in coastal waters off Japan, and their nursery grounds may be further offshore in the Tasman Front, analogous to their early life history in the Kuroshio Extension.

xvii, 141 p. : ill. / Territoriality, defined as an animal or group of animals defending an area, is thought to have evolved as a means to acquire limited resources such as food, nest sites, or mates. Most studies of territoriality have focused on vertebrates, which have large territories and even larger home ranges. While there are many models used to examine territories and territorial interactions, testing the models is limited by the logistics of working with the typical model organisms, vertebrates, and their large territories. An ideal organism for the experimental examination of territoriality would exhibit clear territorial behavior in the field and laboratory, would be easy to maintain in the laboratory, defend a small territory, and have movements and social interactions that were easily followed. Lottia gigantea , the owl limpet, is just such a model animal. With a small territory (< 900 cm 2 ) and slow movements (3 mm/min), the interactions of several L. gigantea can be continuously and simultaneously monitored. Using time-lapse photography, experiments were conducted to observe behaviors of L. gigantea , ranging from how L. gigantea form home ranges to how territorial L. gigantea interact. Lottia gigantea formed home ranges within four weeks, returning to a home scar after each foraging cycle. To determine whether L. gigantea returned to areas with greater food resources, three different algal density treatments were used, and individuals were monitored to see which tiles they frequented the most. Lottia gigantea actually avoided areas with a thick algal covering, potentially due to the loss of suction they experienced while moving across algae. When L. gigantea established territories, home ranges overlapped considerably. Two individuals were placed in one arena, under the assumption that a dominance hierarchy would be established. Dominant status was predetermined, and in four of the seven dyads both individuals were evasive. When subjected to territorial encounters for two weeks, L. gigantea avoided areas where they experienced agonistic losses. Mucus may serve as an olfactory cue to define territorial boundaries. Individuals avoided tiles with conspecific's mucus more often than tiles with self-mucus or no mucus. / Committee in charge: Barbara (“Bitty”) Roy, Chairperson; Alan Shanks, Advisor; Craig Young, Member; Mark Hixon, Member; Frances White, Outside Member