Dissertations / Theses on the topic 'Aquatic biology'

Sensory biology of animals is studied throughout the world for the insight it provides to understanding ecosystems and improving how we manage species. In this research, I designed experiments to investigate the sensory biology and behaviour of two Australian species of freshwater crayfish from the genus Cherax, the yabby (Cherax destructor) and redclaw crayfish (Cherax quadricarinatus). Experimental apparatus were constructed and tailored to test specific questions on physiology, tactile (touch) sensitivity, observation techniques, aggressive behaviour and responses to electrical fields. The outcomes were:
• abdominal muscle mass was positively correlated to the size of the electrical fields produced by swimming crayfish,
• behaviour changed in response to contact with different structures and textures of wall surfaces,
• computer analysis of underwater behaviour was similar to that scored by a human observer,
• the level of aggression in groups of crayfish changed as group size increased, and
• two species of crayfish responded to electrical fields in the water by decreasing their locomotory movement.
These results reveal a way in which physiology relates to behaviour, how crayfish and other crustaceans may sense the invisible and behave in aquaculture ponds, as well as documenting methodology to further investigate these areas in the future.

Species invasions threaten the integrity of biotic communities, as invaders may outcompete and replace resident species. For many aquatic invaders, species replacements are driven by aggression. I explored this phenomenon through a quantitative synthesis and laboratory experiments. A quantitative synthesis of published studies on aggression in aquatic invaders found that body size and prior residency generally mediate the outcome of aggressive encounters, but there is no consistent tradeoff between intra- and interspecific aggression. As the majority of studies on agonistic interactions focus on phylogenetically related species, I investigated such interactions between two unrelated invasive species that occupy a similar niche: the round goby (Neogobius melanostomus) and the spinycheek crayfish (Orconectes limosus), both benthic omnivores that compete for shelter. Laboratory experiments revealed that round gobies were more aggressive than crayfish, regardless of prior residency. Heightened aggression may be a selective advantage for an animal to invade a habitat occupied by another territorial species.
Les invasions d'espèces posent une menace à l'intégrité des communautés biologiques, puisque les espèces envahissantes peuvent gagner la compétition contre les espèces résidentes et en conséquence les supplanter. Le remplacement par des espèces envahissantes est souvent dû à leur comportement agressif. J'ai étudié ce phénomène en employant des méthodes de méta analyse et des expériences en laboratoire. Une méta analyse sur les actes d'agression chez les espèces envahissantes a démontré que la taille du corps et le statut de résidence antérieure affectent généralement le résultat des affrontements, mais il n'y a pas de compromis entre les actes d'agression intra et interspécifique. Puisque la plupart des études sur les interactions agonistes se concentrent sur des espèces apparentées taxonomiquement, j'ai examiné une telle interaction entre deux espèces envahissantes éloignées taxonomiquement qui occupent une niche semblable : le gobie à taches noires (Neogobius melanostomus) et l'écrevisse américaine (Orconectes limosus), deux omnivores qui se font compétition pour leur refuge. Les expériences en laboratoire ont démontré que les gobies à taches noires étaient plus agressifs que les écrevisses, indépendamment du statut de résidence antérieure. Le comportement agressif accru peut être un avantage sélectif qui permet à un animal d'envahir un habitat occupé par une autre espèce territoriale.

While environmental controllers of decomposition have been extensively studied, organic matter quality and biotic controllers of decomposition, such as detritivore preference and manipulation of detritus, are largely understudied. In the studies described in this dissertation, a range of biotic controllers of detrital dynamics in aquatic ecosystems are presented. Crayfish, as model shredders, produce a diverse pool of fine particulate organic matter (FPOM) through fragmentation of coarse particulate organic matter (CPOM) and fecal production in the laboratory. Crayfish process maple leaves at a greater rate than oak leaves, and produced a greater amount of FPOM from maple compared to oak. Crayfish-generated FPOM had lower C:N ratios and increased bacterial abundances compared to original CPOM. Further, hydropsychid caddisfly and simuliid blackfly larvae confer greater growth efficiency when reared on crayfish-generated FPOM compared to mechanically ground FPOM in the laboratory, indicating that crayfish increase bioavailability of FPOM. No differences in growth or metamorphosis of simuliid larvae were observed when larvae were lab-reared on crayfish-generated FPOM from CPOM of different tree species (i.e., sugar maple, sycamore, or white oak) or different stream conditioning times (i.e. , 30 or 150 d). This suggests that crayfish processing reduces organic matter origin effects on bioavailability. Changes in macrophyte abundance in a tropical wetland due to competition and ecosystem management can affect litter availability and litter quality. In two field-based, replacement series experiments with floating-mat macrophytes (Eichhornia crassipes and Neptunia oleracea), no interspecific competition was detected. However, E. crassipes dominated experimental enclosure biomass through attrition. Decomposition rates were faster for E. crassipes litter compared to N. oleracea litter within enclosures, but no differences in decomposition rates were detected by floating-mat species composition. Both synergistic and antagonistic diversity effects were observed on decomposition dynamics in an experiment varying litter richness from one to five species. Additionally, cattail (Typha domingensis ) eradication efforts lead to changes in the decomposition landscape within the wetland, as E. crassipes colonizes managed areas, and decomposition rates were slower for litter of T. domingensis compared to E. crassipes. The compounding effects of litter species, detritivore interactions, and anthropogenic impacts on organic matter dynamics illustrate that it is critical to consider ecosystem function in ecosystem management.

I examined flow-ecology relationships among stream communities in the Ozark Highlands, USA. I sampled fish, crayfish, and benthic macroinvertebrates during two consecutive summers, including a drought year (2012) and a flood year (2013). Biological response variables related to community structure were assessed via two different statistical methods: an Information Theoretic approach relating response variables to a priori selected predictor variables incorporating hydrology, habitat, geomorphology, and water quality, and canonical ordination using forward selection to relate these same response variables to a large assortment of hydrologic metrics. In addition to assessing metrics related to predicted natural flow, flow alteration at gaged sites was also quantified and community metrics were assessed with respect to flow alteration. Additionally, I conducted a manipulative laboratory greenhouse experiment to examine the effects of stream drying, one of the major components of the natural hydrologic disturbance regime in the region, on stream fishes as well as benthic community structure. Hydrologic variation was often less important than other environmental variables and substantial temporal variation existed in flow-ecology relationships. Stream flow magnitude was the most important category of hydrologic metric overall, but there were key differences in which metrics were important for each assemblage and how those assemblages responded to those metrics. Flow alteration has a strong effect on Ozark riverine communities, and the most important categories of flow alteration affecting these communities are magnitude of average flows, and frequency, magnitude, and duration of high flows. The large number of important high flow metrics suggests that flood events may play a particularly crucial role in structuring aquatic assemblages in the region. I found that seasonal stream drying had strong species-specific effects on organisms in pool refuges, and that type of drying specifically affected periphyton growth. Overall, I found that the elucidation of flow-ecology relationships and management decisions that are based on those relationships face a variety of challenges: the complex interaction of hydrology with other kinds of environmental variables, temporal variation in the aquatic community, and the differential effects of flow metrics on different assemblages.

Most quantitative ecological research on aquatic insects has addressed their immature stages. To understand their population dynamics, however, information on the adult stage is essential. This study aimed to obtain quantitative estimates of life cycle features, such as emergence, adult life span and fecundity, and to develop further the methods used. Field studies on adult insects revealed patterns in spatial and temporal distribution and the effect of land use on lateral dispersal. Finally, methods used to estimate dispersal and gene flow were discussed. Studies on Leuctra nigra demonstrated that their emergence is associated with the quantity of emergent substratum locally available. Female L. nigra can be classified as "immature" and "mature", based on the maturity of their eggs, and this was used as an approximate age marker in studies of adult survival and spatial distribution, and to improve estimates of emergence by excluding mature females from catches in pyramidal traps. A female biased sex ratio observed in L. nigra stemmed from a discrepancy in the life span of the genders, with shorter-lived males, combined with a change in habitat by the females. Most adult aquatic insects stayed close to the stream. Thus, half of the stoneflies travelled less than 18 m lateral to the channel and the dispersal ranges of caddis flies and female of mayflies were even shorter. Comparison of the movement along the stream with the lateral dispersal suggests that most dispersal is in the 'stream corridor' itself. Little distinction was found between lateral dispersal in different catchment land uses. It is still too early, however, to conclude that dispersal is unaffected by land use. Temporal and spatial distribution of leuctrid stoneflies differed among neighbouring catchments, with Leuctra inermis and L. nigra dominating in moorland and catchments managed for forestry, respectively. Both physiochemical factors and biological interactions could explain this distribution.

The aim of this study was to improve our understanding of the biology of two alien, invasive, free-floating species, the Water Fern Azollafiliculoides and the Least Duckweed Lemna minUla, which cause severe weed problems in Britain. Hence, control practices, which had been based upon anecdotal information, could be given a scientific foundation. An appraisal of the known distributions of the two species in Britain was undertaken. From an analysis of spread to date, it can be predicted that L. minUla will be present in 150 and A.filiculoides in 500, 10 x 10 km grid squares by the year 2000. Neither A. filiculoides nor L. minuta produce specialised overwintering structures and both rely heavily on ordinary, vegetative plants to overwinter. It was found that vegetative plants of both species can survive encasement in ice and laboratory studies show that they can withstand short exposure to sub-zero temperatures above approximately -4 °C. However, field evidence suggests that both species can survive much more severe temperature conditions, so both are considerably less cold-sensitive than previously suggested. L. minuta is not known to reproduce sexually in Britain. However, A. filiculoides sporulates regularly over a wide geographical range to produce numerous, viable sporocarps. These sporocarps form a 'seed' bank in the sediment and may ensure population survival because they are more freeze- and desiccation- tolerant than adult plants. Sporocarps require temperatures of not less than 10 °C and a short burst of light to germinate. L. min uta plants vary very little seasonally (although larger summer fronds can be easily confused with the common, native duckweed Lemna minor). In contrast, three forms of A. jilicuJoides can be identified; survival, mat and colonising. Competition experiments suggested the following tentative order of decreasing competitive ability; A. filiculoides > L. minuta > L. minor. This was probably a result of the more erect A filiculoides plants growing over the Lemna fronds. Not all field evidence supports this finding. Floating mats of A.filiculoides and L. minuta cause similar ecological problems because they reduce light, pH and oxygen and increase detrit~:s and probably alter nutrient loading. Laboratory studies showed that morphologically and physiologically plastic species of submerged plants, ego Elodea nuttall;;, could withstand these conditions better than less adaptable species, ego Potamogeton crispus. Four chemical control methods were tested over a range of dosages in the laboratory; diquat (as both spray and sub-surface injection), glyphosate (as spray) and terbutryn (as sub-surface application). These treatments were unsuccessful in controlling L. minuta, in contrast to anecdotal field evidence where terbutryn is considered effective. Glyphosate and diquat sprayed at 1.8 kg ai ha-1 and 1 kg ai ha-1 controlled A. jiliculoides. A. jiliculoides sporocarps were resistant to all chemical treatments.

Chitin belongs to the most abundant biopolymers on earth where it has an important role as a structural element in crustaceans, insects, fungi and some phytoplankton. Missing evidence for long-term accumulation of chitin in nature implies fast turnover and as chitin is composed of aminosugar subunits it holds central roles in both carbon and nitrogen cycles. The aim of this thesis was to contribute to a better understanding of organic matter cycling by learning more about the diversity, function and ecology of bacteria that degrade chitin. A metagenome-enabled study of the spatial distribution of chitinolytic bacteria in aquatic ecosystems identified salinity as the major environmental factor for shaping their community composition. To address the role of alternative environmental variables controlling chitinolytic communities, a temporally resolved study was completed in a dimictic freshwater lake. Pronounced seasonal change in the indigenous chitinolytic community was observed and parallel measured environmental parameters pointed to the availability and crystalline form of chitin as significant controlling factors.  The different ecological niches occupied by microbes that utilize chitin for growth were studied in an experimental study. Single-cell quantification of chitinolytic cells and cells incorporating chitin hydrolysis products suggested that commensal use of chitin hydrolysis products without simultaneous chitinase activity could be an important ecological strategy in freshwater bacterioplankton communities. Members of the ubiquitous and often quantitatively dominant group of freshwater Actinobacteria Ac1 were identified as particularly active in this “cheater” lifestyle. Further experiments based on artificially created gradients in bacterial diversity demonstrated the importance of specific bacterial populations and community composition rather than overall community richness in controlling more specific functions such as chitin and cellulose degradation. To conclude, results of this thesis provide insight into the biogeography, niche-separation and species interactions of the functional community of chitin degraders and the influence of general bacterial diversity to the respective system functioning.
Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 700

The appearance and disappearance of large numbers of medusae is a common characteristic of jellyfish populations. Blooms of jellyfish can attain very large biomasses that cover wide areas and can be short-lived, after which time the population may crash rapidly. The sheer biomass of jellyfish during bloom periods and the ‘boom and bust’ population dynamics are likely to have considerable impacts on the surrounding ecosystem. Some species of jellyfish contain symbiotic dinoflagellates called zooxanthellae. Zooxanthellae are able to assimilate nutrients from the surrounding water and transfer photosynthetic products to the host jellyfish. Zooxanthellate jellyfish are likely to acquire and recycle nutrients very differently to non-zooxanthellate species, and are therefore likely to have contrasting influences on nutrient cycling and trophodynamics. However, there are large gaps in our understanding of these processes. This thesis directly compares the role of zooxanthellate and non-zooxanthellate jellyfish on nutrient cycles and trophodynamics, by investigating these processes in zooxanthellate jellyfish, Cassiopea sp. and Phyllorhiza punctata, and the non-zooxanthellate jellyfish, Catostylus mosaicus. An important step in understanding the influence of jellyfish on ecosystem processes is to determine how nutrients are cycled within individual medusae. To do this, the exchanges of nutrients with the surrounding water were compared between zooxanthellate and non-zooxanthellate jellyfish. Experiments were done to compare the net exchanges (uptake and excretion) of organic and inorganic nitrogen and phosphorus with the surrounding water. Changes in nutrient concentrations were measured in tubs housing zooxanthellate Cassiopea sp., non-zooxanthellate C. mosaicus, and water control (no jellyfish). Experiments were repeated during the day, when photosynthesis and respiration could occur, and at night when only respiration could occur. Organic nutrients were found to comprise 25 - 43 % of the total excretion by non-zooxanthellate jellyfish. Organic nutrient excretion by blooms (506 t km-2) of non-zooxanthellate jellyfish were estimated to potentially support 62 – 120 mg C m-2 of bacterial production per day. In addition, excretion of inorganic nutrients by blooms of non-zooxanthellate jellyfish were estimated to potentially support 201- 423 mg C m-2 of primary production per day. In contrast, zooxanthellate jellyfish excreted minimal amounts of inorganic and organic nutrients or took them up from the water column. Therefore, nutrients assimilated by zooxanthellate jellyfish are likely to be retained and temporarily stored in the biomass of the population. The assimilation and retention of nitrogen were compared between zooxanthellate and non-zooxanthellate jellyfish. To do this, firstly, the assimilation and retention of nitrogen were directly compared between Cassiopea sp. and C. mosaicus. Jellyfish were labelled with isotopic nitrogen (15N) from two different sources, 15N-labelled Artemia prey and dissolved ammonium (15NH4+). The incorporation and retention of 15N was measured in the jellyfish tissues over nine days. Secondly, experiments were done to measure the influence of the availability of prey and concentrations of nutrients on the retention of nitrogen by Cassiopea sp. To do this, Cassiopea sp. were labelled with 15NH4+ and then placed in pools that had different combinations of high and low nutrient concentrations and high and low feeding regimes. The retention of 15N was measured in jellyfish over 37 days. Respiration and excretion rates were also measured for animals at the end of the experiment. Cassiopea sp. was found to assimilate nitrogen from both NH4+ and prey, and recycle this nitrogen internally. In contrast, C. mosaicus only assimilated nitrogen from prey and quickly excreted this nitrogen to the external environment, resulting in a short retention time. Cassiopea sp. retained nitrogen more than five times longer than C. mosaicus. Further, the nitrogen retention time of Cassiopea sp. was influenced by the availability of prey and dissolved nutrients, with the availability of prey having the greatest effect. Specifically, medusae exposed to low feeding retained nitrogen twice as long as medusae exposed to high feeding, which suggests that ingestion of prey by the host jellyfish is an important source of nitrogen in Cassiopea sp. Further, daily rates of photosynthesis and respiration suggest that photosynthesis by the zooxanthellae can potentially supply all of the carbon required for respiration and growth of the entire medusa. Jellyfish populations can hold considerable proportions of carbon and nutrients in an ecosystem and when a population crashes, jellyfish may sink to the benthos and decompose. An experiment was done that measured the changes in sediment oxygen demand as well as inorganic and organic nutrients during the decomposition of dead jellyfish, C. mosaicus. Fluxes were measured in tubs housing dead jellyfish over nine days as the jellyfish tissue decomposed. The decomposition of C. mosaicus resulted in a rapid leaching of organic nutrients from the dead tissues. Following this, microbial mineralisation dominated, which consumed oxygen and released dissolved inorganic nutrients. Although this release of nutrients may serve as a trophic link to pelagic primary producers, it may also lead to environmental problems associated with low oxygen concentrations depending on the size of the bloom and the degree of mixing in the system. Lastly, the influence of zooxanthellate and non-zooxanthellate jellyfish on plankton communities was compared. An in situ mesocosm experiment was done to compare the influence of C. mosaicus (non-zooxanthellate) and P. punctata (zooxanthellate). Changes in primary production and plankton assemblages were measured in mesocosms containing C. mosaicus, P. punctata, a combination of these species and compared to controls over six days. Catostylus mosaicus was found to increase chlorophyll a and productivity in the water column due to the large amount of nutrients excreted, causing a bottom-up influence on primary producers. This was in contrast to P. punctata, which were found to have little influence on chlorophyll a and production. This study provided direct experimental evidence that unlike C. mosaicus, P. punctata does not enhance primary production due to the minimal excretion of nutrients. Both P. punctata and C. mosaicus also had a large top-down predation pressure on zooplankton communities, causing significant declines in most species. This was with the exception of bivalve veligers, which were not consumed by either species, and gastropod veligers, which were not consumed by P. punctata. The major findings of this research have been integrated into a conceptual model that compares the influence of zooxanthellate and non-zooxanthellate jellyfish on nutrient cycles and trophodynamics. This model has been discussed in context to existing literature and recommendations have been made for future research. Overall this research found that zooxanthellate and non-zooxanthellate jellyfish assimilate, retain and release nutrients very differently and therefore have contrasting impacts on the nutrient cycling and trophodynamics of their surrounding ecosystem.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

During 1991 and 1992, I studied environmental contamination of the aquatic communities at Imperial National Wildlife Refuge on the lower Colorado River. I collected composite samples of sediment, detritus, aufwuchs, aquatic plants, invertebrates, and fishes from 2 river sites, 5 backwater lakes, and 2 seepage lakes. Selenium concentrations (μg/g, dry weight) were elevated in sediment (geometric mean = 0.93, range = none detected (ND) to 4.1); detritus (4.50, 0.4-27.4); aufwuchs (4.85, 2.6-10.2); Najas marina (5.66, ND-21.0); Corbicula spp. (10.54, 5.8-26.5); Procambarus clarkii (7.70, 1.5-35.8); whole fishes (6.70, 1.6-17.2); and fish fillets (9.72, 5.8-22.6). Ninety-four percent of whole fishes and invertebrates (n = 185) contained concentrations of selenium that exceeded 3 μg/g, a concentration recommended by the U.S. Fish and Wildlife Service to protect aquatic birds from chronic selenium toxicity. Biological samples from seepage lakes had significantly lower (p ≤ 0.05) selenium levels than similar samples from backwater lakes. Selenium is incorporated into plants in backwater lakes and enters consumers primarily through the detrital food web.

Freshwater and terrestrial ecosystems are tightly linked by food web interactions. Naturally occurring carbon and nitrogen stable isotopes provide a tool to quantify nutrient flows across ecological boundaries, however their application to freshwater-terrestrial systems has been limited. This thesis evaluated whether stable isotope analysis can be effective in differentiating freshwater and terrestrial vascular plants at the base of subarctic food webs and found freshwater plants to be consistently enriched in their isotopic signatures relative to terrestrial plants. Stable isotope approaches were then used to investigate spatial and temporal variability in the diet of a population of subarctic beavers (Castor canadensis). Freshwater macrophytes contributed more to the diets of beavers than previously reported. During the winter, beavers from pond habitats consumed more aquatic vegetation than beavers from stream habitats which relied more heavily on food hoards of terrestrial vegetation. Aquatic foraging may enable beavers to persist at the northern periphery of their range by reducing foraging pressure on the subarctic terrestrial ecosystem where their preferred tree species are scarce.
Les écosystèmes d'eau douce et terrestres sont liés par les interactions trophiques. Les isotopes stables naturels de carbone et d'azote offrent une méthode pour quantifier les transferts de nutriments entre les frontières écologiques, mais leurs applications aux systèmes d'eau douce-terrestres sont encore limitées. Cette thèse évalue l'efficacité des isotopes stables pour distinguer les plantes vasculaires d'eau douces et terrestres qui forment la base des chaînes alimentaires subarctiques. Nous avons trouvé qu'en général les plantes aquatiques avaient des signatures isotopiques enrichies par rapport aux plantes terrestres. Nous avons ensuite employé les techniques d'isotopes stables pour évaluer la variabilité spatiale et temporale dans le régime alimentaire d'une population de castors (Castor canadensis) subarctiques. Les macrophytes aquatiques semblent avoir une place plus importante dans le régime alimentaire des castors en comparaison avec la littérature disponible. Durant l'hiver, les castors qui habitaient les lacs ont consommé plus de végétation aquatique par rapport aux castors qui habitaient dans les rivières, ceux-ci comptant plutôt sur les provisions de végétation terrestre. L'accumulation de provisions constituées de plantes aquatiques peut permettre aux castors de persister à la limite de leurs aires de distribution où les arbres préférés des castors sont rares. Ainsi, ce phénomène pourrait réduire la pression des herbivores sur ces écosystèmes terrestres à faible productivité.

Larval Anisakis simplex, Pseudoterranova decipiens, Contracaecum osculatum and larvae and adults of Hysterothylacium aduncum were recovered from specimens of cod, haddock, blue whiting and bull rout; however, only A.simplex were retrieved from long rough dab. The epidemiology of infection by these four nematode species was examined both in whole fish, and in individual host tissues and organs. Frequency distributions of nematodes were found to be generally overdispersed in fish. Preliminary investigations revealed no strong evidence to suggest that competi tive interactions occurred between ascaridoid nematodes wi thin fish. Stomach lesions in gadoids were associated with single (partially penetrated) and mul tiple (throughout stomach wall) worm infections of larval A.simplex; such lesions were discrete and raised in appearance. Lesions associated with 1-3 larval P.decipiens in an open cavity within the stomach of angler fish were diffuse and not significantly raised. Histological examination of each form of ulcer revealed general similarities in pathology, with infil tration of inflamatory cells being the initial response to the nematode\s. Changes in the cephalic morphology of A.simplex, P.decip1ens, C.osculatum and H.aduncu were examined at different life cycle stages under scanning electron microscopy. Due to their small size, newly hatched third stage larvae of P .decip1ens were cultured in a bacterial mat prior to fixation for S.E.M., and the external ultrastructure of these larvae is described. The most prominent external feature at this stage is the cephalic boring tooth. Aspects of the internal ultrastructure of A. simplex, P.decipiens, C.osculatum and H.aduncu were examined using transmission electron microscopy. Newly hatched third stage larvae of P.decipiens show little differentiation of internal organs. The ultrastructure of sensory amphids in H.aduncum and A. simplex is cons i stent wi th that of a chemoreceptor, that of the single papilla in P.decipiens a mechanoreceptor. The ultrastructure of the digestive tract, excretory gland and body wall of marine ascaridoids were also examined.

Sexual reproduction provides submerged aquatic vegetation (SAV) populations unique opportunities for dispersal, genetic mixing, and resilience in the event of catastrophic population declines. Relative to asexual reproduction, sexual reproduction is a risky resource investment and can have a lower probability of success. A wide variety of abiotic and biotic interactions common in both terrestrial and aquatic environments can lead to significant mortality of seeds and seedlings. The goal of this dissertation is to explore the diversity of biological interactions that influence seed and seedling survival in SAV that drive the population dynamics and restoration success of SAV species. A combination of survey and experimental methods were used to test if three biological interactions, disturbance, herbivory, and competition, compromised seedling recruitment for three different SAV species growing in three different coastal environments. Chapter One explored the influence of sediment bioturbators on seedling establishment for the seagrass Posidonia australis in a marine environment. Field surveys demonstrated that dispersed seeds of P. australis overlap with a suite of sediment bioturbators that disturb the sediment in the coastal lagoons of Western Australia. The movement of sediment bioturbators found in these areas (sand dollars, sea stars, and heart urchins) dislodged and moved recently settled P. australis seeds. The overlap in habitat suitability between these animals and P. australis seeds suggests high densities of these animals consistently disturb non-dormant P. australis seeds and may act as a bottleneck to seedling recruitment. Chapter Two explored the role of grazers on seedling recruitment of a freshwater angiosperm. Field surveys recorded high grazing levels of isolated Vallisneria americana propagules in oligohaline areas of the James and Chickahominy Rivers, VA. Camera surveys identified the blue crab, Callinectes sapidus, as a likely herbivore. Subsequent surveys and experiments suggested C. sapidus in this system consumes SAV as part of their diet. The emergence of non-native SAV in the system, but not V. americana, suggests grazing prevents the recruitment of some SAV, but not others. Chapter Three evaluated interactions between adult plants and seedlings and how they impacted seedling establishment of an estuarine seagrass species. Field surveys consistently recorded seedlings establishing among existing Zostera marina shoots in a meso/polyhaline region of Chesapeake Bay, VA. Concurrent experiments indicated that seed supply influenced seedling establishment rates in some areas. Further surveys and experiments showed that negative interactions between seedlings and adult shoots influenced the subsequent survival of these seedlings within existing Z. marina meadows. Results from the research studies in this dissertation, conducted across three diverse coastal habitats, demonstrate that interactions between SAV seeds or seedlings and other biota can be very important in ultimately determining seed or seedling survival. The diverse mechanisms through which biota compromise seedling recruitment and sexual reproduction for SAV observed here suggest there may be many additional, unexplored biological interactions affecting successful sexual recruitment for many SAV species. Because sexual reproduction provides substantial benefits to SAV populations, incorporating risks associated with seedling recruitment into population models and restoration strategies may help better predict SAV population health, resiliency and expansion as well as help optimize SAV restoration efforts.

The South Texas Banks are a mesophotic coral ecosystem (30-150m deep). Understanding the community structure, biodiversity and, geographic connectivity of the South Texas Banks is essential with increasing threats from climate change, ocean acidification, invasive species, and pollution. In this study, a remotely operated vehicle (ROV) was used to examine the fish communities at five of the South Texas Banks: Big Adam, Hospital, Mysterious, North Hospital, and Southern. Reef fish were identified to the lowest possible taxon and enumerated from ROV transect video footage. A total of 3,838 demersal and pelagic fishes were recorded representing 61 species in 22 families including invasive Pterois volitans. Bodianus pulchellus, Holocentrus adscensionis, Priacanthus arenatus, and the Gobiidae family were the only fishes observed at all five banks. Habitat suitability models were created that highlight the rich biodiversity found on the South Texas Bank, which will warrant for future research and conservation efforts.

Natural and sexual selection shape animal communication signals according to the demands of social context and the environment, which results in enormous variation in signal properties. My dissertation uses the electrocommunication signals of South American weakly electric knifefish to compare signal structure across several closely related species, with particular emphasis on signals that are extreme or unusual. Weakly electric fish continuously generate an electric field using an electric organ discharge (EOD). During short-range social interactions, fish produce chirps by rapidly and transiently increasing EOD frequency. I used recordings with playbacks of conspecific signals and hormone manipulation to characterize the sexually dimorphic chirp duration of Parapteronotus hasemani, a species of electric fish with high-frequency, long-duration chirps and huge variation in male morphology. I also described signaling behavior in Distocyclus conirostris , a species of electric fish with a low-frequency EOD and an unusual asymmetrical behavioral response to “jamming” created when EODs of similar frequencies interact. Next, I compared across species to examine how signal properties (EODs and chirping) interact to influence each other’s detection and evolution. Certain signal parameters such as chirp frequency modulation and EOD frequency difference have substantial effects on chirp conspicuousness. Contrary to expectations, there was little support for a strict co-evolution in which a species’ chirps are most conspicuous on their own EOD waveforms. Thus, although EOD properties influence chirp conspicuousness, other factors such as the social or physical environment also likely shape chirp structure. Additionally, I show that EOD waveform may differ in perceptibility based on the EOD waveform complexity of the interacting fish. I consider how chirp conspicuousness could drive the evolution of sexually dimorphic chirps (such as those produced by P. hasemani), and I raise questions about whether low-frequency EODs (such as those produced by D. conirostris) contain sufficient information for fish to detect conspecific EOD frequencies using the neural mechanisms described in fish with high-frequency EODs. Taken together, these results show how the properties of multi-component signals shape each other and impact signal detectability. Finally, my dissertation concludes with a description of an innovative approach to teaching scientific communication skills in a highly structured undergraduate introductory biology lab.

Freshwater environments are threatened worldwide by external stressors and biodiversity decline, with major implications for ecosystem resilience. The genetic consequences so far have been neglected, especially for freshwater invertebrates, though their abundance, diversity, ease of sampling and functional importance renders them ideal candidates for genetic appraisal. For three freshwater invertebrates (Amphinemura sulcicollis, Isoperla grammatica and Baetis rhodani) novel microsatellite markers were developed so that genetic structure, and genetic diversity could be assessed throughout upland Wales. The aim was to investigate dispersal and the genetic response to environmental stressors. Genetic diversity in these species was compared to species diversity across whole macroinvertebrate assemblages to investigate what factors might cause a correlation between these fundamental levels of biodiversity. The demographic history of each species was also investigated with the aim of assessing whether reduced genetic diversity was due to bottlenecks and more broadly, what this indicates in terms of the populations’ resilience. Species differed in their genetic structure and genetic diversity. All three species showed effective dispersal and geneflow, with each species displaying panmixa across catchments in southern and mid-Wales. However, A. sulcicollis and I. grammatica revealed genetic isolation and reduced genetic diversity at specific northern sites. Genetic and species diversity were correlated positively only in A. sulcicollis, where isolation combined with a common driver were the likely cause. There was evidence of recent bottlenecks in all three species. All these results could be explained by an underlying genetic response to post-industrial acidification: reduced genetic diversity correlated significantly with acidity for A. sulcicollis, while reduced species diversity and genetic bottleneck signatures was consistent with chronic and episodic acidification across the Welsh region. Overall, these results show how a positive correlation between species and genetic diversity can never be assumed, and illustrate how assessments of genetic health expand insights available from traditional biodiversity assessment.

During the Late Woodland Period in the American Southeast, the amount of space that any individual group could exploit began to shrink, due to the presence of other groups on the landscape. Resource expansion occurred to augment food supplies, resulting in increased exploitation of mussel beds. Because mussels can be extremely sensitive to the characteristics of the waterways they live in, the specific habitat requirements of these animals can be used to reconstruct the environments they were recovered from. In this thesis I use freshwater mussel assemblages to reconstruct hypothetical aquatic catchments and map them onto modern rivers in the Yazoo River Basin and the Tombigbee River Basin. These are used to test ethnographic models of exploited space. I also use detrended correspondence analysis to test if sites exist in mathematical space like they do in physical space along the Yazoo River basin, as observed in the Tombigbee River basin.

Fishing is a potent ecological force that can impact the density and distribution of fish stocks as well as fitness-related traits. In this thesis I examined eco-phenotypic change in the introduced Nile perch of Lake Nabugabo (East Africa) in response to decades of intense fishing pressure. I quantified temporal (12 years) and spatial variation (wetland vs. exposed habitats) in the a) size, b) catch per unit effort, c) diet, and d) gill morphology of Nile perch, by comparing field data collected in 2007 to earlier studies (1995, 2000 for distribution and diet and 1996 for gill morphology). Nile perch are now less abundant and smaller, and a larger proportion of the population is found near wetlands than in 1995. Relative to open waters, Nile perch near wetlands consume a higher proportion of cichlids, shift to piscivory at a smaller size, and have larger gills. Sustainability of the Nile perch fishery will demand adaptive management that accounts for rapid eco-phenotypic change in the stocks.
La pêche est une force écologique puissante qui peut avoir des impacts non seulement sur la densité et la distribution des stocks de poissons mais également sur les traits reliés à la valeur adaptative. Dans cette thèse, j'ai examiné un changement éco-phénotypique en réponse à plusieurs décennies de pêche intensive chez la Perche du Nil, une espèce introduite, dans le lac Nabugabo (Afrique de l'est). J'ai quantifié la variation temporelle (sur 12 ans) et spatiale (milieux humides vs. habitats exposés) de: a) la taille de la Perche du Nil, b) des prises par unité d'effort, c) de la diète, et d) des branchies en comparant les données de terrain récoltées en 2007 avec des données d'études antérieures (1995, 2000 et 1996 pour les branchies). La Perche du Nil est maintenant moins abondante et de taille inférieure comparé à la population échantillonnée en 1995. En 2007, une plus grande proportion de la population se retrouve près des milieux humides comparé à la population en 1995. La Perche du Nil retrouvée près des milieux humides consomme une plus grande proportion de cichlidés, a modifié son régime alimentaire en devenant piscivore à de petite tailles et a développé des branchies plus larges comparé aux Perches retrouvées en milieu pélagique. Pour perpétuer une exploitation durable des stocks de Perche du Nil, les gestionnaires des pêcheries devront s'adapter et tenir compte de ce rapide changement éco-phénotypique dans la population.

The global human population is expected to exceed 9 billion individuals by 2050, putting greater strain on the natural resources needed to sustain such a population. To feed this many people, some expect agricultural production will have to double and agrochemical use will have to increase anywhere from two- to five-fold relative to the turn of the century. Although industrial agriculture has provided many benefits to society, it has caused declines in biodiversity, both directly (e.g., through conversion of habitat) and indirectly (e.g., through contamination of adjacent natural habitats). Agricultural activity has also been linked to increased prevalence and intensity of trematode infections in wildlife and humans - directly by increasing available aquatic habitat for the snail intermediate hosts of trematode parasites and indirectly by altering the biological composition of aquatic habitats in ways that increase snail density. While the effects of single agrochemical contaminants on aquatic communities and trematode disease risk have been examined, agrochemical pollution typically occurs as mixtures of multiple chemical types in surface waters and the effects of mixtures on aquatic communities have received less attention. Moreover, given the high number of chemicals approved for agricultural use, the number of potential combinations of agrochemicals renders testing all possible combinations implausible. Thus, there is a critical need to develop better risk assessment tools in the face of this complexity. I developed and tested a theoretical framework that posits that the net effects of agrochemical mixtures on aquatic communities can be predicted by integrating knowledge of each functional group's 1) sensitivity to the chemicals (direct effects), 2) reproductive rates (recovery rates), 3) interaction strength with other functional groups (indirect effects), and 4) links to ecosystem properties. I conducted a freshwater mesocosm experiment to quantify community- and ecosystem-level responses to pairwise mixtures of four major agrochemical types (fertilizer, herbicide, insecticide, and fungicide) and single chemical treatments. The responses of biodiversity and ecosystem properties to agrochemicals alone and in mixtures were indeed predictable. Moreover, these results show that community ecology theory holds promise for predicting the effects of contaminant mixtures and offer recommendations on which types of agrochemicals to apply together and separately to reduce their impacts on aquatic ecosystems. I extended this framework to test if the direct effects of pesticides can be predicted by chemical class and/or mode of action. I performed standard toxicity trials on two invertebrate predators of snails (crayfish and giant water bugs) exposed to six insecticides belonging to two chemical classes (organophosphates and pyrethroids) to determine if environmental risk can be generalized to either insecticide class or insecticide exposure. Survival analyses demonstrated that insecticide class accounted for 55.7% and 91.1% of explained variance in crayfish and water bug survival, respectively. Simulated environmental exposures using US EPA software suggested that organophosphate insecticides present relatively low risk (as defined by the US EPA) to both crayfish and water bugs, while pyrethroid insecticides present consistently high risk to crayfish but not to water bugs, where only λ-cyhalothrin produced consistently high-risk exposure scenarios. Thus, risk to non-target organisms is well predicted by pesticide class. Furthermore, identifying insecticides that pose low risk to aquatic macroarthropods might help meet increased demands for food while mitigating against potential negative effects on ecosystem functions. Because evidence from field data and manipulated experiments demonstrated both top-down and bottom-up effects of agrochemical pollution that increased snail densities and trematode infections in wildlife, I conducted an additional agrochemical mixture experiment with freshwater communities containing the snail hosts of schistosomiasis, which has also been linked to agriculture. As expected, top-down and bottom-up effects of insecticide, herbicide, and fertilizer exposure indirectly increased snail densities, individually and as mixtures. Agrochemical exposure and snail density together accounted for 88% of the variation in the density of infected snails. Thus, agrochemical pollution has great potential to increase human exposure to schistosome parasites, and underscores the importance of identifying low-risk alternative pesticides. A subsequent mesocosm experiment with the same six insecticides used previously in laboratory trials confirmed that insecticide exposure indirectly mediates the densities of snail hosts that can transmit schistosomiasis through the direct effects of insecticides on crayfish mortality. Importantly, crayfish mortality in semi-natural mesocosm trials closely matched mortality from controlled laboratory trials. Thus, standard laboratory toxicity tests can be a useful tool for identifying alternative insecticides that might pose lower environmental risks to important predators that regulate snail densities. Identifying practices or agrochemicals that minimize this risk is critical to sustainably improving human health in schistosome-endemic regions. The theoretical framework presented here demonstrates the feasibility of predicting the effects of contaminant mixtures and highlights consistent effects of major agrochemical types (e.g. fertilizers, insecticides, etc.) on freshwater aquatic community composition. Furthermore, the strong top-down effects of invertebrate snail predators highlight that managing for high snail predator densities in might be a particularly effective strategy for reducing the burden of schistosomiasis in tropical countries.

Natural ecosystems are strongly affected by changes in resource supply (bottom-up forces) and by changes in upper trophic levels (top-down forces). The extent to which these processes impact a system depends largely on the responses of organisms at middle trophic levels. In seagrass beds, a group of mid-level consumers known as mesograzers form a critical link in the chain of impact, connecting seagrass and epiphytic algae with predatory fishes and crustaceans. I observed dramatic seasonal and interannual changes in mesograzer abundance and species composition in eelgrass (Zostera marina) beds of lower Chesapeake Bay, Virginia, and endeavored to explain the top-down and bottom-up causes and consequences of those changes with field studies and controlled experiments. A field cage experiment showed that grazing, predation and nutrient enrichment all had strong effects on the eelgrass community, but that the effects of each factor varied for different community components (Chapter 1). A second experiment delved deeper into the predation dynamic by manipulating the diversity of both predators and mesograzers in macroalgal mesocosms. Increasing predator diversity increased the strength of predation, but increasing mesograzer diversity conferred resistance to some types of predation (Chapter 2). to assess the influence of top-down and bottom-up forces in a more natural context, I analyzed the long-term changes in biotic and abiotic components of an eelgrass bed at the Goodwin Islands National Estuarine Research Reserve. I found that abiotic processes had strong effects on both consumer and resource abundance, and could therefore initiate either top-down or bottom-up control of eelgrass community structure (Chapter 3). to examine this top-down and bottom-up control in more detail I explicitly compared the ecological relationships seen in the field to those observed in mesocosm experiments. Mesocosm experiments tended to find a greater influence of top-down effects and a lesser influence of bottom-up effects, relative to field observations (Chapter 4). Finally, I took a snapshot of the eelgrass food web itself by examining the gut contents and stable carbon and nitrogen isotopic ratios of predators, mesograzers, and plants. I found that direct grazing on eelgrass does occur, but that microalgae and detritus provide the main trophic support for the epifaunal community (Chapter 5). Overall, my results suggest that both top-down and bottom-up forces control eelgrass community structure via mesograzers, but that top-down control in the field is more subtle and more intimately tied with bottom-up control than has been indicated by some manipulative experiments.

The general goals of this study were to evaluate transplant methods for Lake Pontchartrain submersed aquatic vegetation (SAV) restoration, and to compare survival and expansion of transplanted SAV among four sites. Two experiments were conducted from summer 2000 through spring 2001 at two north shore and two south shore sites in Lake Pontchartrain. Experiment 1 involved testing the effects of transplanting with matting, staples, exclosures, and interspecific interaction on survival and expansion of Ruppia maritima and Vallisneria americana transplants in Lake Pontchartrain. Experiment 2 involved testing the effects of transplanting with matting, staples, and plugs on Ruppia survival and expansion. After transplanting, areal coverage was monitored in fall 2000 and spring 2001. Unusually high salinities and high wave energy caused Vallisneria numbers to rapidly decrease after transplanting. Matting always had equal or greater Ruppia coverage than staples. Exclosure treatments had no effect on Ruppia coverage. No significant biological interaction was detected between species. Matting provided a stable substrate for Ruppia while staple and plug treatments succumbed to the high-energy environment of Lake Pontchartrain. High wave energy and eutrophication were responsible for the loss of all south shore transplants.

Wetlands exhibit high primary productivity and play a significant role in the global carbon cycle. Brackish and salt marshes co-occur in Southern California; yet, restoration designs often eliminate remnant brackish marshes, along with their ecosystem functions, without evaluation. Vegetation, soil organic matter, and carbon flux were compared between brackish and salt marsh habitats in the Huntington Beach Wetlands. Newland Brackish Marsh had more carbon aboveground in denser and taller vegetation than the other two marshes. Brookhurst Salt Marsh sediments had more organic matter than the other two marshes. CH₄ emissions were negligible at all sites, and there were no differences in CO₂ flux or aerobic and anaerobic microbial respiration among sites. Although these components of the carbon cycle were similar among sites in this project, such quantitative functional evaluations should be part of the restoration planning process.

Information on the movement of migratory demersal fishes such as Pacific halibut, Pacific cod, and sablefish is needed for management of these valuable fisheries in Alaska, yet available methods such as conventional tagging are too coarse to provide detailed information on migration characteristics. In this dissertation, I present methods for characterizing seasonal and annual demersal fish movement at multiple scales in space and time using electronic archival and acoustic tags. In Chapter 1, acoustic telemetry and the Net Squared Displacement statistic were used to identify and characterize small-scale movement of adult female Pacific halibut during summer foraging in a Marine Protected Area (MPA). The dominant movement pattern was home range behavior at spatial scales of less than 1 km, but a more dispersive behavioral state was also observed. In Chapter 2, Pop-up Satellite Archival Tags (PSATs) and acoustic tags were deployed on adult female Pacific halibut to determine annual movement patterns relative to MPA boundaries. Based on observations of summer home range behavior, high rates of year-round MPA residency, migration timing that largely coincided with winter commercial fisheries closures, and the demonstrated ability of migratory fish to return to previously occupied summer foraging areas, the MPA is likely to be effective for protecting both resident and migrant Pacific halibut brood stock year-round. In Chapter 3, I adapted a Hidden Markov Model (HMM) originally developed for geolocation of Atlantic cod in the North Sea for use on demersal fishes in Alaska, where maximum daily depth is the most informative and reliable geolocation variable. Because depth is considerably more heterogeneous in many regions of Alaska compared to the North Sea, I used simulated trajectories to determine that the degree of bathymetry heterogeneity affected model performance for different combinations of likelihood specification methods and model grid sizes. In Chapter 4, I added a new geolocation variable, geomagnetic data, to the HMM in a small-scale case study. The results suggest that the addition of geomagnetic data could increase model performance over depth alone, but more research is needed to continue validation of the method over larger areas in Alaska. In general, the HMM is a flexible tool for characterizing movement at multiple spatial scales and its use is likely to enrich our knowledge about migratory demersal fish movement in Alaska. The methods developed in this dissertation can provide valuable insights into demersal fish spatial dynamics that will benefit fisheries management activities such as stock delineation, stock assessment, and design of space-time closures.

The impacts of a 20,993 L diesel and gasoline spill on the benthic macroinvertebrate (BMI) and diatom communities in Cold Creek and the Santa Ana River (below its confluence with Cold Creek) were assessed by comparing species richness, diversity and compositions between fuel-impacted and reference sites. BMIs and diatoms were sampled four times (13–26 months after the spill) in sites located upstream from the spill (reference) and in sites located 0.5, 1.3, 2.7 and 3.0 km downstream from the spill (impact). BMI communities up to 2.7 km below the spill and in Cold Creek had (1) lower species richness and diversity for at least 25 months after the spill and (2) dissimilar species compositions for up to 26 months after the spill when compared to the reference site. Diatom communities up to 2.7 km below the spill and in Cold Creek had (1) similar or higher species richness and diversity when compared to the reference site and (2) dissimilar species compositions when compared to the reference site for the entirety of the study. BMI and diatom communities located 3.0 km below the spill and in the Santa Ana River had similar species richness, diversity and compositions when compared to the reference site. These results provide evidence that the fuel spill had an impact on the BMI and diatom communities in Cold Creek and that these communities are still changing.

Gamefish populations in North America are experiencing increasingly elevated recreational fishing pressures; however, the impacts of current fishing regulations have not been evaluated for most marine species. Mandatory catch and release often results from size and bag limits with the assumption of fish survival and recovery with minimal sublethal effects. Depending on the intensity and duration of the stressor, acute stress from angling and handling can have deleterious physiological and behavioral impacts with consequences for fish health and fitness. We evaluated the short-term sublethal effects of angling-related stressors on kelp bass, Paralabrax clathratus, one of the most popular gamefish in southern California. Collaborating with recreational anglers to capture fish using standard hook and line practices, we evaluated biochemical responses and recovery by collecting blood samples at different time points after capture (10-120 min), after fish were released and some were recaptured (3h to 186 d). Blood cortisol, glucose, and lactate were significantly elevated and steadily increased in the hour following capture and holding (p < 0.001). Fish caught, released, and recaptured after varying time at liberty were found to have returned to basal levels in < 24 h (p > 0.05). Physiological stress responses were positively correlated with angling and handling duration, but negatively correlated with increasing fish size (p < 0.05), suggesting that larger individuals may be more resilient to capture stress. Likewise, kelp bass exhibited no signs of cumulative or chronic stress from repetitive angling/recapture events and recovered to basal levels in <24 h (p > 0.05). Kelp bass were also tagged with acoustic accelerometer transmitters and tracked to evaluate fine-scale behavioral effects of angling stress on their normal diel movement and activity. Reduced frequency of high acceleration movements (i.e. rapid feeding strikes) was observed for 33 h post-release, followed by recovery and evidence of elevated feeding behavioral activity. Rate of movement and area use size showed high individual and temporal variation; however, reduced movement immediately after release steady increased to normal levels over the first 10 h post-release. There was no discernable effect of angling on area use size, but areas of high relief substratum may be important refuge habitat for angled kelp bass during recovery. By integrating physiological and behavioral endpoints for kelp bass to standard angling induced stress we conclude that this species is able to recover in <24 h; however, smaller individuals may be more susceptible to predation during this recovery period. Based on these findings, it is likely that kelp bass may still fair well under current size and bag limits.

Five species of waterbirds were collected from five sites on Imperial National Wildlife Refuge between April and August of 1993. There were previous baseline contaminants data for all sites. Sites were of two distinct habitat types. Backwater lakes have a direct connection to the mainstem of the Colorado River, and seep lakes receive river water only via seepage through the soil column. Selenium concentrations in liver, kidney, and muscle tissues were consistently higher in birds collected from backwater lakes than those collected from seep lakes. Eighty-one percent of the birds collected on backwater lakes (n = 52) were above the effect threshold for reproductive impairment or embryotoxicity (10 ppm dry weight in livers). Herbivorous birds had significantly (p ≤ 0.05) lower tissue selenium levels than those species feeding on animal matter. Of the birds feeding on fish and invertebrates, 83% (n = 47) had selenium levels in liver above the effect threshold. Differences in selenium concentrations based on diet suggest food chain cycling of selenium. Eggs from waterbirds as well as those from neotropical migrants were above the 3 ppm embryotoxicity threshold.

Understanding the drivers and patterns of biological diversity has been a central tenet for ecologists over the past century. Aquatic ecosystems appear to be particularly sensitive to biodiversity declines and thus comprehending the causes of these biodiversity losses has become a pressing issue. The objectives of this thesis are twofold. First, I wanted to investigate the effect of phosphorus, a surrogate for productivity in aquatic ecosystems, on the diversity of two taxonomic groups across broad spatial and temporal scales. Secondly, I wanted to quantitatively assess the use of biodiversity indicators in aquatic ecosystems, with particular emphasis on the role of body size. In the first chapter of this thesis, I took a palaeolimnological approach to investigate how the species richness of subfossil diatoms and cladocera varies in response to phosphorus. From both our spatial and temporal analyses, a significant decline in species richness of diatoms and cladocera was observed as phosphorus increased. When subdivided according to habitat preference, only the littoral species richness showed a decline in species richness. We attribute this decline in species richness in the littoral taxa to the interplay of nutrients on littoral habitat heterogeneity. At low levels of phosphorus, the littoral zone is thought to be more productive and harbor a greater abundance of submerged macrophytes and is thus able to maintain a more diverse community. The second chapter of this thesis investigated the efficiency of cross-taxon congruence as a method for estimating biodiversity in aquatic ecosystems. I approached this subject by performing a spatial field study coupled to a meta-analysis of the published literature. The field survey and meta-analysis show that organisms of similar size tended to exhibit more congruent diversity patterns. I argue that this pattern arises because organisms of similar body size have similar life history traits and thus similar biodiversity responses to environmental gradients. I demonstrate that cross-taxon biodiversity indicators are most effective when estimating the diversity of communities of most similar body size. Overall, this research has expanded our understanding of patterns, drivers and similarities of biodiversity across trophic levels in aquatic ecosystems.
Au cours du siècle dernier, plusieurs écologistes ont tenté de comprendre les caractéristiques ainsi que les facteurs qui contrôlent la diversité biologique. Les écosystèmes aquatiques semblent être particulièrement sensibles au déclin de la biodiversité et donc en découvrir les causes devient alors une question pertinente. Cette thèse possède deux objectifs. Tout d'abord, je souhaite étudier l'effet du phosphore, un substitut de productivité dans les écosystèmes aquatiques, sur la diversité de deux groupes taxonomiques à travers de grandes échelles spatiales et temporelles. Deuxièmement, je désire évaluer, de façon quantitative, les indicateurs de biodiversité dans les écosystèmes aquatiques, et ce, en mettant l'emphase sur le rôle de la dimension des organismes. Dans le premier chapitre de cette thèse, j'ai utilisé une approche paléolimnologique pour étudier comment la richesse spécifique des diatomées et des cladocères fossilisés varie en fonction du taux de phosphore. Grâce à mes analyses temporelles et spatiales, j'ai noté une baisse significative de la richesse spécifique des diatomées et des cladocères avec une augmentation du phosphore. De plus, lorsque les communautés étaient divisées par leurs préférences d'habitat, seules les richesses spécifiques littorales ont démontré un déclin en fonction du phosphore. J'attribue ce déclin de la richesse spécifique dans les groupes littoraux à l'effet des nutriments sur l'hétérogénéité des habitats littoraux. À de bas niveaux de phosphore, la zone littorale est plus productive et peut accueillir de grandes abondances de macrophytes qui fournissent plus de niches écologiques pour les espèces, donc une plus grande diversité.Le deuxième chapitre de cette thèse porte sur l'utilisation de la richesse spécifique d'une communauté d'organismes pour estimer la richesse spécifique d'une autre. Cette méthode de substitution est utilisée pour estimer la biodiversité dans les écosystèmes aquatiques. J'ai abordé ce sujet en effectuant une étude spatiale jumelée à une méta-analyse des écrits. Mon analyse spatiale et ma méta-analyse illustrent que les groupes taxonomiques ayant des dimensions similaires ont tendance à présenter des patrons de diversité plus conformes. Je suppose que les organismes de tailles similaires démontrent plus de similarité en ce qui concerne leurs traits de vie et à leurs patrons de diversité lors de gradients environnementaux. Je démontre que les indicateurs utilisés pour prédire la biodiversité sont plus efficaces lorsque leurs tailles sont plus similaires. Conséquemment, cette recherche a permis d'agrandir nos connaissances des patrons, des processus et des similitudes de la richesse spécifique dans les écosystèmes aquatiques.

Rates of species invasion are rising globally, particularly in freshwater ecosystems. The impacts of only a small fraction of these invasions have been studied, and some have been found to cause substantial ecological and socio-economic damage. Nevertheless, there have been recent claims that the impacts of non-native species have been exaggerated, that native species have an equal propensity to cause damage, and therefore the biogeographic origins of species should not be considered in management decisions. Here, I address these claims by comparing the socio-economic impacts of native and non-native species in freshwater systems. Using data from North American and European watersheds, I find that non-native species are five times more likely than natives to become pests. Another major issue concerning the impacts of non-native species is that managers lack predictive tools for prioritizing invasion threats, because very few general correlates of impact have been identified. The functional distinctiveness of a non-native species within the invaded assemblage has been proposed as a predictor of its impact on native species populations. Using a global dataset of non-native freshwater molluscs and taxonomic relatedness as a proxy for functional similarity, I find that novel taxa comprise disproportionately large numbers of high-impact invaders. Moreover, more taxonomically distant taxa have the highest proportions of high-impact species. These results support the use of taxonomy and biogeographic origin in invasion risk assessment.
Les taux d'invasions d'espèces sont en hausse dans le monde, et particulièrement dans les écosystèmes d'eau douce. Seuls les impacts d'une petite fraction de ces invasions ont été étudiés. Il a été démontré que certaines d'entre elles peuvent causer des dommages environnementaux et socioéconomiques considérables. Toutefois, certains écologistes suggèrent que l'impact des espèces non indigènes pourrait avoir été exagéré. Selon eux, les espèces indigènes auraient la même propension à causer des dommages environnementaux et socioéconomiques. L'origine biogéographique d'une espèce ne devrait alors pas être considérée lors d'une prise de décision. Je tente ici de vérifier la validité de ces affirmations en faisant la comparaison des impacts socioéconomiques des espèces indigènes et non indigènes dans les écosystèmes d'eau douce. En analysant des données provenant de bassins d'eau douce nord-américains et européens, il s'avère que les espèces non indigènes ont cinq fois plus de chances de devenir nuisibles. Un problème majeur relié à l'impact des espèces invasives est que les preneurs de décisions manquent d'outils de prédiction leur permettant de prioriser les menaces d'invasion. Le caractère distinctif de la fonction écologique d'une espèce non indigènes au sein de la communauté envahie à été proposé comme prédicteur de son impact sur la population indigène. En construisant un ensemble de données mondial sur les mollusques non indigènes et en utilisant la parenté phylogénique comme indicateur de la similarité fonctionnelle des espèces, il ressort que les taxons nouveaux sont plus susceptibles de devenir des envahisseurs à haut impact. De plus, les taxons les plus distants phylogéniquement ont la plus haute proportion d'espèces envahissantes à haut impact. Ces résultats soutiennent l'utilisation de la phylogénie et de l'origine biogéographique pour l'évaluation des risques associés à une invasion par une espèce non indigène.

Distinguishing marine and freshwater animals in the fossil record is a long-standing problem in paleontology. The physiological tolerances of extinct animals usually are inferred from environmental indicators and/or on the physiology of nearest living relatives. These types of evidence are often ambiguous and may be confounded by factors such as post-mortem transport and polymorphism in the living relatives. A solution to this problem is to combine these types of data with analyses of the oxygen isotope compositions of the phosphate (δ¹⁸O(p)) and the carbon isotope compositions of the carbonate (δ¹³C(sc)) of teeth and bones, to determine whether the ingested water and diet, respectively, were fresh or marine. The power of this approach is illustrated here in a study of the early evolution of cetaceans (whales, dolphins and porpoises). Changes in δ¹⁸O(p) and δ¹³C(sc) of the teeth and bones of early cetaceans documented here indicate that fully marine cetaceans existed by the middle Eocene and that some species exploited both marine and freshwater environments. This isotopic approach requires the avoidance of isotopically altered specimens. For this reason, the second component of this work deals with criteria for recognizing isotopically altered fossils. In contrast to one recent study, I found a positive correlation between δ¹⁸O(p) and δ¹⁸O(sc) not only in mammals but also in fish and reptiles. This correlation can be used as a test of whether the original isotopic composition is preserved in fossil specimens. Another approach to this problem is to make analyses of samples taken along growth transect of a fossil tooth or bone. Growth-transect analyses could resolve whether within-species isotopic variation represents differences in preservation or ontogenetic shifts in diet or habitat. In support of this goal, a new method for the analysis of phosphate oxygen is presented. This new method differs from all previous methods in that it involves no chemical reaction, but rather high-temperature (>725°C) equilibrium oxygen isotope exchange between CO₂ and Ag₃PO₄ As the amount of CO₂ is controlled by the analyst, small phosphate samples may be analyzed, making this method potentially useful for growth-transect analyses.

Thesis (M.S.)--East Tennessee State University, 2001.
Title from electronic submission form. ETSU ETD database URN: etd-0711101-121822 Includes bibliographical references. Also available via Internet at the UMI web site.

A continuous culture model system was set up in the laboratory and inoculated with a diverse range of microorganisms, including several bacteria and protozoa, obtained from the local mains water tap supply. This inoculum and was added to the system without any prior culture or other selection process. Biofilms readily developed on glass tiles suspended in the planktonic phase of the system. An avirulent Legionella pneumophila was inoculated into the system and was subsequently isolated from both biofilms and also from the aqueous(planktonic) phase of the chemostat. The attenuation of this strain, determined by its inability to cause disease and death in guinea pigs, remained unaltered despite the long term survival of this strain within the system. Investigations to determine whether the avirulent L. pneumophila was able to infect and proliferate within protozoa were carried out. The results of the present study show that this avirulent L. pneumophila did not proliferate intracellularly and suggest that the association of L. pneumophila with protozoa although probably important in the long term survival of this bacterium especially during periods where adverse conditions prevail, is not essential but opportunistic. In chapter 3 the importance of the presence of these non-legionellae bacteria, which included Flavobacterium sp., Acinetobacter spp. and several species of Pseudomonas, was investigated. The results suggest that the presence of the non-legionellae are relevant to the survival of Legionella especially in environments which favour it's growth, for example water distribution systems. In order that we may gain a further insight into the ecology of microorganisms in their natural environment, it is necessary to visualise them in conditions which allow them to interact in a way which mimics as closely as possible the natural environment. Biofilms were developed on surfaces which could be removed from the model system in their entirety. Direct visualisation techniques, including atomic force microscopy and Hoffman modulation microscopy could then be used which allowed the in vivo examination of biofilms in situ on the surface upon which they had developed. More traditional microscopy methods were also used. Atomic force microscope images of biofilms and individual biofilm bacteria including Legionella were obtained, which clearly showed the presence of exopolymeric substances (EPS). Hoffman modulation contrast microscopy and scanning electron microscopy showed the diverse nature of the biofilms being studied. The results of these investigations suggest that a more complete understanding of the complex nature of biofiims is achieved by the use of a combination of several microscopy techniques. The response of a L. pneumophila serogroup 6 and the avirulent L. pneumophila serogroup 1 to a commercially available biocide, Vantocil IB, was investigated. Both the serogroup 6 and the avirulent serogroup 1 could not be detected following biocide teatment in either the planktonic phase or biofilms. These results suggest that this avirulent L. pneumophila is a suitable model substitute for the virulent L. pneumophila.

Previous studies on the impacts of cattle on the aquatic environment have mainly focused on cold water systems with high intensity grazing, and may be of limited relevance for assessing impacts of cattle grazing on low gradient, low intensity sites such as those in eastern Ontario. The present study looks at changes to the aquatic habitat following the removal of cattle from a watercourse. Biomonitoring was completed at an aquatic restoration site over a four year period encompassing pre- and post-implementation conditions. The initial results indicated modest improvements in the habitat and in the benthic macroinvertebrate and fish communities following exclusion of cattle from the watercourse. Trends over time suggested an increase in the proportion of sensitive benthic macroinvertebrates, a decrease in tolerant benthic species and an increase in fish density. Longer-term monitoring is required to observe changes to the aquatic communities following the growth of woody riparian vegetation.
Par la passé, plusieurs scientifiques ont étudié l'effet du bétail sur le milieu aquatique utilisant des sites où se trouve une haute densité de vaches dans des endroits où les cours d'eaux ont une forte pente. Puisque nous utilisons des sites dans l'Est Ontarien, les résultats de ces recherches auront peu de pertinence en ce qui concerne cette présente étude car la majorité des sites de la région sont ceux où l'on retrouve peu de vaches et des cours d'eaux ayant une faible pente. Cette thèse examine les changements du milieu aquatique suivant l'enlèvement des vaches à proximité du cours d'eau, et ce, depuis les quatre dernières années, incluant les conditions pré et post implémentation. Les résultats indiquent une amélioration modeste d'habitat et des communautés de macroinvertébrées benthiques et de poissons. Les tendances au fil du temps ont suggérées qu'il y eu une amélioration des proportions de macroinvertébrées benthiques sensible, une diminution de macroinvertébrées benthiques insensible et un accroissement dans le nombre de poissons. Plusieurs années seraient nécessaires pour étudier les effets de la croissance des arbres et arbustes sur les communautés aquatiques.

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Programa Santander Universidades
Os ecossistemas lóticos apresentam um gradiente de variáveis ecológicas que se modificam da nascente até a foz, influenciando diretamente a sucessão da biota aquática. Em regiões temperadas os rios diferem-se daqueles localizados em regiões tropicais. Nas regiões tropicais o pulso de inundação exerce uma forte influência nas comunidades de macroinvertebrados. A distribuição e composição da comunidade de macroinvertebrados respondem às variações de fatores bióticos e abióticos e ainda, estão relacionadas com as diferentes regiões e tipos de hábitats disponíveis nos sistemas. Estudos relacionados à diversidade, estrutura e dinâmica de macroinvertebrados fornecem informações fundamentais para o conhecimento, acerca da biodiversidade e para programas de manejo e monitoramento dos recursos hídricos. Neste sentido o objetivo geral desta dissertação de mestrado foi conhecer a riqueza, a abundância, a composição e os grupos tróficos de macroinvertebrados, em nove arroios de pequena ordem em uma bacia hidrográfica do
Lotic ecosystems have a range of ecological variables that change from source to mouth, having direct influence on succession of aquatic biota. In temperate regions rivers are different from those located in tropical regions. In tropical regions the flood pulse has a strong influence on communities of macroinvertebrates. Distribution and composition of the community of macroinvertebrates respond to variations in biotic and abiotic factors and are related to different regions and types of habitat available in the systems. Studies on diversity, structure and dynamics of macroinvertebrates provide essential information on the biodiversity and for programs of management and monitoring of water resources. In this sense, the general objective of this master’s dissertation was to investigate the richness, abundance, composition and trophic groups of macroinvertebrates in nine small-sized streams in a hydrographic basin in southern Brazil and to analyze the influence of physical and chemical parameters of water and d

Dover sole (Microstomus pacificus) is a commercially important, slope dwelling flatfish of the northeast Pacific coast. Its genetic diversity at the mitochondrial DNA control region appears substantially lower than another commercially important flatfish, Pacific sanddab (Citharichthys sordidus). I designed a comparative study along depth and latitudinal gradients using five flatfishes and one brotula. In the control region's left domain, genetic diversity of six species trended lower with increasing habitat depth at Palos Verdes: shallow species had high genetic diversity and deep dwelling species (ex. Dover sole) had low genetic diversity. This diversity gradient may follow decreases in mass specific metabolic rates as Dover sole grow, invade the oxygen minimum zone and assume higher tissue water content. The left domain from 64 Dover sole specimens was compared across 4 latitudinal locations. Genetic diversity trended higher with increasing latitude, possibly due to cold water emergence as biomass shift shallower with increasing latitude.

This thesis qualifies functional and ecological aspects of mucus trails deposited by Elimia potosiensis collected from the Meramec River. Freshwater snails are most often recognized for their significant role in river and stream ecosystem function as primary consumers and prey items. However, their form of locomotion is the most energetically expensive found in the animal kingdom. Found in large numbers and densities, E. potosiensis is capable of coating large swaths of substratum with carbohydrate- and protein-rich mucus. This has the potential to affect ecosystem function at the most basal trophic level both energetically, by contributing nutrients and energy to the surrounding water body, and functionally, as a sticky substance to which microheterotrophs become adhered.

In marine studies, researchers have found that bacteria can readily degrade gastropod mucus and that it can act as the basis for biofilm formation. There have also been studies that show unique employment of energy saving strategies by snails that use their trails to capture food items and to reduce production needs by following trails laid by conspecifics. Very little research has been conducted on freshwater gastropods. This study is the first to focus solely on the ecological and functional aspects of freshwater snail mucus.

For this study, collections of E. potosiensis were made from a single site along the Meramec River to qualify the effect deposited mucus has on the adherence of microalgae and its potential for formation of biofilms. Overall, mucus-coated surfaces significantly more particles in flow than non-coated surfaces. The water velocity at which a trail is laid was not found to have an affect on the thickness, adhesive ability or persistence of a trail. However, the water velocity in which a trail is incubated in stream does have effect on the adherence rate of a trail. In this study, it was found that this was most likely due to the fact that trails in high water velocity come into contact with more particles during a given period of time due, in part, to its higher carrying capacity.

As eel populations decline worldwide, research tools for scientists and managers to better understand eel populations and dynamics will be vitally important. This research focuses on the relatively understudied silver phase eel, the sexually mature adult life stage that will make the single spawning journey to the oceanic spawning grounds. A non-lethal index of eel maturity was designed based on external measurements and was able to correctly classify individuals into one of seven maturity classes 83% of the time overall, yielding similar results to other non-lethal indices. Habitats above and below barriers to migration, at varying levels of watershed urbanization, and different distances from the ocean were compared in terms of eel maturity, size, age, and parasite parameters. Two methods of bioelectrical impedance analysis (BIA) were evaluated in their ability to estimate eel lipid concentration, a key factor in eel maturity and successful spawning.

Streams along the Copper River Delta, southcentral Alaska, exhibit contrasting thermal and hydrologic variability associated with being primarily groundwater-fed (GWF) or surface water-fed (SWF). Groundwater-fed streams are predictable both thermally and hydrologically year round, whereas SWF streams are unpredictable and exhibit more variable thermal and hydrologic regimes. These differences may strongly influence aquatic insect community structure and secondary production. Four streams, two GWF and two SWF, were sampled twice monthly from late April 2013 through August 2013 and once seasonally in fall (September) and early winter (November). Aquatic insect community structure differed markedly in both hydrologic types. Taxa richness was significantly higher in SWF (43) than in GWF (39) streams and non-metric multidimensional scaling of community structure revealed two distinct groups corresponding to the two hydrologic types. Total secondary production was higher in GWF than in SWF streams with Orthocladiinae (Diptera: Chironomidae) representing 56% of insect secondary production in GWF streams. Results from this study have strong implications for aquatic insect communities in GWF and SWF streams because of differing susceptibilities of these systems to the potential effects of climate change. Due to their thermal stability, groundwater-fed streams are less likely to be impacted by climate change, whereas SWF streams are thermally variable and more likely to be influenced. The effects of altered aquatic insect communities can cascade to higher trophic levels such as salmon and ultimately impact stream ecosystem function and the ecosystem services they provide.