Land uses dominated by human activity can have a significant effect on ecological processes. In Florida, oxygen depletion is the most common impairment in lake, stream, and coastal water bodies. The continual growth and development in Florida, along with a conversion to more human intense land uses warrants study and discussion on impacts to dissolved oxygen regimes along a gradient of human disturbance. This research study is designed to identify observable trends in dissolved oxygen regimes along a gradient of increasing human intensity. Twenty-six stations in the Tampa Bay area were selected to represent lotic systems in west-central Florida. Data was collected quarterly, during four-day deployments, using a deployable data sonde. Grab samples for nutrients and chlorophyll-a provided antecedent data to explain observed trends. Physical components of streams, such as channelization were also taken into account. Biological integrity of streams was assessed to identify if altered dissolved oxygen regimes as a result of human land use significantly affect the health of the systems. Analysis included the use of Spearman rank order correlations to identify patterns. Dissolved oxygen regimes were correlated with the Landscape Development Intensity Index (LDI). Nutrients, primary productivity, and physical alteration to the streambed play a significant role in understanding how land use affects dissolved oxygen regimes. Results indicate the intensity of human land use has a significant effect on dissolved oxygen regimes and has significant policy implications for Florida's Total Maximum Daily Load (TMDL) program. Diel variation in oxygen measurements may be a more appropriate indicator of impairment and stream biological integrity.

A total of 670 critical thermal maxima (CTMax) and minima (CTMin) were determined for three freshwater fishes acclimated to three constant temperatures and a diel regimen cycling between the lowest and highest acclimation temperatures. In all species temperature tolerance was directly related to acclimation temperature and slopes relating these variables indicate that acclimation temperature has a greater influence on tolerance of low rather than high temperatures. CTMax and CTMin values generated following exposure to 32 days of oscillating temperatures indicate that in general, fishes had temperature tolerance acclimation states consistent with the average temperature and not either the highest or lowest temperature of the diel cycle.

The intestinal tract microbiota – microbial community of the gut – is an important field in microbiology not only because of its critical role in the host development, but also increasingly large number of diseases are associated with certain state of the gut microbiota. The community structure and function of the gut microbiota is relatively well studied in humans and related higher vertebrates, but is severely understudied in fish. This is especially true for the coral reef fishes, who constitute the most diverse assemblage of vertebrates spread over a very local scale, and are essential for the resilience of the reefs. In order to bridge this gap in knowledge, this dissertation studied the community structure, interactions and functions of the gut microbial community from the surgeonfishes in the Red Sea – with special focus on the surgeonfish enteric symbiont Epulopiscium spp. Initially, I studied the composition of the gut microbiota of nine surgeonfish and three nonsurgeonfish species from the Red Sea using 454 pyrosequencing. Upon discovering the high abundance of Epulopiscium spp. in herbivorous surgeonfishes, I then proceeded to identify their phylogenetic diversity, distribution, as well as deducing their coevolutionary relationship with the host. Because Epulopiscium spp. undergo substantial changes in the cell size (grow up to ~600μm) and the DNA concentration (from 85 to over 250pg per cell) throughout their diel lifecycle, I also studied the temporal changes in their expression pattern using RNA-seq. Overall, this dissertation shed light on the complex structure, interaction and function of an important family of coral reef fish from the Red Sea through range of molecular techniques.

The diel vertical migration (DVM) and feeding periodicity of myctophids (lanternfishes) were studied in the high-latitude Masfjorden, Norway, and the tropical Red Sea. In Masfjorden, a bottom-mounted echo sounder permitted continuous studies throughout the year, and revealed a diverse seasonal DVM behavior. During spring and summer, when zooplankton peaks in the epipelagic zone, migrating glacier lanternfish performed normal DVM (NDVM), ascending to the epipelagic zone during night and residing below ~200m during daytime. During autumn and winter, when Calanus overwinters between ~150–300 m, migrating glacier lanternfish mainly performed inverse DVM (IDVM), ascending to feed on Calanus in mid-waters during daytime. Non migrating (NoDVM) individuals were present all year below ~300 m in Masfjorden. In the Red Sea, where zooplankton has an epipelagic distribution, the whole population of skinnycheek lanternfish performed NDVM, feeding in the epipelagic zone at night, while residing at ~500–750 m during daytime. The warm waters of the Red Sea were hypothesized to limit the time individuals can stay in the mesopelagic zone without migrating to feed in the epipelagic layers. The DVM behavior of myctophids largely seemed to relate to the distribution of zooplankton, and it was hypothesized that NDVM will prevail with epipelagic distribution of prey, while IDVM and NoDVM are common in areas where zooplankton migrate seasonally to mesopelagic depths. Potential predators were continuously present, found to apparently attack glacier lanternfish, at mesopelagic depth in Masfjorden. Thus, myctophids are under threat of predation even at mesopelagic depth.

Monoamine oxidase (MAO) is a mitochondrial membrane-bound enzyme that catalyzes the oxidative deamination of monoamines in a wide array of organisms. While the enzyme monoamine oxidase has been studied extensively in its role in moderating behavior in mammals, there is a paucity of research investigating this role in invertebrates, where the latter utilizes this enzyme in a major pathway to degrade monoamines. There is especially a dismal lack of information on how MAO influences activity in invertebrates, particularly in account of the circadian cycle. Previous studies revealed MAO degrades serotonin and norepinephrine in arachnids, but did not investigate other critically important compounds like octopamine. Larinioides cornutus is a species of orb-weaving spider that exhibits diel fluctuations in behavior, specifically levels of aggression. The monoamines octopamine and serotonin have been shown to influence aggressive behaviors in L. cornutus, thus this species was used to investigate if MAO is a potential site of regulation throughout the day. Not only did gene expression of MAO orthologs and MAO activity fluctuate at different times of day, but the enzymatic activity was substrate-specific producing a higher level of degradation of octopamine as compared to serotonin in vitro. This study further supports evidence that MAO has an active role in monoamine inactivation in invertebrates and provides a first look at how MAO ultimately may be regulating behavior in an invertebrate.

Ayant été formée durant de nombreuses années par la pensée de Paul Diel, j'ai voulu faire le lien entre mon expérience psychologique et les connaissances acquises en Philosophie à l’Université Laval. Paul Diel, m’est alors apparu, comme une jonction entre ces deux domaines antérieurement réunis dans la plupart des philosophies. J’ai retracé la vie de Paul Diel, et essayé de montrer l’originalité spécifique de l’œuvre de Diel dans l’utilisation qu’il a faite des apports de la philosophie, de la psychologie, et de la psychanalyse. J’ai comparé les concepts d’âme, d’imagination et d’intellect issus des œuvres d’Aristote, de Hegel et de Diel en faisant ressortir leur évolution dans le temps. Ceux-ci s'organisent autour de la notion d'universel. La méthodologie utilisée dans ce travail est l'introspection, résultat d'expériences de vie, d'observations, soutenue, par des connaissances en psychologie en philosophie et philosophie des sciences. Elles m'ont amenée à préciser les notions de rationalité, d’émotion, d'universel.

1. Large rivers in the central United States experience a variety of ecological interactions. Both short- and long-term temporal changes affect both fish and zooplankton communities in rivers. Variation in diel patterns of predation could affect differences of behavior in prey. Long term temporal changes across seasons can lead to different areas of rivers providing growth or costing energy. Spatial changes also affect habitat quality and behaviors of the aquatic organisms within large rivers. Spatial variation can be dynamic and occur between longitudinally connected habitats or vary through different sections of the reach and can also change seasonally. 2. Invasive species have major economic and ecological impacts. In aquatic ecosystems, plankton are the base of the food web and a planktivore invader can cause major ecological disruptions. The Wabash River is a large free flowing river with a variable hydrology, which causes dramatic changes in habitat availability through time. Therefore, habitat usage, quality, and availability may differ for native and invasive species through time. The objectives of this study were to assess how habitat quality changes in a large, flashy, free-flowing river over time, and to compare the quantity and overlap of quality macrohabitat for invasive and native fish. Growth rate potential (GRP) was used to quantify habitat quality for Silver Carp (Hypophthalmichthys molitrix; invasive) and Gizzard Shad (Dorosoma cepedianum; native). To calculate GRP, bioenergetic models were used with monthly observations of food abundance (zooplankton, phytoplankton, and detritus), water temperature, dissolved oxygen, and water velocity of various habitat types from the Wabash River’s confluence with the Ohio River upstream to Terre Haute, Indiana, approximately 215 river miles. Negative GRP for both Silver Carp and Gizzard Shad occurred during spring and most of summer. However, in the fall, the majority of the river had a positive GRP for both species. Reduced flows and increases in food abundance were the cause for the switch from negative to positive GRP. There was a high degree of spatial overlap in positive GRP areas between Silver Carp and Gizzard Shad, suggesting that there is a high degree of competition. Acoustically tagged Silver Carp selected for areas predicted to have a positive GRP from the model presented in the study. This model showed that regulation of flows in hydrologically altered systems could potentially lower the impact of Silver Carp in those systems. With Silver Carp selecting for predicted habitats, a bioenergetics model can be used to inform commercial fishers where to focus effort to maximize catch.3. Temporal changes in rivers tend to be quantified at broad seasonal scales. However, river conditions including water flow, water temperature, dissolved oxygen, and availability of zooplankton prey may change daily. In large rivers, these conditions may change in a diel fashion between backwater and main channel habitats. To assess diel changes in the Illinois River, zooplankton, paired with mobile hydroacoustic surveys for fish were sampled from three main channel and three off-channel sites in the LaGrange reach every four hours in a twenty-four-hour period at different depths between October 22 and 26, 2018. Water depth, water temperature, water velocity, and fish (planktivore and nonplanktivore) densities were quantified during each sampling time. Water temperature and water velocity differed between the two habitat types. Water temperature was higher and water velocity was lower in the off-channel. Water temperature was colder in the morning in both the main channel and off-channel. Water velocity did not change throughout the day. The majority of the zooplankton community was comprised of rotifers which were less mobile than larger taxa and did not migrate. When evaluating the more mobile, large body zooplankton, time and depth affected copepod density in off-channel environments, where the deeper depth had a higher copepod density than the shallower depth. In contrast, only time of day affected off-channel cladoceran density, where densities increased at night. Fish did not exhibit diel patterns and the off-channel habitat had a higher density. The most likely mechanism behind the diel movements of the large bodied zooplankton was predation by planktivorous fish. The present study suggests that connections to the off-channel habitats in large rivers will promote quality habitat for both zooplankton and fish.

The aim of this thesis was to explore the use of genome-scale metabolic models to predict metabolic fluxes in plant tissues. Results from this thesis showed that the application of constraint-based modelling, namely flux balance analysis, to an Arabidopsis genome-scale metabolic model gave accurate predictions of metabolic fluxes in heterotrophic cell culture and in photosynthetic leaves. Two major factors important for the accuracy of model predictions were highlighted from the study: 1) the inclusion of energetic costs for transports and cellular maintenance in terms of ATP and NADPH; 2) consideration of the interactions between light and dark metabolism in modelling photosynthetic leaves. This study began with the construction of a well-curated and compartmented genome-scale metabolic model of Arabidopsis. Using the model, cellular maintenance costs in a heterotrophic cell culture under control and two stress conditions were estimated in terms of ATP and reductant usage. The results suggested that the cells were not stressed under hyperosmotic conditions. Comparisons between model predictions and experimentally estimated flux maps showed that the inclusion of transport and maintenance costs was important for obtaining accurate model flux predictions. To model leaf metabolism over a day-night cycle, a diel modelling framework was developed which took into account the interactions between light and dark metabolism. Numerous known features of metabolism in a C₃ leaf were predicted such as the nocturnal accumulation of citrate utilised for diurnal glutamate and glutamine synthesis and the operation of an incomplete TCA cycle during the day. Using the Arabidopsis genome-scale metabolic model and the diel modelling framework, the operation of the CAM cycle was predicted as a direct consequence of blocking the CO₂ exchange with the external air during the day to simulate closure of the stomata. Comparisons between model predictions of C₃ and various subtypes of CAM leaves suggested that photon and nitrogen use efficiencies are unlikely to be the driving forces for the evolution of CAM plants under the current atmospheric CO₂ concentration. Finally, the model was utilised to predict the changes in metabolic fluxes, in particular fluxes through various routes of alternative electron flow, in a C₃ leaf with varying light intensity, nitrogen availability and at different stages of leaf development. From the model flux predictions, it was shown that constraint-based modelling can be utilised to elucidate the distinct metabolic roles of enzymes in different subcellular compartments and the tissue-specific use of distinct forms of enzymes with different coenzyme specificities.

Hyporheic water is thought to infiltrate at the head of a riffle which in turn is complemented by upwelling back to the stream at the tail of the riffle in a pool-riffle-pool (PRP) sequence. Heat tracing is a potentially useful method to characterize these hyporheic flow paths and quantify associated fluxes. Temperature was monitored within a PRP sequence for several days. Temperature in the hyporheic zone reflected the diel temperature change in the river but not uniformly. The observed thermal pattern exhibited deeper penetration of thermal oscillations below the head pool and shallower penetration below the tail pool. This pattern is consistent with the conceptual model of hyporheic exchange over a PRP sequence. One-dimensional analytical heat transport models were used at different points below the PRP sequence to estimate distributed vertical fluid fluxes. The calculated fluxes exhibit a trend that follows the expected distribution for a PRP sequence but modified for a losing stream. Deviation of both magnitude and distribution of fluxes from the conceptual ‘downwelling-to-upwelling’ model is partly due to the dominantly losing conditions at the study site but the trends are consistent with a losing stream undergoing hyporheic exchange. Violation of the assumptions in the analytical models most likely adds error to flux estimates. For this study, flux estimation methods using a temperature time series amplitude analysis more closely matched field measurements than phase methods. / text

I investigated seasonal and inter-site variation in factors influencing diel dissolved oxygen (DO) metabolism at four streams in the Virginia Coastal Plain. Data were collected monthly from January to August 2008 to characterize DO metabolism (diel DO amplitude, production, respiration), incident solar radiation (PAR), dissolved nutrients, fine benthic materials (mass, C:N, Chlα) and hydrology (discharge, water transit time, transient storage). Reach-scale metabolism estimates were determined using the one-station diurnal DO technique and transit time and transient storage were determined by conservative tracer additions. Incident solar radiation was the primary determinant of DO metabolism as streams experiencing higher light levels (Herring and Powell Creeks) exhibited greater diel DO amplitudes, production and respiration. Streams with greater riparian shading (Courthouse and Crump Creeks) exhibited lower DO metabolism despite their higher nutrient concentrations. Higher incident solar radiation was associated with greater benthic algal biomass at some (Herring, Crump, and Courthouse Creeks) but not all (Powell Creek) sites. Diel DO amplitudes were significantly and positively correlated with benthic Chlα and incident solar radiation at less shaded sites. These factors were not significant predictors of DO amplitude, production or respiration at more shaded sites.