Smallmouth bass (Micropterus dolomieu) have experienced substantial range expansions in northern Ontario over the past century, with adverse consequences for native salmonid predators. It is unclear how climate-induced water clarity shifts will affect interactions between native dark-adapted walleye (Sander virteus) and invading smallmouth bass in northern Ontario. This study used stable isotopes of nitrogen (15N/14N) and carbon (13C/12C) in fish muscle tissue to investigate how resource partitioning between walleye and smallmouth bass is related to water clarity in 34 small (100-200 ha) Boreal Shield lakes (ranging from 1 to 8.5 m Secchi depth, and from 3.2 to 13.1 mg/L DOC). Quantitative metrics of trophic niche dimensions (based on the size, position, and dispersion of multivariate ellipses drawn around sampled individuals in δ15N vs. δ13C biplot space) were calculated for each individual population and used to determine trophic interactions and niche overlap between sympatric walleye and smallmouth bass. Linear and multiple regressions were then used to explore potential relationships between trophic interactions and water clarity. Available habitat and fish assemblage data was also explored for potential influences on isotopic niche dimensions and trophic interactions of walleye and smallmouth bass. Total occupied niche space decreased significantly with increasing water clarity for smallmouth bass as populations occupied a narrower range of trophic levels and made greater use of pelagic resources. In contrast, walleye trophic niche dimensions did not respond significantly to water clarity. Isotopic niche overlap ranged from 0 to 65%, but no metric of trophic overlap was significantly related to water clarity. Other abiotic and biotic variables, however, did have a significant influence on the similarity between some aspects of walleye and smallmouth iv bass isotopic niche dimensions (but not interaction). Both species fed on more isotopically similar carbon sources as lakes became shallower, which may be a result of a lack of distinct littoral and limnetic habitats. Walleye and smallmouth bass niche size also became more similar with increasing DOC but this may be a result of lower prey diversity. Both species also occupied more similar average food web positions as yellow perch relative abundance increased, indicating that the exploitation of yellow perch by both species increased with perch abundance. Together with other studies that have found little evidence for an impact of smallmouth bass on walleye fitness and abundance, this research suggests that, unlike salmonid and cyprinid species, walleye may be resilient against smallmouth bass invasions regardless of water clarity conditions in oligotrophic boreal lakes.

Biological processes like species interactions and patterns such as abundance and distribution observed in nature can vary depending on the scale at which the subject of interest is evaluated. Knowing that there is no single natural scale at which systems should be studied, in this thesis, I conducted a series of basic and applied ecological approaches in order to examine the phenomena that can occur at different scales of space, time, and ecological organization. Species abundances can vary over large spatial and temporal scales. By studying the habitat use of an abundant species, which uses a wide range of habitats, insights can be gained into how seascape-scales might influence population-level patterns. Similarly, temporal scales might affect the dynamics of species that have complex life cycles where migration is involved. Therefore, in the first study I used an eight-year dataset to conduct a population-level study at broader time- and seascape- scales of an abundant species in Tampa Bay, Florida. The goal of this study was to provide the first in-depth study on the habitat use of Pinfish on the eastern Gulf of Mexico and to provide insights on how seascape-scales can influence their abundance and distribution. Predator-prey interactions can be influenced by habitat at different spatial scales. In seagrass systems, blade density can provide prey refugia at local scales, which are further embedded within the seascape-scale effect of turbidity. In the second study, I used a combination of in situ field experiments and laboratory-controlled experiments to examine and separate the effects of habitat across these local and seascape scales on the relative predation rates of tethered Pinfish (Lagodon rhomboids). The broad-scale analyses indicated that population-level differences, such as abundance patterns and distribution can be influenced by temporal and spatial scales. Field- studies showed that habitat can influence ecological interactions at local- and seascape- scales. Overall, this research demonstrates the importance of using multiple spatial and temporal scale approaches when studying ecology, especially of those organisms that move over large distances and have complex life histories.

Coral reefs are greatly impacted by the physical characteristics of the water surrounding them. Incidence and severity of mass coral bleaching and mortality events are increasing worldwide due primarily to increased water temperature, but also in response to other stressors. This decline in reef health demands clearer understanding of the compounding effects of multiple stressors, as well as widespread assessment of coral reef health in near-real time. Satellites offer a means by which some of the physical stressors on coral reefs can be measured. The synoptic spatial coverage and high repeat sampling frequency of such instruments allow for a quantity of data unattainable by in situ measurements. Unfortunately, errors in cloudmasking algorithms contaminate satellite derived sea surface temperature (SST) measurements, especially during anomalously cold events. Similarly, benthic interference of satellite-derived reflectance signals has resulted in large errors in derivations of water quality or clarity in coral reef environments. This work provides solutions to these issues for the coral reef environments of the Florida Keys. Specifically, improved SST cloudmasking algorithms were developed for both Advanced Very High Resolution Radiometer (AVHRR; Appendix A) and Moderate Resolution Imaging Spectroradiometer (MODIS) data (Appendix B). Both of these improved algorithms were used to reveal the extent and severity of a January 2010 cold event that resulted in widespread mortality of Florida Keys corals. Applied to SST data from 2010, the improved MODIS cloudmasking algorithm also showed improved quantity of SST retrievals with minimal sacrifice in data quality. Two separate algorithms to derive water clarity from MODIS measurements of optically shallow waters were developed and validated, one focusing on the diffuse downwelling attenuation coefficient (Kd, m-1) in visible bands (Appendix C), the other on Kd in the ultraviolet (Appendix D). The former utilized a semi-analytical approach to remove bottom influence, modified from an existing algorithm. The latter relied on empirical relationships between an extensive in situ training dataset and variations in MODIS-derived spectral shape, determined using a stepwise principal components regression. Both of these algorithms showed satisfactory validation statistics, and were used to elucidate spatiotemporal patterns of water clarity in the Florida Keys. Finally, an approach was developed to use Landsat data to detect concurrent MODIS-derived reflectance anomalies with over 90% accuracy (Appendix E). Application of this approach to historical Landsat data allowed for long-term, synoptic assessment of the water environment of the Florida Keys ecosystem. Using this approach, shifts in seagrass density, turbidity increases, black water events, and phytoplankton blooms were detected using Landsat data and corroborated with known environmental events. Many of these satellite data products were combined with in situ reports of coral bleaching to determine the specific environmental parameters individually and synergistically contributing to coral bleaching. As such, SST and visible light penetration were found to be parsimoniously explaining variance in bleaching intensity, as were the interactions between SST, wind and UV penetration. These relationships were subsequently used to create a predictive model for coral bleaching via canonical analysis of principal coordinates. Leave-one-out-cross-validation indicated that this model predicted `severe bleaching' and `no bleaching' conditions with 64% and 60% classification success, respectively, nearly 3 times greater than that predicted by chance. This model also showed improvement over similar models created using only temperature data, further indicating that satellite assessment of coral bleaching based only on SST data can be improved with other environmental data. Future work should further supplement the environmental parameters considered in this research with databases of other coral stressors, as well as improved quantification of the temperature at the depth of corals, in order to gain a more complete understanding of coral bleaching in response to environmental stress. Overall, this dissertation presents five new algorithms to the field of satellite oceanography research. Although validated primarily in the Florida Keys region, most of these algorithms should be directly applicable for use in other coastal environments. Identification of the specific environmental factors contributing to coral bleaching enhances understanding of the interplay between multiple causes of reef decline, while the predictive model for coral bleaching may provide researchers and managers with widespread, near real-time assessments of coral reef health.

Water quality in Tampa Bay was examined using concurrent in situ and satellite remote sensing observations. Chlorophyll and suspended sediment concentrations showed large short-term variability, primarily driven by tide and wind forcing. Superimposed on these high frequency variations were recurrent phytoplankton blooms stimulated by decreases in turbidity 1-2 days after wind-induced bottom sediment resuspension events; the blooms were particularly strong if neap tides occurred after the wind events. The in situ data show that observations once per month are inadequate to sample short-term variability and that therefore the current monthly water quality surveys may have uncertainties of -50 to 200% if they are used to represent the monthly mean concentrations of chlorophyll or suspended sediment. Such uncertainties make it difficult to identify trends and interannual variability based on the in situ monitoring program. Colored dissolved organic matter (CDOM) generally showed good relationship with salinity and primarily delivered by riverine inputs but showed conservative and non-conservative mixing behaviors for the dry and wet seasons, respectively. CDOM in Old Tampa Bay (OTB), however, showed properties that were different from those in other Bay segments, and the non-conservative CDOM mixing behavior may be simply due to a three-end-member mixing scenario in which Hillsborough Bay and Middle Tampa Bay also receive water from Old Tampa Bay. A turbidity algorithm was successfully developed for application of MODIS/Aqua 250 m imagery. The MODIS turbidity images showed distinct spatial and temporal patterns related to river runoff in the upper bay and wind-induced sediment resuspension events in the middle and lower portions of the Bay. Similarly, light attenuation from SeaWiFS estimated using a new semi-analytical algorithm confirmed that water clarity was related to river runoff and to wind-induced sediment resuspension events. Wind is shown repeatedly to be another important factor controlling water quality in the Bay. The study shows that remote sensing products have the potential to be an important tool to help resource managers assess conditions in a large estuary like Tampa Bay synoptically, frequently and repeatedly.

No description available.

The availability of light is a primary limiting factor for seagrass recovery and sustainability. Understanding not only the quantity but the quality of light reaching the bottom is an important component to successful seagrass management and the key focus of this study. This study explores the spectral properties of the sub-surface light field in four shallow Seagrass Management Areas (SMA) in Tampa Bay. Wavelength-specific photosynthetically active radiation (PAR(λ)) and the spectral light attenuation coefficient (Kd(λ)) are used to estimate the percent blue, green, and red light remaining at the bottom relative to the surface. LIDAR Bathymetry is combined with Kd(λ) to produce high-resolution maps of percent subsurface light along the seagrass deep edge. The absorptance spectra from two seagrass species together with PAR(λ) is used to calculate the photosynthetically useable radiation (PUR(λ)), a term describing the actual wavelengths of light being used by the seagrass. Based on the average annual Kd(λ) , 32% - 39% percent of PAR reached the bottom at the seagrass deep edge, while only 14% - 18% of blue light reached bottom, suggesting that seagrass may be blue-light limited. Analysis of PUR(λ) data further confirmed that seagrass are blue-light limited. Each SMA was characterized in terms of the inherent optical properties (IOP) of absorption and scatter. Tampa Bay is considered a chlorophyll-dominated estuary. However, in this study, colored dissolved organic matter (CDOM) was the major absorber of blue light, accounting for 60% of the total absorption. To infer past light conditions, the IOPs were related to parameters more commonly used in routine monitoring programs. To estimate Kd(λ) an empirically-derived model using only the total absorption and scatter coefficients was used and resulted in a good fit between measured Kd(480) and modeled Kd(480). A deck-mounted flow-through system was used to survey each SMA for CDOM and chlorophyll a fluorescence, among other properties. A series of SMA-specific predictor equations were empirically derived to relate raw fluorescence to the IOPs. The Kitchen SMA was used as a case study. Survey results show a strong connection between CDOM-rich waters and the mangrove-dominated shoreline.