<p> The low-lying topographic nature of salt marshes makes plants in these communities particularly vulnerable to increased salinity and inundation exposure associated with sea level rise. Both increased salinity and inundation have been cited as major causes of reduced plant performance and survival in marsh and areas fringing marsh. In addition to limitations imposed by physical stress, interspecific interactions have also been shown to mediate the performance and survival of salt marsh and salt marsh fringing species. The Stress Gradient Hypothesis (SGH) postulates that species interactions shift from competitive to facilitative as stress levels increase and predicts that (a) the frequency and intensity of facilitative interactions increase as conditions become more stressful for plants and (b) the strength of competitive interactions increases as abiotic stress levels diminish. The SGH has been rigorously tested to examine how both the frequency and intensity of species interactions change under varying physical stress levels. Studies conducted in salt marsh systems have shown facilitation to be as strong of a driving force as competition in influencing plant performance and survival and have shown that while competition appears to be the pervasive force in the less physically stressful terrestrial zones fringing salt marshes, facilitation influences the performance and survival of species in harsher marsh areas. Under conditions of sea level rise, it remains unclear if the nature of interspecific interactions would shift as stress levels change. This research endeavors to examine the interplay between abiotic stresses and biotic interactions under conditions of increased salinity and inundation exposure. </p><p> The first study presented here investigated the effects of increased inundation and soil salinity associated with sea level rise on four salt marsh fringing species, and assesses how competition and facilitation impact survival of salt marsh fringing plant survival under these changing conditions. All plant species experienced reduced growth and photosynthetic inhibition below their current distributional positions, both in the presence and absence of neighboring above ground vegetation. The findings also signal a potential shift in the nature of interspecific interactions from competition to facilitation to neutral as plants begin to experience increased salt and inundation exposure. </p><p> The second study aimed to disentangle the effects of increased soil salinity and increased soil moisture on four salt marsh fringing species, and to examine the effects of plant neighbors. The results showed that fringe plants exposed to increased inundation experienced a two-fold reduction in performance and survival over 750 g pure salt addition, suggesting that inundation may be a more important limiting factor than salinity with rising sea levels. Landward transplants at the forest-fringe margin exposed to lower soil salinity and decreased inundation exhibited a three-fold increase in performance and survival when compared to controls. Neighbor manipulation studies, which consisted of trimming neighboring vegetation to ground level, again suggested that interspecific interactions in salt marsh fringing species may shift from competitive to facilitative with climate-induced sea level rise. Overall, our findings suggest that salt marsh fringing species may not be able to tolerate changing conditions associated with sea level rise and their survival may hinge on their ability to migrate towards higher elevations. </p><p> The final experiment tested the Stress Gradient Hypothesis and investigated the relative importance of facilitation and competition in a salt marsh system under varying stress levels. This study also ascertained whether salt or inundation exposure is the primary influence on salt marsh plant performance and survival. As in previous studies, our findings suggest that many salt marsh plants don't require, but merely tolerate harsher abiotic conditions. The results showed that plants at higher elevations were depressed by strong competitive pressure from neighboring fringe species while plants at lower elevations benefited from the presence of neighbors. Collectively, the results of these studies indicate that species interactions are an integral driver of plant distribution in salt marsh communities. Furthermore, our findings indicate that changing stress levels may not always result in a shift in the nature of interspecific interactions. These studies have endeavored to show that the interplay between competition and facilitation interacts with physical processes to determine the growth and performance of both fringe and marsh plant species. The paucity of studies examining the roles of species interactions and changing abiotic stress levels on multiple salt marsh and salt marsh fringing species warrants the need for additional research. The responses of salt marsh and salt marsh fringing species to sea level rise can not only serve as very valuable and sensitive indictors of climate change, but will also aid in predicting the future location of the marsh-fringe-forest ecotone, which is predicted to shift inland as sea levels continue to rise.</p>

<p> Ocean general circulation models of the IPCC class have biases even when simulating present-day conditions, which may bring into question their predictions of future conditions. This dissertation is about tools for, and results from assessing biases in the Community Earth System Model (CESM) ocean component, by itself and when combined with the Biological Ecosystem Cycling (BEC) model. Newly developed tools and their applications are listed. 1. An offline matrix tracer transport model for the ocean component of CESM. 2. A fast Newton-Krylov implicit tracer equilibrium solver for both the annually-averaged and the seasonally-varying circulation. 3. An effective preconditioner for the solver simulating radiocarbon. Application results: For a natural radiocarbon simulation, an equilibrium solution was obtained in 23 model-years, a dramatic decrease from the 4000 model-years reported for time-stepping. The modeled circulation in the deep Pacific Ocean produced radiocarbon ages twice those of observations. 4. A capability for computing the surface origin of water mass fractions as well as the age of the various water masses. </p><p> Application results: The North Atlantic was the major supplier of ventilated water to not only the Atlantic, but also the Pacific and Indian Oceans. A lack of formation of bottom water in the Southern Ocean was discovered. 5. A capability for restricting the tracer simulation domain to a limited region of the ocean while retaining the effectiveness of advection and diffusion fields on the boundary. This reduces computational costs and allows separating local versus remote impacts of tracer sources on the biogeochemical tracer concentrations. This capability has the potential to provide a platform for further biogeochemical studies. </p><p> Application results: The Indian Ocean region was isolated. Global versus regional circulation effects were determined using radiocarbon. Most of the bias within the region was eliminated by using observational, rather than globally calculated values, on the boundaries. Oxygen production and consumption from a CMIP5 BEC simulation were used to drive a regional oxygen model. Boundary values of oxygen from the CMIP5 BEC simulation were replaced with observations, resulting in less bias within the region. However, significant bias in the location of the Arabian Sea oxygen minimum zone remained.</p>

<p> Benthic foraminifers that host algal symbionts are similar to corals in that they rely on their algal endosymbionts for their energy needs, calcify prolifically, and are sensitive to changes in environmental conditions. They are abundant in the benthos of coastal coral-reef areas and are found throughout the tropical and subtropical regions. Pulse Amplitude Modulated (PAM) chlorophyll fluorometry and chlorophyll a extraction techniques were used to quantify and compare the photosynthetic responses of the benthic foraminifera, <i> Archaias angulatus</i> and their isolated endosymbionts, <i>Chlamydomonas hedleyi</i>, to short-term changes in temperature. Maximum quantum efficiency (Fv/Fm) and rapid light curves (RLCs), from which relative electron transport rates (rETR) of photosystem II (PSII) were derived, were investigated over a thermal range from 4.4&deg; to 33.9 &deg;C in three experiments that were 7 to 31 days in duration. Typical mean yields (Fv/Fm) for healthy holobionts (symbionts in hospite) were 0.6 - 0.7, and for isolated symbionts 0.5 - 0.6. Chronic photoinhibition, indicated by significant decreases in Fv/Fm, occurred at temperatures above 31.0&deg;C; there was minimal reduction in efficiency in cooler treatments. The trends between holobiont and symbionts were very similar in all of the photophysiological parameters measured [yield, photoefficiency (&aacute;), ETRmax and minimum saturating irradiance (Ek)] and supported the temperature range findings in terms of the tolerance of the specimens in the low temperatures up to 31.0 &deg;C. For all photochemical measurements assessed, the holobiont values tended to be somewhat higher than those for the symbionts, with the exception of Ek, possibly indicating a tight coupling in the host-symbiont response during photosynthesis. Chlorophyll a (&igrave;g/foram) was negatively correlated with temperature (r = -0.37, p &lt; 0.001) in Experiments 1 and 2. However, in all 3 experiments, chlorophyll a was variable, suggesting a high degree of individual variability in <i>A. angulatus</i> and the ability to acclimate. Some differences observed among treatments may be related to differences in seasons when the specimens were collected and in length of time in culture prior to experiments. Holobiont median rETR light curve trends and photophysiological derived parameters recorded median Ek ranges of ~100-150 &igrave;mol photons m^-2 s^-1, observed ETR_max light intensities of ~200 &igrave;mol photons m-2 s-1 and photoinhibition, induced by increasing irradiance intensities, which occurred > 500 &igrave;mol photons m^-2 s^-1. These light curve trends and derived parameters generally supported previous photosynthesis O₂ and CO₂ gas production studies of A. angulatus. The differences in responses associated with acclimation should be considered in design of future experimental studies. This was the first known physiological study of the viable temperature range and photobiology of A. angulatus using chlorophyll fluorometry methods. Though commonly found in Caribbean and Atlantic waters ranging from 14.0 &ndash; 31.0 &deg;C, these results indicate a wider thermal-tolerance range for A. angulatus than was previously known.</p>

<p> 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.</p><p> 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 <i> in situ</i> 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.</p><p> 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.</p><p> 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 (K_d, m^-1) in visible bands (Appendix C), the other on K_d 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 <i>in situ</i> 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.</p><p> Many of these satellite data products were combined with <i>in situ </i> 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.</p><p> 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.</p>

Thesis (Ph.D.)--Louisiana State University and Agricultural & Mechanical College, 2003. / (UnM)AAI3182902. Source: Dissertation Abstracts International, Volume: 66-07, Section: B, page: 3592. Director: Donald M. Baltz.

Thesis (Ph.D.)--University of Washington, 2006. / (UnM)AAI3205846. Adviser: Charles A. Nittrouer. Source: Dissertation Abstracts International, Volume: 67-02, Section: B, page: 0763.

Thesis (Ph.D.)--University of California, San Diego, 2006. / (UnM)AAI3214542. Adviser: John A. Hildebrand. Source: Dissertation Abstracts International, Volume: 67-04, Section: B, page: 1862.

Thesis (Ph.D.)--University of California, Santa Cruz, 2006. / (UMI)AAI3241212. Advisers: John S. Pearse; Rich Mooi. Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6203.

Thesis (Ph.D.)--The University of Alabama at Birmingham, 2006. / (UMI)AAI3227075. Adviser: James B. McClintock. Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3554.

Thesis (Ph.D.)--University of California, Berkeley, 2006. / (UMI)AAI3253898. Source: Dissertation Abstracts International, Volume: 68-02, Section: B, page: 1133. Adviser: Harvey Blanch.