Many coastal ecosystems around the world are dominated by submerged aquatic vegetation (SAV) habitats. These SAV habitats are known to provide many highly valuable ecosystem services such as habitat for commercial important species and increased water clarity. Water flow is an environmental variable which can have measurable effects on the ecosystem services provided by SAV, but is often not considered in studies assessing these services. This dissertation sought to investigate the links between SAV, primarily seagrasses, and hydrodynamics, paying special attention to the effects on sediments and fauna. Three main areas are discussed: (1) the effects of SAV on flow, (2) the effects of SAV and flow on deposition in SAV beds, and (3) the effects of SAV and flow on faunal communities in SAV beds. Seagrasses and other SAV reduce currents, attenuate waves, and dampen turbulence within their vegetative canopies, which in turn can enhance deposition and reduce the resuspension of sediment, organic matter, and passively settling larvae. The ability of SAV to retard flow may be further enhanced by increases in vegetated structure, such as shoot density, biomass, or canopy height, which can promote increased abundance and diversity of in- and epifauna within SAV beds. Ultimately, it is clear that hydrodynamics is an important factor that shapes SAV communities both physically (e.g. deposition, sediment structure, etc.) and biologically (e.g. faunal community composition, predation pressure, food availability, etc.).

Coastal marine ecosystems are among the most impacted globally, attributable to individual and cumulative effects of human disturbance. Anthropogenic nutrient loading is one stressor that commonly affects nearshore ecosystems, including seagrass beds, and has positive and negative effects on the structure and function of coastal systems. An additional, previously unexplored mechanistic pathway through which nutrients may indirectly influence nearshore systems is by driving blooms of benthic jellyfish. My dissertation research, conducted on Abaco Island, Bahamas, focused on elucidating the role that benthic jellyfish have in structuring systems in which they are common (i.e., seagrass beds), and explored mechanistic processes that may drive blooms of this taxa. To establish that human disturbances (e.g., elevated nutrient availability) may drive increased abundance and size of benthic jellyfish, Cassiopea spp., I conducted surveys in human-impacted and unimpacted coastal sites. Jellyfish were more abundant (and larger) from human-impacted areas, positively correlated to elevated nutrient availability. In order to elucidate mechanisms linking Cassiopea spp. with elevated nutrients, I evaluated whether zooxanthellae from Cassiopea were higher from human-disturbed systems, and whether Cassiopea exhibited increased size following nutrient input. I demonstrated that zooxanthellae population densities were elevated in human-impacted sites, and that nutrients led to positive jellyfish growth. As heightened densities of Cassiopea jellyfish may exert top-down and bottom-up controls on flora and fauna in impacted seagrass beds, I sought to examine ecological responses to Cassiopea. I evaluated whether there was a relationship between high Cassiopea densities and lower benthic fauna abundance and diversity in shallow seagrass beds. I found that Cassiopea have subtle effects on benthic fauna. However, through an experiment conducted in a seagrass bed in which nutrients and Cassiopea were added, I demonstrated that Cassiopea can result in seagrass habitat modification, with negative consequences for benthic fauna. My dissertation research demonstrates that increased human-driven benthic jellyfish densities may have indirect and direct effects on flora and fauna of coastal marine systems. This knowledge will advance our understanding of how human disturbances shift species interactions in coastal ecosystems, and will be critical for effective management of jellyfish blooms.

Seagrass beds are among the most ecologically important systems in the marine environment. They provide the primary production to nearby coral reef and mangrove communities, and seagrasses comprise a large component of the diets of many marine organisms including fishes, small invertebrate species, and many protected species such as manatees and sea turtles. This consumption provides a pathway for many contaminants to enter the marine food web via the seagrasses. The coastal location of seagrass beds causes them to be especially susceptible to anthropogenic pollution, including accumulation of heavy metals, which has been shown to have many adverse health effects in the seagrasses and marine organisms that feed on them. This study assessed the heavy metal concentrations of seagrasses in three regional locations in South Florida: Port of Miami, Card Sound Aquatic Preserve, and Florida Bay. Three species of seagrasses, Thalassia testudinum, Halodule wrightii, and Syringodium filiforme, which comprise the majority of South Florida seagrass beds, were collected monthly for a period of one year and analyzed for ten heavy metals: (arsenic (As), cadmium (Cd), copper (Cu), iron (Fe), mercury (Hg), manganese (Mn), nickel (Ni), lead (Pb), selenium (Se), zinc (Zn)). Concentrations were compared across locations, season, species, and plant part (leaves, shoots, roots, and rhizomes). Concentration ranges, in µg/g (ppm), found in seagrass tissues for all included locations, species, and plant parts were: As (0.02-2.95), Cd (0.09-10.72), Cu (0.38-33.68), Fe (1.52-1877.43), Pb (0.78-156.20), Mn (0.79-300.15), Hg (0.03-16.46), Ni (0.67-87.74), Se (0.01-4.79), Zn (1.48-669.44). Statistical analysis showed significant difference in concentrations among locations, season, species, and plant morphology.

Bahia de la Ascension (BA) is a pristine, shallow, karst bay located in the Mexican Caribbean, a region experiencing rapid population growth stimulated by intense tourism development. The overall objective of this study was to address the natural hydrographic variability of this inherently vulnerable ecosystem and assess its influence on a key habitat, the seagrass. The chapters follow the three-branched nature of the study which tackled the connected ecosystem issues of coastal hydrology, physical dynamics of flow and circulation, and the ecological dynamics of the seagrass species Thalassia testudinum in BA. Freshwater input to BA is primarily by submerged groundwater discharges and surface runoff; both sources are derived from fissures in the aquifer but feature distinct water quality due to the interaction with adjacent wetlands. Hurricanes explain 36 percent of the interannual precipitation variability in the region. The water balance indicates a persistent net outflow from BA to the adjacent shelf, suggesting an intense exchange across inlets. Both diurnal and semidiurnal tidal frequencies are attenuated in the inner bay, where a meteorologically-induced subtidal water level increase may occur during four-day southeasterly winds. A clear SW-NE salinity gradient was established during dry and rainy seasons, with a strong tidally-driven marine influence throughout the central basin, and a perennial mesohaline ambient in the southwestern-most bay, where hydrodynamics are primarily controlled by wind stress. Thalassia testudinum is the dominant seagrass species in BA, occupying ~90 percent of the substrate, including the freshwater-influenced inner bay. High nutrient inputs, including phosphorus which might have limiting effects in karst environments, along with the wind-driven circulation controlling water residence times are associated with the successful development of T. testudinum (up to 1,461.23 g DW m-2) within the SW bay. Farthest into the central basin, Thalassia consistently exhibited an inverse correlation between abundance and density of shoots. This pattern was enhanced under exceptional precipitation and inputs of denuded organic matter resulting from hurricanes making landfall on this region. The relationship between nutrient distribution and the above/belowground ratio suggested that Thalassia growing in BA favors the development of the aerial component as nutrients availability increases. This study provides a basic understanding of the most important processes molding the patterns of variability exhibited by T. testudinum in Bahia de la Ascension. The salinity gradient and external nutrient supply, along with the hydrodynamic component, define the spatial scale at which the connectivity between the adjacent wetland, the bay, and the shelf may occur.

In the past century, seagrasses have experienced massive die off episodes in what has been collectively referred to as “wasting disease.” Researchers generally agree that wasting disease is caused by a protist of the Labyrinthula genus, and that environmental stressors can make some populations of seagrasses more susceptible to infection. The purpose of this study was to examine the combined effects of elevated salinity, elevated temperature, elevated sulfide and night-time hypoxia on Thalassia testudinum health and its response to Labyrinthula sp. infection under controlled conditions. To test these effects, microcosms were utilized and individual seagrass shoots were randomly assigned to treatment groups consisting of various combinations of abiotic stressors. They were then infected with Labyrinthula sp. and monitored for lesion formation and a reduction in photosynthetic efficiency. It was hypothesized that seagrasses incubated under the application of a given stressor would show evidence of declining health, and, in turn, would be more prone to infection, as quantified by lesion size and reduced photosynthetic capacity. Results indicated that abiotic stressors have little effect on T. testudium’s ability to resist infection from Labyrinthula sp. However, the Labyrinthula sp. was highly sensitive to abiotic stressors, specifically salinity, indicating that the health of the pathogen greatly contributed to the severity of the disease. Therefore, the stress thresholds of both the host seagrass and the pathogen need to be considered. Indeed, the interaction(s) among T. testudinum, Labyrinthula spp. and the environment are complex and not as linear as previously thought.

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