Seagrass habitats are highly productive ecosystems that support marine food webs and provide essential habitat for a variety of species. Seagrass coverages are declining in abundance worldwide. For southeastern Florida in particular, one of the main causes of the decline is disturbance from dredging and removal of substrate. Seagrass beds at three locations in the vicinity of Port Everglades, Florida were assessed for their trophic contribution to the marine organisms in the area. Seagrasses, algae, invertebrates, and vertebrates from the beds were identified and analyzed for stable carbon and nitrogen isotope ratios to determine their contribution as a food source. Significant differences were found in both δ13C and δ15N between both seagrass species and among the three sites. The δ13C of Johnson’s seagrass Halophila johnsonii ranged from -16.28 to -11.27‰ while shoal grass Halodule wrightii ranged from -15.78 to -13.36‰. The δ15N for H. wrightii were more constrained than those of H. johnsonii, 4.69 to 7.08‰ versus 0.80 to 7.86‰, respectively. Neither seagrass species appeared to be a dominant food source for marine organisms at all three study sites. However, the δ13C and δ15N of both seagrass species, Halophila johnsonii and Halodule wrightii, did fall in the fractionation range of potential consumers, -28.78 to -17.11‰ and 1.96 to 12.63‰, indicating that these animals could be ingesting pieces of seagrass while grazing on epiphytes and other primary producers in the area. Epiphytes found on the seagrass blades appeared to be a greater trophic contributor to local organisms. So while the seagrass species in question may not have been major contributors to the diet of many of the local consumers, the seagrasses nontheless played a vital role as habitat for the epiphytes that did serve as a trophic resource in these communities.

Caridean shrimp are a prominent element of seagrass faunal communities and play an important role in the energy transfer between trophic levels. They are a food source for other organisms and play an integral role in the ecosystem by feeding on algae and assisting with the breakdown of organic matter. Carideans are also fundamental to the marine fishery industry in that they are a food source for potentially valuable juvenile commercial fish. Ectoparasitic isopods (Cymothoida: Bopyridae) that infest caridean shrimps decrease the energy level of the shrimp, resulting in slower reaction time, greater predation rate, slower growth rate, and/or reduced egg production. However, in South Florida, little is known about the distributions and effects of parasitism among caridean shrimp in seagrass habitats. This research investigates the relationship of caridean shrimps and ectoparasitic isopods throughout several marine and brackish basins of coastal South Florida ranging from Lostmans River on the lower southwest mangrove coast through Florida Bay and Biscayne Bay. Samples were collected at the end of the wet season in 2010 and the dry season in 2011 using a 1-m2 throw-trap. Relations among isopods, carideans and environment were determined based on a series of biotic (host preference and availability) and abiotic (salinity, temperature, turbidity, water depth) factors. Bopyrid isopods were most abundant in Manatee Bay and Barnes Sound adjacent to the C-111 canal located in southern Biscayne Bay region and predominantly associated with Hippolyte spp. Logistical regression revealed that the likelihood of parasite presence is associated with higher temperatures, lower salinity, increasing depth, less seagrass coverage and greater macroalgae coverage. The results suggest that increased stressors in an environment, such as anthropogenic runoff, may also negatively impact host resistance to parasitism.

Seagrasses are considered highly important CO2 sinks, with the capacity to store substantial quantities of organic carbon in the living biomass and sediments, and thereby acting as a buffer against climate change. In this thesis, I have studied carbon storage variability in temperate and tropical seagrass habitats and identified factors influencing this variation. In addition, as seagrass areas are decreasing worldwide, I have assessed effects of different anthropogenic disturbances on carbon sequestration processes. The result from this thesis showed that there was a large variation in carbon storage within and among temperate, tropical and subtropical regions. The highest organic carbon stocks were found in temperate Zostera marina meadows, which also showed a larger carbon storage variability than the subtropical and tropical seagrass habitats. The tropical and subtropical seagrass meadows had inorganic carbon pools exceeding the organic carbon accumulation, which could potentially weakens the carbon sink function. The variability in organic carbon stocks was generally strongly related to the sediment characteristics of the seagrass habitats. In Z. marina meadows, the strength of the carbon sink function was mainly driven by the settings of the local environment, which in turn indicates that depositional areas will likely have higher organic carbon stocks than more exposed meadows, while in the tropics seagrass biomass was also influencing sedimentary carbon levels. Furthermore, locations with large areas of seagrass were associated with higher carbon storage in tropical and subtropical regions, which could be related to increased accumulation of both autochthonous and allochthonous carbon. In an in situ experiment, impacts on carbon sequestration processes from two types of disturbances (with two levels of intensity) were tested by simulating reduced water quality (by shading) and high grazing pressure (through removal of shoot biomass). At high disturbance intensity, reductions in the net community production and seagrass biomass carbon were observed, which negatively affected carbon sequestration and could impact the sedimentary organic carbon stocks over time. In the treatments with simulated grazing, erosion was also seen, likely due to an increase in near-bed hydrodynamics. When experimentally testing effects of increased current flow on organic carbon suspension in Z. marina sediment, a ten-fold release of organic carbon with higher current flow velocities was measured, which resulted in an increase in the proportion of suspended organic carbon by three times in relation to other sediment particles. Therefore, periods with enhanced hydrodynamic activity could result in a removal of organic carbon and thereby likely reduce the seagrass meadows’ capacity to store carbon. The findings of this thesis add to the emerging picture that there is a large natural variability in seagrasses’ capacity to store carbon, and highlight how human-induced disturbances could negatively affect the carbon sink function in seagrass meadows. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

Efforts that are underway to rehabilitate the Florida Bay ecosystem to a more natural state are best guided by a comprehensive understanding of the natural versus human-induced variability that has existed within the ecosystem. Benthic foraminifera, which are well-known paleoenvironmental indicators, were identified in 203 sediment samples from six sediment cores taken from Florida Bay, and analyzed to understand the environmental variability through anthropogenically unaltered and altered periods. In this research, taxa serving as indicators of (1) seagrass abundance (which is correlated with water quality), (2) salinity, and (3) general habitat change, were studied in detail over the past 120 years, and more generally over the past ~4000 years. Historical seagrass abundance was reconstructed with the proportions of species that prefer living attached to seagrass blades over other substrates. Historical salinity trends were determined by analyzing brackish versus marine faunas, which were defined based on species’ salinity preferences. Statistical methods including cluster analysis, discriminant analysis, analysis of variance and Fisher’s α were used to analyze trends in the data. The changes in seagrass abundance and salinity over the last ~120 years are attributed to anthropogenic activities such as construction of the Flagler Railroad from the mainland to the Florida Keys, the Tamiami Trail that stretches from the east to west coast, and canals and levees in south Florida, as well as natural events such as droughts and increased rainfall from hurricanes. Longer term changes (over ~4000 years) in seagrass abundance and salinity are mostly related to sea level changes. Since seawater entered the Florida Bay area around ~4000 years ago, only one probable sea level drop occurring around ~3000 years was identified.

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Globally, human populations are increasing and coastal ecosystems are becoming increasingly impacted by anthropogenic stressors. As eutrophication and exploitation of coastal resources increases, primary producer response to these drivers becomes a key indicator of ecosystem stability. Despite the importance of monitoring primary producers such as seagrasses and macroalgae, detailed studies on the response of these benthic habitat components to drivers remain relatively sparse. Utilizing a multi-faceted examination of turtle-seagrass and sea urchin-macroalgae consumer and nutrient dynamics, I elucidate the impact of these drivers in Akumal, Quintana Roo, Mexico. In Yal Ku Lagoon, macroalgae bioindicators signified high nutrient availability, which is important for further studies, but did not consistently follow published trends reflecting decreased δ15N content with distance from suspected source. In Akumal Bay, eutrophication and grazing by turtles and fishes combine to structure patches within the seagrass beds. Grazed seagrass patches had higher structural complexity and productivity than patches continually grazed by turtles and fishes. Results from this study indicate that patch abandonment may follow giving-up density theory, the first to be recorded in the marine environment. As Diadema antillarum populations recover after their massive mortality thirty years ago, the role these echinoids will have in reducing macroalgae cover and altering ecosystem state remains to be clear. Although Diadema antillarum densities within the coral reef ecosystem were comparable to other regions within the Caribbean, the echinoid population in Akumal Bay was an insufficient driver to prevent dominance of a turf-algal-sediment (TAS) state. After a four year study, declining coral cover coupled with increased algal cover suggests that the TAS-dominated state is likely to persist over time despite echinoid recovery. Studies on macroalgal diversity and nutrients within this same region of echinoids indicated diversity and nutrient content of macroalgae increased, which may further increase the persistence of the algal-dominated state. This study provides valuable insight into the variable effects of herbivores and nutrients on primary producers within a tropical coastal ecosystem. Results from this work challenge many of the currently accepted theories on primary producer response to nutrients and herbivory while providing a framework for further studies into these dynamics.

The loss of large-bodied herbivores and/or top predators has been associated with large-scale changes in terrestrial, freshwater, and marine ecosystems around the world. Understanding the consequences of these declines has been hampered by a lack of studies in relatively pristine systems. To fill this gap, I investigated the dynamics of the relatively pristine seagrass ecosystem of Shark Bay, Australia. I began by examining the seagrass species distributions, stoichiometry, and patterns of nutrient limitation across the whole of Shark Bay. Large areas were N-limited, P-limited, or limited by factors other than nutrients. Phosphorus-limitation was centered in areas of restricted water exchange with the ocean. Nutrient content of seagrasses varied seasonally, but the strength of seasonal responses were species-specific. Using a cafeteria-style experiment, I found that fast-growing seagrass species, which had higher nutrient content experienced higher rates of herbivory than slow-growing species that are dominant in the bay but have low nutrient content. Although removal rates correlated well with nutrient content at a broad scale, within fast-growing species removal rates were not closely tied to N or P content. Using a combination of stable isotope analysis and animal borne video, I found that green turtles (Chelonia mydas) – one of the most abundant large-bodied herbivores in Shark Bay – appear to assimilate little energy from seagrasses at the population level. There was, however, evidence of individual specialization in turtle diets with some individuals foraging largely on seagrasses and others feeding primarily on macroalgae and gelatinous macroplankton. Finally, I used exclusion cages, to examine whether predation-sensitive habitat shifts by megagrazers (green turtles, dugongs) transmitted a behavior-mediated trophic cascade (BMTC) between sharks and seagrasses. In general, data were consistent with predictions of a behavior-mediated trophic cascade. Megaherbivore impacts on seagrasses were large only in the microhabitat where megaherbivores congregate to reduce predation risk. My study highlights the importance of large herbivores in structuring seagrass communities and, more generally, suggests that roving top predators likely are important in structuring communities - and possibly ecosystems - through non-consumptive pathways.

The seagrass extent has been declining globally. The human activities that are most likely to cause seagrass loss are those which affect the water quality and clarity. However, turbidity following coastal erosion is often left out from marine ecosystem vulnerability indices. This study quantified the coastal erosion for Tsimipaika Bay in northwestern Madagascar by using change detection analysis of satellite imageries. The annual coastal erosion data was then used to create an index for seagrass vulnerability to turbidity following coastal erosion. Considering that the height of seagrass species plays an important role in their survival following turbidity, the seagrass vulnerability index (SVI) was based on two factors; seagrass species height and their distance to the nearest possible erosion place. The results for the coastal erosion showed that the amount of erosion was particularly high in 1996, 2001 and 2009 for Tsimipaika Bay. The highest erosion occurred in 2001 with a land loss area of about 6.2 km2 . The SVI maps revealed that 40% of the seagrass communities had minimum mean SVI values in 2001 and 50% had the maximum mean SVI during the year 2009. This study showed that it is possible to use coastal erosion to measure seagrass vulnerability; however, the index requires configuration such as including the total amount of annual coastal erosion and incorporating bathymetric data. The entire project was built and automated in Jupyter Notebook using Python programming language, which creates a ground for future studies to develop and modify the project.

This study aimed to understand the ecology of the threatened, habitat-forming seagrass, Zostera capensis in Langebaan Lagoon, a marine protected area that forms part of the West Coast national park, South Africa; and the physiological strategies that allow this habitat to persist in sub- and supra-optimal temperatures. First, the environmental drivers responsible for spatial and temporal variability in Zostera and its associated macro-epifauna were determined. Secondly, the effects of temperature and the role of algal grazing in maintaining seagrass performance under temperature stress were investigated. Seasonal field collections of seagrasses and their associated macro-epifauna were undertaken, along with regular measurements of key environmental variables. Thereafter, mesocosm experiments were performed to measure the responses of Zostera to thermal stress and grazing using morphometry, fluorometry, chromatography and biochemistry. Significant seasonal variability in seagrass distributions with severe diebacks in summer were found, which influenced associated macro-epifauna communities. Populations responded to environmental stress by changing their growth form producing small-leaves in high densities in the high intertidal, while those in low intertidal and subtidal areas produced sparse, large-leaved populations. These distinct populations supported unique faunal diversities, which were dominated by grazing invertebrates. Temperature was a consistent driver of seagrass density and leaf size, while turbidity and exposure were key environmental factors that influenced macro-epifaunal patterns. Macro-epifaunal abundances were highly positively correlated with seagrass leaf width and biomass. Different growth forms displayed different responses to thermal stress, including a higher photosynthetic rate, and accumulations of carbon and nitrogen as phenolic compounds, in small- compared to large-leaved plants. This implies that large-leaved populations are more vulnerable to stress from fouling, which was evident in their larger epiphyte loads, compared to small-leaved populations. In addition, grazers were ineffectual at regulating epiphyte growth which increased under warming conditions. These findings suggest differences in resilience between sub-populations of Zostera, and attest to their capacity to recover from environmental stress. They further emphasise the significance of identifying characteristics and acclimation strategies that allow habitats to persist under climate change, and thus sustain biodiversity and productivity, as well as continue to provide important ecosystem services.

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.).