The goal of this project was to determine the effects of oyster reef restoration on oyster coverage, wave height dissipation and seagrass recruitment. First, to assess the current versus historical coverage of natural, dead and restored oyster reefs within Mosquito Lagoon, aerial photographs from 2009, provided by Saint Johns River Water Management District, were digitized using ArcGIS software. Live reefs, restored reefs and dead reefs were screen digitized using a reef ‘signature’ in order to estimate the area of each type of reef. The 2009 maps were used as a guide to digitizing the historical aerial photographs (1943, 1951, 1967, 1971, 1984, 1995, 2006). Dead reefs increased both in number and aerial extent during the study period (1943 – 2009), with 2009 having over 10 acres of dead reef coverage. Dead reefs were more likely to be found along major boating channels. Several dead reefs exhibited migration into the mangrove islands located landward of the 1943 footprint, with some dead reefs completely washing up into the shoreline. Restoration of dead reefs added 0.5 acres of live oysters to the Mosquito Lagoon area as of January 2009. Second, I examined how different oyster reef types (natural reef, restored reef, dead reef) reduced wave height. To determine wave height attenuation on each reef type, experiments were conducted in a 9 meter long wave tank using sensors that measured changes in wave height. For each reef type, replicate reefs were created in the wave tank. Shoreline sediment without oysters was used as a control. Using the wave generator, wave heights similar to Mosquito Lagoon boat wakes were created. Restored reefs reduced the incoming wave height by 25% compared to sediment without oysters. iii Lastly, I examined the potential link between oyster reef restoration and recruitment of seagrass fragments. Monthly surveys were performed to quantify the number of seagrass fragments encountering the three oyster reef types: dead reefs, natural reefs and restored reefs. The quantity of seagrass fragments was found to be similar on the three different reef types, but did show a significant trend of seasonality, which corresponds with the growing season of Halodule wrightii. Next, I tested retention of experimentally manipulated seagrass fragments on five natural and five restored reefs. Restored reefs retained seagrass fragments for significantly longer than natural reefs. I also measured seagrass fragment entanglement on each reef type inside the wave tank. I found that seagrass fragments were significantly more likely to become entangled and retained on restored reefs compared to dead and natural reefs. Overall, these metrics are important for determining the success of long-term oyster restoration project in Mosquito Lagoon, Florida. This project has found that oyster restoration is increasing the area of oyster habitat as well as providing important ecosystem services.

Seagrass is a valuable and important habitat, providing services such as coastal protection, supporting fisheries, and carbon sequestration. However, it is challenging to map accurately, as remote sensing has limits to how deep in the water column it can penetrate, and uncertainties such as distinguishing between algae and seagrass. Seagrass can exist at depths of theoretically 90 m deep in ultraoligotrophic waters, meaning that there is much of this habitat that cannot be mapped by remote sensing. Green turtles are an ideal candidate to help find seagrass blue carbon resources in the Red Sea. They go through an ontogenetic dietary shift to become almost completely herbivorous, and have a high fidelity to foraging sites. In this study we aim to assess the use of green turtles Chelonia mydas in discovering seagrass blue carbon. We use telemetry from 53 turtles tagged over 2018, 2019, and 2021 to map their foraging areas. 50 out of the 53 (94.34%) foraging sites had not been visited by previous seagrass studies in the Red Sea. We visited 18 locations in 14 of these foraging sites to ground truth them, and all 14 foraging sites (100%) had seagrass present. Comparatively, 18 out of 30 sites where seagrass was indicated by the remote sensing-based Allen Coral Atlas showed no seagrass. The turtles were seen to favour travelling shorter distances, thus it will be necessary to expand the area of tagging in order to achieve complete coverage of the Red Sea. Approximately 1/3 of the visited sites were deeper than 8 m, and so out of range of remote sensing, showing that considerable blue carbon resources may be discovered with the use of turtles. Samples were taken for carbon stock estimation from the ground truthed sites. A mean carbon stock of 4.89 ± 0.83 kg Corg m-2 was estimated for 1 m depth sediment. In the future it is important to develop methods for mapping the surface areas of the deep and inaccessible seagrass habitats that the turtles discover.

Algal blooms have caused significant losses in seagrass and macroalgae in the Indian River Lagoon, FL. To gain an understanding of these effects, samples of Gracilaria sp., Halodule wrightii, pinfish, and white mullet were taken throughout October and November of 2013. Samples from 2001 of Gracilaria sp., Halodule wrightii, Syringodium filiforme, Thalassia testudinum, pinfish, spotted seatrout, and white mullet were also obtained. Stable isotope data were obtained from these samples and compared by year and species. Halodule wrightii and pinfish had a significantly larger 2013 [delta]C13 values. Halodule wrightii also displayed lower total %C and total %N averages for 2013 when compared to 2001 data. These results may indicate a link between Halodule wrightii and pinfish, with pinfish consuming organisms that use Halodule wrightii as their source of nutrients. The location of collections also seemed to play a role in stable isotope values, as indicated by samples of Halodule wrightii.

No description available.

Examining how ecological processes are influenced by spatial variation can provide valuable insights into how communities are formed and how they may change in dynamic landscapes. In this thesis I address three objectives surrounding the spatial and temporal variation in species’ recruitment and predation, the influence of habitat isolation on consumer-resource relationships, and the influence of habitat fragmentation on a multi-trophic system. I used marine invertebrates, specifically crustaceans, bivalves, and sessile species as a model system. First, I address the spatial and temporal variation in local and regional processes in a multispecies assemblage of marine sessile invertebrates. Using diverse communities of marine sessile invertebrates as a model system I tested the hypothesis that spatial and temporal variation in recruitment and predation would shape local communities, and that both recruitment and predation would have significant effects on the abundance and structure of adult communities. I found that both recruitment and predation vary through time and space leading to the emergence of regional community divergence. I also address how habitat isolation interacts with top-down and bottom-up processes in seagrass ecosystems. Spatial structure of the habitat may mediate top-down and bottom-up controls of species abundances through decreased habitat connectivity and increased habitat isolation. I manipulated top down and bottom up processes by excluding mesograzers, adding resources, or altering both factors in isolated and contiguous patches of artificial seagrass. I then measured epiphyte recruitment, epiphyte abundances, and macroalgae abundance. I paired this with epiphyte sampling from isolated natural seagrass patches. I found that habitat isolation significantly decreased the abundance of epiphytes settling on seagrass blades due to dispersal limitation for epiphytic invertebrates. I found that consumers had strong effects on epiphyte biomass in continuous habitats, but not isolated habitats. Resource additions increased macroalgae cover and epiphyte biomass only in isolated habitats. The results suggest that isolated habitats may be nutrient limited and that top-down effects are stronger in continuous habitats, while bottom-up effects may dominate in isolated habitats. In my third objective, I address how habitat fragmentation may alter marine food webs. I examined whether predation rates, prey, and predator behavior differed between continuous and fragmented seagrass habitat in a multi-trophic context at two sites in Barnegat Bay, NJ. I hypothesized that blue crab predation rates and foraging would decrease in fragmented seascapes, due to a reduction in adult blue crab densities, increasing survival rates of juvenile blue crabs and hard clams. I expected hard clams to exhibit weaker predator avoidance behavior in fragmented habitats because of decreased predation. I found that species’ responses to fragmentation were different based on trophic level. Clams experienced higher predation and burrowed deeper in continuous habitats at both sites. Densities of blue crabs, the primary predator of hard clams, were higher in continuous habitats at both sites. Predation on juvenile blue crabs was significantly higher in fragmented seagrass at one site. Our results suggest that in fragmented seascapes, the impact of fragmentation on higher trophic level predators may drive predation rates and prey responses across the seascape, which may lead to trophic cascades in fragmented habitats. / Biology

Inshore tropical and subtropical estuaries harbor a relatively high abundance and diversity of organisms. Specifically within estuaries, mangrove and seagrass habitats provide shelter and food for a plethora of organisms, through some or all their life histories. Given the biological connection between offshore coral reefs and coastal estuaries, there is a critical need to understand the underlying processes that determine distribution and abundance patterns within mangrove-seagrass habitats. The predatory fish assemblage within the mangrove and seagrass beds of Biscayne Bay, Florida (USA), was examined over 24-hr. time periods along a distance and habitat gradient from the mangrove edge and nearshore environment (0–300 m) to farshore (301–700 m) seagrass beds. This thesis also investigated the occurrence, distribution and timing of reef fish movement between offshore coral reef habitat and inshore seagrass beds over 24-hr periods. Results indicate that fish predators differed over both the sampling period and with distance from mangrove edge. The results also demonstrated reef fishes move into Biscayne Bay at dusk and exit at dawn by utilizing Broad Creek Channel as a passageway. This work supports the idea of diel migration of selected reef fishes to inshore seagrass beds and highlights the importance of connective channels between habitats. The results suggest that the degradation or loss of seagrass habitat could differentially impact the life-history stages of reef fish species.

L’objectif général était d’évaluer la réponse du macrobenthos à la dynamique d’un herbier marin à Zostera noltii (colonisation, maturation, destruction, restauration), dans le Bassin d’Arcachon, une lagune du sud-ouest de la France. Quand l’herbier commence à se développer, la structure de la macrofaune diverge immédiatement entre habitats d’herbier et de sables nus, sans cependant que les indice biotiques testés (BENTIX, BOPA, AMBI) varient. De même, la population du bivalve dominant, la coque (Cerastoderma edule), souffre du développement de l’herbier. Sa communauté parasitaire (trématodes) est modifiée, sans que cela n’influe sur la dynamique des coques. A l’échelle du Bassin, le développement de l’herbier (considéré comme un signe de “bonne santé”) a été comparé à la santé de deux bivalves endogés dominants, la palourde japonaise (Ruditapes philippinarum) et la coque (C. edule), évaluée en termes de prévalence de maladie. Aucune corrélation n’existe entre le taux de recouvrement d’herbier et la prévalence de trois maladies (trématodiase, perkinsose, maladie du muscle marron). Entre 2002 et 2010, la surface d’herbier a diminué de 1/3. En termes de structure de communautés et d’espèces dominantes, peu de différences sont notées au sein de chaque année (entre les 12 stations) et entre années, indépendamment du déclin de l’herbier. Parmi les indicateurs biotiques, l’indice multivarié MISS est en adéquation avec la relative similarité de la structure de la macrofaune benthique entre les groupes discriminés par l’analyse MDS. En 2005, des activités de dragage dans le Bassin d’Arcachon ont abouti à l’enfouissement de 0,32 km2 d’herbier à Z. noltii. La structure du macrobenthos a été immédiatement modifiée sans retour à l’état initial sur les zones couvertes de sable. En revanche, le macrobenthos (endofaune) s’est rapidement rétabli dans les zones couvertes de vase alors que l’herbier n’a commencé à se développer qu’au bout de 5 ans après les travaux. Le dernier chapitre de cette thèse donne un bref aperçu des connaissances actuelles sur les herbiers vietnamiens et des possibles travaux scientifiques à mener. / The overall objective was to assess macrobenthos response to marine Zostera noltii seagrass dynamics (colonization, maturation, destruction, restoration), in Arcachon Bay, a French Southwestern lagoon.When seagrass starts to develop, the structure of macrofauna community immediately diverges between sand and seagrass habitats, without however modifying tested biotic indices (BENTIX, BOPA, AMBI). As well, population of the dominant bivalve, the cockle (Cerastoderma edule), suffers from seagrass development. Their parasite (trematode) community are impacted, but not sufficiently to explain cockle deficit in seagrass.At the scale of the Bay, seagrass development (considered as a sign of “good health”) is compared to the fitness of the two dominant infaunal bivalves, the Manila clam (Ruditapes philippinarum) and the cockle (Cerastoderma edule), measured in terms of disease prevalence. There was no correlation among seagrass cover rate and the prevalence of three diseases: trematodiosis, perkinsosis and Brown Muscle Disease.Between 2002 and 2010, seagrass cover decreased by 1/3. When looking at community structure and dominant species, there were moderate differences within (among 12 stations) and among years, independently of seagrass decline. Among biotic indicators, multivariate index MISS was in adequation with the relative similarity of macrofauna structure among groups discriminated by MISS analysis.In 2005, dredging activities in Arcachon Bay led in burying 0.32 km2 of Z. noltii. Macrobenthos structure was immediately modified and did not recover in places buried by sand. Conversely, macrobenthos (infauna) recovered rapidly in areas cover by mud, while seagrass began to develop again five years after work. The last chapter of the thesis provides a brief insight of the seagrass in Vietnam, the actual knowledge and what could be investigated.

Seagrass meadows may play a substantial role in climate change mitigation as they are capable to sequester and store substantial amounts of anthropogenic carbon in plant biomass and, more importantly, in their underlying sediments. In this PhD thesis, the carbon-burial potential was assessed by quantifying the amount of organic carbon stored in different seagrass meadows, each dominated by one of the four major seagrass species in the Western Indian Ocean region. Impacts of anthropogenic disturbances on biomass carbon allocation, greenhouse gas emission (methane and nitrous oxide) and production of sulphide were investigated in Chwaka Bay, Zanzibar. The findings showed that east African seagrass meadows generally have high carbon sink capacity. The storage of sedimentary organic carbon, however, varied among seagrass habitats and across sites, and was up to five-fold higher in seagrass sediment to those of nearby unvegetated sediments. Seagrass meadows in eutrophicated sites had higher sedimentary organic carbon content, and substantially higher emission rates of nitrous oxides and methane, compared to more pristine meadows. Disturbances in terms of shading and simulated grazing of seagrass affected several processes, with major decreases in seagrass primary productivity, net community production and biomass carbon, in turn influencing seagrass carbon sequestration as well as stimulating anaerobic microbial processes. In addition, production of sulphide in the sediment and methane emissions from the sediment surface increased significantly when disturbed. At present, seagrass meadows in the Western Indian Ocean have high carbon sink capacity. This important ecosystem service is, however, highly threatened due to regional anthropogenic pressure, which may change the role of blue carbon rich habitats, such as seagrass meadows, from being a sink to a source of greenhouse gases. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 2: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.</p>

This thesis applies the food security concept to assess the significance of seagrass-associated invertebrate gleaning for providing food security in Kaole, Tanzania. It assesses the availability, accessibility, utilisation and stability over time of this food source. To explore this, a multi-strategy research design was used. Structured interviews were held with 30 gleaning women in Kaole, using a self-developed questionnaire designed to address the four components of the food security framework. Two focus group discussions were thereafter held to explore how local ecosystem services, in particular seagrass meadows, and their food provisioning services have developed over time. The findings show that a great majority of the women who engage in seagrass- associated gleaning in Kaole rate this activity as important or very important for providing food to the household. The seagrass-associated gleaning activities were perceived as important, despite the fact that most women also glean in the mangrove area and that almost all women have alternative incomes. However, seen from a strict food security perspective, it is questionable how significant this activity currently is for food security. The study found that availability has decreased and it is not a food source that is stable throughout the year. The findings also suggest that the mangrove-associated Terebralia palustris may be easier to utilise, considering that you can store it in a sack, without being kept cold. If mangrove related gleaning hence seems to play an increasingly important role in local food security, and is a fishery that is available in all seasons, this area is less accessible to potential gleaners with small children, elderly and people with physical disabilities. The study also found that the decline in seagrass-associated gleaning activities have coincided with a number of human stressors and deteriorating seagrass meadows. Despite its’ declining signinficance for food security, most women rate the seagrass-associated gleaning as important and want to protect this food source. Action should therefore be taken to sustainably preserve this provisioning resource. Bearing in mind the fine balance between ecological and food security needs, such measures need to be interdisciplinary. It also needs to involve different community members, as well as other stakeholders. More research would be needed to determine the nutritional content and potential toxic contents in the most fished invertebrate species.

Aquaculture is of growing importance in the global seafood production. The environmental impact of aquaculture will largely depend on the type of environment in which the aquaculture system is placed. Sometimes, due to the abiotic or biotic conditions of the seascape, certain aquaculture systems tend to be placed within or near specific ecosystems, a phenomenon that in this thesis is referred to as aquaculture system - ecosystem links. The exposed ecosystems can be more or less sensitive to the system specific impacts. Some links are known to be widespread and especially hazardous for the subjected ecosystem such as the one between the shrimp aquaculture and the mangrove forest ecosystem. The aim of this thesis was to identify and investigate causes and consequences of other spatial links between aquaculture and ecosystems in the tropical seascape. Two different aquaculture system - ecosystem links were identified by using high resolution satellite maps and coastal habitat maps; the link between sea cage aquaculture and coral reefs, and the one between seaweed farms and seagrass beds. This was followed by interviews with the sea cage- and seaweed farmers to find the drivers behind the farm site selection. Many seaweed farmers actively choose to establish their farms on sea grass beds but sea cage farmers did not consider coral reefs when choosing location for their farms. The investigated environmental consequences of the spatial link between sea cage aquaculture and coral reefs were considerable both on the local coral reef structure, and coral associated bacterial community. Furthermore, coral reef associated fish are used as seedlings and feed on the farms, which likely alter the coral food web and lower the ecosystem resilience. Unregulated use of last resort antibiotics in both fish- and lobster farms were also found to be a wide spread practice within the sea cage aquaculture system, suggesting a high risk for development of antibiotic resistant bacteria. The effects of seaweed farms on seagrass beds were not studied in this thesis but have earlier been shown to be rather substantial within the borders of the farm but less so outside the farm. Further, a nomenclature is presented to facilitate the discussion about production system - ecosystem links, which may also be used to be able to incorporate the landscape level within eco-certifying schemes or environmental risk assessments. Finally - increased awareness of the mechanisms that link specific aquaculture to specific habitats, would improve management practices and increase sustainability of an important and still growing food producing sector - the marine aquaculture. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p>