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.

The tropical seascape is herein defined as a landscape made up of five ecosystems: coastal terrestrial forests, mangrove forests, seagrass beds, coral reefs and the deep sea. Previous studies have shown that men and women use the tropical seascape in different ways. If the seascape was to change as a result of anthropogenic climate change, then men and women could potentially be affected differently by those changes. The seascape is particularly vulnerable to the predicted rise in sea-level and ocean warming, but the coastal terrestrial forests and mangrove forests are in addition vulnerable to the increased storms and hurricanes a warmer climate is predicted to lead to. While men and women utilizes these ecosystems in many different ways, this study found, based on the literature reviewed, that in a worst-case scenario all parts of the seascape could potentially be destroyed and none of the activities performed there today could be performed in the future. The deep sea would not be destroyed, but the fish living there would move to higher latitudes and deeper waters, effectively ending the fishing practices in the tropical waters. To save the tropical seascape anthropogenic climate change would have to stop on a global scale, since the problem cannot be solved on a local or regional level.

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.

Les Invertébrés de l’épifaune vagile présents dans les herbiers de Magnoliophytes marins ont un rôle essentiel dans le transfert d’énergie des producteurs primaires vers les niveaux trophiques supérieurs. L’objectif de ce travail a été d’analyser la relation entre la complexité de l’herbier et la structure des communautés de l’épifaune vagile, et d’étudier le rôle de ce compartiment dans le fonctionnement des réseaux trophiques des herbiers à Thalassia testudinum. Deux sites d’herbiers ont été comparés, l’un proche de la mangrove côtière et l’autre près de la barrière récifale, au cours de deux saisons. L’utilisation de différentes sources trophiques par les Invertébrés a été montrée en utilisant les méthodes des isotopes stables du carbone et de l’azote et de la composition en acides gras. L’herbier côtier, qui présente une structure complexe du fait de ses longues feuilles, de sa litière abondante et de sa forte charge en épiphytes, abrite une faune abondante et diversifiée de Crustacés. La préférence alimentaire de ces Invertébrés pour les micro-algues et les fines particules détritiques favorise la contribution du biofilm au réseau trophique de l’herbier côtier. L’herbier du large, moins complexe, abrite une communauté d’Invertébrés dominée par les Gastéropodes Cerithiidae. La limitation de la disponibilité en nourriture existant dans cet herbier explique la contribution plus élevée de la litière et des feuilles vivantes de Thalassia au réseau trophique par rapport à l’herbier côtier. Le couplage de l’analyse des isotopes stables à celle des contenus stomacaux réalisé sur les poissons a montré le rôle essentiel des Crevettes en tant que proies. L’herbier côtier, qui présente des ressources en nourriture plus abondantes et diversifiées, assure mieux son rôle de « nurserie » pour les juvéniles de poissons que l’herbier du large. / In seagrass beds, vagile epifauna plays a major role in the energy transfer from primary producers to higher trophic levels. The main aim of the work was to examine the relationship between the seagrass complexity and the vagile epifauna community structure, and to study the role of this compartment within the food web of Thalassia testudinum seagrass beds. Two seagrass sites were compared, one near the coastal mangrove and another one near the barrier reef, during two seasons. Trophic resources used by primary consumers were assessed by combining stable isotopes analysis and fatty acid compositions. The coastal seagrass bed is complex due to its long leaves and its great biomass of litter and epiphytes. It shelters a great abundance and diversity of Crustaceans. The feeding preference of them for micro-algae and detrital particles promotes biofilm contribution to food web of the coastal seagrass bed. The seagrass bed located seawards, lesser complex, harbors an Invertebrate community dominated by the Gastropods Cerithiidae. The reduced food availability in that seagrass bed explains the higher contribution of litter and Thalassia leaves to that food web compared to the coastal seagrass bed. By coupling stable isotopes and stomach contents analyses, it was possible to highlight the major role of shrimps in the feeding diet of fishes. The coastal seagrass bed, where the trophic resources are more abundant and diverse, better plays its role of nursery for juveniles fishes than the seaward seagrass bed.

À l'interface bentho-pélagique, les herbiers marins présentent une multitude de rôles écosystémiques. Historiquement, les scientifiques et décideurs de La Réunion se sont focalisés sur l'écosystème récifal. Néanmoins, des prairies monospécifiques à Syringodium isoetifolium sont présentes de manière pérenne (3 hectares) au sein du complexe récifal de l'Ermitage / La Saline (côte ouest). L'objectif principal de cette étude était d'apporter les premières données sur l'écologie de ces herbiers marins. Ainsi, une approche pluridisciplinaire a été développée : 1. L'étude de la dynamique spatiale du paysage herbier sur 65 ans (dès 1950), et à l'échelle saisonnière (2013-2015) qui a permis de définir le rôle majeur des forçages hydrodynamiques et de l'eutrophisation. 2. L'analyse de la productivité de l'écosystème herbier et sa réponse métabolique face à des apports nutritifs, révèle des bilans métaboliques opposés (autotrophie/hétérotrophie) en fonction des conditions environnementales, ainsi qu'un rôle de tampon sur les flux de nutriments. 3. Des analyses isotopiques (δ13C et δ15N) ont permis d'identifier les sources de matière entrant dans l'écosystème et alimentant les réseaux trophiques associés aux herbiers. L'étude a permis d'établir un lien trophique entre Holothuria leucospilota et les herbiers marins ainsi qu'un rôle essentiel dans le maintien des populations de poisson herbivores récifaux. 4. Des enquêtes locales ont révélé une méconnaissance de cet écosystème malgré leur potentiel économique et écologique. À la lumière de ces travaux de thèse, la prise en considération des herbiers marins dans la gestion du milieu marin réunionnais est nécessaire. / Located at the benthos-pelagos interface, seagrass beds have many ecosystemic roles such as coastal protection or biodiversity. Historically, scientists and decision-makers at Reunion Island have been focusing on reef ecosystems. However, for several decades, monospecific (Syringodium isoetifolium) seagrass beds have been observed (3 hectares – 2013) within Ermitage / La Saline reef (West coast). The main objective of this study was to give the first data on seagrass ecology at Reunion Island. Therefore, a multi-disciplinary study was developed. First, seascape ecology of seagrasses is analyzed at decadal (since 1950) and seasonal scales (2013-2015). Physical settings (swell) and eutrophication were driving factors on the spatial dynamics of seagrass beds. Second, seagrass community metabolism and response to nutrient loads (nitrate and phosphate) show variations in metabolic budget (autotrophy to heterotrophy) and make seagrass beds a nutrient sink following the environmental conditions. Third, stable isotope analysis (δ13C and δ15N) identified sources of particulate matter entering the ecosystem and fueling food webs. The trophic roles of seagrass beds are assessed for echinoderm and herbivorous fish communities. This study highlighted a trophic link between seagrass and Holothuria leucospilota, and proved some species to be heavily dependent on seagrass ecosystem (Leptoscarus vaigiensis, Siganus sutor). Finally, interviews showed a lack of knowledge about this ecosystem despite crucial economic and ecologic roles. Considering their major functions, seagrass beds have to be considered in future management of the coastal marine systems at Reunion Island.

La méiofaune joue un rôle important dans le fonctionnement des habitats benthiques à substrat meuble (ex. flux de matière) en relation avec sa production élevée, sa position trophique intermédiaire et les importants transferts d’énergie vers les niveaux trophiques supérieurs qui y sont lié. Les relations trophiques et les flux de matière organique liés à la méiofaune restent néanmoins mal connus ou peu pris en compte. Afin de mieux appréhender le rôle de la méiofaune, la structure des communautés et les relations trophiques entre les sources de nourriture et ces consommateurs ont été déterminées dans cinq habitats à substrat meuble (i.e., vasière nue, herbier, zone à sables) de la baie de Marennes-Oléron, France, et de la baie de Sylt-Rømø, Allemagne, en tenant compte des variations temporelles. Le peuplement de méiofaune s’est trouvé être dominé par les nématodes et les copépodes benthiques. Les biomasses de microphytobenthos et de matière organique du sédiment sont apparues comme étant deux facteurs structurants pour les communautés. L’utilisation combinée de différents traceurs de la matière (i.e., isotopes stables, acides gras) a démontré que le microphytobenthos et les bactéries étaient les ressources trophiques majeures de la méiofaune dans les cinq habitats étudiés. Les mesures réalisées sur la structure des communautés et les données issues des traceurs de la matière ont été implémentées dans des modèles de réseaux trophiques. Dans tous les habitats, ces modèles ont mis en évidence que le flux de carbone dominant était issu du microphytobenthos, ceci démontrant les très faibles changements de comportements alimentaires malgré les importantes différences de sources trophiques en termes de disponibilité et de production des sources de nourriture entre ces différents habitats. Tous les groupes trophiques de nématodes, à l’exception des déposivores sélectifs, étaient particulièrement sélectifs et s’alimentaient majoritairement à partir de microphytobenthos, ceci étant à l’origine d’une forte production et d’un court temps de renouvellement de la méiofaune. En conclusion, cette thèse démontre le rôle important de la méiofaune dans les habitats à substrat meuble ainsi que l’importance de la relation trophique entre le microphytobenthos et la méiofaune dans le fonctionnement de ces réseaux trophiques. / Meiofauna play an important role in ecosystem processes in soft-bottom benthic habitats, e.g. food web dynamics, related to their highproduction, their intermediate trophic position and the energy they transfer towards higher trophic levels. The trophic linkages and flows of organic matter related to the meiofauna remain poorly known or taken into account. To better assess the role of meiofauna, the community structure and trophic relationships between food sources and meiofauna were determined in five intertidal soft-bottom habitats (i.e., mudflat, seagrass bed, sandflat) of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany, taking temporal variations into account. Meiofauna communities were dominated by nematodes and benthic copepods. Biomass of microphytobenthos and of sediment organic matter were two of the major drivers of community structure. The combination of trophic markers (i.e., stable isotopes, fatty acids) demonstrated that microphytobenthos and bacteria were the major food sources of meiofauna in the five habitats. Information from community structure assessments and trophic marker analyses were implemented in food web models. In all habitats, these models demonstrated that the main flow of carbon to meiofauna originated from microphytobenthos, highlighting negligible changes in meiofauna feeding behavior besides the large differences in availability and productivity of food sources between these habitats. All trophic groups of nematodes, except for selective deposit feeding nematodes, were highly selective and mainly fed on microphytobenthos, resulting in a high production and a short turn-over time of meiofauna. In conclusion, this thesis demonstrated the important role of meiofauna in soft-bottom habitats as well as the importance of the trophic pathway from microphytobenthos to meiofauna in the functioning of these food webs.