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>

Small-scale fisheries employ many millions of people around the world, and are particularly important in developing countries, where the dependency on marine resources is high and livelihood diversification options are scarce. In many areas of the world however, small-scale fisheries are at risk which threatens the food security and wellbeing of coastal people. Small-scale fisheries management has in many cases been insufficient and new comprehensive approaches are recommended to achieve social-ecological sustainability in the long-term. The aim of this thesis is to analyze empirically how social-ecological elements of seagrass-associated small-scale fisheries in the Western Indian Ocean region can be addressed for a transformation from the current mostly degraded state to more sustainable social-ecological systems and secure future livelihoods. The main method used was semi-structured interviews with local fishers. The main findings show the crucial contributions seagrass-associated small-scale fisheries make to food security and income generation and highlight the need to acknowledge the social-ecological importance of seagrasses in the seascape (Paper I). A discrepancy between low societal gains of the fishing of sea urchin predator fish species and their crucial importance in the food web (in controlling sea urchin populations and the associated grazing pressure on seagrasses) was identified (Paper II). These results suggest catch-and-release practice of sea urchin predator fish species, which could contribute to more balanced predator – sea urchin – seagrass food webs in the long run. The use of illegal dragnets was identified as a major threat to local seagrass meadows (Paper IV). Institutional elements influencing the use of such destructive dragnet were identified to be normative, cultural-cognitive and economic, which constitutes an institutional misfit to the current emphasis on regulative elements in a hierarchical manner (Paper III). Concerning future co-management initiatives, gear restrictions and education were the favoured management measures among all fishers (Paper IV). A majority of fishers were willing to participate in monitoring and controls, and most fishers thought they themselves and their communities would benefit most from seagrass-specific management. These findings highlight the need for actions on multiple scales, being the local-, management-, policy- and governance levels. The suggested actions include: education and exchange of ecological and scientific knowledge, gear management including the cessation of dragnet fishing, strengthening of local institutions, an active participation of fishers in enforcement of existing rules and regulations and an introduction of adequate alternative livelihood options. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Manuscript.</p>

Les écosystèmes marins côtiers subissent de nombreuses perturbations naturelles et anthropiques. Dans le contexte socio-économique actuel, mieux comprendre le fonctionnement et transfert des contaminants dans ces écosystèmes est primordial. L’étude du transfert de la matière organique et des contaminants aux interfaces, constitue un enjeu crucial. Les principaux objectifs sont de caractériser l’ichtyofaune des herbiers de posidonie et comprendre les relations trophiques ; d’établir les niveaux et variabilité spatiale de la contamination en éléments traces ETs et polluants organiques persistants POPs dans les compartiments de l’écosystème ; et d’identifier les sources et les processus influençant les niveaux de contamination le long du réseau trophique à Marseille et Hyères. La caractérisation du peuplement de poissons et des relations trophiques au sein de l’écosystème est nécessaire pour comprendre les niveaux de contamination. Chez les poissons, le phénomène de bioaccumulation des ETs est difficile à mettre en évidence, excepté pour le mercure. L’influence du régime alimentaire, taille et besoins physiologiques et métaboliques est manifeste. La grande stabilité et la rémanence des POPs leur confèrent des propriétés de bioconcentration et de bioamplification importantes. Les concentrations en contaminants mesurées, ainsi que la détection de pesticides toxiques interdits, attestent de la nécessité de considérer cette pollution avec attention, plus forte à Marseille. / The marine ecosystems undergo frequent disturbances. In the current socio-economic context characterized by intensive urban development and industrialization, it is of primordial importance for the management of the environment to achieve a better understanding of the functioning and the transfer of contaminants within these ecosystems. The study of the transfer of organic matter and contaminants to the interfaces is thus a crucial issue. The main objectives are to characterize the fish fauna and to determine the food webs; to establish the levels and patterns of spatial variability of contamination by trace elements TEs and persistent organic pollutants POPs; and to identify the sources and the processes having an influence on the levels of contamination throughout the food webs. The characterization of the fish populations and the trophic relations between the compartments of the ecosystem is necessary in order to understand the levels of contamination in TEs and POPs. For the fishes, it is difficult to provide evidence of the phenomenon of bioaccumulation of TEs, except for mercury, but the influence of diet, size and physiological and metabolic requirements is obvious. The great stability, liposolubility and persistence of the POPs confer on them significant bioconcentration and bioamplification capabilities. The concentrations in TEs and POPs recorded, and the detection of banned toxic pesticides, attest to the necessity of paying close attention to this pollution.

The aim of this study was to develop and examine the use of backscatter data collected with multibeam sonar (MBS) systems for benthic habitat mapping. Backscatter data were collected from six sites around the Australian coastal zone using the Reson SeaBat 8125 MBS system operating at 455 kHz. Benthic habitats surveyed in this study included: seagrass meadows, rhodolith beds, coral reef, rock, gravel, sand, muddy sand, and mixtures of those habitats. Methods for processing MBS backscatter data were developed for the Coastal Water Habitat Mapping (CWHM) project by a team from the Centre for Marine Science and Technology (CMST). The CMST algorithm calculates the seafloor backscatter strength derived from the peak and integral (or average) intensity of backscattered signals for each beam. The seafloor backscatter strength estimated from the mean value of the integral backscatter intensity was shown in this study to provide an accurate measurement of the actual backscatter strength of the seafloor and its angular dependence. However, the seafloor backscatter strength derived from the peak intensity was found to be overestimated when the sonar insonification area is significantly smaller than the footprint of receive beams, which occurs primarily at oblique angles. The angular dependence of the mean backscatter strength showed distinct differences between hard rough substrates (such as rock and coral reef), seagrass, coarse sediments and fine sediments. The highest backscatter strength was observed not only for the hard and rough substrate, but also for marine vegetation, such as rhodolith and seagrass. The main difference in acoustic backscatter from the different habitats was the mean level, or angle-average backscatter strength. However, additional information can also be obtained from the slope of the angular dependence of backscatter strength. / It was shown that the distribution of the backscatter. The shape parameter was shown to relate to the ratio of the insonification area (which can be interpreted as an elementary scattering cell) to the footprint size rather than to the angular dependence of backscatter strength. When this ratio is less than 5, the gamma shape parameter is very similar for different habitats and is nearly linearly proportional to the ratio. Above a ratio of 5, the gamma shape parameter is not significantly dependent on the ratio and there is a noticeable difference in this parameter between different seafloor types. A new approach to producing images of backscatter properties, introduced and referred to as the angle cube method, was developed. The angle cube method uses spatial interpolation to construct a three-dimensional array of backscatter data that is a function of X-Y coordinates and the incidence angle. This allows the spatial visualisation of backscatter properties to be free from artefacts of the angular dependence and provides satisfactory estimates of the backscatter characteristics. / Using the angle-average backscatter strength and slope of the angular dependence, derived by the angle cube method, in addition to seafloor terrain parameters, habitat probability and classification maps were produced to show distributions of sand, marine vegetation (e.g. seagrass and rhodolith) and hard substrate (e.g. coral and bedrock) for five different survey areas. Ultimately, this study demonstrated that the combination of high-resolution bathymetry and backscatter strength data, as collected by MBS, is an efficient and cost-effective tool for benthic habitat mapping in costal zones.

Les écosystèmes côtiers présentent une forte production biologique, soutenue par une grande diversité de sources de matière organique particulaire (autochtones : phytoplancton, microphytobenthos, phanérogames marines, macroalgues, épiphytes ; allochtones : apports continentaux), pouvant contribuer à la production secondaire. La diversité de ces sources complexifie de manière considérable le fonctionnement écologique des systèmes côtiers — e.g. cycles biogéochimiques, réseaux trophiques — et en rend sa compréhension difficile.Une étude spatio-temporelle réalisée en 2009 dans le Bassin d’Arcachon, une lagune semi-fermée qui abrite le plus grand herbier à Zostera noltii d’Europe, a été menée afin d'estimer l’origine et la composition des matières organiques particulaire en suspension (MOPS) et sédimentaire (MOS) et d'appréhender le devenir des différentes sources de matière organique dans le réseau trophique macrobenthique. Cette approche quantitative a été effectuée principalement à l’aide des rapports isotopiques et élémentaires (δ15N, δ13C et C/N) et/ ou des acides grasA l’échelle annuelle et en moyenne pour les trois stations étudiées, la MOPS est composée principalement de phytoplancton (48 ± 2%) mais aussi de matériel continental (19 ± 4%) et de microphytobenthos (16 ± 2%), les macroalgues et les phanérogames ne contribuant que peu (8 ± 1% et 5 ± 1%, respectivement). Cette composition, qui présente une saisonnalité (faible contribution du phytoplancton en hiver au profit des apports continentaux), est principalement dépendante du climat (température) et de l’hydrodynamique / hydrodynamique sédimentaire (apports continentaux, remise en suspension du sédiment). A l’échelle annuelle et en moyenne pour les six stations ayant fait l’objet du suivi annuel, la MOS est composée principalement de sources benthiques (phanérogames : 23 ± 3% ; microphytobenthos : 19 ± 1% ; macroalgues : 19 ± 5%), mais également de matériel continental (27 ± 8%) et de phytoplancton (11 ± 2%). A l’échelle de l’écosystème (étude printanière) la composition de la MOS est similaire — avec toutefois une plus forte contribution du phytoplancton, au dépend de la matière continentale. Elle est géographiquement homogène, ce que semble favoriser l’hydrodynamique du bassin d’Arcachon associée à sa faible profondeur. La principale différence spatiale apparaît entre le sédiment subtidal (faible contribution des macrophytes au profit du matériel continental) et le sédiment de l’herbier intertidal. L’étude des voies de transfert trophique de la matière organique particulaire a mis en évidence une organisation trophique complexe avec l’existence de sous-groupes au sein des déposivores d’interface et des brouteurs. A l’échelle annuelle et à l’échelle du Bassin d’Arcachon, le microphytobenthos et les phanérogames (incluant leurs épiphytes) soutiennent 90% de la production macrozoobenthique. Cette production secondaire est principalement effectuée par les déposivores (60%). Une forte bactérivorie a été mise en évidence notamment chez les déposivores et chez le suspensivore invasif Crepidula fornicata. Les bactéries représentent ainsi un intermédiaire important dans le transfert de MOP des producteurs primaires vers les consommateurs primaires. Toutefois la pression trophique qu’exercent les consommateurs primaires de la macrofaune benthique sur les producteurs primaires est relativement modeste puisque le macrozoobenthos n’absorbe que 10% de la production primaire totale du système, ce qui rend cette dernière potentiellement disponible pour d’autres compartiments biologiques. Malgré cela l’herbier à Zostera noltii représente une ressource importante pour la macrofaune benthique. Dans le contexte de sa régression, une disparition de l’herbier engendrerait une diminution de la biomasse du macrozoobenthos. / Abstract