[Truncated abstract] There is a well-documented global decline of seagrass meadows in response to anthropogenic pressures. Transplantation of rhizome fragments into denuded areas has been used to enhance natural recovery but nutrient limitation and poor root growth may contribute to low success rates. Addition of nutrients to sediments has been proposed as a means of enhancing growth and survival of seagrass transplants by alleviating nutrient limitation but there is limited information of the effects of nutrient additions to seagrass transplants, particularly root development and morphology. In addition to nutrient limitation, sulphide accumulation in sediments with high organic matter has been shown to reduce seagrass growth and experimental iron additions have been shown to enhance seagrass growth by buffering the development of reduced conditions in organic rich sediments. This thesis examines responses (growth, morphology and nutrient status) of Posidonia australis and Posidonia sinuosa transplants to nitrogen (N), phosphorus (P) and chelated iron (Fe EDTA) additions, and includes a detailed investigation of root growth and morphology in response to these additions. Experiments were carried out in underwater plots in Oyster Harbour, a sheltered estuarine inlet with seasonal river flow, located on the southern coast of Western Australia. In the first experiment, nutrients (N, P and N+P) and Fe EDTA were added to sediment underlying transplants at the end of summer (March 2005). ... Nitrogen (both N and N+P) addition also reduced overall biomass allocation to roots. Nitrogen concentrations increased with N addition in P. sinuosa only but both species had more negative d15N values with N and N+P addition indicating that added N had been taken up. In contrast, P addition had little effect on root growth, and P concentrations only increased in P. australis. However, tissue concentrations of Zn, Co, and Mo in both species increased with P addition. Roots showed limited morphological variation (total root length, mean root diameter, root fineness, specific root length, surface area) in response to nutrient addition. Combined N and P addition increased lateral root density (branches m-1) but had no effect on other morphological parameters of the root compartment. Iron addition had no effect on P. sinuosa but P. australis transplants significantly reduced root growth and productivity, particularly in spring/summer growth period, due to lower primary and lateral growth rates. Overall, N or P additions did not enhance growth although these nutrients were taken up. Iron additions also had little effect on transplant growth. Seagrass transplants had significant root growth although they appeared not to respond to nutrient or iron addition. Both species produced extensive root systems capable of taking up sediment nutrients, which suggests that root development was not a limiting factor in establishment and growth of transplants in the temperate estuary, Oyster Harbour.

Les relations interspécifiques sont un indicateur naturel de l'état de santé d'un écosystème et de son éventuelle évolution. Dans le contexte actuel de changement climatique et d'intensification des activités humaines, nous décrivons, par une approche intégrée, les interactions existant entre les tortues vertes et leurs ressources trophiques, afin de contribuer à la compréhension de la dynamique de la biodiversité marine. La tortue verte est la seule tortue marine herbivore aux stades sub-adulte et adulte. Elle se nourrit principalement sur des herbiers de phanérogames marines et des algueraies en milieu côtier relativement peu profonds et constitue ainsi un modèle privilégié pour étudier l'écologie trophique et fonctionnelle des tortues marines en conditions naturelles. Le travail présenté dans ce manuscrit étudie deux populations de tortues vertes : la première s'alimentant de phanérogames marines sur le site de N'Gouja à Mayotte et la seconde d'algues benthiques sur la côte ouest de l'Ile de La Réunion. A ce stade de l'étude, le système tortues vertes-herbier est le mieux connu. Nous proposons une synthèse des relations existant entre le comportement de plongée et d'alimentation d'individus juvéniles et adultes avec la disponibilité trophique au sein d'un herbier marin plurispécifique. Ceci a été obtenu à partir de systèmes d'acquisition embarqués, d'observation directes de tortues vertes et de relevés phyto-écologiques conventionnels. Par ailleurs, notre étude a permis d'engager le suivi du système tortues vertes – herbier marin de N'Gouja et d'en décrire les premières tendances. En quatre ans, une diminution de près de 80 % de la biomasse végétale du site de N'Gouja accentue la pression d'herbivorie des tortues vertes sur l'herbier. Ce phénomène entraîne l'appauvrissement de la diversité spécifique des phanérogames en faveur des espèces végétales pionnières. La diminution parallèle de l'effectif de la population de tortues vertes du site de N'Gouja suggère un modèle alimentaire basé sur le principe de densité-dépendance. Les conséquences d'une surexploitation de l'herbier par les tortues vertes sont alors en opposition avec celles obtenues suite à la simulation d'une pression d'herbivorie nulle. Nous montrons que sous une pression d'herbivorie modérée, un stade successionel intermédiaire de l'herbier est maintenu et la diversité spécifique est favorisée par la diminution des capacités compétitives des espèces consommées. Il découle ainsi de notre étude des indicateurs du stade phytodynamique d'un herbier plurispécifique et de la pression d'herbivorie exercée par les tortues vertes qui permettent d'envisager les réponses écosystémiques d'un système tel que celui de N'Gouja sous différents scénarios environnementaux. Enfin, dans un cadre plus large, nous posons la question de savoir si l'évolution statutaire de Mayotte peut contribuer à approfondir et pérenniser la protection des tortues marines qui se trouvent sur son territoire. Nous décrivons la départementalisation comme un moyen d'accentuer le processus de clarification du droit applicable à Mayotte et d'assurer des moyens humains, matériels, et financiers nécessaires à la protection de l'environnement. Des recensements aériens réalisés au dessus de la côte ouest de l'île de La Réunion révèlent la présence d'individus sexuellement matures et immatures, dont le nombre augmente depuis 1996. Cette approche nous aura permis d'identifier une fréquentation préférentielle des habitats coralliens et de décrire, à partir d'observations sous-marines parallèles, la côte ouest de l'île comme un site d'alimentation d'individus matures et d'individus en phase de croissance. Ce travail renforce les bases scientifiques nécessaires à la mise en place de stratégies de conservation des tortues marines et de leurs habitats. / Reproduction of sea turtles primarily relies on body reserves stored during the time spent on foraging grounds prior to the nesting season. Accordingly, the investigation of foraging behaviour of sea turtles is critical for better assessing their biology but also for conservation issues of these endangered species. Sea turtles contribute significantly to the consuming biomass of their ecosystem and hence to its functioning, thus providing natural indications of the health of the ecosystem. Yet the trophic ecology of sea turtles is poorly documented because their feeding grounds remain poorly known and for most of them hardly accessible. Among sea turtles the green turtle is the only species where sub-adults and adults are mostly herbivorous feeding on seagrass and algae patches in shallow coastal waters. Such fairly accessible marine ecosystems provide a unique opportunity to investigate sea turtle ecology under natural conditions. The study was conducted in two foraging sites of green turtles located in the south-western Indian Ocean: Mayotte (seagrass meadow) and Reunion Island (algae spots). Thanks to fine-scale sampling of feeding activities, we addressed the lack of research investigating the food requirements and the trophic role of green turtles. To day, feeding activities of green turtles are better known on seagrass. We described the habitat use, the food intake, and the herbivory pressure of green turtles exploiting a multi-sepcies seagrass meadow of Mayotte. In Reunion Island, first results provide some information about the habitat use of green turtles. Such results are paramount for the management and conservation sea turtles and their habitats.

Trophic downgrading of ecosystems necessitates a functional understanding of trophic cascades. Identifying the presence of cascades, and the mechanisms through which they occur, is particularly important for seagrass meadows, which are among the most threatened ecosystems on Earth. Shark Bay, Western Australia provides a model system to investigate the potential importance of top-down effects in a relatively pristine seagrass ecosystem. The role of megagrazers in the Shark Bay system has been previously investigated, but the role of macrograzers (i.e., teleosts), and their importance relative to megagrazers, remains unknown. The objective of my dissertation was to elucidate the importance of teleost macrograzers in transmitting top-down effects in seagrass ecosystems. Seagrasses and macroalgae were the main food of the abundant teleost Pelates octolineatus, but stable isotopic values suggested that algae may contribute a larger portion of assimilated food than suggested by gut contents. Pelates octolineatus is at risk from numerous predators, with pied cormorants (Phalacrocorax varius) taking the majority of tethered P. octolineatus. Using a combination of fish trapping and unbaited underwater video surveillance, I found that the relative abundance of P. octolineatus was greater in interior areas of seagrass banks during the cold season, and that the mean length of P. octolineatus was greater in these areas compared to along edges of banks. Finally, I used seagrass transplants and exclosure experiments to determine the relative effect of megagrazers and macrograzers on the establishment and persistence of three species of seagrasses in interior microhabitats. Teleost grazing had the largest impact on seagrass species with the highest nutrient content, and these impacts were primarily observed during the warm season. My findings are consistent with predictions of a behaviorally-mediated trophic cascade initiated by tiger sharks (Galeocerdo cuvier) and transmitted through herbivorous fishes and their predators.

As climate change continues, climactic extremes are predicted to become more frequent and intense, in some cases resulting in dramatic changes to ecosystems. The effects of climate change on ecosystems will be mediated, in part, by biotic interactions in those ecosystems. However, there is still considerable uncertainty about where and how such biotic interactions will be important in the context of ecosystem disturbance and climactic extremes. Here, I review the role of consumers in seagrass ecosystems and investigate the ecological impacts of an extreme climactic event (marine heat wave) and subsequent widespread seagrass die-off in Shark Bay, Western Australia. Specifically, I compare seagrass cover, shark catch rates, and encounter rates of air breathing fauna in multiple habitat types before and after the seagrass die-off to describe post-disturbance dynamics of the seagrass community, shifts in consumer abundances, and changes in risk-sensitive habitat use patterns by a variety of mesoconsumers at risk of predation from tiger sharks (Galeocerdo cuvier). Finally, I conducted a 16 month field experiment to assess whether xi loss of top predators, and predicted shifts in dugong foraging, could destabilize remaining seagrass. I found that the previously dominant temperate seagrass Amphibolis antarctica is stable, but not increasing. Conversely, an early-successional tropical seagrass, Halodule uninervis, is expanding. Following the die-off, the densities of several consumer species (cormorants, green turtles, sea snakes, and dugongs) declined, while others (Indo-Pacific bottlenose dolphins, loggerhead sea turtles, tiger sharks) remained stable. Stable tiger shark abundances following the seagrass die-off suggest that the seascape of fear remains intact in this system. However, several consumers (dolphins, cormorants) began to use dangerous but profitable seagrass banks more often following seagrass decline, suggesting a relaxation of anti-predator behavior. Experimental results suggest that a loss of tiger sharks would result in a behaviorally mediated trophic cascade (BMTC) in degraded seagrass beds, further destabilizing them and potentially resulting in a phase shift. My work shows that climactic extremes can have strong but variable impacts on ecosystems mediated in part by species identity, and that maintenance of top predator populations may by important to ecological resilience in the face of climate change.

The endemic eelgrass (Zostera marina) community of Morro Bay Estuary, located on the central coast of California, has experienced an estimated decline of 95% in occupied area (reduction of 344 acres to 20 acres) from 2008 to 2017 for reasons that are not yet definitively clear. One possible driver of degradation that has yet to be investigated is the role of herbicides from agricultural fields in the watershed that feeds into the estuary. Thus, the primary research goal of this project was to better understand temporal and spatial trends of herbicide use within the context of San Luis Obispo (SLO) County and Morro Bay Watershed by analyzing data of application by mass, area, and intensity to identify herbicides with the highest potential for local environmental pollution. California Pesticide Use Annual Summary Reports (PUASR) from the years 2000 to 2017 were used to obtain data for conducting a meta-analysis to estimate total herbicide application by weight within every township, range, and section for each of the eight selected herbicides: oxyfluorfen, glyphosate, diuron, chlorthal-dimethyl, simazine, napropamide, trifluralin, and oryzalin. A second goal was to select an analytical laboratory that would be best suited for herbicide analysis of estuary sediments to determine the presence, or lack thereof, of the eight selected herbicides. Criteria of consideration in laboratory selection included herbicides detection capabilities, detection/reporting limits, testing prices, chain of custody protocols, turnaround times, and laboratory site locations. The meta-analysis yielded results showing high herbicide application rates in SLO County with glyphosate, oxyfluorfen, and chlorthal-dimethyl being identified as three herbicides of elevated risk for local environmental contamination due high rates of use by mass, by area, and/or intensity during the study timeframe. Additionally, Morro Bay Watershed exhibited moderate rates of herbicide application with chlorthal-dimethyl and glyphosate being of highest risk for contamination and accumulation within the estuary because of high application rates by mass, by area, and/or intensity. Finally, Environmental Micro Analysis (EMA) and Primus Group, Inc. (PrimusLabs) were identified as the top candidates for analytical laboratory testing of Morro Bay Estuary sediment samples to be obtained and tested for the selected herbicides. These laboratories provide superior analytical capabilities of the eight herbicides, impressive reporting limits or lower detection limits, competitive testing prices for detecting multiple constituents in multiple samples, robust chain of custody protocols, options for quick turnaround times, and laboratory site locations within California.

Cumulative effects from multiple anthropogenic stressors over the past three centuries have severely impacted estuarine and coastal habitats, with cascading effects on the species that rely upon them. Pacific salmon (Oncorhynchus sp.) are migratory species that use estuaries as juveniles and as adults and deliver critical nutrients to coastal ecosystems as they move between fresh and marine waters. Many once abundant salmon populations have been extirpated or are in severe decline relative to historic levels, yet the strength of the relationship between habitat loss and population productivity has been challenged. In this dissertation, I applied field studies, otolith analyses, and conservation decision science tools to investigate the relative importance of estuarine habitat to salmon populations, with the aim of advancing effective management solutions for these species and their habitats. First, I conducted a two-year field survey of fish communities in the Fraser River estuary, British Columbia, Canada comparing the species richness and relative catch amongst three distinct habitats. I found that this impacted estuary still supported a rich community of migratory marine and anadromous fishes, as well as resident estuarine fish species. Each habitat supported some unique fish assemblages, with eelgrass supporting the highest catch and diversity of fishes overall but brackish marsh supporting the highest and most consistent catch of salmonids. Next, I used otolith analyses to quantify the residency and growth of juvenile Chinook salmon in the estuary. I found that for one of the only two remaining Chinook salmon stocks abundant enough to still support limited harvest in the Fraser River, the estuary provides vital rearing habitat, with juveniles residing in the estuary for an average of 6 weeks, during which time they had mean daily growth rates of 0.57 mm fork length, approximating growth in healthier estuarine systems. The use of these habitats by juvenile Chinook salmon had not been quantified previously, so these findings directly inform management of this population, which was recently designated as Threatened by the Committee on the Status of Endangered Wildlife in Canada. Finally, I applied Priority Threat Management, a conservation decision science framework, to predict the future status of Pacific salmon in the lower Fraser River and identify the most cost-effective conservation solutions out of a suite of alternative management strategies. On our current trajectory none of these populations were predicted to be assessed as ‘green’ or healthy status at the end of 25 years. In contrast, implementation of broad scale habitat restoration, protection, and watershed management could considerably improve the viability of the lower Fraser to support these salmon, such that many (14/19) of these populations would have a >50% likelihood of being assessed as healthy. Together, this research provides novel evidence of active and selective use of estuarine habitats by juvenile salmon, reliance on estuarine habitat for early marine growth by juvenile Chinook salmon, and a direct link between habitat health and population status for lower Fraser River salmon populations. / Graduate / 2023-04-13

Seagrass populations are in decline worldwide. Zostera marina (eelgrass), one of California’s native seagrasses, is no exception to this trend. In the last 8 years, Morro Bay, California has lost 95% of its eelgrass. Eelgrass is an ecosystem engineer, providing important ecosystem services such as sediment stabilization, nutrient cycling, and nursery habitats for fish. The failure of recent restoration efforts necessitates a better understanding of the causes of eelgrass decline in this estuary. Previous research on eelgrass in California has demonstrated a link between population genetic diversity and eelgrass bed health, ecosystem functioning, and resilience to disturbance and extreme climatic events. The genetic diversity and population structure of Morro Bay eelgrass populations has not been assessed until this study. Additionally, we compare Morro Bay eelgrass to Bodega Bay eelgrass in northern California. We conducted fragment length analysis of 9 microsatellite loci on 133 Morro Bay samples, and 20 Bodega Bay samples. We found no population differentiation within the bay, and no difference among samples growing at different tidal depths. Comparison with Bodega Bay in northern California revealed that Morro Bay eelgrass contains three first generation migrants from a northern eelgrass population, but remains considerably genetically differentiated. Despite the precipitous loss of eelgrass in Morro Bay between 2007 and 2017, genetic diversity remains comparable to other populations on the west coast.

No description available.

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.