Cette étude a été menée afin de mieux comprendre l’influence de l’herbier à Zosteranoltii du Bassin d’Arcachon, herbier affecté par une sévère régression depuis les années2000, sur la dynamique biogéochimique des sédiments intertidaux de cette lagune. Dans cet environnement côtier dynamique, il s’agissait de caractériser cette influence sur demultiples échelles spatiales (i.e. de la racine à l'écosystème) et temporelles (i.e. tidale, diurne, saisonnière et interannuelle). Des mesures par voltammétrie in situ de la composition des eaux porales des sédiments intertidaux non végétalisés ont montré que (i) les distributions verticales des espèces réduites variaient avec les marées et que (ii) la dynamique de l’oxygène dissous en réponse aux cycles tidaux et diurnes était contrôlée par l’activité photosynthétique et les migrations verticales du microphytobenthos. L’étude de l’influence de l’herbier sur cette dynamique via des pertes d’oxygène au niveau des racines a été initiée en mesurant les variations des concentrations en oxygène à l’intérieur des lacunes aérifères de ces plantes. L’organisation des lacunes de Zostera noltii est présentée pour la première fois dans cette étude. La distribution verticale de nutriments dans les eaux porales de sédiments végétalisés et de sédiments nus a été caractérisée pendant la période de croissance de l’herbier. La présence de Zostera noltii a induit une zonation verticale marquée de cette distribution qui reflète l’évolution avec la profondeur de l’équilibre entre la production de nutriments résultant de l’exsudation de matière organique labile par les parties souterraines de la plante (source) et le pompage de ces nutriments par les racines (puits). L’existence d’un pompage de carbone inorganique dissous et de silice dissoute par les racines de l’herbier a été mise en évidence. Des mesures d’échanges benthiques d’oxygène dissous sur des sédiments nus et colonisés par Zostera noltii ont permis de caractériser la saisonnalité et l’hétérogénéité spatiale du métabolisme benthique (respiration et production primaire brute) en relation avec les distributions d’herbier et/ou de macrofaune benthique. Dans les sédiments végétalisés, la forte variabilité spatio-temporelle de ce métabolisme benthique était largement contrôlée par la biomasse de feuilles d’herbier. A l’échelle de la lagune, nos calculs ont montré que la regression de l’herbier à Zostera noltii entre 2005 et 2007 a induit une diminution significative des taux de respiration et de production de la zone intertidal de la lagune. L’évolution interannuelle de la biogéochimie de sédiments colonisés par Zostera noltii a été étudiée en 2006 et en 2010/2011 sur une zone située dans une partie du Bassin d’Arcachon particulièrement affectée par le déclin des herbiers (secteur de Cassy). Contrairement aux observations réalisées sur l’herbier bien portant en 2006, l’herbier en déclin augmenterait le relargage de nutriments dans les sédiments via la stimulation de la production d’ammonium ou de la dissolution du phosphore particulaire. La régression des herbiers fournirait un apport significatif de phosphore vers la colonne d’eau de la lagune, d’une magnitude comparable aux apports par les rivières ou à ceux liés au pompage tidal. / The aim of this study was to improve our understanding of the influence of the Zostera noltii meadows of the Arcachon Bay, a seagrass meadow affected by a severe regression since the 2000’s, on the biogeochemical dynamic of the intertidal sediment of this lagoon. In such a changing coastal environment, it was important to characterize this influence on a wide range of spatial (i.e. from roots to the ecosystem) and temporal scales(i.e. tidal, diurnal, seasonal and inter-annual). In situ voltammetric measurements of the composition of porewater in an intertidal unvegetated sediment showed that (i) the vertical distribution of reduced species varied with tides and (ii) the oxygen dynamic in response to tidal and diurnal cycles was controlled by the photosynthetic activity and vertical migrations of microphytobenthos.The study of the influence of seagrasses on this dynamic by radial oxygen loss around roots was initiated with measurements of oxygen concentrations inside the lacunae of these plants. The organization of the lacunae of Zostera noltii is presented for the first time inthis study. The vertical distribution of porewater nutrients in vegetated and unvegetated sediments was characterized during the growth period of seagrasses. The presence of Zostera noltii induced a strong vertical zonation related to the depth-evolution of the balance between nutrient production stimulated by the root exudation of labile organic matter (source) and the root uptake of nutrients (sink). This study revealed the occurence of a root uptake of dissolved inorganic carbon and dissolved silica. Measurements of benthic oxygen exchanges on sediments colonized or not by Zostera noltii enabled the characterization of the seasonality and spatial heterogeneity of benthic metabolism (respiration and gross primary production) related to macrofaunal and macrophytic distribution. In vegetated sediments, the spatio-temporal variability of this benthic metabolism was highly controlled by leaves biomass. At the lagoon scale, our calculations showed that the regression of Zostera noltii meadows induced a significant decresase of mean annual respiration and production rates of the intertidal area of the lagoon.The inter annual evolution of the biogeochemistry of sediments colonized by Zostera noltii was studied in 2006 and in 2010/2011 in an area of the Arcachon Bay highly affected by the seagrass decline. In contrast to the healthy meadow in 2006, the declining meadow has increased nutrient release in sediments stimulating the production of ammonium or the dissolution of particulate phosphorus. This study shows that seagrass decay may result in a significant supply of phosphorus to the water column of a magnitude comparable to annual inputs to the lagoon from the rivers and the tidal pump.

L’influence de la diversité génétique sur la stabilité démographique des populations constitue un paradigme de l’écologie évolutive. Au sein des populations naturelles, l’étude de cette relation est complexifiée par l’influence réciproque de la stabilité sur la diversité, et leur degré d’interconnexion. Ces interrelations ont été explorées chez la plante marine Zostera marina et les coraux d’eau froide Lophelia pertusa et Madrepora oculata, des espèces partiellement clonales. Ce trait d’histoire de vie, influençant profondément la dynamique démographique et la trajectoire évolutive des espèces, a constitué le fil d’Ariane de ce travail. L’échantillonnage dans l’espace (échelle régionale) et le temps (un pas de trois ans) d’herbiers de Zostère a permis de mieux comprendre la dynamique clonale de ces plantes. L’architecture et la diversité clonale apparaissent comme la résultante de l’équilibre entre dispersion/recrutement de nuages de graines dispersées collectivement, et la compétition pour l’espace entre clones. Les perturbations affectent localement l’équilibre de l’herbier. Cette dynamique originale rend impossible l’identification des contours populationnels. En revanche, nos résultats semblent indiquer que la diversité génétique au sens strict (hétérozygotie et nombre d’allèles) des herbiers de Zostères constitue un facteur de stabilité démographique, via sa potentielle influence sur les capacités de résistance aux perturbations saisonnières. Les coraux d’eau froide, quant à eux, présentent des patrons biogéographiques en accord avec l’hypothèse d’une extinction dans le Golfe de Gascogne, lors des derniers épisodes glaciaires. Les marques visibles des activités de pêche posent la question des capacités de résilience de ces écosystèmes, qui dépendent entre autres du potentiel de dispersion de ces espèces. L’absence de structure génétique observée chez L. pertusa suggère, au moins pour cette espèce, un fort degré d’interconnexion entre les récifs, tandis que M. oculata montre davantage de structure régionale. La sensibilité de ces espèces aux variations climatiques et à la pression des activités anthropiques souligne la nécessité d’études approfondies, pour leur conservation.Les résultats obtenus pendant cette thèse permettent de mieux comprendre la dynamique populationnelle des herbiers et récifs profonds, le taux de clonalité et la connectivité des populations. Ces informations sont essentielles pour avancer vers une meilleure compréhension de la dynamique et la résistance de ces espèces structurantes, et sont donc primordiales pour la conservation de ces écosystèmes clé. / The influence of genetic diversity on the demographic stability of populations constitutes a paradigm in evolutionary ecology. The complexity of this relationship within natural populations is enhanced by the reciprocal effect of stability on diversity, and the degree of interconnection among populations. This interaction was explored within the seagrass Zostera marina and the cold-water corals Lophelia pertusa and Madrepora oculata, three partially clonal species. This life history trait, deeply influencing the population dynamics and evolutionary trajectory of species, constituted the underlying theme of this work.The sampling in space (regional scale) and time (a three-years step) of eelgrass meadows allowed us to better understand the clonal dynamics of these plants. The clonal architecture and diversity may result from the equilibrium between dispersal/recruitment of collectively dispersed clouds of seeds, and the competition for space among clones. Perturbations locally affect the equilibrium of meadows. This original dynamic makes impossible the identification of population contours. Yet, our results suggest that the genetic diversity sensu stricto (heterozygosity and number of alleles) represents a factor of demographic stability, through its putative influence on resistance capacity for seasonal disturbances. Cold-water corals show biogeographic pattern in line with the hypothesis of glacial extinction, within the Bay of Biscay. The noticeable footprints of fishing activities question the capacity of resilience of these ecosystems, depending on dispersal potential of the structuring species, which showed low levels of clonality. The lack of genetic structure observed for L. pertusa suggest, at least for this species, a high degree of interconnection among reefs at large scale, while M. oculata revealed a stronger regional structure. Sensitivity of these two species to climatic variations and the pressures of human activities highlight the need of thorough studies for their conservation. Results obtained during this thesis allow a better understanding of the populations dynamics of both seagrass and deep reefs and their levels of clonality and connectivity. This information constitutes the first step toward a better understanding of dynamics and resistance of these structuring species, and is also primordial for the conservation of their key ecosystems.

Seagrass ecosystems are some of the most productive in the world and provide a variety of ecosystem services but are facing global decline chiefly due to anthropogenic disturbance. Mechanical disturbances to seagrass meadows from anchoring, propeller scars, and mooring scars result in losses or damage to both shoots and the underlying rhizome. I conducted a literature synthesis on the extent of, recovery from, and ecological impacts of these mechanical disturbances to seagrass meadows. The literature suggests that anchoring damage tends to be worst in deeper water where larger vessels anchor and can cause large (>100m2) loss per anchoring and recovery may take decades to over a century. Propeller damage is of largest concern in shallow (<2m) areas experiencing heavy boat traffic because propeller damage can only occur where the propeller can come close to the seagrass. Mooring damage is highly variable depending on the type of mooring used (>10m2 to >1000m2 scoured per mooring). Seagrass patches experiencing these mechanical disturbances have, in some studies, been found to have lower seagrass percent cover and shoot density than reference areas. This indicates scars can have "halos" of impacted seagrass meadow. Some seagrass systems cannot recover within a century (e.g. Posidonia oceanica meadows at the extent of their depth tolerance) while others recover annually from some disturbances (e.g., anchor scars <1m2). Systems face altered species composition when scars are preferentially recolonized by certain species and patterns of recovery are affected by altered biogeochemical conditions following disturbances. Additionally, mooring, anchoring, and propeller scarring frequently alter meadow density, cover, patch size, patch shape, patch isolation, edge area, and ratios of edge to interior meadow leading to changes in faunal community structure. Correlations between these disturbances and faunal abundances, densities, and richness in seagrass ecosystems are complex, vary temporally (sometimes on the scale of days), and may result in species showing positive, negative, or no responses to a wide range of disturbance regimes. To explore the connections between mooring scarring, the surrounding seagrass meadow condition and epifaunal community, in the second part of this thesis I measured 30 mooring scars to determine average scar size. To explore any potential "halo" effect around mooring scars for seagrass or epifauna and to seek any difference in epifaunal community between mooring and reference sites I also sampled paired sites at eight locations in Nantucket Harbor, Massachusetts three times each in the summer of 2015. Each location consisted of a meadow site actively experiencing mooring scarring and a reference site without moorings. My conservative sampling methods of the 30 sampled mooring scars found scars to average 21.1m2. Across my paired sites, seagrass was found to have lower cover and lower canopy height in mooring versus reference sites. Seagrass cover and canopy height were lower in the first few meters (typically 2-3m) surrounding each scar in comparison to paired reference quadrats indicating a "halo" effect of each scar. I did not detect a difference in epifaunal community composition or density per blade between mooring and reference sites; however, the relatively constant per blade concentration of epifauna combined with the differences in seagrass biomass between the mooring versus reference sites indicate an overall increase in the total amount of epifauna in areas with less disturbance. Epifaunal community composition was different and between locations and sampling dates indicating these factors are more important than proximity to mooring scarring in determining epifaunal abundance and richness. When considering scar area and the "halo" of each scar I estimate that at least 32ha (2%) of Nantucket Harbor was impacted by mooring scarring. Given that the estimates of seagrass do not include areas previously denuded of this plant and that my measurements were conservative, likely a larger portion of this harbor's potential seagrass habitat is impacted. Combined with the findings of loss due to these direct boat-related physical disturbances of seagrass meadows worldwide across regions, this halo effect is likely to also be found for moorings globally. I encourage management of the issue by employing and fine-tuning mooring methods (such as deploying moorings with anchor connections that do not drag on the sea floor) to minimize these unintentional but strong effects of mooring on the recipient habitat.

Les herbiers de Zostera noltii constituent des habitats remarquables dans les zones intertidales des baies et estuaires bordés par l'Atlantique Nord. Ces herbiers étant soumis à des pressions naturelles et anthropiques, l'estimation de la dynamique spatio-temporelle se révèle alors primordiale afin de mettre en place des mesures de gestion et de protection appropriées. La télédétection visible - proche infra-rouge à partir de capteurs aéroportés et satellitaux a été utilisée pour leur identification et leur cartographie à macro-échelle. La méthodologie proposée repose sur l'analyse des spectres de réflectance des feuilles (partie épigée de l'herbier) pour des longueurs d'ondes allant de 400 à 900 nm. A partir de librairies spectrales réalisées en laboratoire par spectroradiométrie, des relations quantitatives entre la biomasse et des indices de végétation ont été obtenues, intégrant l'influence du substrat et des variations phénologiques. Cette approche spectroradiométrique a facilité l'interprétation et le traitement d'images multi et hyperspectrales (SPOT et HySpex) couvrant la baie de Bourgneuf (2°10'O, 46°57'N), révélant une extension régulière des herbiers de 1991 à 2011, probablement expliquée par un phénomène d'accrétion naturelle dans la baie, entrecoupée cependant de brèves périodes de régression (2006-2009) dont les causes ne sont pas expliquées.

Cette étude a été menée afin de mieux comprendre l'influence de l'herbier à Zosteranoltii du Bassin d'Arcachon, herbier affecté par une sévère régression depuis les années2000, sur la dynamique biogéochimique des sédiments intertidaux de cette lagune. Dans cet environnement côtier dynamique, il s'agissait de caractériser cette influence sur demultiples échelles spatiales (i.e. de la racine à l'écosystème) et temporelles (i.e. tidale, diurne, saisonnière et interannuelle). Des mesures par voltammétrie in situ de la composition des eaux porales des sédiments intertidaux non végétalisés ont montré que (i) les distributions verticales des espèces réduites variaient avec les marées et que (ii) la dynamique de l'oxygène dissous en réponse aux cycles tidaux et diurnes était contrôlée par l'activité photosynthétique et les migrations verticales du microphytobenthos. L'étude de l'influence de l'herbier sur cette dynamique via des pertes d'oxygène au niveau des racines a été initiée en mesurant les variations des concentrations en oxygène à l'intérieur des lacunes aérifères de ces plantes. L'organisation des lacunes de Zostera noltii est présentée pour la première fois dans cette étude. La distribution verticale de nutriments dans les eaux porales de sédiments végétalisés et de sédiments nus a été caractérisée pendant la période de croissance de l'herbier. La présence de Zostera noltii a induit une zonation verticale marquée de cette distribution qui reflète l'évolution avec la profondeur de l'équilibre entre la production de nutriments résultant de l'exsudation de matière organique labile par les parties souterraines de la plante (source) et le pompage de ces nutriments par les racines (puits). L'existence d'un pompage de carbone inorganique dissous et de silice dissoute par les racines de l'herbier a été mise en évidence. Des mesures d'échanges benthiques d'oxygène dissous sur des sédiments nus et colonisés par Zostera noltii ont permis de caractériser la saisonnalité et l'hétérogénéité spatiale du métabolisme benthique (respiration et production primaire brute) en relation avec les distributions d'herbier et/ou de macrofaune benthique. Dans les sédiments végétalisés, la forte variabilité spatio-temporelle de ce métabolisme benthique était largement contrôlée par la biomasse de feuilles d'herbier. A l'échelle de la lagune, nos calculs ont montré que la regression de l'herbier à Zostera noltii entre 2005 et 2007 a induit une diminution significative des taux de respiration et de production de la zone intertidal de la lagune. L'évolution interannuelle de la biogéochimie de sédiments colonisés par Zostera noltii a été étudiée en 2006 et en 2010/2011 sur une zone située dans une partie du Bassin d'Arcachon particulièrement affectée par le déclin des herbiers (secteur de Cassy). Contrairement aux observations réalisées sur l'herbier bien portant en 2006, l'herbier en déclin augmenterait le relargage de nutriments dans les sédiments via la stimulation de la production d'ammonium ou de la dissolution du phosphore particulaire. La régression des herbiers fournirait un apport significatif de phosphore vers la colonne d'eau de la lagune, d'une magnitude comparable aux apports par les rivières ou à ceux liés au pompage tidal.

The aim of this research was to assess three hierarchical aspects of alga-grazer interactions in intertidal communities on a small scale: spatial heterogeneity, grazing effects and spatial stability in grazing effects. First, using semivariograms and cross-semivariograms I observed hierarchical spatial patterns in most algal groups and in grazers. However, these patterns varied with the level on the shore and between shores, suggesting that either human exploitation or wave exposure can be a source of variability. Second, grazing effects were studied using manipulative experiments at different levels on the shore. These revealed significant effects of grazing on the low shore and in tidal pools. Additionally, using a transect of grazer exclusions across the shore, I observed unexpected hierarchical patchiness in the strength of grazing, rather than zonation in its effects. This patchiness varied in time due to different biotic and abiotic factors. In a separate experiment, the effect of mesograzers effects were studied in the upper eulittoral zone under four conditions: burnt open rock (BOR), burnt pools (Bpool), non-burnt open rock (NBOR) and non-burnt pools (NBpool). Additionally, I tested spatial stability in the effects of grazing in consecutive years, using the same plots. I observed great spatial variability in the effects of grazing, but this variability was spatially stable in Bpools and NBOR, meaning deterministic and significant grazing effects in consecutive years on the same plots. Both the significance in grazing effects and spatial stability depended on the level of resolution (species, functional, biomass) at which the algal assemblage was evaluated, suggesting hierarchical variability. In order to be able to predict spatial variability in the effects of grazers in the upper eulittoral zone using biotic and abiotic micro- and macrofactors, a conceptual model was proposed, based on data from several multiple-regressions. This linked the interactions among three elements: idiosyncratic heterogeneity, micro and macrofactors. This suggests that spatial variability can be a product of these factors, while spatial stability can be caused by the same or different combinations of factors. In conclusion, grazing and other ecological phenomena must be studied hierarchically, not only through spatiotemporal scales, but also at different levels of resolution, as these also influence our perception of patterns.

Most of what is known about the ways in which strongly interacting species affect ecological communities stems from changes to community structure revealed in contemporary research. However, trophic downgrading has limited the temporal extent to which inferences can be drawn. The aim of my Dissertation was to expand on the strongly interacting species concept by examining species interactions at a historical scale, in a textbook example of a strongly interacting and keystone predator. The sea otter, Enhydra lutris, was driven to near-extinction but is recovering in parts of its range, providing a mosaic of areas with and without sea otters. This mosaic allowed for a series of natural experiments, which I conducted using behavioural observations, genetic tools, and archaeological methods, to examine sea otter effects spanning contemporary (last ~40 yrs.), and late-Holocene (~3500-150 yrs. ago) timeframes, and on an evolutionary scale that inferred middle-Pleistocene interactions. In Chapter 2, my coauthors and I found that sea otter use of clam-based niches increased as occupancy-time increased, and that bachelor groups of male otters primarily inhabited these niches, findings that informed and inspired subsequent questions. In Chapter 3, we found that where sea otters were established for 20-30 years, the disturbance to eelgrass (Zostera marina), caused by sea otters digging for clams and other infaunal prey, was correlated with ~25% greater eelgrass allelic richness than where otters were present <10 yrs, or absent. We posit that sea otter digging has long-influenced the genetic diversity and resilience of eelgrass – perhaps since the middle Pleistocene. In Chapter 4, we asked how two strongly interacting species – people and sea otters – co-existed for millennia where they both consumed clams. We used assemblages of live and otter-cracked butter clams (Saxidomus gigantea), to confirm the ecological effects that sea otters exert today. We measured clams from archaeological assemblages in areas densely populated with clam gardens – terraced beaches that enhance clam habitat and productivity – and found that sea otters reduced the sizes of ancient clams, acting as ecologically effective predators in the mid-to-late Holocene. However, clam harvests were stable for thousands of years, with or without otters. We suggest that clam gardening supported coexistence of people and otters in the past, and could function the same way today. Collectively, we found that a few, perhaps long-forgotten, interactions increased the breadth of the strongly interacting species concept. In Chapter 5, I suggest that such rediscoveries could occur in other systems. Many large vertebrates have suffered population declines, but the most insidious losses accompanying these, are the losses of ecological interactions that become unknowable, and thus cannot be intentionally restored. By searching out ancient interactions, long-forgotten relationships have the potential to be recovered, and to inform our understanding of contemporary systems. / Graduate / 2022-09-10

The objectives of the present study are to: (1) Describe the macro-invertebrate species composition and seasonal changes in abundance of the benthic infauna within an eelgrass bed; (2) Observe what immediate effects occur to the benthic community as a result of experimental removal of eelgrass plants from plants within the Zostera bed; (3) Measure the seasonal variation of eelgrass turion length over an annual cycle and determine its correlation to biomass (dry weight); (4) Examine, by means of field experiments, the importance of incident solar irradiation in affecting the seasonal growth of Zostera; and (5) Determine the relationship, if any, between the abundance of major invertebrate species and the abundance of eelgrass as determined by mean turion length.

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.

The capacity of the world’s coastal ecosystems to sequester carbon dioxide (CO2), termed “Blue Carbon,” has been a major focus of research in recent decades due to its potential to mitigate climate change. Vegetated coastal ecosystems such as mangroves, seagrass beds, and salt marshes represent a global area that is one to two orders of magnitude smaller than that of terrestrial forests, yet their contribution to long-term carbon sequestration is much greater per unit-area, in part because of their high productivity and efficiency in trapping suspended matter and associated organic carbon. Despite the value that Blue Carbon (BC) systems offer in sequestering carbon, as well as providing numerous other goods and services, these habitats are being lost at critical rates and require urgent action in order to prevent further degradation and loss. Recognition of the carbon sequestration value of vegetated coastal ecosystems provides a strong argument for their protection and restoration, and global efforts are now underway to include BC ecosystems into global carbon offset budgets, focusing on their optimal management to optimize CO2 sequestration and minimize CO2 emissions. Here, BC was investigated in the Cowichan Estuary in relation to habitat type (salt marsh, eelgrass meadow, non-vegetated mudflats, and oyster shell beds), and habitat degradation. Stored organic carbon (OC) and inorganic carbon (IC) were quantified in the top 20 cm depth of sediment cores, as well as in eelgrass and salt marsh vegetation, and then extrapolated to the areal extent of each habitat type based on a high resolution 1:12,000 scale base map of the estuary. Rates of sedimentation and carbon sequestration were quantified in each habitat type using 210Pb radiometric dating, and organic matter (OM) sources and quality were assessed in each habitat type using δ13C, C/N ratios and photopigment content in the sediments. A particular focus on the lower intertidal zone allowed us to examine the potential impact of industrial activity (log transport and storage) on the estuary’s capacity for carbon storage, as a result of a reduction of suitable habitat for eelgrass and microphytobenthos (MPB). Additionally, IC was quantified in aboveground oyster shell beds and buried oyster shell to assess inorganic storage. Finally, potential valuation of Blue Carbon in the Cowichan Estuary was investigated by comparing carbon sequestration to provincial greenhouse gas (GHG) emission equivalents as well as carbon sequestration in B.C. forests. We found that the salt marsh was the most important carbon reservoir, with a mean per-hectare sediment organic carbon (SOC) stock of 49.1 ± 19.9 Mg C ha-1, total ecosystem carbon stock (TECS) of 5443.75 Mg C, and carbon accumulation rate of 74 ± 23 g C m-2 yr-1. In the other habitats, we found SOC stocks and TECS respectively 19.1 ± 3.78 Mg C ha-1 and 3651.6 ± 72.3 Mg C in the upper mudflats, 16.9 ± 4.36 Mg C ha-1 and 1058.85 Mg C in the lower mudflats, 17.9 ± 1.21 Mg C ha−1 and 324.57 Mg C in the eelgrass meadow, and 9.43 ± 1.50 Mg C ha-1 and 59.4 Mg C in the oyster beds. The eelgrass meadow had a carbon accumulation rate of 38 ± 26 g C m-2 yr-1, while the mudflats could not successfully be dated due to erosion and/or mixing. Furthermore, the salt marsh contained the highest proportion of recalcitrant, terrestrial-derived root material which was more protected from hydrodynamic forces compared to other habitats. No pattern differences were observed between the carbon reservoirs or bulk properties of the log boom area (lower mudflat) compared to the upper mudflat, and thus there was no evidence that the log booms significantly decrease carbon sequestration in the areas where they make frequent contact with the seafloor. However, decreased chlorophyll a (chl a) concentrations in the lower mudflat sediment suggests a possible detrimental impact on microphytobenthos in addition to preventing the recolonization of the seagrass Zostera marina (Z. marina). Carbon stocks in the eelgrass meadow were similar to those of the mudflats. These carbon stocks were lower than global averages but consistent with those recently reported in low Z. marina meadows in the Pacific Northwest. Evidence of significant eelgrass vegetation outwelling necessitates further investigation to elucidate the degree to which these primary products are being decomposed or buried elsewhere in the estuary or open ocean. Since approximately half of the historical salt marsh habitat is currently reclaimed for agricultural and industrial use, consideration should be given to the role of the marsh system as a carbon reservoir in future land-use policy in the Cowichan Estuary. / Graduate / 2022-04-30