Benthic microalgal community composition on an ephemerally submerged sandflat at East Beach, Galveston Island, Texas was studied to determine the spatial and temporal variability of total biomass and community composition and its responses to experimental manipulations of two environmental factors (salinity and nutrients). Four field studies were conducted between August 2004 and February 2005. The community consisted of two major algal groups, diatoms, and cyanobacteria with two less abundant groups, green algae, and phototrophic bacteria. Spatial variability showed that patch sizes of 12 - 25 m were detected over larger scales with smaller scale (cm) patches of approximately 28 - 201 cm^-2 contained within the larger patches. The second study examined the spatio-temporal variability of BMA over a 21-month period in a 1,000 m^2 area. Sampling location and date explained a significant amount of the variability in the abundances of algal groups, which were positively correlated with the water content of the sediments and negatively correlated with temperature (sediment and water). All of the algal groups showed a seasonal pattern with higher abundances measured in the winter months and lower abundances found during the summer. BMA biomass (100 mg Chl a m^-2 or greater) maxima occurred at temperatures less than 22 degrees C and sediment water content greater than 15% (g water g sediment^-1). BMA response to different salinities and nutrient (N+P) amended sediments was assessed in four bioassays conducted over a 6-month period (Aug. 2004, Oct. 2004, Dec. 2004, and Feb. 2005). In the salinity study, the treatments that were either 100% or partially diluted with deionized water had the lowest BMA biomass over all. Chlorophyll a and fucoxanthin were significantly affected by salinity with higher abundances found in salinities that averaged 15 with a preference for salinities greater than 22. Chlorophyll b was affected by salinity with higher abundances measured in the treatments with lowest salinity (DL and DI); and was affected by the time of year. This would suggest that this algal group prefers an environment with salinity less than 2 but can easily adapt to environments with higher salinities. BMA abundances were not significantly affected by the nutrient amended sediment, but were significantly affected by stations with higher water content, and during the cooler months (Dec. 2004 and Feb. 2005).

La compréhension des processus écologiques affectant la matière transitant ou produite dans les estuaires nécessite une bonne connaissance des facteurs qui contrôlent le développement des différents groupes biologiques et leurs relations trophiques dans le milieu.Les milieux estuariens macrotidaux sont le plus souvent caractérisés par des fortes turbidités qui limitent généralement la production primaire locale. Ils présentent cependant une forte productionsecondaire et des concentrations en chlorophylle non négligeables dans la colonne d’eau. L’une des problématiques demeure donc l’origine de cette production primaire dans les eaux turbides de ces milieux. Cette thèse s’inscrit dans cette logique ; dans la continuité des travaux réalisés précédemment. Elle vise à analyser l’importance et le rôle de la production primaire dans la production globale de l’estuaire de la Gironde. Le présent manuscrit résume ainsi l’ensemble des travaux réalisés et lesrésultats obtenus sur les principaux groupes de producteurs primaires (phytoplancton et microphyto-benthos) présents le long du continuum fluvio-estuarien de la Gironde. Les principales questions qui sont développées dans ce travail structurent ce rapport en trois axes de recherche. Le premier axe permet, au moyen d’une modélisation 1D de transport et réaction, de simuler,dans l’espace et le temps, la dynamique de la chlorophylle-a et des sels nutritifs, témoins d’uneproduction primaire dans le milieu. Les résultats indiquent que la dynamique de la chlorophylle-adans la Gironde reste fortement dépendante des débits et des temps de résidence très courts des massesd’eau, renforçant ainsi une origine allochtone du phytoplancton. Parmi les sources potentielles deproduction d’origine allochtone présents dans la colonne d’eau, les microalgues benthiques jouent unrôle majeur puisqu’elles peuvent être remises en suspension au cours de chaque marée. L’analyse dece compartiment et de sa production a permis dans un second axe de travail, de montrer que les zonesintertidales situées en aval de l’estuaire sont les plus productives et sont majoritairement autotrophes.Elles produiraient relativement plus de matière que les zones situées en amont qui elle, sont fortementinfluencées par les débits des fleuves.Finalement dans le troisième axe, les différentes voies de transfert de la matière organique au seindu réseau trophique, où les copépodes occupent une place prépondérante, sont analysées au moyendu traçage par les isotopes stables de carbone et de l’azote (13C et 15N) / Abstract

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

Diatomáceas são importantes constituintes do epifíton em ambientes costeiros. Estratégias de fixação conferem a estas algas vantagem adaptativa, no entanto, as mesmas estão sujeitas às variações ambientais, podendo responder com alterações da composição e estrutura da comunidade. Embora a relação entre epifíton e substrato seja pouco compreendida, a arquitetura do substrato parece influenciar na comunidade aderida. A composição, estrutura e variação sazonal de diatomáceas epifíticas foram avaliadas em ambientes de marismas no estuário da Lagoa dos Patos, sul do Brasil. Três sítios foram amostrados, Saco do Silveira, Ilha da Pólvora e São José do Norte, distantes 36, 18 e 9 km do oceano Atlântico, respectivamente. O epifíton aderido à Spartina alterniflora Loisel., Spartina densiflora densiflora Brogn., Scirpus maritimus L. e Juncus kraussii Hochst. foi removido dos substratos com lâmina metálica, oxidado e montado em lâminas permanentes para a análise das diatomáceas. Ao total cento e vinte e sete táxons foram encontrados, destacaram-se pelo maior número de espécies os gêneros Navicula Bory, Nitzschia Hassall e Tryblionella W. Smith. A sazonalidade, espacialidade, salinidade e tipo de substrato tiveram influência na composição e estrutura da comunidade. A maior distância da desembocadura do estuário proporcionou uma maior influência de águas continentais no sítio Saco do Silveira, resultando na formação de uma comunidade caracterizada pela presença de táxons dulciaquícolas. O período de inverno se caracterizou por maiores valores dos atributos da comunidade (riqueza, diversidade e equitabilidade). A maior complexidade da superfície de Scirpus maritimus proporcionou a formação de uma comunidade epifítica mais rica. A investigação taxonômica de Nitzschia e Tryblionella foi aprofundada, analisando-se também o microfitobentos da região. A espécie Nitzschia papillosa Bertolli et al. foi registrada pela primeira vez para a ciência, ocorrendo no epifíton e microfitobentos dos sítios Ilha da Pólvora e São José do Norte. A espécie possui formato linear-lanceolado, ápices cuneados e fíbulas irregularmente distribuídas como várias espécies do gênero, sua característica diagnóstica é a presença de excrecências de sílica arredondadas a quadradas situadas na costa transapical interna das valvas. O estudo do gênero Tryblionella revelou a presença de 11 espécies, duas foram registradas pela primeira vez para o Rio Grande do Sul e uma para o sul do Brasil. Além disso, duas espécies novas para a ciência são propostas, Tryblionella Bertolli et Torgan, espécie semelhante a T. debilis Arnott ex O’Meara em microscopia óptica, mas que apresenta costelas transapicais assimétricas em microscopia eletrônica, e Bertolli et al., espécie que apresenta um padrão de ornamentação na face valvar semelhante à trama de uma renda. As espécies de Tryblionella e N. papillosa ocorreram concomitantemente no epifíton e no microfitobentos, evidenciando a interação entre as duas comunidades, promovida pela dinâmica do ambiente. / Diatoms are an important component of the epiphyton in coastal environments. The strategies of attachment provide adaptive advantages to these algae; however, they are susceptible to the environmental fluctuations, responding to them with changes in the community composition and structure. Although the relationship between epiphyton and substrate is poorly understood, the architecture of the substrate seems to influence the attached community. The composition, structure and seasonal variations of the epiphytic diatoms were evaluated in Patos Lagoon salt marshes. Three sampling sites were defined, Saco do Silveira, Ilha da Pólvora and São José do Norte, distant 36, 18 and 9 km from the Atlantic Ocean, respectively. The epiphyton attached to Spartina alterniflora Loisel., Spartina densiflora densiflora Brogn., Scirpus maritimus L. e Juncus kraussii Hochst. was scraped with metal blade, oxidized and mounted on permanent slides for the analysis of the diatoms. A total of a hundred and twenty seven taxa were found. The genus Navicula Bory, Nitzschia Hassall e Tryblionella W. Smith showed the highest number of species. The seasonality, spatiality, salinity and substrate influenced the composition and structures of the community. The higher distance of the estuary mouth provided a higher influence of continental waters in the site Saco do Silveira, resulting in a community characterized by freshwater taxa. The winter was characterized by higher values of the community attributes (richness, diversity and evenness). The more complex structure of S. maritimus surface provided the establishment of a richer community. The taxonomic investigation of Nitzschia and Tryblionella was more detailed, including the analysis of the microphytobenthos of the sites. The species Nitzschia papillosa Bertolli et al. was registered for the first time to science in Ilha da Pólvora and São José do Norte. The species has linear-lanceolate outline, cuneate apices and fibulae irregularly distributed, as many other species of the genus. Its main feature is the presence of rounded to squarer silica excrescences, situated on the transapical costae in the internal valve view. The study of the genus Tryblionella showed 11 species, two of them were registered for the first time in Rio Grande do Sul State and one in Southern Brazil. Besides that, two species new to science were proposed, Tryblionella Bertolli et Torgan, which is similar to T. debilis Arnott ex O’Meara in light microscopy, but present asymmetrical transapical ribs in scanning electron microscopy, and T. Bertolli et al. which presents an ornamentation pattern similar to a lace texture in the valve face. The species of Tryblionella and N. papillosa occurred concomitantly in the epiphyton and microphytobenthos, evidencing the interaction between both communities, promoted by the environment dynamics.

Diatomáceas são importantes constituintes do epifíton em ambientes costeiros. Estratégias de fixação conferem a estas algas vantagem adaptativa, no entanto, as mesmas estão sujeitas às variações ambientais, podendo responder com alterações da composição e estrutura da comunidade. Embora a relação entre epifíton e substrato seja pouco compreendida, a arquitetura do substrato parece influenciar na comunidade aderida. A composição, estrutura e variação sazonal de diatomáceas epifíticas foram avaliadas em ambientes de marismas no estuário da Lagoa dos Patos, sul do Brasil. Três sítios foram amostrados, Saco do Silveira, Ilha da Pólvora e São José do Norte, distantes 36, 18 e 9 km do oceano Atlântico, respectivamente. O epifíton aderido à Spartina alterniflora Loisel., Spartina densiflora densiflora Brogn., Scirpus maritimus L. e Juncus kraussii Hochst. foi removido dos substratos com lâmina metálica, oxidado e montado em lâminas permanentes para a análise das diatomáceas. Ao total cento e vinte e sete táxons foram encontrados, destacaram-se pelo maior número de espécies os gêneros Navicula Bory, Nitzschia Hassall e Tryblionella W. Smith. A sazonalidade, espacialidade, salinidade e tipo de substrato tiveram influência na composição e estrutura da comunidade. A maior distância da desembocadura do estuário proporcionou uma maior influência de águas continentais no sítio Saco do Silveira, resultando na formação de uma comunidade caracterizada pela presença de táxons dulciaquícolas. O período de inverno se caracterizou por maiores valores dos atributos da comunidade (riqueza, diversidade e equitabilidade). A maior complexidade da superfície de Scirpus maritimus proporcionou a formação de uma comunidade epifítica mais rica. A investigação taxonômica de Nitzschia e Tryblionella foi aprofundada, analisando-se também o microfitobentos da região. A espécie Nitzschia papillosa Bertolli et al. foi registrada pela primeira vez para a ciência, ocorrendo no epifíton e microfitobentos dos sítios Ilha da Pólvora e São José do Norte. A espécie possui formato linear-lanceolado, ápices cuneados e fíbulas irregularmente distribuídas como várias espécies do gênero, sua característica diagnóstica é a presença de excrecências de sílica arredondadas a quadradas situadas na costa transapical interna das valvas. O estudo do gênero Tryblionella revelou a presença de 11 espécies, duas foram registradas pela primeira vez para o Rio Grande do Sul e uma para o sul do Brasil. Além disso, duas espécies novas para a ciência são propostas, Tryblionella Bertolli et Torgan, espécie semelhante a T. debilis Arnott ex O’Meara em microscopia óptica, mas que apresenta costelas transapicais assimétricas em microscopia eletrônica, e Bertolli et al., espécie que apresenta um padrão de ornamentação na face valvar semelhante à trama de uma renda. As espécies de Tryblionella e N. papillosa ocorreram concomitantemente no epifíton e no microfitobentos, evidenciando a interação entre as duas comunidades, promovida pela dinâmica do ambiente. / Diatoms are an important component of the epiphyton in coastal environments. The strategies of attachment provide adaptive advantages to these algae; however, they are susceptible to the environmental fluctuations, responding to them with changes in the community composition and structure. Although the relationship between epiphyton and substrate is poorly understood, the architecture of the substrate seems to influence the attached community. The composition, structure and seasonal variations of the epiphytic diatoms were evaluated in Patos Lagoon salt marshes. Three sampling sites were defined, Saco do Silveira, Ilha da Pólvora and São José do Norte, distant 36, 18 and 9 km from the Atlantic Ocean, respectively. The epiphyton attached to Spartina alterniflora Loisel., Spartina densiflora densiflora Brogn., Scirpus maritimus L. e Juncus kraussii Hochst. was scraped with metal blade, oxidized and mounted on permanent slides for the analysis of the diatoms. A total of a hundred and twenty seven taxa were found. The genus Navicula Bory, Nitzschia Hassall e Tryblionella W. Smith showed the highest number of species. The seasonality, spatiality, salinity and substrate influenced the composition and structures of the community. The higher distance of the estuary mouth provided a higher influence of continental waters in the site Saco do Silveira, resulting in a community characterized by freshwater taxa. The winter was characterized by higher values of the community attributes (richness, diversity and evenness). The more complex structure of S. maritimus surface provided the establishment of a richer community. The taxonomic investigation of Nitzschia and Tryblionella was more detailed, including the analysis of the microphytobenthos of the sites. The species Nitzschia papillosa Bertolli et al. was registered for the first time to science in Ilha da Pólvora and São José do Norte. The species has linear-lanceolate outline, cuneate apices and fibulae irregularly distributed, as many other species of the genus. Its main feature is the presence of rounded to squarer silica excrescences, situated on the transapical costae in the internal valve view. The study of the genus Tryblionella showed 11 species, two of them were registered for the first time in Rio Grande do Sul State and one in Southern Brazil. Besides that, two species new to science were proposed, Tryblionella Bertolli et Torgan, which is similar to T. debilis Arnott ex O’Meara in light microscopy, but present asymmetrical transapical ribs in scanning electron microscopy, and T. Bertolli et al. which presents an ornamentation pattern similar to a lace texture in the valve face. The species of Tryblionella and N. papillosa occurred concomitantly in the epiphyton and microphytobenthos, evidencing the interaction between both communities, promoted by the environment dynamics.

Diatomáceas são importantes constituintes do epifíton em ambientes costeiros. Estratégias de fixação conferem a estas algas vantagem adaptativa, no entanto, as mesmas estão sujeitas às variações ambientais, podendo responder com alterações da composição e estrutura da comunidade. Embora a relação entre epifíton e substrato seja pouco compreendida, a arquitetura do substrato parece influenciar na comunidade aderida. A composição, estrutura e variação sazonal de diatomáceas epifíticas foram avaliadas em ambientes de marismas no estuário da Lagoa dos Patos, sul do Brasil. Três sítios foram amostrados, Saco do Silveira, Ilha da Pólvora e São José do Norte, distantes 36, 18 e 9 km do oceano Atlântico, respectivamente. O epifíton aderido à Spartina alterniflora Loisel., Spartina densiflora densiflora Brogn., Scirpus maritimus L. e Juncus kraussii Hochst. foi removido dos substratos com lâmina metálica, oxidado e montado em lâminas permanentes para a análise das diatomáceas. Ao total cento e vinte e sete táxons foram encontrados, destacaram-se pelo maior número de espécies os gêneros Navicula Bory, Nitzschia Hassall e Tryblionella W. Smith. A sazonalidade, espacialidade, salinidade e tipo de substrato tiveram influência na composição e estrutura da comunidade. A maior distância da desembocadura do estuário proporcionou uma maior influência de águas continentais no sítio Saco do Silveira, resultando na formação de uma comunidade caracterizada pela presença de táxons dulciaquícolas. O período de inverno se caracterizou por maiores valores dos atributos da comunidade (riqueza, diversidade e equitabilidade). A maior complexidade da superfície de Scirpus maritimus proporcionou a formação de uma comunidade epifítica mais rica. A investigação taxonômica de Nitzschia e Tryblionella foi aprofundada, analisando-se também o microfitobentos da região. A espécie Nitzschia papillosa Bertolli et al. foi registrada pela primeira vez para a ciência, ocorrendo no epifíton e microfitobentos dos sítios Ilha da Pólvora e São José do Norte. A espécie possui formato linear-lanceolado, ápices cuneados e fíbulas irregularmente distribuídas como várias espécies do gênero, sua característica diagnóstica é a presença de excrecências de sílica arredondadas a quadradas situadas na costa transapical interna das valvas. O estudo do gênero Tryblionella revelou a presença de 11 espécies, duas foram registradas pela primeira vez para o Rio Grande do Sul e uma para o sul do Brasil. Além disso, duas espécies novas para a ciência são propostas, Tryblionella Bertolli et Torgan, espécie semelhante a T. debilis Arnott ex O’Meara em microscopia óptica, mas que apresenta costelas transapicais assimétricas em microscopia eletrônica, e Bertolli et al., espécie que apresenta um padrão de ornamentação na face valvar semelhante à trama de uma renda. As espécies de Tryblionella e N. papillosa ocorreram concomitantemente no epifíton e no microfitobentos, evidenciando a interação entre as duas comunidades, promovida pela dinâmica do ambiente. / Diatoms are an important component of the epiphyton in coastal environments. The strategies of attachment provide adaptive advantages to these algae; however, they are susceptible to the environmental fluctuations, responding to them with changes in the community composition and structure. Although the relationship between epiphyton and substrate is poorly understood, the architecture of the substrate seems to influence the attached community. The composition, structure and seasonal variations of the epiphytic diatoms were evaluated in Patos Lagoon salt marshes. Three sampling sites were defined, Saco do Silveira, Ilha da Pólvora and São José do Norte, distant 36, 18 and 9 km from the Atlantic Ocean, respectively. The epiphyton attached to Spartina alterniflora Loisel., Spartina densiflora densiflora Brogn., Scirpus maritimus L. e Juncus kraussii Hochst. was scraped with metal blade, oxidized and mounted on permanent slides for the analysis of the diatoms. A total of a hundred and twenty seven taxa were found. The genus Navicula Bory, Nitzschia Hassall e Tryblionella W. Smith showed the highest number of species. The seasonality, spatiality, salinity and substrate influenced the composition and structures of the community. The higher distance of the estuary mouth provided a higher influence of continental waters in the site Saco do Silveira, resulting in a community characterized by freshwater taxa. The winter was characterized by higher values of the community attributes (richness, diversity and evenness). The more complex structure of S. maritimus surface provided the establishment of a richer community. The taxonomic investigation of Nitzschia and Tryblionella was more detailed, including the analysis of the microphytobenthos of the sites. The species Nitzschia papillosa Bertolli et al. was registered for the first time to science in Ilha da Pólvora and São José do Norte. The species has linear-lanceolate outline, cuneate apices and fibulae irregularly distributed, as many other species of the genus. Its main feature is the presence of rounded to squarer silica excrescences, situated on the transapical costae in the internal valve view. The study of the genus Tryblionella showed 11 species, two of them were registered for the first time in Rio Grande do Sul State and one in Southern Brazil. Besides that, two species new to science were proposed, Tryblionella Bertolli et Torgan, which is similar to T. debilis Arnott ex O’Meara in light microscopy, but present asymmetrical transapical ribs in scanning electron microscopy, and T. Bertolli et al. which presents an ornamentation pattern similar to a lace texture in the valve face. The species of Tryblionella and N. papillosa occurred concomitantly in the epiphyton and microphytobenthos, evidencing the interaction between both communities, promoted by the environment dynamics.

Microphytobenthos (MPB), a mixed community of microscopic, photosynthetic organisms, algae and cyanobacteria, inhabiting the top few millimetres of bottom sediment, is a key component of intertidal mudflats. It accounts for a significant proportion of estuarine primary production, forms the base of the food chain and influences sediment distribution and resuspension (through production of extracellular polymeric substances (EPS)). Diatoms dominate the microphytobenthos community in the mid-latitudes of the Northern Hemisphere. Estuarine sediments, are a sink for metal contaminants derived from fluvial, marine and atmospheric sources. Whilst metal releases to estuaries have declined in recent years due to increased regulation and declining industrial activity, metals previously discharged and which are now locked up in saltmarsh sediments remain a concern. For example, there are indications that saltmarshes are already being eroded, due to climate change related sea level rise, in some locations. This erosion may result in the redistribution of historically contaminated sediment to locations, such as the mudflats, where it is more available to biota, such as the MPB. In addition to causing redistribution, climate change effects, such as increasing temperatures and storminess, may also alter the bioavailability of metals to MPB. Increased concentrations of metals within the MPB could potentially increase their transfer to higher organisms through the food chain with potential impacts for biota. Whilst planktonic algae have been well studied with respect to metal uptake from the water column, there has been little research involving MPB and uptake of metals from sediment. The extent to which contaminant uptake by microphytobenthic algae occurs and under what conditions is therefore poorly understood. The research presented uses laboratory, mesocosm and field studies, to gain an understanding of processes governing metal bioavailability and mechanisms for uptake from sediment to the diatoms of the MPB under the complex and variable conditions of intertidal mudflats. A laboratory study using a single diatom species Cylindrotheca closterium found that uptake of cadmium (Cd) varied with sediment properties revealing the importance of sediment particle size and organic matter content in metal bioavailability to diatoms. Additionally, this study showed that the presence of diatoms altered Cd partitioning between sediment, overlying and pore water. Specifically there was an increase in Cd in the overlying and pore water when diatoms were present, indicating that diatoms mobilise metals from the sediment to the water column potentially increasing metal bioavailability to other biota. A study was conducted using an intertidal mesocosm to increase the realism of the study system and examine uptake to a natural MPB community. Diatoms were found to have higher concentrations of all the metals analysed (except tin) than other types of algae (filamentous and sheet macroalgae), confirming their importance as a study organism with respect to metal uptake and potential mobilisation through the food chain. Sediment disturbance was shown to increase metal uptake (iron, aluminium, vanadium and lead) from the sediment to algae. This is of concern due to predicted increases in storminess which are likely to increase sediment disturbance, with the likelihood that uptake of metals to diatoms will increase in the future. However, there were also indications of an antagonistic effect of temperature on disturbance, whilst disturbance increased bioavailability and uptake, increasing temperatures reduced uptake of some metals. This highlights the importance of considering the effects of multiple stressors in complex systems. Field studies showed that concentrations of some metals were related to their position on the mudflat whilst others were related to sampling date, indicating that there may be seasonal controls, such as to the presence of greater diatom biomass in spring and autumn, on metal uptake from the sediment. The research conducted has increased understanding of metal uptake to microphytobenthic diatoms from sediment and the influence they have in transferring metals from sediment to water, however the research also raises a number of new questions. For example, there appeared to be a link between sediment organic matter content and bioavailability of metals to diatoms, although the relative contribution of the diatoms, other algae, cyanobacteria and EPS to the sediment organic matter warrants further investigation. Furthermore, it has shown that the use of laboratory and mesocosm studies for this type of research can produce similar outcomes to those observed in the field but under more controlled and easily manipulated conditions, although field studies will continue to be vital in improving understanding of metals availability and transfer.

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.

Les zones côtières ne sont prises en compte dans les budgets globaux de CO2 atmosphérique que depuis peu. Il s’avère que bien qu’elles ne représentent globalement que de faibles superficies, les flux de carbone et de nutriments y sont très significatifs à l’échelle globale. On sait peu de chose sur le comportement des écosystèmes lagunaires vis-à-vis du CO2 et, encore moins des zones intertidales où les échanges avec l’atmosphère ont lieu alternativement avec l’eau et le sédiment. Les objectifs de cette étude ont été d’une part, d’établir le bilan de carbone échangé entre la lagune d’Arcachon, l’atmosphère et le milieu terrestre, et d’autre part de mettre en relation ces flux avec la production nette de l’écosystème (NEP) afin de mieux caractériser le statut métabolique de celle-ci ainsi que les facteurs environnementaux clés. Pour cela, nous avons mis en place pour la première fois et à différentes saisons et stations, des mesures directes de flux de CO2 par Eddy Corrélation, une méthode fonctionnant en continu pendant l’immersion et l’émersion. En parallèle, les apports de carbone terrestre sous ses différentes formes ont été quantifiés par un suivi annuel sur 9 rivières alimentant la lagune. L’export total de carbone par le bassin versant à travers les eaux de surface des rivières est estimé à 116 t C km-2 an-1 dont 39% est exporté à la lagune sous forme organique dissoute (DOC) du fait de la prédominance de podzols dans le bassin versant. La forte minéralisation de la matière organique terrestre dans les sols et eaux souterraines sursature largement les eaux en CO2 et l’export sous forme de carbone inorganique dissoute (DIC) représente environ 21%. La formulation d’un modèle mathématique, le « StreamCO2-DEGAS », basé sur les mesures de pCO2, de concentrations et de compositions isotopiques en DIC a permis de montrer que 43% de l’export total de carbone était dégazé sous forme de CO2 depuis les rivières vers l’atmosphère, réduisant alors le flux net entrant dans la lagune à 66 t C km-2 an-1. Concernant la mesure de flux verticaux, l’analyse cospectrale ainsi que les résultats obtenus en adéquation avec les contrôles physiques et biologiques aux différentes échelles tidale, diurne et saisonnières, ont permis de valider la méthode de l’Eddy Covariance en zone intertidale. Sur l’ensemble de la période de mesures, les flux de CO2 étaient faibles, variant entre -13 et 19 µmol m-2 s-1. Des puits de CO2 atmosphérique à marée basse le jour ont été systématiquement observés. Au contraire, pendant l’immersion et à marée basse la nuit, des flux positifs ou négatifs ou proche de zéro ont été observés suivant la saison et la station étudiées. L’analyse concomitante des flux de CO2 et des images satellites du platier à marée basse le jour a clairement permis de discriminer l’importance relative des deux cycles métaboliques distincts des principaux producteurs primaires avec (1) les herbiers de Zostera noltii à cycle annuel long, dominant la NEP en été et en automne à la station la plus centrale et (2) les communautés microphytobenthiques, dominant la production primaire brute (PPB) au printemps à la même station et en automne au fond du bassin. Un recyclage rapide de cette production durant l’immersion et l’émersion a aussi clairement été mis évidence. Au vue des différents résultats, la technique d’Eddy Covariance utilisée en zone intertidale laisse envisager d’intéressantes perspectives en termes de connaissances sur les budgets de carbone et les processus écologiques et biogéochimiques dans la zone côtière. / The coastal zone is only taken into account since recently in global carbon budgeting efforts. Although covering globally modest surface areas, carbon and nutrient fluxes in the coastal zone appear significant at the global scale. However, little is known about the CO2 behaviour in lagoons and even less in intertidal zones where exchanges with the atmosphere occur alternatively with the water and the sediment. The purposes of this work are, on one hand, to establish the carbon budget between the Arcachon lagoon, the atmosphere and the terrestrial watershed and on the other hand, to link these fluxes with the net ecosystem production (NEP) and better characterize its metabolic status along with the relevant environmental factors. For the first time, CO2 flux measurements by Eddy Correlation have been carried out at different seasons and stations in the tidal flat. In parallel, the total terrestrial carbon export from river waters has been quantified throughout a complete hydrological cycle in nine watercourses flowing into the lagoon. The total carbon export from the watershed through surface river waters is estimated at 116 t C km-2 yr-1 on which 39% is exported to the lagoon as dissolved organic carbon (DOC) owing to the predominance of podzols in the watershed. Intense organic matter mineralization in soils and groundwaters largely over-saturate river waters in CO2 on which export accounts for 21% as dissolved inorganic carbon (DIC). The mathematical “StreamCO2-DEGAS” model formulation based on water pCO2, DIC concentrations and isotopic composition measurements permits to show that 43% of the total carbon export was degassed as CO2 from the riverine surface waters to the atmosphere, lowering then this latter to 66 t C km-2 yr-1. With respect to the CO2 flux measurements in the lagoon, cospectral analysis and the well accordance of results with physical and biological controls at the tidal, diurnal and seasonal time scales permit to validate the Eddy Correlation technique over tidal coastal zone. CO2 fluxes with the atmosphere, during each period, were generally weak and ranged between -13 and 19 µmol m-2 s-1. Low tide and daytime conditions were always characterized by an uptake of atmospheric CO2. In contrast, during the immersion and during low tide at night, CO2 fluxes where either positive or negative, or close to zero, depending on the season and the site. The concomitant analysis of CO2 fluxes with satellite images of the lagoon at low tide during the day clearly discriminate the relative importance of the two distinct metabolic carbon cycling involving the main primary producers, i.e. (1) the Zostera noltii seagrass meadow predominance on the NEP in autumn and summer in the more central station, with an annual cycling and (2) the microphytobenthos community predominance on the gross primary production (GPP) in spring at the same station and in autumn in the inner part of the bay where a rapid carbon cycling during the immersion and the emersion was clearly highlighted. The different results obtained with the Eddy Correlation technique over tidal flats opens interesting perspectives on the knowledge of the carbon budget and the biogeochemical and ecological processes within the coastal zone.