No description available.

No description available.

Large areas of mesotidal estuaries become subaerial during low tide. Here we study the effect of nutrient enrichment and several meteorological and hydrodynamic parameters on the erodability of mudflat substrates when they are emergent. We tested the impact of nutrient fertilization on tidal flat sediments over a two week period in September 2011 in Plum Island Sound, Massachusetts (USA). High resolution measurements from our experiment indicate that daily nutrient enrichment at 70 μM NO3‾ using our experimental approach does not change the critical shear stress of the muddy substrate, nor affect the concentration of chlorophyll a at the surface. Sediment erodability is instead directly related to the potential evaporation rate and to the duration of the subaerial period. Chlorophyll a concentration decreases when evaporation is high, possibly due to the downward migration of diatoms. Sediment concentrations in the water column during submergence strongly depend on bottom shear stresses triggered by tidal currents. Surprisingly, they are also related to the total evaporation that occurred in the previous emergence period. We conclude that subaerial desiccation at low tide decreases the erodability of mudflat sediments. This strengthening effect is not lost during the following submerged period, thus limiting the erosive effect of tidal currents. For the first time we show that not only subaqueous but also subaerial processes control the erodability of mudflats. Global warming and other climatic variations regulating long-term evaporation rates can therefore directly affect the stability of mudflats in mesotidal environments.

No description available.

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

Les vasières intertidales sont des environnements complexes et changeants, qui abritent des invertébrés enfouis dans le sédiment (la macrofaune benthique) et sont visités de manière saisonnière par de grands migrateurs : les oiseaux limicoles. Ce travail de recherche s’intéresse aux relations proie-prédateur entre les oiseaux limicoles et leur ressource alimentaire : la macrofaune benthique. La thèse est articulée en 8 chapitres qui présentent des études à différentes échelles spatio-temporelles : des saisons à la décennie, et de la baie à la route migratoire. Ces études sont basées sur un échantillonnage régulier des vasières intertidales du Golfe de Gascogne (France) ainsi que d’échantillonnages en mer des Wadden (Pays-Bas) et au Banc d’Arguin (Mauritanie). Les données de macrofaune (qualité, taille, densité, biomasse) sont couplées aux données de comptages de leurs prédateurs ainsi qu’à leur comportement alimentaire (reconstruction du régime alimentaire d’après les isotopes, les fécès, la modélisation ou l’observation de vidéos). Ces huit études apportent un éclairage sur l’écologie de leurs interactions (en intégrant des variables environnementales telles que le temps d’inondation, la granulométrie, la température, la production primaire, ou encore la latitude). Une attention particulière est portée à la variabilité des proies et du comportement alimentaire de leurs prédateurs, dans l’espace et le temps. Des encarts viennent illustrer pour l’un les techniques de reconstruction du régime alimentaire, pour l’autre les défenses développées par les mollusques marins, ou encore la relation entre énergie à disposition et sélection du site pour les limicoles. / Intertidal mudflats are complex ecosystems undergoing constant changes, home to infaunal invertebrates (benthic macrofauna), and migratory sites for particular birds : shorebirds. This research focuses on predator-prey interactions between shorebirds and their macrobenthic prey. The present thesis is composed of 8 chapters which illustrate different spatio-temporal scales : from seasons to the decade, and from the bay to the migratory flyway. These studies are based on regular benthic sampling of intertidal flats along the Bay of Biscay (France), as well as sampling data from the Dutch Wadden Sea and the Mauritanian Banc d’Arguin. Macrobenthic data (quality, sizes, densities, biomass) are linked with shorebird counts and data about their feeding behaviour (diet reconstruction from isotopes, faeces, modeling and video observations). These eight studies shed light on particular relationships between some prey and their predators, and the ecology of these interactions (including environmental variables such as inundation time, grain size, temperature, primary production, or even latitude). Particular attention is given to the variability of prey and predator behaviour in time and space. Inserts are included in between chapters to illustrate for instance different diet reconstruction techniques, anti-predation traits in marine molluscs, or relation between energy available and site selection in shorebirds.

Dans les vasières intertidales dominées par les diatomées, la production primaire est particulièrement forte à marée basse. Ce microphytobenthos peut être limité par les nutriments azotés en lien avec les communautés de procaryotes impliquées dans le cycle de l’azote. Ainsi, ce travail de thèse cherche, via une approche écologique, à décrire le rôle des communautés de procaryotes benthiques notamment liées au cycle de l’azote et ce, suivant différentes échelles temporelles liées aux cycles du microphytobenthos. Des échantillons de sédiment ont été prélevés dans la baie de Marennes-Oléron (Côte Atlantique, France) entre 0 et 10 cm de profondeur suivant 5 couches (0-0,5 cm, 0,5-1 cm, 1-2 cm, 2-5 cm, 5-10 cm). Différents facteurs biotiques et abiotiques ont été mesurés et mis en relation avec la production bactérienne, les activités enzymatiques et les gènes fonctionnels liés au cycle de l’azote (impliqués dans la nitrification, la dénitrification et l’anammox). De plus, la diversité bactérienne et archéenne a été évaluée par pyroséquençage 454 afin de caractériser les communautés et leurs dynamiques en lien avec les facteurs forçants biotiques et abiotiques. Dans le but d’évaluer l’influence des paramètres abiotiques et de la production du microphytobenthos, des mesures in situ ont été couplées avec des mesures en conditions semi-contrôlées. / In diatoms-dominated intertidal mudflats, at low tide the primary production is particularly high and microphytobenthos that can be limited by nitrogen-related nutrients is linked with N-related prokaryotic communities. Thus, this PhD thesis aim at describing by ecological approach, the role of benthic prokaryotic communities especially N-related ones, at various temporal scales linked to microphytobenthos life cycles. Sediment samples from Marennes-Oleron mudflat (Atlantic coast, France) were collected according to 5 layers : 0-0.5 cm, 0.5-1 cm, 1-2 cm, 2-5 cm and 5 to 10 cm below sediment surface (bsf). Various biotic (i.e. chlorophyll a) and abiotic parameters (i.e. nutrients, exopolymeric substances, water content, salinity, pH, temperature…) were recorded and linked with benthic bacterial production, enzymatic activities and N-related functional genes (i.e. implied in nitrification, denitrification, and anammox). Furthermore, the bacterial and archaeal diversity was assessed by 454 pyrosequencing in order to characterize the communities and shift in link with biotic and abiotic drivers. Aiming at evaluating the influence of abiotic parameters and microphytobenthic activities on the prokaryotic communities, in situ measurements were coupled to a semi-controlled approach.

Les vasières intertidales sont le siège d’une forte production primaire sous la forme d’un biofilmmicrophytobenthique qui se développe en surface à marée basse. Ce biofilm se compose principalement de diatomées et de bactéries hétérotrophes. Ces deux composantes sécrètent des substances polymériques extracellulaires (EPS) qui jouent différents rôles dans le biofilm. Le travail présenté s’est basé sur différentes échelles d’observation (in situ à 2 saisons, mésocosme en laboratoire, et échelle fine du biofilm en microscopie confocale) et a permis de mettre en évidence les interactions des diatomées et des bactéries à différents moments de la marée et du nycthémère. L’utilisation d’une nouvelle méthode d’extraction des EPS a permis d’éclaircir leur rôle en évitant les contaminations par les substances internes provoquées par les méthodes classiques. Les EPS colloïdales particulièrement riches en glucose s’associent au déplacement des diatomées, notamment lors d’un stress (sursalure, carence en nutriments) et sont préférentiellement consommées par les bactéries, après leur dégradation par les enzymes ou leur hydrolyse dans l’eau interstitielle. Les EPS liées au frustule, et plus particulièrement les sucres, inhiberaient le développement bactérien à proximité de la cellule algale. Elles sont surtout sécrétées lors de la mise en place du biofilm et pour protéger la cellule quand les conditions sont osmotiquement défavorables et leur richesse en protéine leur confère un potentiel intéressant pour les bactéries qui peuvent les utiliser comme substrat azoté en cas de carence. D’autres substances ont été plutôt sécrétées parles bactéries telles que les N-acétylglucosamines et les protéines colloïdales de bas poids moléculaire,certainement des enzymes bactériennes, ainsi que le glucose qui semble être associé au EPS colloïdaux des diatomées mais aussi aux EPS bactériens selon l’analyse en microscopie confocale en utilisant des lectines comme marqueurs d’EPS. / Microphytobenthic biofilms that develop at the intertidal mudflat surface are responsible of a substantialprimary production. These biofilms are composed of diatoms and heterotrophic bacteria, both excretingextracellular polymeric substances (EPS) that have various functions into the biofilm. The present thesis is basedon different observation scales that have highlighted the complex interactions between diatoms and bacteria fordifferent moment of the biofilm development (in situ at 2 seasons, in laboratory mesocosm and at the scale of thebiofilm at confocal microscopy). Furthermore, a new extraction method that avoids contamination with internalsubstances was used and provides new insights about the role of EPS. Colloidal EPS are excreted during thediatom migrations, notably in case of environmental stress (nutrient depletion, high salinity). They arepreferentially consumed by bacteria, after hydrolysis or enzymatic cleavage. Bound EPS are associated to abacterial inhibition, especially sugars. These EPS are mainly excreted during biofilm formation and also in caseof osmotic stress, if diatoms cannot migrate toward favorable slices. Some substances are associated to bacterialdevelopment, such as N-acetylglucosamine, low molecular weight proteins that probably consist of bacterialenzymes and also glucose that seems to be associated to colloidal EPS secreted by diatoms as well as bacterialEPS, when analyzing the biofilm with confocal microscopy by using lectins as EPS biomarkers.

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.