Dans le bassin d’Arcachon, le crustacé thalassinidé Upogebia pusilla habite préférentiellement les vasières intertidales colonisées par les zostères naines (Zostera noltei) où il trouve la stabilité sédimentaire indispensable à l’établissement durable de son terrier. Du fait de la profondeur de ce dernier (> 30 cm) et de sa grande mobilité, cette espèce ingénieure a souvent été négligée dans les études antérieures ayant pour objectif de mieux comprendre le rôle des communautés macro-benthiques dans le fonctionnement des herbiers de phanérogames et les conséquences de leur régression rapide. Ce manuscrit présente une étude intégrée du rôle d’U. pusilla dans le fonctionnement de son écosystème en s’attachant particulièrement à caractériser et quantifier les relations entre (1) ses différentes activités (fouissage, ventilation, locomotion, …), (2) les modes de bioturbation qui en résultent et (3)leurs impacts respectifs sur la dynamique biogéochimique sédimentaire. Ce travail montre qu’U. pusilla engendre un remaniement et une bioirrigation intenses de la matrice sédimentaire qui l’entoure. Sa présence stimule ainsi fortement la reminéralisation de la matière organique sédimentée et les échanges de solutés à travers l’interface eau-sédiment.Bien que l’influence d’U. pusilla sur ces processus écologiques et biogéochimiques soit très dépendante des conditions environnementales (e.g., saisonnalité, prévalence parasitaire),l’ensemble de mes résultats suggère que le déclin progressif de ses populations, conséquence directe de la dégradation de son habitat, est susceptible de fortement altérer le fonctionnement global des écosystèmes du bassin d’Arcachon. / In Arcachon bay, the endobenthic thalassinid crustacean Upogebia pusilla is tightly associated with the intertidal dwarf grass Zostera noltei providing the sediment stability required for the construction of (semi-)permanent burrows. Because of the depth and complex architecture of their burrow (> 30 cm), this high mobile engineer species have been largely ignored in previous studies aiming at better understanding the role of macrobenthic communities in the functioning of seagrass ecosystems and the consequences of their rapid decline. This manuscript presents an integrated study regarding the role played by U. pusillain the functioning of its ecosystem, with particular emphasis on the characterisation and quantification of the relationships between (1) its different activities (burrowing, ventilating,walking…), (2) both bioturbation modes and rates and (3) their respective impacts on the sedimentary biogeochemical dynamics. This work shows that mud shrimp activity leads tohigh mixing and bioirrigation of the surrounding sediment matrix, thus strongly enhancing organic matter mineralisation processes and solute exchanges across the sediment-water interface. Although the influence of U. pusilla on ecological and biogeochemical processes largely depends on environmental conditions (e.g., seasonality and parasitism), altogether my results suggest that the gradual decline of its population in Arcachon bay, as a direct consequence of benthic habitat degradation, may greatly alter the overall functioning of this vulnerable marine ecosystem.

L’objectif de cette thèse concerne la quantification des flux benthos-pélagiques dans une lagune soumise à un régime climatique tropical rythmé de périodes humides et périodes sèches. La lagune de Terminos, située au sud du golfe du Mexique est le plus vaste écosystème laguno-estuarien du Mexique (2000 km2). Du fait de sa faible profondeur (3.5 m en moyenne), les processus benthiques sont sensés participer activement à l’ensemble du cycle biogéochimique de cet Ecosystème. Les mesures de flux benthiques ont eu lieu au cours de un réseau de 13 stations pendant une saison sèche (mars 2009 et 2010) et une saison humide (octobre 2009 et novembre 2010). Quatre stations ont fait l’objet de mesures plus fréquentes du 2008 au 2010. Des incubations ex-situ de carottes de sédiment prélevées ont permis de mesurer la variabilité spatio-temporelle des taux de respiration benthique (SOD) et des flux de sels nutritifs. Les SOD sont significativement différents entre les périodes sèches et humides (1327±161 et 2248±359 µmol m-2 h-1 respectivement). Les flux de silicates sont significativement plus importants pendant la saison des pluies (89.4±15.9 µmol m-2 h-1) que pendant la saison sèche (46.5±11.4 µmol m-2 h-1). Les flux de phosphates, faibles tout au long des périodes étudiées, n’ont pas montré de différence significative. Les flux d’azote dissous (DIN) sont de même intensité mais de sens opposé (2.9±18.8 µmol m-2 h-1 et 24.3±7.3 µmol m-2 h-1). Ces flux caractérisés par un fort signal saisonnier sont fortement corrélés avec les caractéristiques biogéochimiques des sédiments (Corg, N et chloropigments) et contribuent significativement au bilan du carbone et des éléments associés. / The goal of this study concerns the quantification of sediment-water fluxes in a tropical lagoon under climatic forcing regulated by successive dry and wet periods. Terminos lagoon on the South coast of Gulf of Mexico (Campeche sound) is a shallow (3.5 m) but vast estuarine system (2000 km2) where the sediments are supposed to contribute largely to the overall biogeochemical cycling. Benthic flux measurements were performed twice over a network of 13 stations during dry (March 2009 and 2010) and wet periods (October 2009 and November 2010). A selection of 4 stations from this network were visited more frequently between 2008 and 2010. Sediment Oxygen Demand (SOD) and nutrient fluxes were measured through ex-situ incubations of sediment cores sampled manually. SOD were significantly different between both dry and wet seasons (1327±161 and 2248±359 µmol m-2 h-1 respectively). Silicates fluxes were significantly more intense during the wet season (89.4±15.9 µmol m-2 h-1) than during the dry one (46.5±11.4 µmol m-2 h-1). Phosphate fluxes, low during all periods did not show a temporal trend. Finally DIN fluxes showed a net uptake during the wet season (2.9±18.8 µmol m-2 h-1) and conversely an efflux during the dry season (24.3±7.3 µmol m-2 h-1). These fluxes depicted a pronounced seasonal signal, showed a significant correlation to sediment characteristics (Corg, N and chloropigments) and finally contributed to the overall carbon and nutrient budget of the lagoon.

À l'interface bentho-pélagique, les herbiers marins présentent une multitude de rôles écosystémiques. Historiquement, les scientifiques et décideurs de La Réunion se sont focalisés sur l'écosystème récifal. Néanmoins, des prairies monospécifiques à Syringodium isoetifolium sont présentes de manière pérenne (3 hectares) au sein du complexe récifal de l'Ermitage / La Saline (côte ouest). L'objectif principal de cette étude était d'apporter les premières données sur l'écologie de ces herbiers marins. Ainsi, une approche pluridisciplinaire a été développée : 1. L'étude de la dynamique spatiale du paysage herbier sur 65 ans (dès 1950), et à l'échelle saisonnière (2013-2015) qui a permis de définir le rôle majeur des forçages hydrodynamiques et de l'eutrophisation. 2. L'analyse de la productivité de l'écosystème herbier et sa réponse métabolique face à des apports nutritifs, révèle des bilans métaboliques opposés (autotrophie/hétérotrophie) en fonction des conditions environnementales, ainsi qu'un rôle de tampon sur les flux de nutriments. 3. Des analyses isotopiques (δ13C et δ15N) ont permis d'identifier les sources de matière entrant dans l'écosystème et alimentant les réseaux trophiques associés aux herbiers. L'étude a permis d'établir un lien trophique entre Holothuria leucospilota et les herbiers marins ainsi qu'un rôle essentiel dans le maintien des populations de poisson herbivores récifaux. 4. Des enquêtes locales ont révélé une méconnaissance de cet écosystème malgré leur potentiel économique et écologique. À la lumière de ces travaux de thèse, la prise en considération des herbiers marins dans la gestion du milieu marin réunionnais est nécessaire. / Located at the benthos-pelagos interface, seagrass beds have many ecosystemic roles such as coastal protection or biodiversity. Historically, scientists and decision-makers at Reunion Island have been focusing on reef ecosystems. However, for several decades, monospecific (Syringodium isoetifolium) seagrass beds have been observed (3 hectares – 2013) within Ermitage / La Saline reef (West coast). The main objective of this study was to give the first data on seagrass ecology at Reunion Island. Therefore, a multi-disciplinary study was developed. First, seascape ecology of seagrasses is analyzed at decadal (since 1950) and seasonal scales (2013-2015). Physical settings (swell) and eutrophication were driving factors on the spatial dynamics of seagrass beds. Second, seagrass community metabolism and response to nutrient loads (nitrate and phosphate) show variations in metabolic budget (autotrophy to heterotrophy) and make seagrass beds a nutrient sink following the environmental conditions. Third, stable isotope analysis (δ13C and δ15N) identified sources of particulate matter entering the ecosystem and fueling food webs. The trophic roles of seagrass beds are assessed for echinoderm and herbivorous fish communities. This study highlighted a trophic link between seagrass and Holothuria leucospilota, and proved some species to be heavily dependent on seagrass ecosystem (Leptoscarus vaigiensis, Siganus sutor). Finally, interviews showed a lack of knowledge about this ecosystem despite crucial economic and ecologic roles. Considering their major functions, seagrass beds have to be considered in future management of the coastal marine systems at Reunion Island.

La production sonore biologique, étudiée par acoustique passive, doit être évaluée comme méthode complémentaire pour l’étude des effets des perturbations anthropiques sur les milieux côtiers.Alors que les sons émis par les mammifères marins et les poissons sont largement documentés, ceux issus des invertébrés benthiques restent peu décrits, même si ces derniers peuvent assurer des fonctions-clés dans les systèmes marins. L’enjeu principal de cette thèse était d’évaluer la pertinence de l’utilisation de l’acoustique passive comme outil écologique en s’appuyant sur la biophonie des invertébrés benthiques d’habitats côtiers tempérés et plus particulièrement en prenant comme habitat-modèle les bancs de maërl de la rade de Brest. Nous avons mis en évidence l’existence d’espèces sonifères remarquables qui constituent de bons candidats pour leur suivi en milieu naturel. Ces travaux ont de plus montré l’importante contribution de certains invertébrés benthiques dans le paysage sonore sous-marin, encourageant à ne plus imputer systématiquement les sons benthiques uniquement aux « crevettes claqueuses ». Le deuxième volet de cette thèse a montré que les variations de production sonore des invertébrés benthiques, à l’échelle individuelle ou collective, offrent des informations précieuses sur la mise en évidence de stress tels qu’un bloom d’algues toxiques ou l’impact du dragage. Ainsi, le nombre de mouvements sonifères des coquilles Saint-Jacques est doublé en présence de fortes concentrations d’algues toxiques, et le paysage sonore des bancs de maërl fortement pêchés est trois fois plus silencieux et moins complexe que celui du maërl préservé. Les résultats de ce travail de thèse, discutés dans un contexte de développement d’outils pour l’évaluation de l’état de santé des écosystèmes marins, permettent l’émergence de nouvelles hypothèses de travail en écologie marine. / Biological sound production, as studied by passive acoustics, should be considered as a complementary method to study the effect of anthropogenic disturbances on coastal systems. While sounds emitted by marine mammals and fish are well documented, those from benthic invertebrates are poorly described, although they can play key roles in marine ecosystems. The main goal of this PhD work was to evaluate the suitability of passive acoustics as an ecological tool based on sound production by benthic invertebrates living in temperate coastal habitats, and particularly in maerl beds of the Bay of Brest.We highlighted the existence of interesting soniferous species that appear to be good candidates to monitor in the field. This work also showed the important contribution of some benthic invertebrates to the underwater soundscape, suggesting that benthic sounds should not be attributed only to snapping shrimps. The second part of this PhD thesis emphasized that changes in benthic invertebrate sound production, at individual or collective scales, provides valuable information on the detection of stress such as a toxic algal blooms or the impact of dredging. Thus, the number of soniferous movements made by the great scallop doubles in the presence of high concentrations of toxic algae, and the soundscape of heavily fished maerl beds is three times quieter and less complex than preserved ones. The results of this PhD thesis, which are discussed in the context of tool development for the assessment of marine ecosystem health, raise new working hypotheses in marine ecology.

Les estuaires, situés à l’interface entre les domaines continental et marin, constituent des zones essentielles dans les échanges de matières. Ils jouent dès lors un rôle capital pour les cycles biogéochimiques et biologiques et subissent, par ailleurs, des pressions climatiques et anthropiques croissantes depuis plusieurs décennies. Le présent travail a été focalisé sur les peuplements benthiques et pélagiques présents dans la partie fluviale (Garonne et Dordogne) de l’estuaire de la Gironde, zone àtrès faible salinité où ces peuplements n’avaient encore jamais été étudiés. Alors que la méiofaune, composée principalement de Nématodes, s’est avérée relativement abondante dans les domaines intertidal et subtidal, le macrobenthos est apparu composé essentiellement d’Oligochètes en intertidal et complètement absent en subtidal. La grande plasticité du copépode dominant Eurytemora affinis a été confirmée, celui-ci occupant une niche écologique différente dans la partie fluviale de l’estuaire par rapport à la zone haline. L’importance de la température plutôt que la qualité du pool nutritif sur la productivité d’E. affinis a été démontrée, mettant en évidence une fois de plus la grande adaptabilité de cette espèce dans un habitat très fluctuant. L’étude de l’habitat benthique et pélagique, notamment en terme de qualité du pool nutritif disponible pour les organismes, a démontré que la contribution de la matière organique réfractaire d’origine terrestre est dominante. La contribution du micro phytobenthos à la composition de la matière organique sédimentaire et pélagique a aussi été mise en évidence. Enfin,l’étude des communautés planctoniques dans la partie fluviale de l’estuaire de la Gironde a montré que l’espèce E. affinis y occupe une position clef. / Being at the interface between continental and marine systems, estuaries are essential areas for matter exchanges. Therefore, they play a crucial role in biological and biogeochemical cycles. In addition to natural fluctuations, these systems have also undergone increasing climate and anthropogenic pressures for several decades. The present work focused on the benthic and pelagic assemblages in the fluvial section (Garonne and Dordogne rivers) of the Gironde estuary, a low salinity area where these communities had never been studied. Meiofauna, mainly composed ofnematodes, was found in relatively high abundance in both intertidal and subtidal zones.Macrozoobenthos was essentially composed of oligochaetes in the intertidal, while it was totally absent in the subtidal areas. The high plasticity of the dominant copepod Eurytemora affinis was confirmed, with a different ecological niche in the freshwater section of the estuary compared to the haline area downstream. The importance of temperature rather than the quality of the nutrient pool on the productivity of E. affinis was demonstrated, thereby confirming the great adaptability of thisspecies to a highly fluctuating habitat. Study of benthic and pelagic habitat, especially in terms of quality of the nutrient pool available to the organisms, showed that the contribution of refractoryorganic matter with a terrestrial origin is dominant. A significant contribution of microphytobenthos to the composition of sedimentary and pelagic organic matter was also highlighted. Finally, the study of planktonic communities in the fluvial part of the Gironde estuary showed that the species E. affinis occupies a key position in this part of the estuary.

The trophic state of lakes is commonly defined by the concentration of nutrients in the water column. High nutrient concentrations generate high phytoplankton production, and lakes with low nutrient concentrations are considered low-productive. This simplified view of lake productivity ignores the fact that benthic primary producers and heterotrophic bacteria can be important basal producers in lake ecosystems. In this thesis I have studied clear-water and brown-water lakes with respect to primary production, respiration and bacterial production based on allochthonous organic carbon. These processes were quantified in pelagic and benthic habitats on temporal and spatial scales. I also calculated the net ecosystem production of the lakes, defined as the difference between gross primary production (GPP) and respiration (R). The net ecosystem production indicates whether a lake is net heterotrophic (GPP < R), net autotrophic (GPP > R) or in metabolic balance (GPP = R). Net heterotrophic lakes are sources of carbon dioxide (CO2) to the atmosphere since respiration in these lakes, by definition, is subsidized by an external organic carbon source. External organic carbon is transported to lakes from the terrestrial environment via inlets, and can serve as a carbon source for bacteria but it also limits light availability for primary producers by absorbing light. On a seasonal scale, four of the clear-water lakes studied in this thesis were dominated by primary production in the soft-bottom benthic habitat and by respiration in the pelagic habitat. Concentrations of dissolved organic carbon (DOC) were low in the lakes, but still high enough to cause the lakes to be net heterotrophic. However, the lakes were not low-productive due to the high production in the benthic habitat. One of the clear-water lakes was studied also during the winter and much of the respiration under ice was supported by the benthic primary production from the previous summer. This is in contrast to brown-water lakes where winter respiration is suggested to be supported by allochthonous organic carbon. By studying lakes in a DOC gradient (i.e. from clear-water to brown-water lakes) I could draw two major conclusions. The lakes became less productive since benthic primary production decreased with increasing light extinction, and the lakes became larger sources of CO2 to the atmosphere since pelagic respiration was subsidized by allochthonous organic carbon. Thus, lake carbon metabolism can have an important role in the global carbon cycle due to their processing of terrestrial organic carbon and to their possible feedback effects on the climate system.

Oyster reefs are declining worldwide, as well as the economic and ecological value of oysters to their respective systems. Numerous restoration efforts have been undertaken in hopes of re-establishing these shellfish populations. This study evaluated a restoration project within the Guana Tolomato Matanzas estuary in northeast Florida, U.S.A., to investigate community structure as well as seasonal patterns in species abundance and diversity of juvenile fish and benthic macrofauna within restored and unrestored intertidal habitats along the Guana Peninsula. The first objective was to determine whether the artificially created reefs provided similar quantity and diversity of benthic macrofauna as adjacent unrestored habitats. The second objective was to specifically characterize resident and transient fish assemblages associated with the artificial reef and adjacent unrestored habitats. Benthic macrofauna were quantified using plastic settlement trays deployed in triplicate at each site and sampled monthly for a year. Community structure differed by habitat, confirmed through an analysis of similarity. High abundances of Petrolisthes armatus on the natural reef sites largely contributed to dissimilarity in community composition between the natural reef and the restored sites. Fish assemblages were quantified using monthly seine and gill nets set adjacent to restored and unrestored intertidal habitats. Diversity was similar between the restored and unrestored sites, however, there was very little species overlap between the two sites. The dominance of post-larval and juvenile spot (Leiostomus xanthurus), anchovies (Anchoa mitchelli and A. hepsetus) and mullet (Mugil sp.) led to high density and low diversity in seine collections during the winter months. Overall, the gill net survey did not show any patterns in fish abundance associated with particular habitats in the area, however this is the first assessment in this region using gill netting. Constructed oyster reefs created immediate habitat for resident species and enhanced habitat value compared to unstructured mud bottom.

The purpose of this study was to analyze the water quality of the micro-basin of Córrego da Areia Branca, through analysis of hydrologic (temperature, dissolved oxygen, pH, conductivity and clarity) and analysis of the benthic community of macroinvertebrates. Samplings were carried out at each fifth day in three distinctive sites of the micro-basin, from September 2005 to January 2006. The macroinvertebrates were identified at maximum level of family. It was carried out analysis of diversity and similarity to compare communities and Principal Component Analysis (PCA) of biotic and hydrologic factors. Seven families were found: Chironomidae, Tipulidae, Simuliidae, Psychodidae, Glossiphoniidae, Tubificidae and Lymnaeidae. The family Chironomidae was the most abundant in the three sites sampled. The origin (Site 1) showed the best water quality compared as the other sites due to riparian vegetation around. The Site 2, located at 500m from the origin, had decreased water quality, however, showed the highest diversity. The worst water quality was observed in Site 3 which had near zero dissolved oxygen coupled with the high conductivity values (average 537,2 S/cm). In such site, the taxons Chironomus, Psychodidae and Tipulidae were the most abundant. Conductivity and water clarity were the principal factors determining the low diversity of macroinvertebrates in the micro-basin. The findings of this study can be used as a baseline for further environmental monitoring for the future recovery of the Córrego da Areia Branca micro-basin. / Este trabalho teve como objetivo analisar a qualidade da água da microbacia do Córrego da Areia Branca por meio de análises de variáveis hidrológicas (temperatura, oxigênio dissolvido, pH, condutividade e transparência) e da composição da comunidade de macroinvertebrados bentônicos. Amostragens foram realizadas quinzenalmente no período de setembro de 2005 a janeiro de 2006 em três trechos distintos da microbacia, incluindo a nascente. Os macroinvetebrados foram identificados ao nível máximo de família. Foram efetuadas análises de diversidade e eqüidade para comparar as comunidades e Análise de Componentes Principais com os fatores bióticos e abióticos. Sete famílias foram amostradas: Chironomidae, Tipulidae, Simuliidae, Psychodidae, Glossiphoniidae, Tubificidae e Lymnaeidae. A família Chironomidae foi dominante nos três pontos de amostragens. A nascente apresentou melhor qualidade da água em relação aos outros dois trechos por apresentar vegetação ripária em seu entorno. O ponto 2, localizado a 500m a da nascente apresentou reduzida qualidade da água, entretanto, mostrou maior diversidade. O ponto 3 apresentou pior qualidade da água, com valores de OD próximos de 0 e condutividade média de 537,2 S/cm. Neste trecho, os táxons Chironomus, Psychodidae e Tipulidae foram os mais abundantes. A condutividade e a transparência da água foram os principais fatores determinando a baixa diversidade na microbacia. Os resultados deste estudo poderão servir como base para futuro monitoramento ambiental visando a recuperação da microbacia do Córrego da Areia Branca.

The biostratigraphy and isotope stratigraphy of the upper Aptian to lower Cenomanian interval including oceanic anoxic events OAE1b, 1c and 1d are investigated in ODP Site 763, drilled on the Exmouth Plateau offshore northwest Australia. Benthic foraminifera suggest that Site 763 was situated in outer neritic to upper bathyal water depths (~150-600 m). OAEs of the Atlantic basin and Tethys are typically associated with organic carbon-rich black shales and δ13C excursions. However, OAEs at this high latitude site correlate with ocean acidification and/or pyrite formation under anoxic conditions rather than black shales. Ocean acidification maybe responsible for sporadic low abundances of planktic foraminifera compared to radiolarians and benthic foraminifera associated with increased volcanogenic CO2 production during the formation of the Southern and Central Kerguelen Plateaus. Sea surface temperature may have cooled to 11°C in the late Aptian but increased gradually during the Albian. The Aptian/Albian boundary is placed at a negative carbon isotope excursion associated with the lowest occurrence of Microhedbergella renilaevis, typically found within the Niveau Kilian black shale of OAE1b. Third-order sea level cycles, particularly in the middle Albian, produced cyclic changes in the abundance of inoceramid prisms that increased during inferred times of falling sea level. The late Albian OAE1c and OAE1d coincide with horizons of intense pyritization and the absence of all biocomponents suggesting the development of euxinia. Warm Tethyan waters reached the Exmouth Plateau during the latest Albian based on the presence of thermocline dwelling keeled planktic foraminifera including Planomalina buxtorfi.

No description available.