Dans le contexte actuel de changement global et particulièrement de réchauffement climatique et de pollution chimique chronique, se pose la question de la vulnérabilité des écosystèmes côtiers et notamment des populations d’invertébrés filtreurs jouant un rôle structurant dans la plupart de ces écosystèmes. Dans ces travaux de thèse, une approche couplée d’écophysiologie et de génomique fonctionnelle a été mise à profit afin de mieux comprendre les processus moléculaire, cellulaire et physiologique de réponse à une contamination chimique chronique modérée et d’évaluer la capacité à faire face à une augmentation de température chez des populations naturelles de moules bleues (Mytilus spp.) de la Rade de Brest. Les résultats obtenus révèlent qu’une contamination chronique modérée induit des réponses adaptatives au niveau subcellulaire chez les moules exposées, prévenant ainsi l’apparition de souffrances physiologiques et permettant aux populations de se maintenir dans un environnement variable. Ces réponses impliquent en particulier, une activation des mécanismes de défense cellulaire (métabolisme énergétique et défenses antioxydantes) et d’élimination des xénobiotiques. Par ailleurs, l’exposition à une augmentation de température en conditions expérimentales ne met pas en évidence de sensibilité particulière au stress thermique chez les moules provenant d’un site exposé à une contamination chronique modérée. En revanche, les résultats indiquent que ces dernières pourraient avoir une plus grande capacité à compenser grâce à des réponses adaptatives, les effets délétères générés par une augmentation de température. Cependant, le fort coût énergétique généré par la contamination chimique ainsi que les effets importants du stress thermique mis en évidence dans ces travaux indiquent que la combinaison de ces deux sources de stress pourrait provoquer des dysfonctionnements métaboliques et représenter à l’avenir, une menace pour les populations naturelles de moules bleues. Ces travaux de thèse ont également contribué au développement de nouvelles méthodologies permettant respectivement, de quantifier des contaminants environnementaux dans des tissus biologiques marins, d’étudier des réponses génomiques précoces de stress et de mesurer des paramètres physico-chimiques in situ. Ces méthodologies pourront contribuer à améliorer les performances du diagnostic de l’état de santé des populations naturelles de moules et au delà, d’espèces-sentinelles de mollusques bivalves dans un contexte de contamination chimique mais également de changements climatiques. / In the current context of chronic chemical pollution and on-going climate change, coastal ecosystems, and in particular keystone filter-feeding bivalve populations inhabiting them, appear vulnerable. In this thesis, an approach coupling ecophysiology and functional genomics was used to study the molecular, cellular and physiological responses of wild blue mussel populations of the Bay of Brest to a moderate chronic chemical contamination, and to assess the ability of these populations to face a heat stress. Results indicate a moderate chronic chemical contamination induces adaptive responses in wild mussel populations from the Brest harbour area, which prevents severe physiological disturbances and sustain long-term population survival. These responses include an activation of cellular stress response [energetic metabolism and antioxidant defences) and xenobiotic elimination mechanisms. Furthermore, experimental heat stress exposure does not highlight a higher sensitivity to a temperature increase in mussels sampled in a moderately contaminated area but suggests that these mussels could have a better ability to offset the adverse effects of heat stress thanks to adaptive responses. However, the high energetic cost of chemical contamination and the strong effects of heat stress presented in this work, suggest combined chemical and heat stress could be a future threat for wild blue mussel populations. This work also contributes to the development of new methodologies to, respectively, quantify environmental contaminants in marine biota, study early warning genomic stress responses and to survey physicochemical parameters in situ. These methodologies contribute to improving the health diagnostics of natural mussel populations and thus, appear as useful tools to assess health of bivalve sentinel species populations in biomonitoring studies, in a context of chemical contamination and climate change.

A wave energy park has been established on the Swedish west coast outside Lysekil and pioneer work about its interactions with the marine environment has been conducted. So far, little is known about the effects of offshore energy installations on the marine environment, and this thesis assists in minimizing environmental risks as well as in enhancing potential positive effects on the marine environment. The Lysekil research site is situated about two kilometres offshore and has been under development since 2005. During this time 26 “environmental devices”, without generators, consisting of a steel buoy attached via a wire to a foundation on 25 m depth have been placed out for ecological studies on macrofauna in surrounding sediments and on colonization of the foundations and the buoys. Sediment samples to examine macrofauna in the seabed have been taken during five seasons. Biomass, abundance and diversity of infauna in the test site were generally low, but higher than in a nearby control site. The species composition was typical for the area and depth. In addition to sediment analysis, the effect of wave power concrete foundations on the marine environment has been investigated by scuba diving. The surface orientation and its effect on colonization by sessile organisms was examined on the first five foundations, placed out in 2005, and observations of habitat use by fish and crustaceans were made. The results show a succession of colonization over time (three years of investigation) with a higher cover by sessile organisms on vertical surfaces. Mobile fauna abundance on and around the foundations was generally low. Three months after the deployment of the 21 new foundations in 2007, assemblages of mobile organisms were examined visually. Also here, mobile species exhibit a low density, but still higher than on surrounding soft bottoms. The edible crab used artificial holes in the foundations frequently. The foundations were placed in two different clusters, north and south, and the degree to which early recruits covered the foundations and the succession of epibenthic communities were documented during two years. Sessile organisms colonized the northern foundations more rapidly, producing a higher diversity which suggests that the placement of wave energy devices affects colonization patterns. Biofouling on buoys was examined and blue mussels, Mytilus edulis, dominated with a cover about 90%. Wave exposed buoys were particularly favoured by M. edulis which there had a higher biomass and larger shells compared to those on sheltered buoys. Biofouling on wave power buoys, independent whether these had a cylindrical or toroidal shape, was insufficient to markedly affect their energy production. Finally, the thesis incorporates a review describing wave power projects in general pointing out the need of future research on for instance no-take zones, marine bioacoustics and electromagnetic fields. The main conclusions are that large-scale renewable wave energy conversion will cause ecological impact primarily by adding new hard substrate to an area but not by harming organisms or decreasing biodiversity within wave power parks.

Chez les invertébrés benthiques marins à cycle de vie bentho-pélagique, le taux de fixation-métamorphose est l'un des facteurs déterminant du succès de recrutement et donc du renouvellement des populations. Relié à l'abondance et au comportement des stades péri-métamorphiques (larves compétentes et post-larves), le taux de fixation est régulé par l'interaction de multiples facteurs endo- et exogènes. Prérequis du fonctionnement vital des organismes hétérotrophes, la ressource trophique est un facteur exogène biotique d'importance puisqu'elle affecte leur condition physiologique. Son influence sur le recrutement n'est souvent envisagée que d'un point de vue quantitatif alors que les recherches menées en laboratoire attestent de l'importance de sa qualité lipidique. Dans ce contexte, la présente étude a pour objectif principal d'évaluer l'influence de la qualité de la ressource trophique sur le succès de recrutement et implique la moule bleue (Mytilus edulis, L 1758) comme modèle biologique. La recherche se concentre sur les sources de nourriture potentiellement disponibles pour les stades péri-métamorphiques soit, le plancton et le biofilm. Une emphase est portée aux acides gras polyinsaturés (PUFA) et essentiels (EFA), dont le caractère indispensable aux organismes aquatiques est largement admis. De plus, les études menées sur le recrutement décrivent un découplage bentho-pélagique entre larves et recrues, une importante variabilité spatio-temporelle de la fixation, ainsi qu'une synchronisation du pic de fixation. La disponibilité en larves et le comportement sont souvent les facteurs incriminés, mais l'origine de tels phénomènes demeure encore incertaine. La présente étude propose donc d'apporter des éléments de réponse supplémentaires en fournissant une analyse fine de la variabilité spatio-temporelle au cours de l'ontogénie larvaire. Ce projet est constitué de trois grands axes de recherche dans lesquels nous définissons la fixation comme le processus par lequel les individus s'associent au substrat, et le recrutement comme le nombre d'individus présents à un temps t de la vie benthique : i) Considérant la théorie de " match/mismatch " de Cushing, nous posons les hypothèses que la concentration en EFA dans la nourriture influence les succès de fixation et de recrutement. Nous avons suivi simultanément le développement larvaire et les conditions trophiques pendant deux saisons de reproduction successives (2007 et 2008); ii) Considérant le biofilm comme une ressource trophique potentielle, nous posons les hypothèses que le taux de fixation augmente avec l'âge du biofilm et son contenu en EFA. Nous avons conditionné et caractérisé finement des biofilms en milieu naturel afin de tester leur influence sur le succès de fixation des moules; iii) Considérant le rôle important du comportement et des conditions physiologiques des stades péri-métamorphiques, nous posons les hypothèses d'une importante variabilité spatiale à petite échelle, d'un découplage bentho-pélagique et d'un avantage physiologique lors du pic de fixation. Nous avons suivi le développement larvaire dans plusieurs sites, ainsi que la qualité lipidique des post-larves et de leur nourriture. Nos résultats mettent en évidence le contrôle prédominant des communautés phytoplanctoniques sur le succès de recrutement de la moule bleue via deux processus novateurs : i) le " match/mismatch " avec la qualité lipidique du plancton et ii) le déclencheur trophique de la fixation (" trophic settlement trigger ", TST). Le rôle nutritionnel des PUFA/EFA semble important pour le recrutement de l'année, mais leur teneur dans les compartiments benthiques et pélagiques ne semble pas pour autant affecter le comportement et la physiologie des jeunes moules au cours de la saison. Ces dernières semblent répondre fortement aux variations d'abondance du picoplancton autotrophe (picoeucaryotes, < 2 μm) au sein de ces deux compartiments. Enfin, nos résultats montrent un couplage bentho-pélagique entre larves et recrues, et suggèrent pour la première fois que le découplage dépende de deux traits comportementaux typiques des bivalves : le retard de métamorphose et la dérive bysso-pélagique. Cette recherche apporte de nouvelles pistes de réflexion quant à l'écologie des invertébrés benthiques et souligne l'importance de considérer la composante planctonique et le comportement au cours de l'ontogénie larvaire et post-larvaire lors des travaux menés sur la dynamique des populations en milieu naturel. Une emphase particulière devrait être portée sur la qualité lipidique et la composition taxonomique de la ressource trophique, et la séparation des différents stades de développement semble nécessaire pour comprendre la dynamique des populations. La notion de TST constitue le point majeur de l'étude puisqu'il s'agirait d'un signal indépendant de l'habitat prospecté qui synchroniserait un comportement de fixation, peu importe la qualité du substrat et/ou l'histoire de vie des individus.

Environmental change is a major threat to marine ecosystems worldwide. Understanding the key biological processes and environmental factors mediating spatial and temporal species' responses to habitat alterations underpins our ability to forecast impacts on marine ecosystems under any range of scenarios. This is especially important for calcifying species, many of which have both a high climate sensitivity and disproportionately strong ecological impacts in shaping marine communities. Although geographic patterns of calcifiers' sensitivity to environmental changes are defined by interacting multiple abiotic and biotic stressors, local adaptation, and acclimation, knowledge on species' responses to disturbance is derived largely from short- and medium-term laboratory and field experiments. Therefore, little is known about the biological mechanisms and key drivers in natural environments that shape regional differences and long-term variations in species vulnerability to global changes. In this thesis, I examined natural variations in shell characteristics, both morphology and biomineralisation, under heterogeneous environmental conditions i) across large geographical scales, spanning a 30° latitudinal range (3,334 km), and ii) over historical times, using museum collections (archival specimens from 1904 to 2016 at a single location), in mussels of the genus Mytilus. The aim was to observe whether plasticity in calcareous shell morphology, production, and composition mediates spatial and temporal patterns of resistance to climate change in these critical foundation species. For the morphological analyses, the combined use of new statistical methods and multiple study systems at various geographical scales allowed the uncoupling of the contribution of development, genetic status, and environmental factors to shell morphology. I found salinity had the strongest effect on the latitudinal patterns of Mytilus shape. Temperature and food supply, however, were the main predictor of mussel shape heterogeneity. My results suggest the potential of shell shape plasticity in Mytilus as a powerful indicator of rapid environmental changes. I found decreasing shell calcification towards high latitudes. Salinity was the best predictor of regional differences in shell deposition, and its mineral and organic composition. In polar, low-salinity environments, the production of calcite and organic shell layers was increased, while aragonite deposition was enhanced under temperate, higher-salinity regimes. Interacting strong effects of decreasing salinity and increasing food availability on compositional shell plasticity predict the deposition of a thicker external organic layer (periostracum) at high latitudes under forecasted future conditions. This response potential of Mytilus shell suggests an enhanced protection of temperate mussels from predators and a strong capacity for increased resistance of polar and subpolar individuals to dissolving water conditions. Analyses of museum specimens indicated increasing shell calcification during the last century. Deposition of individual shell layers was more closely related to temporal changes in the variability of key environmental drivers than to alterations of mean habitat conditions. Calcitic layer and periostracum showed marked responses to alterations of biotic conditions, suggesting the potential of mussels to trade-off between the deposition of calcareous and organic layers as a compensatory response to strategy-specific predation pressure. These changes in biomineralisation indicated a marked resistance to environmental change over the last century in a species predicted to be vulnerable, and how locally heterogeneous environments and predation levels can have a stronger effect on Mytilus responses than global environmental trends. My work illustrates that biological mechanisms and local conditions, driving plastic responses to the spatial and temporal structure of multiple abiotic and biotic stressors, can define geographic and temporal patterns of unforeseen species resistance to global environmental change.

Mollusc shells are unique adaptations that serve to protect the organisms that make them, and are a defining feature of the phylum. However the molecular underpinnings of shell forming processes are still largely unexplored. To further understand mollusc shell formation, I studied three bivalve species in this project: the blue mussel Mytilus edulis, the Pacific oyster Crassostrea gigas, and the king scallop Pecten maximus. While previous analyses of the shell proteomes showed species specificity, transcriptomes of the mantle tissues revealed more commonalities. To reconcile these differences, I studied differential gene expression in shell damage-repair experiments and during the formation of the first larval shell, to produce a comprehensive overview of shell formation processes. Expression data showed large biological variability between individuals, requiring matched-pair experimental designs to detect differential gene expression during shell repair. Loci differentially expressed during shell repair and in the larvae encoded shell matrix proteins, transmembrane transporters, and novel transcripts. A large number of shell matrix proteins, encoded in differentially expressed loci, were common in all three species during shell formation, indicating that shell forming proteins between different species may be more common than previously thought. Differential expression of transmembrane transporters during shell repair indicated that the animals may be regulating bicarbonate ions during shell formation. Finally, the experiments revealed novel transcripts, with unknown annotations to public datasets, that may putatively be involved in shell formation.

The biogeographic distribution of organisms is determined by physiological characteristics that enable a population to persist in a specific location. Global climate change effects are anticipated to increase the physiological stress experienced by organisms. Consequently, it is important to understand physiological responses to environmental stress and the mechanisms used by animals to cope with variable conditions. I investigated the physiological response to environmental stress in two species of mussel from New Zealand, Perna canaliculus and Mytilus galloprovincialis, using quantitative PCR and ecological field experiments. A series of laboratory and field experiments were done to manipulate stress levels and the expression levels of three heat shock protein genes (hsp24, hsp70, hsp90) were measured. A transcription regulatory gene (elf2) and a cell cycle regulatory gene (tis11d) were also measured. The dynamics of stress response gene expression in response to acute stress and gene expression changes in the natural population due to varying forms of environmental stress were tested. Between-zone translocations of different sized M. galloprovincialis and P. canaliculus were done at two sites in both east and west regions of the South Island of New Zealand. Site was found to be the most important factor in stress response. Apparent low food and high exposure stress interacted to create the particularly elevated stress response at the Timaru site. The adaptive ability of mussels transplanted between sites with varying environmental conditions was also tested. Results suggest that acclimation may be limited under stressful conditions. Furthermore, I found that P. canaliculus, the predominantly low-zone species, had a lower stress response than M. galloprovincialis, which was contradictory to predictions. The investigations described in this thesis suggest that interactive effects of abiotic stress and food limitations are particularly challenging for animals. With the severity of climate change scenarios predicted, changes in water quality and aerial and seawater temperature suggest mussel populations are likely to be negatively affected in the future. This work also illustrates the great potential to utilise molecular techniques for analysis of physiological processes of non-model organisms in a real-world setting.

L'objectif de travail a été d'évaluer l'effet de deux types de polluants, le tributylétain (TBT) et les hydrocarbures aromatiques polycycliques (HAPs), sur l'activation de la voie des MAP kinases et sur l'induction de l'apoptose chez deux invertébrés marins, la moule Mytilus galloprovincialis et l'éponge Suberites domuncula. Il a été montré, chez ces deux espèces exposées aux deux composés, une activation systématique de p38 en réponse à toutes les conditions expérimentales testées. JNK est également activée suite à leur exposition au TBT. En revanche, une exposition aux HAPs, dans les conditions expérimentales choisies, induit l'activation de JNK, chez la moule et de ERK, chez l'éponge. En outre, une induction de l'expression de Bcl-xS a été observée chez la moule, protéine impliquée dans la voie intrinsèque de l'apoptose. Chez l'éponge, l'induction de l'apoptose est dépendante de l'activation de la caspase 3 alors que chez la moule, comme chez d'autres bivalves, le processus apoptotique n'est dépendant de la caspase 3 que pour certaines concentrations de polluant. Par ailleurs, l'analyse des échantillons de moules prélevées in situ dans dix neuf stations de la côte adriatique (Croatie), polluées à des degrés divers notamment par le TBT et les HAPs, durant l'hiver et l'été, a montré une activation des trois MAPKs p38, JNK et ERK. Le niveau d'activation est corrélé au degré de pollution et à la température. Pour conclure, ce travail permet de noter l'intérêt de la p38 comme biomarqueur d'exposition et celui de l'apoptose comme marqueur d'effet.

In South Africa, the indigenous mussel Perna perna is threatened by both an invasive species and excessive human exploitation. The Mediterranean mussel Mytilus galloprovincialis is an invasive species that has been introduced to many parts of the world. In South Africa, this species arrived in the 1970s and spread rapidly along the west coast where today it is the dominant mussel species. Along the west coast, M. galloprovincialis is competitively superior in all aspects to the indigenous mussel species, and, as a result, has displaced some of them. On the south coast, M. galloprovincialis found more oligotrophic waters, higher species richness, and a stronger competitor in the indigenous mussel P. perna. The rate of spread of M. galloprovincialis along the south coast has decreased over the last 10 years and the present eastern limit of its distribution in South African is East London. On the south coast, M. galloprovincialis has not yet completely replaced P. perna; instead, the two exhibit spatial segregation, with P. perna dominating the low shore, M. galloprovincialis the high shore and an overlap zone between the two. An experiment on competition was carried out at one site on the south coast. The results showed that, on the low shore, P. perna is a more dominant competitor for space than M. galloprovincialis. Also byssus attachment of the two species differs, P. perna being much stronger than M. galloprovincialis, which suffers high mortality due to wave action on the low shore, especially in monospecific beds. As a result, mortality of M. galloprovincialis through wave action is reduced by the presence of P. perna, which seems to confer protection against dislodgement. However, in the absence of strong wave action, P. perna competitively excludes M. galloprovincialis. Human exploitation along 160 km of coast was examined by sampling mussel populations and using aerial surveys to determine where harvesters were distributed. Collectors did not seem to discriminate between species. The study has shown that higher abundances of mussels were found in protected or inaccessible sites, while in unprotected sites mussels were scarce. Coastal nature reserves are being proven to be effective in protecting mussel populations.

Within landscapes, spatial heterogeneity is common and specific landscape features can influence propagule dispersal by wind or water, affecting population connectivity and dynamics. Coastline topographic features, such as bays and headlands, have a variety of biophysical effects on nearshore oceanography, larval transport, retention and supply, and the processes of larval settlement and recruitment. Although this has been demonstrated in several parts of the world, engendering a perception of a general ‘bay effect’, few studies have investigated this generality in a single experiment or region, by replicating at the level of ‘bay’. The Agulhas biogeographic region of the south coast of South Africa is a useful system within which to test for such generality. Using the intertidal mussels Mytilus galloprovincialis and Perna perna as model organisms, patterns of adult distribution were surveyed across four large ‘halfheart’ bays and intervening stretches of open coast, providing replication at the level of ‘bay’ and duplication of ecologically similar species. In support of a general, pervasive influence of bays on intertidal populations, mussel cover was found to be greater in bays than on the open coast for both species, although the effect was strongest for M. galloprovincialis. To explain this adult distribution, settlement, post-settlement mortality and recruitment were examined over 12mo at the same sites, with the prediction that rates of each would favour larger bay populations. Contrary to this, an interaction between month and bay-status was found, with greater settlement and recruitment on the open coast than in bays reflecting extreme settlement and recruitment events at 3 westerly open coast sites during summer. Re-analysis excluding these outliers, revealed the expected effect, of greater settlement and recruitment in bays. While this indicates the broad generality of the bay effect, it highlights exceptions and the need for replication in time and space when examining landscape effects. Measuring post-settlement mortality required testing small-scale settlement behaviour on established and newly deployed settler collectors. It was found that all settlers preferred collectors with biofilm, but that primary settlers avoided conspecific settlers, while secondary settlers were attracted to them. With discrepancies in settler attraction to new and established collectors accounted for, initial (over 2d) and longer-term (over 7d) post-settlement mortality rates were found to be substantial (ca 60 %) for both species. No topographic effect on p-s mortality was evident. Finally, recruit-settler, adult-recruit and interspecies correlations were examined at regional and local scales. Synergistic (or neutral) effects maintained the initial settlement pattern in recruit and adult populations regionally, but not at local scales; striking interspecies correlations suggested the influence of common regional transport processes. Ultimately, the results emphasize the importance of the direction of effects in different life stages and at different spatial scales, and the possibility that antagonistic effects may mask even strong patterns.

Yes / The Mg/Ca ratios of biogenic calcite is commonly seen as a valuable palaeo-proxy for reconstructing past ocean temperatures. The temperature dependence of Mg/Ca ratios in bivalve calcite has been the subject of contradictory observations. The palaeoceanographic use of a geochemical proxy is dependent on initial, rigorous calibration and validation of relationships between the proxy and the ambient environmental variable to be reconstructed. Shell Mg/Ca ratio data are reported for the calcite of two bivalve species, Mytilus edulis (common mussel) and Pecten maximus (king scallop), which were grown in laboratory culturing experiments at controlled and constant aquarium seawater temperatures over a range from 10 to 20 C. Furthermore, Mg/Ca ratio data of laboratory- and fieldgrown M. edulis specimens were compared. Only a weak, albeit significant, shell Mg/Ca ratio¿temperature relationship was observed in the two bivalve species: M. edulis (r2=0.37, p<0.001 for laboratory-cultured specimens and r2=0.50, p<0.001 for field-cultured specimens) and P. maximus (r2=0.21, p<0.001 for laboratory-cultured specimens only). In the two species, shell Mg/Ca ratios were not found to be controlled by shell growth rate or salinity. The Mg/Ca ratios in the shells exhibited a large degree of variability among and within species and individuals. The results suggest that the use of bivalve calcite Mg/Ca ratios as a temperature proxy is limited, at least in the species studied to date. Such limitations are most likely due to the presence of physiological effects on Mg incorporation in bivalve calcite. The utilization is further limited by the great variability both within and among shells of the same species that were precipitated under the same ambient conditions