Caribbean coral reefs have undergone changes in coral cover, structural complexity and assemblage composition since the 1970s. Although some of the ecological consequences associated with these changes have been well documented, the consequences for ecosystem functions dependent on reef structure are less well understood. In particular, there has been little research into the effects of change, on carbonate production and bioerosion; both are critical controls of structural complexity. Currently, there is only a very limited understanding of how both processes vary within and between different habitat types and what this means for ecosystem functioning. Carbonate framework production and bioerosion were investigated within three habitat types (hardgrounds, Acropora palmata reef and Orbicella reef) under sheltered and exposed wave energy regimes on Grand Cayman. Census based assessments were used, allowing the identification of functionally important species. Additionally, habitat specific calcification rates were measured for calcareous encruster communities to improve estimations of carbonate production; mean rates of calcification ranged from 0.19 to 1.14 G (1G = 1 kg CaCO3 m-2 yr-1) within hardgrounds (4–7 m), Acropora palmata reef (1–8 m) and Orbicella reef habitats (8–15 m) and were significantly higher at wave exposed sites. The rates of bioerosion for two sponge species, Siphonodictyon brevitubulatum and Cliona tenuis, were also measured and new approaches to estimating excavating sponge community bioerosion were developed to improves bioerosion estimates. Mean carbonate framework production was 0.38 G within hardgrounds, 2.65 G within Acropora palmata reef habitat and 3.54 G within Orbicella reef habitat but not significantly different between wave exposure regimes. Calcareous encruster communities, dominated by coralline algae, were identified as key carbonate producers within shallow reef habitats on the exposed south coast. They may be important to the maintenance of reef structure in these degraded reef habitats. Orbicella species were the most important carbonate producers within all reef habitats. Mean total bioerosion was 1.32, 2.27 and 2.28 G within hardgrounds, Acropora palmata reef and Orbicella reef habitats respectively. 4 Total bioerosion was not significantly different between wave exposure regimes for any habitat type, but almost completely dominated by parrotfish (29–86 %). On Grand Cayman, both carbonate framework production and bioerosion were less than that measured in comparative habitats, across the Caribbean, despite the presence of a well-managed marine protected area on the sheltered west coast. The highest rates of net carbonate production occurred in the deepest habitat - Orbicella reef (exposed: +1.45 G, sheltered: +1.07 G). Sheltered and exposed Acropora palmata reef habitat had net production rates of +0.53 and +0.30 G respectively. Hardgrounds were net erosional (-0.94 G). Overall the results suggest a change in the focal point for reef accumulation on Grand Cayman that may alter geomorphology over time. Additionally, Acropora palmata reef habitats are likely to be in a state of accretionary stasis, which may have shutdown reef growth in reef crest environments as carbonate framework produced within these habitats is a major contributor to reef accumulation at the reef crest.

In the past, oceans have strongly influenced atmospheric CO2 levels through organic and inorganic carbon cycling. The inorganic carbon pump relies on the formation of calcium carbonate which releases CO2 into the surface ocean and traps alkalinity in solid form which sinks to deeper ocean layers and sediments. After sinking, calcium carbonate can either then become trapped in the sediments or dissolve increasing the alkalinity of deeper ocean layers. The net effect is of acidifying surface oceans and encouraging release of CO2 to the atmosphere. The present thesis focuses on marine teleost (bony) fish in temperate areas as previously poorly understood but potentially major producers of calcium carbonate in the ocean. Fish in temperate areas may be contributing to carbonate sediment production and as such the inorganic carbon pump. Prior to this thesis only tropical fish have been investigated as major piscine sediment producers. The present thesis describes the composition and morphology of carbonates produced by many different species of temperate fish providing a basis for the understanding the fate of these carbonates in the environments and their potential contribution to sediment production and the inorganic carbon cycle. Characteristics of carbonates produced by fish in the wild were fairly consistent within a species upon examination of carbonates produced by poor cod (Trisopterus minutus) over the course of a year. However, despite the likely consistent and distinct characteristics of fish carbonates, little evidence of them was found in temperate shallow sediments beneath pens of farmed Atlantic salmon (Salmo salar) where there theoretically should be very high production rates. Reduced salinity, often a feature of temperate areas compared to tropical areas, was found to reduce production rates of carbonate from fish compared to higher salinities. However, salinity reductions below the ocean average of 35 psu (practical salinity units) had less impact on production rates than increases above 35 psu. As such it is argued that production rates in temperate environments should still be relatively high considering high fish biomasses in some temperate regions and could still mean fish in temperate areas are an important source of carbonate production and potential sediment production.

Les coccolithophoridés sont des algues marines photosynthétiques et planctoniques qui produisent des plaques micrométriques de carbonate de calcium (CaCO3) appelés coccolithes. Ces algues sont apparues il y 210 Ma et produisent actuellement la majeure partie du CaCO3 dans les océans modernes, jouant ainsi un rôle majeur dans le cycle du carbone. Cependant, l’émergence de la production de CaCO3 océanique par les coccolithophoridés au cours du Jurassique, ainsi que son impact sur le cycle du carbone, restent très mal compris. Cette étude s’est donc focalisée sur une période du Jurassique Moyen (Bajocien inférieur, -170 Ma) enregistrant la diversification de Watznaueria, un genre de coccolithophoridé qui a ensuite dominé la production de CaCO3 océanique pendant plus de 80 Ma. L’analyse des assemblages de coccolithes du Jurassique Moyen du Portugal et du sud de la France, réalisée à l’aide d’une méthode de reconnaissance automatique appliquée pour la première fois aux coccolithes du Jurassique, a permis de quantifier l’importance de cette période de diversification sur la production de CaCO3 pélagique. En outre, la durée de cet intervalle clé a été réévaluée grâce à l’analyse cyclostratigraphique des séries sédimentaires du Sud de la France. Les variations de production de CaCO3 pélagique ainsi reconstituées ont été comparées aux perturbations du cycle du carbone enregistrées par les rapports des isotopes du carbone, et indiquent un lien probable avec une augmentation marquée de la fertilité des océans. Par ailleurs, l’analyse paléontologique montre que cette diversification correspond à l’apparition successive de différentes espèces vraisemblablement opportunistes du genre Watznaueria. Enfin, les flux obtenus de CaCO3 pélagiques, largement inférieurs à ceux observés dans les océans actuels, semblent insuffisants pour avoir eu une influence significative sur le cycle global du carbone du Jurassique Moyen. / Coccolithophorids are photosynthetic and planktonic marine algae that produce micrometric calcium carbonate (CaCO3) platelets called coccoliths. These algae appeared about 210 Ma ago and produce today most of the CaCO3 in the modern oceans, hence playing a major role in the carbon cycle. Nevertheless, the onset of oceanic CaCO3 production by these organisms during the Jurassic and its impact on carbon cycling remain poorly understood. This study therefore focused on the Middle Jurassic interval (Early Bajocian, -170 Ma) which records the diversification of Watznaueria, an evolutionary important coccolith genus that subsequently dominated oceanic CaCO3 production for more than 80 Myr. The analysis of coccolith assemblages from the Middle Jurassic of southern France and Portugal, based on an automaticcoccolith recognition device used for the first time on Jurassic coccoliths, allowed quantifying the impact of this diversification on CaCO3 production. In addition, the duration of this key interval has been revaluated by the cyclostratigraphic analysis of sedimentary strata from southern France. The reconstructed changes in CaCO3 production were compared to carbon cycle perturbations recorded by carbon isotope ratios and indicate a probable link with a marked increase of ocean fertility. Besides, paleontological analyses show that this diversification episode correspond to the successive appearance of different, probably opportunistic Watznaueria species. The obtained fluxes of pelagic CaCO3 production, by far lower than those recorded in modern oceans, seems too low to have significantly impacted theMiddle Jurassic carbon cycle.

This thesis examines functional relationships between the morphologic, hydrodynamic, ecological and sedimentological characteristics of the Warraber reef platform, an inter-tidal reef island system, Central Torres Strait, Australia (10[degrees] 12??? S, 142 [degrees] 49??? E). Hydrodynamic and sediment-transport experiments were conducted on the reef flat using current meters, water level recorders and directional sediment traps. Results showed dominantly SE flows during the dry season and more variable NW to SE flows during the wet season. Topography and reefal water levels modulated the direction and strength of currents and the generation of wind-waves on the reef flat as well as the passage of waves over the reef rim. These hydrodynamic conditions are sufficient to induce significant transport of moderately fast to slow settling sediment (&gt-5.25 symbol psi) on the reef flat, though the platform as a whole is a relatively closed transport system. Carbonate production was estimated based on the key ecological variables of live assemblage distribution and cover. Overall, only 24% of the reef flat was occupied by carbonate-producing organisms. The average estimated carbonate-production rate for the reef was 1.6 kgm -2y-1 (0.07-4.37 kgm-2y-1). Production is dominated by coral (73%), with subordinate proportions contributed by coralline algae (19%). And molluscs, foraminifera and Halimeda (&lt4%) though actual reef-flat sediments did not reflect this potential. Instead, they were dominated by molluscs (35-55%), coralline algae (16-26%), coral (8-13%), Halimeda (7-8%) and foraminifera (5-10%). Differential rates of carbonate to sediment conversion meant the reef-platform sediments were more closely related to the cover of live organisms than to the contribution of carbonate production by each parent organism. The settling properties of the least altered particles of the five commonest constituents were measured and these provided the basis for an eco-sedimentological model of the reef-platform system. Modelled textures were compared to the actual textures, indicating the degree of textural alteration resulting from a combination of biological and physical processes, including sediment production, hydraulic sorting and mechanical breakdown. This analysis, integrated with the hydrodynamic, exposure and other data, was used to determine reef-platform surface-sediment sources, sinks and transport pathways. In using both the textual and constituent compositional properties of sediments, as well as information on local biological and physical processes, the model approach developed offers progress towards an integrative, interdisciplinary analysis of carbonate environments.

This thesis examines functional relationships between the morphologic, hydrodynamic, ecological and sedimentological characteristics of the Warraber reef platform, an inter-tidal reef island system, Central Torres Strait, Australia (10[degrees] 12??? S, 142 [degrees] 49??? E). Hydrodynamic and sediment-transport experiments were conducted on the reef flat using current meters, water level recorders and directional sediment traps. Results showed dominantly SE flows during the dry season and more variable NW to SE flows during the wet season. Topography and reefal water levels modulated the direction and strength of currents and the generation of wind-waves on the reef flat as well as the passage of waves over the reef rim. These hydrodynamic conditions are sufficient to induce significant transport of moderately fast to slow settling sediment (&gt-5.25 symbol psi) on the reef flat, though the platform as a whole is a relatively closed transport system. Carbonate production was estimated based on the key ecological variables of live assemblage distribution and cover. Overall, only 24% of the reef flat was occupied by carbonate-producing organisms. The average estimated carbonate-production rate for the reef was 1.6 kgm -2y-1 (0.07-4.37 kgm-2y-1). Production is dominated by coral (73%), with subordinate proportions contributed by coralline algae (19%). And molluscs, foraminifera and Halimeda (&lt4%) though actual reef-flat sediments did not reflect this potential. Instead, they were dominated by molluscs (35-55%), coralline algae (16-26%), coral (8-13%), Halimeda (7-8%) and foraminifera (5-10%). Differential rates of carbonate to sediment conversion meant the reef-platform sediments were more closely related to the cover of live organisms than to the contribution of carbonate production by each parent organism. The settling properties of the least altered particles of the five commonest constituents were measured and these provided the basis for an eco-sedimentological model of the reef-platform system. Modelled textures were compared to the actual textures, indicating the degree of textural alteration resulting from a combination of biological and physical processes, including sediment production, hydraulic sorting and mechanical breakdown. This analysis, integrated with the hydrodynamic, exposure and other data, was used to determine reef-platform surface-sediment sources, sinks and transport pathways. In using both the textual and constituent compositional properties of sediments, as well as information on local biological and physical processes, the model approach developed offers progress towards an integrative, interdisciplinary analysis of carbonate environments.

Le Crétacé inférieur est ponctué de perturbations du cycle du carbone associées à des épisodes de préservation de matière organique et à des crises de la production carbonatée néritique et pélagique. Ces évènements coïncident également avec des refroidissements à très court terme (<1Ma) dont l’origine et les conséquences sont encore imprécises en raison de la faible résolution des courbes de températures dans les eaux de surface. Les études récentes réalisées à partir de modèles climatiques couplés à des modèles géochimiques laissent penser qu’une crise de la production carbonatée pourrait engendrer un refroidissement climatique sur une échelle de temps inférieure à 1 Ma (Donnadieu et al., accepté). Basées sur les dépôts d’âge Valanginien des coupes de La Charce–Vergol et d’Ollioules (Sud-est de la France) et sur les sédiments de l’Aptien du sous-Bassin de Galvé (Nord-est de l’Espagne), des études stratigraphiques, paléoécologiques et géochimiques ont été menées pour établir les relations entre la production carbonatée et le climat au cours du Valanginien et de l’Aptien. Pour cela, des courbes de température à haute résolution pour les eaux de surface ont été établies et mises en regard des évolutions des producteurs néritiques et pélagiques de carbonate. Le Valanginien et l’Aptien présentent tous deux des arrêts polyphasés de la production carbonatée néritique. Certains arrêts précèdent des refroidissements à court terme, dont ceux datés du Valanginien supérieur, du début et de la fin de l’Aptien inférieur. Cette succession suggérerait un lien de cause à effet entre les crises de la production et les fluctuations climatiques. Toutefois, les refroidissements du Valanginien supérieur et de la fin de l’Aptien inférieur sont respectivement précédés par un enfouissement de matière organique continentale et océanique, qui est un processus pouvant également générer une diminution de CO2 et un refroidissement. Ce travail a permis de mettre en évidence les répercutions des changements climatiques sur la production carbonatée par l’intermédiaire de changements de producteurs dans les domaines néritiques et pélagiques. Dans un premier temps, la mise en place de conditions froides au Valanginien supérieur et à la fin de l’Aptien inférieur est suivie de remplacements floro-fauniques caractérisés par l’évolution de communautés hétérozoaires à photozoaires. Les bouleversements observés suggèrent un changement drastique des conditions trophiques sous le développement de conditions arides relatives au refroidissement. Dans un second temps, l’évolution des communautés pélagiques au Valanginien répondraient également aux changements climatiques : ces communautés marquées d’un déclin depuis la fin du Valanginien inférieur présentent une courte reprise du début au milieu du Valanginien supérieur. Cette reprise coïncide avec le développement de conditions froides et plus arides occasionnant des conditions trophiques plus faibles / The Early Cretaceous is punctuated by carbon cycle perturbations, associated with organic matter burial episodes and carbonate production crises. These events coincide with short-term cooling (<1Ma), yet the mechanisms are still unclear, because of low resolution in sea surface temperature reconstructions. Recent climatic models suggest that carbonate-platform-collapse events may trigger a short-term ocean cooling episode (Donnadieu et al., accepted). In order to establish relations between climates and carbonate productions, we performed stratigraphic, palaeoecologic and geochemical analyses on Valanginian sediments from the La Charce-Vergol and the Ollioules sections (South-East France) and Aptian sedimentary record of the Galvé subasin (North East Spain). Therefore, high-resolution sea surface temperature curves were reconstructed with regard to the pelagic and neritic carbonate producer evolution. Both Valanginian and Aptian stages are marked by polyphased neritic production drawdown. Moreover, the Late Valanginian, basal and latest Early Aptian carbonate-platform demises predate a short-term cooling occurrence. The chronology of these events may imply that carbonate production decrease may have affected the atmospheric CO2 pool and the climate. Nevertheless, the decreases of water temperature that took place in the Late Valanginian and the latest Early Aptian are also prior to episodes of continental and oceanic organic matter burial, respectively. This process is also known as a CO2 drawdown and cooling generator. The present study allowed establishing climate feedbacks on the pelagic and neritic carbonate producers triggering fluctuations of the carbonate production fluxes. At first, cooler conditions during the Late Valanginien and latest Early Aptian are posterior to floro-faunal changes characterised by heterozoan to photozoan replacements. These suggest a trophic level decrease relative to cool and dryer climatic condition. Subsequently, nannoconid communities seem to record a response to the Late Valanginian climatic change: these producers are characterised by a decline from the latest Early Valanginian onward, interrupted by a recovery from the earliest Late Valanginian up to the mid-Late Valanginian. This recovery coincides with the development of cooling and dryer conditions, triggering low trophic level and thus promoting a subsequent pelagic production recovery.

This thesis presents a new stratigraphic forward numerical model to simulate the carbonate production of marine sedimentary basin through ecological model which is implemented in the SIMSAFADIM-CLASTIC program. This ecological model is based on the Generalized Lotka Voltera equations that model the population evolution of species. These populations are controlled by biological factors (growth rate, carrying capacity and interaction among species), and by the environmental conditions (light, energy of the medium, nutrients, bottom slope and concentration of clastic sediments in suspension) which are combined forming a unique environmental factor that downscale the intrinsic rate of growth. The algorithm to apply in the code uses an explicit Runge-Kutta numerical method of order (4)5 to solve the differential equations formulated in the ecological model. Finally, a 3D visualization output files for the interpretation and analysis are generated using the VTK format. The obtained code has been applied in three sample experiments in order to discuss the possibilities and the limitations of the code. The first example is the model of a theoretical basin. The results are compared with real cases. The second example is an actual basin sited in western Mediterranean Sea. The results are discussed to show the applicability and the limitations of the model. The third example applies several configurations to the Aptian Galve sub-basin (Maestrat Basin, E Iberia), allowing to define the environmental conditions.

This thesis presents a new stratigraphic forward numerical model to simulate the carbonate production of marine sedimentary basin through ecological model which is implemented in the SIMSAFADIM-CLASTIC program. This ecological model is based on the Generalized Lotka Voltera equations that model the population evolution of species. These populations are controlled by biological factors (growth rate, carrying capacity and interaction among species), and by the environmental conditions (light, energy of the medium, nutrients, bottom slope and concentration of clastic sediments in suspension) which are combined forming a unique environmental factor that downscale the intrinsic rate of growth. The algorithm to apply in the code uses an explicit Runge-Kutta numerical method of order (4)5 to solve the differential equations formulated in the ecological model. Finally, a 3D visualization output files for the interpretation and analysis are generated using the VTK format. The obtained code has been applied in three sample experiments in order to discuss the possibilities and the limitations of the code. The first example is the model of a theoretical basin. The results are compared with real cases. The second example is an actual basin sited in western Mediterranean Sea. The results are discussed to show the applicability and the limitations of the model. The third example applies several configurations to the Aptian Galve sub-basin (Maestrat Basin, E Iberia), allowing to define the environmental conditions.