Among tools that are used to fill knowledge gaps on natural systems, ecological modelling has been widely applied during the last two decades. Ecological models are simple representations of a complex reality. They allow to highlight environmental drivers of species ecological niche and better understand species responses to environmental changes. However, applying models to Southern Ocean benthic organisms raises several methodological challenges. Species presence datasets are often aggregated in time and space nearby research stations or along main sailing routes. Data are often limited in number to correctly describe species occupied space and physiology. Finally, environmental datasets are not precise enough to accurately represent the complexity of marine habitats. Can we thus generate performant and accurate models at the scale of the Southern Ocean ?What are the limits of such approaches ?How could we improve methods to build more relevant models ?In this PhD thesis, three different model categories have been studied and their performance evaluated. (1) Mechanistic physiological models (Dynamic Energy Budget models, DEB) simulate how the abiotic environment influences individual metabolism and represent the species fundamental niche. (2) Species distribution models (SDMs) predict species distribution probability by studying the relationship between species presences and the environment. They represent the species realised niche. (3) Dispersal lagrangian models predict the drift of propagules in water masses. Results show that physiological models can be developed for marine Southern Ocean species to simulate the metabolic variations in link with the environment and predict population dynamics. However, more data are necessary to highlight detailed physiological contrasts between populations and to accurately evaluate models. Results obtained for SDMs suggest that models generated at the scale of the Southern Ocean and future simulations are not relevant, given the lack of data available to characterise species occupied space, the lack of precision and accuracy of future climate scenarios and the impossibility to evaluate models. Moreover, model extrapolate on a large proportion of the projected area. Adding information on species physiological limits (observations, results from experiments, physiological model outputs) was shown to reduce extrapolation and to improve the capacity of models to estimate the species realised niche. Spatial aggregation of occurrence data, which influenced model predictions and evaluation was also succefully corrected. Finally, dispersal models showed an interesting potential to highlight the role of geographic barriers or conversely of spatial connectivity and also the link between species distribution, physiology and phylogeny history. This PhD thesis provides several methodological advice, annoted codes and tutorials to help implement future modelling works applied to Southern Ocean marine species. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Sea ice in the Antarctic Marginal Ice Zone (MIZ) plays a pivotal role in regulating heat and energy exchange between oceanic and atmospheric systems, which drive global climate. Current understanding of Southern Ocean sea ice dynamics is poor with temporal and spatial gaps in critical seasonal data-sets. The lack of in situ environmental and wave data from the MIZ in the Antarctic region drove the development of UCT's first generation of in situ ice-tethered measurement platform as part of a larger UCT and NRF SANAP project on realistic modelling of the Marginal Ice Zone in the changing Southern Ocean (MISO). This thesis focuses on the firmware development for the device and the design process taken to obtain key measurements for understanding sea ice dynamics and increasing sensing capabilities in the Southern Ocean. The buoy was required to survive the Antarctic climate and contained a global positioning system, temperature sensor, digital barometer and inertial measurement unit to measure waves-in-ice. Power was supplied to the device by a power supply unit consisting of commercial-grade batteries in series with a temperature-resistant low dropout regulator, and a power sensor to monitor the module. A satellite modem transmitted data through the Iridium satellite network. Finally, Flash chips provided permanent data storage. Firmware and peripheral driver files were written in C for an STMicroelectronics STM32L4 Arm-based microcontroller. To optimise the firmware for low power consumption, inactive sensors were placed in power-saving mode and the processor was put to sleep during periods of no sampling activity. The first device deployment took place during the SCALE winter expedition in July 2019. Two devices were deployed on ice floes to test their performance in remote conditions. However, due to mechanical and power errors, the devices failed shortly after deployment. A third device was placed on the deck of SA Aghulas II during the expedition and successfully survived for one week while continuously transmitting GPS coordinates and ambient temperature. The second generation featured subsequent improvements to the mechanical robustness and sensing capabilities of the device. However, due to the 2020 COVID-19 pandemic, subsequent Antarctic expeditions were cancelled resulting in the final platform evaluation taking place on land. The device demonstrates a proof of concept for a low-cost, ice-tethered autonomous sensing device. However, additional improvements are required to overcome severe bandwidth and power constraints.

A formação de águas profundas na Antártica afeta diretamente o clima global, uma vez que este processo conecta os ramos superior e inferior da circulação termohalina global (MOC). Avaliar os impactos das mudanças climáticas nestes processos é importante para compreensão do transporte global de calor pelos oceanos e para realização de projeções climáticas. Aplicando a forçante interanual Coordinated Ocean-Ice Reference (CORE), foi realizada uma simulação de 60 anos (1948-2007) utilizando o ROMS com módulos de gelo marinho e plataforma de gelo ativos. Uma rodada preliminar de 100 anos foi realizada com forçante do ano normal CORE, para gerar campos estáveis de inicialização da rodada interanual. Para ambos os experimentos adotou-se uma grade circumpolar periódica com resolução variável, alcançando cerca de 5 km na borda sul. Para investigar as massas de água foi aplicada a Análise Multiparamétrica Ótima - OMP. As principais massas de água do Mar de Ross foram identificadas: Água de Superfície Antártica (AASW), Água Circumpolar Profunda (CDW), Água de Fundo Antártica (AABW) e Água de Plataforma (SW), posteriormente separadas em Água da Plataforma de Gelo (ISW) e Água de Plataforma de Alta Salinidade (HSSW). Os resultados são consistentes com observações prévias (Bergamasco, 2002; Orsi & Wiederwohl, 2009; Budillon, 2011). A simulação interanual sugere que o Oceano Austral vem sofrendo um processo de aquecimento e diminuição de salinidade. Houve um aumento do calor advectado pela CDW e uma diminuição da salinidade das águas de plataforma e da AABW, consistente com as observações de Johnson & Doney (2006). A capacidade do modelo regional ROMS de reproduzir as águas de plataforma ISW, HSSW e a AABW é uma importante contribuição para estudos climáticos, visto que os modelos globais não conseguem representar tais processos. A inclusão de parametrizações explícitas dos processos de gelo marinho e plataforma de gelo capacita o ROMS para reproduzir os processos associados a criosfera, possibilitando a obtenção de projeções mais realísticas. / Dense water formation around Antarctica is recognized as a significant process that significantly impacts the global climate, since that\'s where the linkage between the upper and lower limbs of Global Thermohaline Circulation takes place. Assessing whether these processes may be affected by rapid climate changes and all the eventual feedbacks is crucial to fully understand the ocean heat transport and to provide quality future climate projections. Applying the Coordinated Ocean-Ice Reference (CORE) interannual forcing we have run a 50-year simulation (1948-2007) using ROMS with a new sea ice/ice shelf thermodynamics module. Another 100-year simulation forced with CORE normal year was previously run to provide stable starting fields. The normal year consists of single annual cycle of all the data that are representative of climatological conditions over decades and can be applied repeatedly for as many years of model integration as necessary. The 60-year forcing has interannually varying data from 1948 to 2007, which allows validation of model output with ocean observations. Both experiments employed a periodic circumpolar variable resolution grid reaching less than 5 km at the southern border. By applying the OMP water masses separating scheme, we were able to identify the main Ross Sea water masses: Antarctic Surface Water (AASW), Circumpolar Deep Water (CDW), Antarctic Bottom Water (AABW) and Shelf Water (SW), further separated into Ice Shelf Water (ISW) and High Salinity Shelf Water (HSSW). Results are consistent with previous observational studies (Bergamasco, 2002; Orsi & Wiederwohl, 2009; Budillon, 2011). The interannual simulation indicates that the Southern Ocean is becoming warmer and less salty. The CDW poleward heat transport increased while shelf waters salinity as well as the AABW salinity decreased during the simulation period, consistent with Johnson & Doney (2006), who have reported the export of less dense AABW. ROMS capability to represent ISW, HSSW and AABW is an important contribution to climate studies, since IPCC class models seem unable to provide reliable representations of such important processes, which may lead to projections of more realistic scenarios. This is significantly improved in this study by including more explicit sea ice/ice shelf parameretization. ROMS is able to reproduce cryosphere-linked mechanisms of dense water formation around Antarctica.

Der Südozean ist die Schlüsselregion zur Kenntnis der neogenen Klimaentwicklung. In diesem Zusammenhang ist die Untersuchung von planktonischen Gemeinschaften in Hinblick auf die Umweltentwicklung von großer Bedeutung. In antarktischen neogenen Sedimenten sind Radiolarien reichlich, in großer Diversität und einheitlich gut erhalten. Sie sind nicht nur perfekte Testobjekte für paläobiologischen Studien, sondern auch eine wichtige Quelle für eine verbesserte Biostratigraphie – bisher behinderte nämlich das Fehlen einer verlässlichen Geochronologie detaillierte Studien. Es wurde ein Datensatz aller Taxa von mehreren Standorten des Südozeans gesammelt: für alle der 98 Proben je ca. 7000 Radiolarien. Die Fauna enthält ca. 500 Arten (inclusive 120 neuer Taxa). Die Untersuchung der Makroevolutionsgeschichte dieser Fauna zeigt, dass eine wesentliche ökologische Umwälzung, ohne Aussterbeereignis, bezogen auf den Verlauf der Artengleichheit und den Anstieg der Gattung Antarctissa, bei ca. 8 Ma erfolgte. Dann, 3 My später, folgte ein wesentlicher Diversitätsverlust. Obwohl das ökologische Ereignis eventuell mit einer Änderung der Primärproduzenten assoziiert sein kann, ist der auslösende Faktor des Diversitätsabfalls unbekannt. Außerdem zeigt der Vergleich zwischen der Diversitätsgeschichte dieser Fauna und einer Paläodiversitätsrekonstruktion südozeanischer Faunen, beruhend auf der Neptune Datenbank, daß der generelle Verläufe mit den Probenteilungsmethodologien nachgezeichnet wird, jedoch diese Methodologien aufgrund grober Verzerrungen nicht geeignet für Detailstudien sind. Schließlich wurde eine biostratigraphische Analyse für die komplette Fauna vom Obermiozän bis Pliozän durchgeführt. Obwohl diese Analyse noch vorlaüfig ist, zeigt sich eine Angleichung des aktuellen Altersmodells um mehr als 1 My. Diese Studie zeigt auch 94 neue, sichere Ereignisse, die für die stratigraphische Einordnung der Antarktischen Sedimente genutzt werden können. / The Southern Ocean is the key to understand the Neogene climate evolution. Unfortunately the lack of a robust geochronological framework has hindered precise studies. Equally of interest is understanding how planktonic communities changed in relation with the evolution of these environments. Radiolarians are abundant in Antarctic Neogene sediments, diversified and consistently well-preserved. They should constitute not only an ideal testing ground for paleobiological studies but also a major resource for improved biostratigraphy. In this study, a quantitative, taxonomically-complete dataset have been collected in various sites of the Southern Ocean, using 98 samples and ca. 7000 specimens per sample. Ca. 500 species were uncovered in this fauna, including 120 new to science. The study of the macroevolutionary history of this fauna reveals that a significant, extinctionless ecological turnover, linked to a decrease in the evenness of the species'' abundances and the rise of genus Antarctissa to dominance, occured at ca. 8 Ma, followed 3 My later by a significant diversity loss. Although the ecological event can be tentatively associated with a regional change in the composition of primary producers, the triggering event of the diversity loss is yet to be found. The whole-fauna diversity history was compared to paleodiversity reconstructions computed using subsampling methodologies from the occurrences gathered in the Neptune database. The comparison shows that the main trends are retrieved by the subsampling procedures but also that substantial distortions make them poorly suited for detailed studies. Finally a biostratigraphical analysis was conducted on this whole-fauna dataset for the late Miocene - Pliocene sequence. Although this analysis is still very much preliminary, it shows a coherent readjustement of the current age models by more than 1 My. This study also shows that 94 events seem reliable enough to be used to correlate Southern Ocean sites together.

Quels sont les grands patrons de distribution des espèces et quels sont les facteurs qui les contrôlent? Ces questions sont au cœur des problématiques macroécologiques et prennent un intérêt tout particulier au regard du réchauffement climatique global actuel. L’objectif principal de ce travail de thèse était de déterminer les patrons de distribution actuels des espèces d’oursins antarctiques et subantarctiques à l’échelle de l’océan Austral et de mettre en évidence les facteurs qui contrôlent ces distributions. La modélisation des niches écologiques d’une vingtaine d’espèces d’oursins a permis de mettre en évidence deux grands patrons de distribution : (1) un premier représenté par les espèces dont la distribution n’est pas limitée au sud du Front Polaire et s’étend des côtes antarctiques aux zones subantarctiques et tempérées froides et (2) un deuxième constitué d’espèces restreintes à la zone antarctique. Au sein de ces deux patrons, cinq sous-patrons ont également pu être défini sur la base de différences de distribution latitudinale et bathymétrique entre groupes d’espèces. Cette approche biogéographique par modélisation de niche écologique a été complétée par l’analyse de similarité de l’ensemble des faunes d’oursins, de bivalves et de gastéropodes, au niveau spécifique et générique, entre biorégions de l’océan Austral. Cette analyse démontre qu’il existe chez les oursins et les bivalves des connexions fauniques entre l’Amérique du Sud et les zones subantarctiques ainsi qu’une séparation entre l’Est et l’Ouest antarctique. Au contraire, les faunes de gastéropodes subantarctiques montrent des affinités plutôt antarctiques que sud-américaines, l’Antarctique ne formant qu’une unique province pour ce clade. Ces différences entre clades sont interprétées comme étant le résultat d’histoires évolutive et biogéographique distinctes entre oursins et bivalves d’une part et gastéropodes d’autre part. L’hypothèse d’une réponse évolutive différente des clades aux changements environnementaux survenus au cours du Cénozoïque est avancée. Enfin, l’existence de connexions fauniques trans-antarctiques est mise en évidence dans l’étude des trois clades ; celles-ci sont interprétées comme le résultat de la dislocation de la calotte ouest-antarctique et l’ouverture de bras de mer trans-antarctiques au cours du Pléistocène. Parmi les paramètres environnementaux utilisés dans la modélisation des niches écologiques, les résultats montrent que trois paramètres jouent un rôle majeur dans la distribution des oursins : la profondeur, la couverture de glace et la température des eaux de surface. Toutefois, l’importance relative de ces paramètres diffère selon les espèces d’oursins étudiées. L’étude du genre Sterechinus souligne tout particulièrement ces différences. En effet, l’espèce S. neumayeri est plus sensible aux conditions environnementales qui prédominent près des côtes antarctiques (température des eaux de surface et couverture de glace), alors que S. antarcticus semble être beaucoup moins contraint par ces mêmes paramètres. La distribution potentielle de S. antarcticus est d’ailleurs beaucoup plus étendue en latitude. Cependant, S. antarcticus n’est pas présent sur l’ensemble de son aire de distribution potentielle, ceci pouvant être expliqué alternativement par le résultat (1) de facteurs océanographiques (rôle de barrière biogéographique joué par le Front Polaire), (2) d’interactions biotiques (phénomènes de compétition inter-spécifique) et (3) du contexte temporel (colonisation toujours en cours). / What are the forcing factors and main patterns of species distribution? This question is the core of macroecological issues and is of particular interest in the present context of global warming. The main objectives of this thesis were to determine the current distribution patterns of Antarctic and sub-Antarctic echinoid species at the scale of the whole Southern Ocean and to highlight the forcing factors that control them. The ecological niche modelling of 19 echinoid species showed that distribution is mainly structured in two patterns: (1) a first one represented by species that are not limited to the south of the Polar Front and distributed from the Antarctic coasts to the sub-Antarctic and cold temperate areas, and (2) a second one with species restricted to the Antarctic area. Within these two main patterns, five sub-patterns were also identified that depend on differences in the latitudinal and depth range of species groupings. In addition to this approach of biogeography by ecological niche modelling, a similarity analysis of echinoid, bivalve and gastropod fauna between bioregions of the Southern Ocean was performed at species and genus levels. This analysis reveals faunal connections between southern South America and sub-Antarctic areas in echinoids and bivalves, along with a partition between the East and West Antarctic. On the contrary, sub-Antarctic gastropod fauna show Antarctic rather than South American affinities and the Antarctic form a sole and unique province in this clade. These differences between clades are interpreted as the result of distinct biogeographic and evolutionary histories between echinoids and bivalves on the one hand, and gastropods on the other hand. The proposed hypothesis is that clades developped different evolutionary responses to the environmental changes that occurred during the Cenozoic. Finally, in the three clades, trans-Antarctic faunal connections are shown and interpreted as a result of West Antarctic Ice Sheet collapses and the setting up of trans-Antarctic sea-ways during the Pleistocene. Among the environmental parameters used for the ecological niche modelling, results show that the three following parameters play the main part in echinoid distribution: depth, sea-ice cover and sea surface temperature. However, the relative importance of these parameters depends on the species under studies. These differences are particularly emphasized in the case study of the genus Sterechinus. The species S. neumayeri is indeed the most dependent on environmental conditions that prevail along the Antarctic coasts (sea surface temperature and sea-ice cover), while S. antarcticus doesn’t seem to be so much under the control of these parameters. Accordingly, the potential distribution of S. antarcticus in latitude is the most extended. However, S. antarcticus is not present over the whole area of its potential distribution, what can be explained as the result of either (1) oceanographic factors (role of the Polar Front as a biogeographical barrier), (2) biotic interactions (inter-specific competition) or (3) the temporal context (still ongoing colonization).

A formação de águas profundas na Antártica afeta diretamente o clima global, uma vez que este processo conecta os ramos superior e inferior da circulação termohalina global (MOC). Avaliar os impactos das mudanças climáticas nestes processos é importante para compreensão do transporte global de calor pelos oceanos e para realização de projeções climáticas. Aplicando a forçante interanual Coordinated Ocean-Ice Reference (CORE), foi realizada uma simulação de 60 anos (1948-2007) utilizando o ROMS com módulos de gelo marinho e plataforma de gelo ativos. Uma rodada preliminar de 100 anos foi realizada com forçante do ano normal CORE, para gerar campos estáveis de inicialização da rodada interanual. Para ambos os experimentos adotou-se uma grade circumpolar periódica com resolução variável, alcançando cerca de 5 km na borda sul. Para investigar as massas de água foi aplicada a Análise Multiparamétrica Ótima - OMP. As principais massas de água do Mar de Ross foram identificadas: Água de Superfície Antártica (AASW), Água Circumpolar Profunda (CDW), Água de Fundo Antártica (AABW) e Água de Plataforma (SW), posteriormente separadas em Água da Plataforma de Gelo (ISW) e Água de Plataforma de Alta Salinidade (HSSW). Os resultados são consistentes com observações prévias (Bergamasco, 2002; Orsi & Wiederwohl, 2009; Budillon, 2011). A simulação interanual sugere que o Oceano Austral vem sofrendo um processo de aquecimento e diminuição de salinidade. Houve um aumento do calor advectado pela CDW e uma diminuição da salinidade das águas de plataforma e da AABW, consistente com as observações de Johnson & Doney (2006). A capacidade do modelo regional ROMS de reproduzir as águas de plataforma ISW, HSSW e a AABW é uma importante contribuição para estudos climáticos, visto que os modelos globais não conseguem representar tais processos. A inclusão de parametrizações explícitas dos processos de gelo marinho e plataforma de gelo capacita o ROMS para reproduzir os processos associados a criosfera, possibilitando a obtenção de projeções mais realísticas. / Dense water formation around Antarctica is recognized as a significant process that significantly impacts the global climate, since that\'s where the linkage between the upper and lower limbs of Global Thermohaline Circulation takes place. Assessing whether these processes may be affected by rapid climate changes and all the eventual feedbacks is crucial to fully understand the ocean heat transport and to provide quality future climate projections. Applying the Coordinated Ocean-Ice Reference (CORE) interannual forcing we have run a 50-year simulation (1948-2007) using ROMS with a new sea ice/ice shelf thermodynamics module. Another 100-year simulation forced with CORE normal year was previously run to provide stable starting fields. The normal year consists of single annual cycle of all the data that are representative of climatological conditions over decades and can be applied repeatedly for as many years of model integration as necessary. The 60-year forcing has interannually varying data from 1948 to 2007, which allows validation of model output with ocean observations. Both experiments employed a periodic circumpolar variable resolution grid reaching less than 5 km at the southern border. By applying the OMP water masses separating scheme, we were able to identify the main Ross Sea water masses: Antarctic Surface Water (AASW), Circumpolar Deep Water (CDW), Antarctic Bottom Water (AABW) and Shelf Water (SW), further separated into Ice Shelf Water (ISW) and High Salinity Shelf Water (HSSW). Results are consistent with previous observational studies (Bergamasco, 2002; Orsi & Wiederwohl, 2009; Budillon, 2011). The interannual simulation indicates that the Southern Ocean is becoming warmer and less salty. The CDW poleward heat transport increased while shelf waters salinity as well as the AABW salinity decreased during the simulation period, consistent with Johnson & Doney (2006), who have reported the export of less dense AABW. ROMS capability to represent ISW, HSSW and AABW is an important contribution to climate studies, since IPCC class models seem unable to provide reliable representations of such important processes, which may lead to projections of more realistic scenarios. This is significantly improved in this study by including more explicit sea ice/ice shelf parameretization. ROMS is able to reproduce cryosphere-linked mechanisms of dense water formation around Antarctica.

L’océan Austral abrite encore des populations exceptionnelles de prédateurs marins (manchots, albatros, phoques…). Bien qu’activement étudiés, l’approche fonctionnelle des relations proies-prédateurs souffre encore d’un manque de connaissances chez les prédateurs marins. Etudier comment ces animaux utilisent les habitats est essentiel pour mieux comprendre leur écologie. Par ailleurs, dans une période où les écosystèmes sont soumis à d’importantes pressions d’origine anthropique (surpêche, pollutions, changement climatique), la connaissance de l’écologie d’une espèce est primordiale pour bien caractériser les aires à protéger. Le gorfou macaroni Eudyptes chrysoplophus est un oiseau marin pélagique et constitue l’espèce de manchot la plus abondante dans l’océan Austral (> 6 millions de couples). Au cours des 30 dernières années, les effectifs des populations de Géorgie du Sud et de l’île Marion ont fait face à une diminution drastique (> 30%). Actuellement, les populations de gorfou macaroni des Terres Australes et Antarctiques Françaises (archipel des îles Crozet et îles Kerguelen) abritent encore plus de 50% des effectifs mondiaux. Cependant, les comportements de recherche alimentaire de ces deux populations étaient jusqu’à présent encore mal connues. Au cours de cette thèse, nous avons étudié les stratégies de recherche alimentaire du gorfou macaroni, au cours de l’intégralité de son cycle de reproduction (incubation, élevage et crèche) de Kerguelen et Crozet, îles caractérisées par des environnements océanographiques contrastés. Les ajustements du comportement alimentaire face aux contraintes énergétiques liées à la reproduction et aux variations de la production biologique de leurs environnements ont été examinés en détail. Grace à des mesures biologiques d’origine télémétrique et/ou d’appareil embarqué (trajectoires, comportement de plongées) couplées à des données satellitaires (données environnementales), nous avons pu mettre en évidence l’existence : 1) d’un comportement de recherche alimentaire spécifique et de genre : sur les 2 sites étudiés, un ajustement similaire des déplacements, de l’effort d’approvisionnement, du régime alimentaire a été observé en réponse aux contraintes énergétiques imposées par la reproduction. En incubation, les deux sexes ciblent principalement les fronts océanographiques, les tourbillons et les zones filamentaires situées en eaux pélagiques au cours de longs trajets. En période d’élevage, les femelles s’approvisionnent plus près des côtes, majoritairement sur le plateau et au bord des talus afin de pouvoir alimenter régulièrement la progéniture. En crèche, les mâles ciblent à nouveau les structures frontales tandis que les femelles s’éloignent tout en restant inféodées aux talus. A l’aide de la littérature, nous avons pu observer que cette stratégie semble opérer à l’échelle de l’aire de répartition de l’espèce. 2) d’une plasticité phénotypique inattendue : l’approche comparative entre les îles Kerguelen et Crozet a permis d’étudier les points communs et les différences des stratégies d’approvisionnement entre les deux localités, liées aux conditions environnementales locales. Les deux populations semblent toutes deux très dépendantes des pics saisonniers de productivité primaire. En revanche, des variations d’éloignements à la colonie inter - site et intra – sexe plus importantes qu’attendues ont été observées mettant en évidence une flexibilité phénotypique insoupçonnée pour un prédateur marin pélagique. Cette étude est l’une des rares ayant couvert l’ensemble d’un cycle de reproduction chez les manchots. L’importante variabilité comportementale démontrée réitère le besoin impératif de prendre en compte l’intégralité d’un cycle pour mieux comprendre et définir les stratégies d’approvisionnement d’une espèce. / The Austral Ocean still hosts a great population of marine predators (i.e. penguins, albatross, and seals). Despite well studied, the functional approach investigating the relationship between prey and predators in the marine ecosystem is still poorly known. Knowledge on habitat selection and use of marine species is essential to better understand their ecology and behaviour. The knowledge about the ecology of key species is essential to characterise and identify the areas to protect and to predict the future of populations that may be affected by global changes. This is particularly true in an area where the natural ecosystems are more and more perturbed by anthropogenic activities (i.e. over-fishing, pollution, and climate change). The Macaroni penguin is the most abundant penguin species in the Austral Ocean (> 6 millions pairs). It is also the biggest consumer of secondary resources, in terms of biomass, in the world. Over the past 30 years the Macaroni penguin populations situated in South Georgia and Marion Island suffered of 30% population decline. At the moment, Kerguelen and Crozet Islands (French Southern Territories) still host more than 50% of their global population, however the foraging behaviour of this species is still poorly known. The objective of this research is to study the different foraging behaviour strategies of a pelagic seabird : the Macaroni penguin Eudyptes chrysoplophus during its whole breeding cycle (incubation, brood, crèche). The populations’object of study breed in different oceanographic conditions : the Kerguelen and Crozet archipelagos. The variation in foraging behaviour driven by energetic constraints, which is associated to the reproduction and to the biological production, has been studied in details. Telemetry data (i e. trajectories and diving behaviour) combined with environmental data obtained by remote sensing allowed determining that : 1) Foraging strategies of Macaroni penguin breeding in two different locations differ in terms of movement, foraging effort and foraging niche during their breeding cycle in response to reproduction constraints. In incubation, both sexes carried out long journeys and targeted large oceanographic structures such as fronts, eddy and transport fronts. During the brooding phase, the females foraged closer to the colony adjusting their foraging behaviour based on their offspring needs, targeting the shelf and the slope. When crèche started, males targeted large scale structures whereas females still foraged on the slope. At this time, a shift in the diet composition was observed. 2) The comparative approach between Kerguelen and Crozet allowed to highlighting differences in foraging strategies, in response to local environmental conditions. However, greater than expected variations in foraging areas were observed inter-site and inter-sex. These results have pointed out an unexpected phenotypic flexibility for a pelagic marine predator. This research investigated the entire breeding cycle of a penguin, a fact still rare in ecology. The observed degree of behavioural variability reiterates the imperative to take into account an entire cycle to better understand and define the foraging strategies of a species.

Les foraminifères planctoniques vivants (LPF) contribuent à la pompe biologique du carbone océanique en générant des flux de Corg (cytoplasme) et de Cinorg (test calcaire). Dans cette étude, la morphométrie des tests, les abondances et les compositions spécifiques des assemblages de LPF dans l'océan Indien Sud (30°S-60°S, 50°E-80°E), ont été caractérisées à partir de la collecte par filet à plancton stratifié (Multinet) sur 19 stations échantillonnées pendant trois étés consécutifs (2012- 2014). En démontrant l'efficacité d'échantillonnage du Continuous Plankton Recorder pour spatialiser les données observées en 19 stations, l’étude de la dynamique de population des LPF montre l'effet de la position des fronts sur la production des LPF. Pour mieux contraindre l'impact des LPF dans la pompe biologique du carbone des hautes latitudes, la biomasse protéique et la masse calcique de plus de 2000 foraminifères ont été mesurées. Les différences de biomasse protéique et de poids normalisé par la taille entre années, espèces et masses d'eau suggèrent que les paramètres environnementaux affectent la production de Corg et de Cinorg des LPF. Le rôle des LPF sur la pompe biologique de carbone marin dépend des conditions hydrologiques et trophiques du milieu. Le rapport Corg/Cinorg est très différent selon les espèces considérées. L'applicabilité des tests de foraminifères planctoniques comme proxy de paléopompe du carbone dans les hautes latitudes dépendrait donc de l'effet exercé par les variations des conditions écologiques, et de la composition de l’assemblage. Cette étude propose une première estimation des budgets Corg et Cinorg produits par les LPF dans l’Océan Indien Austral. / Planktonic foraminifera contribute to the marine biological carbon pump by generating organic (cytoplasm) and inorganic (shell) carbon fluxes. In this study, we characterized LPF total abundances, assemblages and test morphometry (minimum diameter) along 19 stations sampled by stratified plankton net (Multinet), during three consecutive austral summers (2012-2014) in the Southern Indian Ocean (30°S-60°S, 50°E-80°E). By demonstrating the efficiency of CPR for LPF sampling, we analysed population dynamic between 19 multinet sampling stations, showing the effect of frontal position on LPF production. To better constrain the impact of those organisms in the biological carbon pump at high latitudes, we have quantified the individual protein-biomass and test calcite mass of more than 2000 LPF. Differences in size-normalized protein-biomass and in size-normalized weight between years, species, and water bodies suggest that environmental parameters affect the production of planktonic foraminifera organic and inorganic carbon to varying degrees. Consequently, planktonic foraminifera are assumed to affect the biological carbon pump, depending on ecological conditions and biological prerequisites. The applicability of planktonic foraminifera tests as proxy of the past biological carbon pump in high latitudes would hence critically depend on the effect exerted by changing in ecological conditions, and the presence of different species. This study proposes a first estimation of planktonic foraminifera Corg and Cinorg standing stock and fluxes in the Southern Indian Ocean.

Respiration, metabolic enzyme assays, and body composition parameters were measured in the Antarctic krill Euphausia superba during the summer, fall and winter on the Western Antarctic Peninsula (WAP). E. superba of all sizes decrease their metabolism from the summer to the winter. These same parameters were also measured along the WAP during the austral fall 2010. E. superba's enzyme activity indicated that there was a latitudinal gradient to the decline in metabolism along the WAP with the more northerly sites having significantly higher metabolic enzyme activities than the sites to the south. Carbon (δ13C) and nitrogen (δ15N) stable isotopes were measured in E. superba along the WAP to determine if there were any latitudinal trends. δ13C showed a significant trend with latitude with more depleted δ13C values in the southern portion of the WAP. Carbon (δ13C) and nitrogen (δ15N) stable isotopes were also measured in two important prey fishes along the WAP, the silverfish Pleuragramma antarcticum and the myctophid Electrona antarctica. P. antarcticum had a more variable and more enriched δ13C value than E. antarctica indicative of P. antarcticum's more neritic habitat. There were no significant differences between the δ15N values of the two fish, indicating that although they feed in different areas they were feeding at the same trophic level. Carbon (δ13C) and nitrogen (δ15N) stable isotopes were measured in twenty species in the marginal ice zone (MIZ) of the Weddell Sea at the beginning of the austral summer. Samples were taken from under the ice, at the ice edge and in the open ocean. A significant trend in the δ13C values of all species was found with the under-ice δ13C values being more depleted than those in the open ocean. This is most likely due to the reduced atmospheric exchange of CO2, upwelled water with depleted δ13C values, and continuous biological respiration under the ice, all of which contribute to very depleted δ13C values. δ15N values were significantly lower in the open ocean than the other ice conditions due to the increased reliance on primary production. The diapausing copepods Calanoides acutus and Rhincalanus gigas showed similar patterns in their isotopic signatures across the ice zones. Cluster analysis revealed trophic shifts between the different ice zones. The ice edge zone proved to contain the most species and was the best habitat for most species. The trophic shifts observed within species in the differing ice conditions mimicked the seasonal changes they undergo during the course of the productive season every year.

Both physical circulation and biogeochemical characteristics are unique in the Southern Ocean (SO) region, and are fundamentally different from those of the northern hemisphere. Moreover, according to previous research, the oceanic response to the trend of the Southern Annual Mode (SAM) has profound impacts on the future oceanic uptake of carbon dioxide in the SO. In other words, the climate and circulation of the SO are strongly coupled to the overlying atmospheric variability. However, while we have understanding on the SO physical circulation and have the ability to predict the future changes of the SO climate and physical processes, the link between the SO physical processes, the air-sea carbon flux, and correlated climate variability remains unknown. Even though scientists have been studying the spatial and temporal variability of the SO carbon flux and the associated biogeochemical processes, the spatial patterns and the magnitudes of the air-sea carbon flux do not agree between models and observations. Therefore, in this study, we utilized a modified version of a general circulation model (GCM) to performed realistic simulations of the SO carbon on seasonal to interannual timescales, and focused on the crucial physical and biogeochemical processes that control the carbon flux. The spatial pattern and the seasonal cycle of the air-sea carbon dioxide flux is calculated, and is broadly consistent with the climatological observations. The variability of air-sea carbon flux is mainly controlled by the gas exchange rate and the partial pressure of carbon dioxide, which is in turn controlled by the compensating changes in temperature and dissolved inorganic carbon. We investigated the seasonal variability of dissolved inorganic carbon based on different regional processes. Furthermore, we also investigated the dynamical adjustment of the surface carbon flux in response to the different gas exchange parameterizations, and conclude that parameterization has little impact on spatially integrated carbon flux. Our simulation well captured the SO carbon cycle variability on seasonal to interannual timescales, and we will improve our model by employ a better scheme of nutrient cycle, and consider more nutrients as well as ecological processes in our future study.