Dissertations / Theses on the topic 'Carbon biological pump'

The biological carbon pump (BCP) exports 5 - 12 Gt C yr−1 to the deep sea and is important for the distribution of carbon within the ocean. Previous studies proposed that the phytoplankton community structure and availability of dense biominerals are key in defining regional export. This thesis examines these factors and their influence on export in the Southern Ocean and the Arctic through the examination of upper ocean species composition, distribution and marine snow particles. In the Southern Ocean, the samples were collected from the high reflectance feature known as the Great Calcite Belt (GCB). The marine snow catcher was used to capture sinking particles and allowed the examination of both the large, fast sinking particles and the slow sinking fraction of particulate organic carbon (POC). The GCB was dominated by nanophytoplankton (<20μm), where the coccolithophore Emiliania huxleyi and diatoms Fragilariopsis nana, Fragilariopsis pseudonana and Pseudonitzschia sp. were the dominant species driving the variation in biogeography. The variation in biogeography was best described by a combination of temperature, nutrients and pCO2. E. huxleyi forms distinct features in the GCB on the Patagonian Shelf, near South Georgia and the Crozet Islands. A southwards progression of E. huxleyi occurs within High Nutrient Low Silica Low Chlorophyll waters in post-bloom conditions after silicic acid and iron drawdown by diatoms. When examined in terms of biomass, the diatoms dominate the GCB, although E. huxleyi was the single biggest contributor as a species. A statistical comparison of surface species and slow sinking material indicated that there was a degree of similarity between the surface and exported community but was regionally variable. Coccolithophores and diatoms contributed minimally (<10%) to upper ocean biomass and total carbon export. The results of this thesis indicate that even though the coccolithophores and diatoms are important phytoplankton for primary production, their direct contribution as cells to carbon export is low. POC flux correlated with opal flux but not calcite flux indicating that the opal was more important in driving POC flux in the GCB. Two types of sinking particles were examined, marine snow aggregates and faecal pellets and there was no significant difference between the sinking velocities. Marine snow sinking velocity was not dependent on size of the aggregate. The concentrations of biominerals and POC in the surface waters and the biominerals in the sinking particles did not influence the sinking velocity. This indicates that porosity and POC content could be more important in determining the sinking velocity and the carbon flux. The synthesis includes the species composition and biomass of the Arctic, which displayed similar trends to the GCB. The results from this thesis suggest that the slow sinking carbon export may not be significantly affected by potential changes in upper ocean biomineralising phytoplankton community structure and upper ocean chemistry. The effects of porosity and POC contents of the particles are here considered to be just as important for determining the export flux than upper ocean community structure and biomineral ballast availability. This implies that the impacts of ocean acidification will become more important deeper in the water column as biominerals become more important within sinking particles as POC is removed.

Since the 1800s, carbon dioxide emissions due to human activities have contributed significantly to the amount of carbon in the atmosphere. Approximately a third of this carbon is absorbed by the ocean, through air-sea fluxes at the ocean surface (Sabine, 2004). Increased CO2 has changed the carbon chemistry of the ocean and hence the pH. pH is expected to drop by 0.4 by the year 2100. It is unclear how this lower pH will affect carbon cycling and sequestration with respect to the biological carbon pump. Most studies have focused on open ocean phytoplankton or bacterial communities in large, stationary mesocosms. Few studies have coupled both phytoplankton and bacterial processes and even fewer have investigated coastal communities, where pH and pCO2 can vary drastically. This study focused first on developing and evaluating a mesocosm and alternative method for elevating pCO2. The second goal was to determine how potential changes in phytoplankton DOC release and community structure and the resulting carbon pool may affect bacterial secondary production and ectoenzyme activity in a natural coastal community. Mesocosms aimed to mimic natural pCO2 fluctuations by maintaining CO2 concentration of 1250 ppm in the headspace, as aqueous pCO2 may change with biological processes. Six mesocosms were filled with 40L of water from the Chesapeake Bay (three ambient pCO2 and three 1250 ppm) and monitored over 15 days. Chlorophyll a, DOC, bacterial respiration, bacterial production, and enzyme activity were measured. Bacterial production and respiration were used to calculate bacterial growth efficiency (BGE). Results showed that there was no significant difference between the ambient and elevated groups with respect to chlorophyll a, DOC, BGE and enzymes activity. However, differences in bacterial respiration and bacterial production during the first four days of the experiment may suggest that bacteria require time to acclimate to elevated pCO2. Phytoplankton and bacteria in coastal areas are exposed to a wide range of abiotic factors such as seasonal temperature variations, salinity, mixing, and terrestrial inputs. The pH of the Chesapeake Bay ranges between 7.5 and 8.3, and it is possible that the phytoplankton and bacteria are adapted to cope with a wide range of pH (Wong, 2012). This study suggests that the biological carbon pump may not be significantly altered in our future ocean.

Thesis advisor: Hilary Palevsky
The ocean plays a key role in global carbon cycling, taking up CO2 from the atmosphere. A fraction of this CO2 is converted into organic carbon through primary production in the surface ocean and sequestered in the deep ocean through a process known as the biological pump. The ability of the biological pump to sequester carbon away from the atmosphere is influenced by the interaction between the annual cycle of ocean mixed layer depth (MLD), primary production, and ecosystem processes that influence export efficiency. Gravitational sinking of particulate organic carbon (POC) is the largest component of the biological pump and the aspect that is best represented in Earth System Models (ESMs). I use ESM data from CESM2, an ESM participating in the Coupled Model Intercomparison Project Phase 6 (CMIP6), to investigate how a high-emissions climate change scenario will impact POC flux globally and regionally over the 21st century. The model simulates a 4.4% decrease in global POC flux at the 100 m depth horizon, from 7.12 Pg C/yr in the short-term (2014-2034) to 6.81 Pg C/yr in the long-term (2079-2099), indicating that the biological pump will become less efficient overall at sequestering carbon. However, the extent of change varies across the globe, including the largest POC flux declines in the North Atlantic, where the maximum annual MLD is projected to shoal immensely. In the future, a multi-model comparison across ESMs will allow for further analysis on the variability of these changes to the biological pump
Thesis (BS) — Boston College, 2021
Submitted to: Boston College. College of Arts and Sciences
Discipline: Departmental Honors
Discipline: Earth and Environmental Science

Export of photosynthetically produced organic matter, from the sunlit to the dark ocean, in the form of sinking particles represents the major mechanism of the biological carbon pump that removes CO2 from the atmosphere. Most of the organic matter bound in sinking particles undergoes microbial remineralisation while traversing the water column, thereby causing CO2 and inorganic nutrients to be released. Increasing evidence indicates that most remineralisation does not occur directly on sinking particles, but rather on suspended particles and dissolved organic matter resulting from their disaggregation and solubilisation. Most particulate organic carbon in the mesopelagic ocean is bound to suspended particles, which represent a major substrate for heterotrophic organisms. Despite their crucial importance, suspended particles and their associated microbial communities have been largely overlooked in favour to sinking particles. This thesis presents the first comparison of diversity and functionalities between microbial communities associated with suspended and sinking particles. Using amplicon sequencing of small-subunit ribosomal RNA genes on particles collected with a marine snow catcher deployed in the Southern Ocean, this thesis demonstrates that prokaryotic communities associated with suspended and sinking particles differ significantly. Particle-associated remineralising bacteria showed a clear preference for either particle-type likely relating to differential organic matter composition. Suspended particles from the upper-mesopelagic were predominately composed of prymnesiophytes and soft-tissue animals, while more efficient carbon export from diatoms was indicated by their prevalence in sinking particles. Eukaryotic sequences associated with suspended and sinking particles were largely dominated by heterotrophic protists, highlighting their major contribution to particulate organic matter remineralisation in the upper-mesopelagic. Finally, remineralisation activities, as well as nitrogen and sulphur cycling, were investigated by comparing metatranscriptomes of various particle-types collected in the North Atlantic. Free-living, small sinking and small suspended particle-associated microbes appeared most active in the remineralisation of simple organic compounds, while large suspended particles acted as the main venue of complex organic matter remineralisation. Additionally, actively expressed genes related to anaerobic processes in small particles corroborate recent postulations that marine particles may serve as oxygen-deficient microniches, and hence, may be key to redox cycling of elements in the ocean. Overall, this dissertation highlights differences between suspended and sinking particles as well as their potential biogeochemical implications in the ocean and provides further insights into constraints shaping the oceanic biological carbon pump.

The Southern Ocean (ca. 20% of the world ocean surface) is a key place for the regulation of Earth climate thanks to its capacity to absorb atmospheric carbon dioxide (CO2) by physico-chemical and biological mechanisms. The biological carbon pump is a major pathway of absorption of CO2 through which the CO2 incorporated into autotrophic microorganisms in surface waters is transferred to deep waters. This process is influenced by the extent of the primary production and by the intensity of the remineralization of organic matter along the water column. So, the annual cycle of sea ice, through its in situ production and remineralization processes but also, through the release of microorganisms, organic and inorganic nutrients (in particular iron)into the ocean has an impact on the carbon cycle of the Southern Ocean, notably by promoting the initiation of phytoplanktonic blooms at time of ice melting.

The present work focussed on the distribution of organic matter (OM) and its interactions with the microbial network (algae, bacteria and protozoa) in sea ice and ocean, with a special attention to the factors which regulate the biological carbon pump of the Southern Ocean. This thesis gathers data collected from a) late winter to summer in the Western Pacific sector, Western Weddell Sea and Bellingshausen Sea during three sea ice cruises ARISE, ISPOL-drifting station and SIMBA-drifting station and b) summer in the Sub-Antarctic and Polar Front Zone during the oceanographic cruise SAZ-Sense.

The sea ice covers were typical of first-year pack ice with thickness ranging between 0.3 and 1.2 m, and composed of granular and columnar ice. Sea ice temperature ranging between -8.9°C and -0.4°C, brines volume ranging between 2.9 to 28.2% and brines salinity from 10 to >100 were observed. These extreme physicochemical factors experienced by the microorganisms trapped into the semi-solid sea ice matrix therefore constitute an extreme change as compared to the open ocean. Sea ice algae were mainly composed of diatoms but autotrophic flagellates (such as dinoflagellates or Phaeocystis sp.) were also typically found in surface ice layers. Maximal algal biomass was usually observed in the bottom ice layers except during SIMBA where the maxima was localised in the top ice layers likely because of the snow and ice thickness which limit the light available in the ice cover. During early spring, the algal growth was controlled by the space availability (i.e. brine volume) while in spring/summer (ISPOL, SIMBA) the major nutrients availability inside sea ice may have controlled algal growth. At all seasons, high concentrations of dissolved and particulate organic matter were measured in sea ice as compared to the water column. Dissolved monomers (saccharides and amino acids) were accumulated in sea ice, in particular in winter. During spring and summer, polysaccharides constitute the main fraction of the dissolved saccharides pool. High concentrations of transparent exopolymeric particles (TEP), mainly constituted with saccharides, were present and their gel properties greatly influence the internal habitat of sea ice, by retaining the nutrients and by preventing the protozoa grazing pressure, inducing therefore an algal accumulation. The composition as well as the vertical distribution of OM in sea ice was linked to sea ice algae.

Besides, the distribution of microorganisms and organic compounds in the sea ice was also greatly influenced by the thermodynamics of the sea ice cover, as evidenced during a melting period for ISPOL and during a floodfreeze cycle for SIMBA. The bacteria distribution in the sea ice was not correlated with those of algae and organic matter. Indeed, the utilization of the accumulated organic matter by bacteria seemed to be limited by an external factor such as temperature, salinity or toxins rather than by the nature of the organic substrates, which are partly composed of labile monomeric saccharides. Thus the disconnection of the microbial loop leading to the OM accumulation was highlighted in sea ice.

In addition the biofilm formed by TEP was also involved in the retention of cells and other compounds(DOM, POM, and inorganic nutrients such as phosphate and iron) to the brine channels walls and thus in the timing of release of ice constituents when ice melts. The sequence of release in marginal ice zone, as studied in a microcosm experiments realized in controlled and trace-metal clean conditions, was likely favourable to the development of blooms in the marginal ice zone. Moreover microorganisms derived from sea ice (mainly <10 µm) seems able to thrive and grow in the water column as also the supply of organic nutrients and Fe seems to benefit to the pelagic microbial community.

Finally, the influence of the remineralization of organic matter by heterotrophic bacterioplankton on carbon export and biological carbon pump efficiency was investigated in the epipelagic (0-100 m) and mesopelagic(100-700 m) zones during the summer in the sub-Antarctic and Polar Front zones (SAZ and PFZ) of the Australian sector (Southern Ocean). Opposite to sea ice, bacterial biomass and activities followed Chl a and organic matter distributions. Bacterial abundance, biomass and activities drastically decreased below depths of 100-200 m. Nevertheless, depth-integrated rates through the thickness of the different water masses showed that the mesopelagic contribution of bacteria represents a non-negligible fraction, in particular in a diatom-dominated system./

L’océan Antarctique (± 20% de la surface totale des océans) est un endroit essentiel pour la régulation du climat de notre planète grâce à sa capacité d’absorber le dioxyde de carbone (CO2) atmosphérique par des mécanismes physico-chimique et biologique. La pompe biologique à carbone est un processus majeur de fixation de CO2 par les organismes autotrophes à la surface de l’océan et de transfert de carbone organique vers le fond de l’océan. Ce processus est influencé par l’importance de la production primaire ainsi que par l’intensité de la reminéralisation de la matière organique dans la colonne d’eau. Ainsi, le cycle annuel de la glace via sa production/reminéralisation in situ mais aussi via l’ensemencement de l’océan avec des microorganismes et des nutriments organiques et inorganiques (en particulier le fer) a un impact sur le cycle du carbone dans l’Océan Antarctique, notamment en favorisant l’initiation d’efflorescences phytoplanctoniques dans la zone marginale de glace.

Plus précisément, nous avons étudié les interactions entre le réseau microbien (algues, bactéries et protozoaires) et la matière organique dans le but d’évaluer leurs impacts potentiels sur la pompe biologique de carbone dans l’Océan Austral. Deux écosystèmes différents ont été étudiés :la glace de mer et le milieu océanique grâce à des échantillons prélevés lors des campagnes de glace ARISE, ISPOL et SIMBA et lors de la campagne océanographique SAZ-Sense, couvrant une période allant de la fin de l’hiver à l’été.

La glace de mer est un environnement très particulier dans lequel les microorganismes planctoniques se trouvent piégés lors de la formation de la banquise et dans lesquels ils subissent des conditions extrêmes de température et de salinité, notamment. Les banquises en océan ouvert étudiées (0,3 à 1,2 m d’épaisseur, températures de -8.9°C à -0.4°C, volumes relatifs de saumure de 2.9 à 28.2% et salinités de saumures entre 10 et jusque >100) étaient composées de glace columnaire et granulaire. Les algues de glace étaient principalement des diatomées mais des flagellés autotrophes (tels que des dinoflagellés ou Phaeocystis sp.) ont été typiquement observés dans les couches de glace de surface. Les biomasses algales maximales se trouvaient généralement dans la couche de glace de fond sauf à SIMBA où les maxima se trouvaient en surface, probablement en raison de l’épaisseur des couches de neige et de glace, limitant la lumière disponible dans la colonne de glace. Au début du printemps, la croissance algale était contrôlée par l’espace disponible (càd le volume des saumures) tandis qu’au printemps/été, la disponibilité en nutriments majeurs a pu la contrôler. A toutes les saisons, des concentrations élevées en matière organique (MO) dissoute et particulaire on été mesurées dans la glace de mer par rapport à l’océan. Des monomères dissous (sucres et acides aminés) étaient accumulés dans la glace, surtout en hiver. Au printemps et été, les polysaccharides dissous dominaient le réservoir de sucres. La MO était présente sous forme de TEP qui par leurs propriétés de gel modifie l’habitat interne de la glace. Ce biofilm retient les nutriments et gêne le mouvement des microorganismes. La composition et la distribution de la MO dans la glace étaient en partie reliées aux algues de glace. De plus, la thermodynamique de la couverture de glace peut contrôler la distribution des microorganismes et de la MO, comme observé lors de la fonte de la glace à ISPOL et lors du refroidissement de la banquise à SIMBA. La distribution des bactéries n’est pas corrélée avec celle des algues et de la MO dans la glace. En effet, la consommation de la MO par les bactéries semble être limitée non pas par la nature chimique des substrats mais par un facteur extérieur affectant le métabolisme bactérien tel que la température, la salinité ou une toxine. Le dysfonctionnement de la boucle microbienne menant à l’accumulation de la MO dans la glace a donc été mis en évidence dans nos échantillons.

De plus, le biofilm formé par les TEP est aussi impliquée dans l’attachement des cellules et autres composés aux parois des canaux de saumure et donc dans la séquence de largage lors de la fonte. Cette séquence semble propice au développement d’efflorescences phytoplanctoniques dans la zone marginale de glace. Les microorganismes originaires de la glace (surtout ceux de taille < 10 μm) semblent capables de croître dans la colonne d’eau et l’apport en nutriments organiques et inorganiques apparaît favorable à la croissance des microorganismes pélagiques.

Enfin, l’influence des activités hétérotrophes sur l’export de carbone et l’efficacité de la pompe biologique à carbone a été évaluée dans la couche de surface (0-100 m) et mésopélagique (100-700 m) de l’océan. Au contraire de la glace, les biomasses et activités bactériennes suivaient les distributions de la chlorophyll a et de la MO. Elles diminuent fortement en dessous de 100-200 m, néanmoins les valeurs intégrées sur la hauteur de la colonne d’eau indiquent que la reminéralisation de la MO par les bactéries dans la zone mésopélagique est loin d’être négligeable, spécialement dans une région dominée par les diatomées.

Doctorat en Sciences agronomiques et ingénierie biologique
info:eu-repo/semantics/nonPublished

Iron (and silicate) (co-)limitation of phytoplankton is considered a primary cause of the Southern Ocean's inefficient biological pump. However, the role of phytoplankton community structure and response to nutrient cycling remains poorly understood. In a mass balance sense, phytoplankton consumption of new nitrogen (N; e.g., allochthonous nitrate) is proportional to net carbon (C) export, while growth fueled by recycled N (e.g., ammonium) yields no net C flux. The N isotope ratio (δ15N) of surface biomass has long been used as an integrative tracer of new versus regenerated uptake. This approach is rendered more accurate by coupling either fluorescence-activated cell sorting (FACS; of nano- and picophytoplankton; 0.4-20 μm) or microscopy (for microphytoplankton; >20 um) with groupspecific δ15N measurements. Samples were collected for the analysis of nutrients and nitrate-, FACS-, and microscopy-δ15N on a mid-summer transect of the Subantarctic Indian basin during the 2016/17 Antarctic Circumnavigation Expedition (ACE) cruise. The data show that all phytoplankton populations preferentially utilize nitrate (≥55%) across the Indian Sector of the Subantarctic, potentially driving higher C export potential than previously estimated. Indeed, near the Subantarctic islands, 72% of microand >80% of nano- and picophytoplankton growth is supported by nitrate. This is likely due to the partial alleviation of phytoplankton iron and silicate stress, largely as a result of bathymetric upwelling, which constitutes a manifestation of the island mass effect. C export potential is lower in the open ocean region away from the islands where iron stress has been shown to be higher; here, nitrate supports >55% of micro- and picophytoplankton and 7 to 79% of nanophytoplankton growth. In terms of relative abundance (RA), the open Subantarctic is dominated by picoeukaryotes (64%), although there exists a large disconnect between relative abundance and potential contribution to C export. The three largest surface-ocean phytoplankton populations included in this study – microphytoplankton, cryptophytes, and nanoeukaryotes – each contribute ~30% to the total C export potential across the Subantarctic Indian sector while picophytoplankton contribute ~5%. Thus, as has been concluded previously, the larger phytoplankton size classes are disproportionately important drivers of the Subantarctic biological pump. Other interesting ecological findings include diatom-dominated microphytoplankton populations apparently fueled by a significant fraction of regenerated N, even in areas of iron supply, and Synechococcus relying near-exclusively on new N, in contrast to subtropical observations. Additionally, the abundance of Synechococcus appears to be controlled by the availability of iron across the Subantarctic, with silicate and temperature playing a supporting role.

Le terme plancton désigne l'ensemble des organismes dérivant au grès des courants marins. On distingue le plancton végétal et principalement photosynthétique, "le phytoplancton", du plancton animal hétérotrophe, "le zooplancton". Au cours des dernières décennies, de nombreuses études ont documenté une croissance de l'abondance et de la distribution spatiale du zooplancton gélatineux à travers diverses régions. Même si le terme "gélification" des océans doit être utilisé avec beaucoup de précaution, des régions comme la mer Méditerranée montre une constante augmentation des méduses au cours de ces 40 dernières années. L'espèce Pelagia noctiluca (Forsskål, 1775) est considérée comme étant la méduse la plus abondante du bassin méditerranéen depuis les années 70. Du fait de leur présence massive dans cette région, il est primordial d'évaluer précisément l'impact de P. noctiluca à la fois sur les cycles biogéochimiques et sur la structuration des écosystèmes pélagiques. Pour cela, les deux processus majeurs de transfert de matière dans l'écosystème doivent être étudiés : la séquestration de carbone via la pompe biologique et le transfert de carbon au travers des réseaux trophiques. Cette thèse s'articule autour de trois axes majeurs: (i) réaliser un premier bilan de l'export de carbone organique particulaire (POCtotal) et dissous (DOC) en mer Méditerranée, (ii) construire un modèle écophysiologique de P. noctiluca pour déterminer la contribution de cette méduse à la pompe biologique, et (iii) évaluer le niveau trophique de P. noctiluca et son potentiel impact sur les niveaux trophiques inférieurs
The term “plankton” refers to all the organisms drifting in the water following the currents. Commonly, the vegetable autotrophic and mainly photosynthetic, “phytoplankton” is distinguished from the heterotrophic and animal “zooplankton”. In the last decades, many studies reported an increase in the abundances and spatial distributions of gelatinous zooplankton in many oceans. Even if the concept of “jellyfication of the oceans” needs to be used with caution, jellyfish populations show an increase in Mediterranean Sea over the last 40 years. The species Pelagia noctiluca (Forsskål, 1775) is considered as the most abundant jellyfish in the Mediterranean basin since the 70s. Due to its massive presence in this area, it is essential to evaluate precisely the impact of P. noctiluca on both biogeochemical cycles and pelagic ecosystem structure. Thus, the contribution of P. noctiluca to the two main factors regulating the biological carbon transfer in the oceans: carbon sequestration via the biological carbon pump and carbon transfer through trophic networks. This manuscript is divided in 3 main sections : (i) providing an initial budget of the particulate (POCtotal) and dissolved organic carbon (DOC) in the Mediterranean sea, (ii) building an ecophysiological model of P. noctiluca to estimate its contribution to the biological carbon pump, and (iii) assessing the trophic level of P. noctiluca and its potential impact on lower trophic levels

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

Les rivières sont une source importante de constituants biogéochimiques pour les océans. Jusqu’à présent, les modèles océaniques globaux représentaient de manière inadéquate ou ignoraient simplement les apports continentaux de nutriments, de carbone, d’alcalinité provenant des rivières. En particulier, les perturbations anthropiques des apports fluviaux au cours du 20 ème siècle et leurs conséquences sur l’état physique et biogéochimique des océans - notamment la zone côtière - n’ont pas encore été analysées à l’aide d’un modèle global prenant en compte la circulation tridimensionnelle de l’océan. L’objectif principal de cette thèse était donc d’intégrer les apports biogéochimiques provenant des rivières dans un modèle océanique global afin d’améliorer la compréhension du cycle du carbone de l’océan côtier et son évolution au cours du 20 ème siècle. Dans un premier temps, mon travail a visé à l’amélioration des connaissances concernant le rôle des apports biogéochimiques fluviaux sur le cycle du carbone océanique à long-terme, en se focalisant sur la période préindustrielle. Pour cela, j’ai estimé les apports des rivières en utilisant des modèles permettant d’estimer l’érosion chimique et le transfert de matière organique desécosystèmes terrestres à l’océan. Ces apports fluviaux ont ensuite été ajoutés dans le modèle biogéochimique océanique HAMOCC et leurs impacts sur la production primaire océanique et les flux de CO2 entre l’atmosphère et l’océan ont été analysés. Les résultats nous ont permis de quantifier un dégazage de CO 2 préindustriel de 0.23 Pg C yr -1 pour l’océan global, principalement localisé à proximité de l’embouchure des rivières. Le modèle a également démontré l’existence d’un transfert inter-hémisphèrique de carbone, avec un plus grand apport des rivières à l’océan dans l’hémisphère nord, et un transfert de l’hémisphère nord à l’hémisphère sud où un dégazage net se produit. Une augmentation considérable de la production primaire océanique induite par les apports des rivières a également été prédite.La modélisation biogéochimique de l’océan côtier a ensuite été améliorée, en augmentant la vitesse de minéralisation de la matière organique dans les sédiments côtiers et en incluant la dégradation de la matière organique dissoute d’origine terrestre (tDOM) dans l’océan. Par ailleurs, notre analyse suggère un temps de résidence des eaux dans la zone côtière significativement plus courte (14-16 mois en moyenne) que celui estimé jusqu’à présent (>4 ans). Ce temps de courte résidence implique un transfert efficace de matière organiquede l’océan côtier à l’océan ouvert, un état autotrophe net de l’océan côtier, ainsi qu’un puit de CO 2 (0.06-0.08 Pg C yr -1) pour la période préindustrielle, contrairement aux hypothèses précédemment proposées dans la littérature.Dans le dernier chapitre, les perturbations océaniques induites par les changements de la concentration en CO 2 dans l’atmosphère, de la physique de l’océan et des apports biogéochimiques fluviaux au cours du 20 ème siècle ont été analysées. Les résultats indiquent que la réduction de production primaire nette (NPP) observée dans les océans tropicaux et subtropicaux, pourrait être entièrement compensée par une augmentation de la NPP dans l’océan austral et dans les systèmes côtiers de type «EBUS». Les simulations montrent aussi que l’augmentation des apports fluviaux provoque une augmentation de NPP océanique à l’échelle de l’océan côtier (+15 %) et à l’échelle globale (+ 4 %). En conclusion, cette thèse a permis de démontrer l’importance d’inclure la variabilité spatio-temporelle des apports fluviaux et des processus biogéochimiques de l’océan côtier dans la description du cycle du carbone océanique global. Les améliorations apportées au modèle océanique global HAMOCC permettront d’affiner les prédictions du rôle de l’océan dans le cycle du carbone au cours du 21 ème siècle.
River deliver vast amounts of terrestrially derived compounds to the ocean. These fluxes are of particular importance for the coastal ocean, which is recognized as a region of disproportionate contribution to global oceanic biological fluxes. Until now, the riverine carbon, nutrient and alkalinity inputs have been poorly represented or omitted in global ocean biogeochemistry models. In particular, there has yet to be a model that considers the pre-industrial riverine loads of biogeochemical compounds to the ocean, and terrestrial inputs of organic matter are greatly simplified in their composition and reactivities in the ocean. Furthermore, the coastal ocean and its contribution to the globalcarbon cycle have remained enigmatic, with little attention being paid to this area of high biological productivity in global model analysis of carbon fluxes. Lastly, 20 th century perturbations in riverine fluxes as well as of the physical and biogeochemical states of the coastal ocean have remained unexplored in a 3-dimensional model. Thus, the main goals of this thesis are to integrate an improved representation of riverine supplies in a global ocean model, as well as to improve the representation of the coastal ocean in the model, in order to solve open questions with respect its global contributions to carbon cycling.In this thesis, I first aimed to close gaps of knowledge in the long-term implications of pre-industrial riverine loads for the oceanic cycling of carbon in a novel framework. I estimated pre-industrial biogeochemical riverine loads and their spatial distributions derived from Earth System Model variables while using a hierarchy of state-of-the-art weathering and organic matter land-ocean export models. I incorporated these loads into the global ocean biogeochemical model HAMOCC and investigated the induced changes in oceanic biological production and in the air-sea carbon flux, both at the global scale and in a regional shelf analysis. Finally, I summarized the results by assessing the net land sink of atmospheric carbon prescribed by the terrestrial models, and comparing it to the long-term carbon outgassing determined in the ocean model. The study reveals a pre-industrial oceanic outgassing flux of 231 Tg C yr -1 ,which is found to a large degree in proximity to the river mouths. The model also indicates an interhemispheric transfer of carbon from dominant northern hemisphere riverine inputs to outgassing in the southern hemisphere. Furthermore, I observe substantial riverine-induced increases in biological productivity in the tropical West Atlantic (+166 %), the Bay of Bengal (+377 %) and in the East China Sea (+71 %), in comparison to a model simulation which does not consider the riverine inputs.In addition to considering supplies provided by riverine fluxes, the biogeochemical representation of the coastal ocean is improved in HAMOCC, by firstly increasing organic matter remineralization rates in the coastal sediment and by secondly explicitly representing the breakdown process of terrestrial dissolved organic matter (tDOM) in the ocean. In an analysis of the coastal fluxes, the model shows a much shorter residence time of coastal waters (14-16 months) than previously assumed, which leads to an efficient cross-shelf transport of organic matter and a net autotrophic state for both the pre-industrial timeframe and the present day. The coastal ocean is also revealed as a CO2 sink for the pre-industrial time period (0.06-0.08 Pg C yr -1 ) in contrary to to the suggested source in published literature. The sink is however not only caused by the autotrophic state of the coastal ocean, but it is likely also strongly influenced by the effects of biological alkalinity production, as well as both physical and biogeochemical characteristics of open ocean inflows.In the final chapter, 20 th century oceanic perturbations due to changes in atmospheric CO 2 concentrations and in the physical climate, and to increases in riverine nutrient supplies were investigated by using sequential model simulations. The model results show that the decrease in the net primary production (NPP) in the tropical and subtropical oceans due to temperature-induced stratification may be completely compensated by increases in the Southern Ocean and in Eastern Boundary Upwelling Systems (EBUS). The model also reveals that including increases in riverine supplies causes a global ocean NPP increase of +4 %, with the coastal ocean being a particularlystrongly affected region (+15 %).This thesis shows a strong necessity to represent spatio-temporal changes in riverine supplies and of the coastal ocean state in spatially explicit global models in order to assess changes of the global cycling of carbon in the ocean in the past and potentially in the future.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

Les cycles océaniques du carbone et des principaux nutriments sont mal connus car ils sont affectés par de nombreux puits et sources physiques, chimiques ou biologiques difficiles à estimer par des mesures directes. Une manière de mieux contraindre ces processus importants est d’utiliser l’information contenue dans des traceurs plus simples : les proxies. Le radium 228 (228Ra), émis par les plateaux continentaux, est utilisé comme proxy des flux d’eau et d’éléments minéraux de la côte vers l’océan ouvert. Il permet en particulier d’estimer les flux d’eau souterraine ou SGDs (Submarine Groundwater Discharge). Le thorium 234(234Th), insoluble, permet quant à lui de contraindre la dynamique des particules par lesquelles il est adsorbé. Il est régulièrement utilisé pour estimer la pompe biologique du carbone (PBC), c’est-à-dire le flux de carbone de la surface vers l’océan profond.Au cours de cette thèse, un modèle numérique à une résolution de 2° a été construit pour chacun de ces deux radio-isotopes, en s’appuyant sur la circulation du modèle NEMO-OPA et les champs de particules du modèle PISCES. Plusieurs paramètres inconnus des modèles ont été contraints par des observations dans le cadre d’une méthode inverse.La modélisation inverse du 228Ra a permis d’estimer les flux de 228Ra venant de 38 régions côtières. En revanche, l’estimation des SGDs est imprécise, car les SGDs sont difficiles à distinguer d’une autre source de 228Ra: la diffusion par les sédiments.La modélisation inverse du 234Th a permis d’estimer les coefficients de partage du 234Th, qui représentent l’affinité de différents types de particules pour cet isotope. Elle a aussi permis d’estimer les erreurs associées à quelques simplifications courantes dans les études de la PBC fondées sur le 234Th
The oceanic cycles of carbon and the main nutrients are poorly known since they are affected by many physical, chemical or biological sources and sinks that are difficult to estimate by direct measurements.One way to better constrain these important processes is to use the information contained in more simple tracers called "proxies". As radium 228 (228Ra) flows from the continental shelves, it is used as a proxy of water and mineral elements fluxes from the coast to the open ocean. In particular, it is often used to estimate the SGD (Submarine Groundwater Discharge). For its part, thorium 234 (234Th), an insoluble radio-isotope, is used to constrain the dynamics of the solid particles onto which it is adsorbed. The carbon flux from the surface to the deep ocean, called "biological carbon pump" (BCP), is often estimated by a 234Th-based method.During this PhD, a numerical model with a resolution of 2°, based on the circulation of the NEMO-OPA model and the particle fields of the PISCES model, was built for each of the two radioisotopes.Several unknown model parameters were constrained by observations using an inverse technique.The inverse modeling of 228Ra was used to constrain 228Ra fluxes from 38 coastal regions.However, the SGD fluxes are poorly constrained by this method, because SGD can be confused with another source of 228Ra: diffusion from sediments.The inverse modeling of 234Th produced estimates of partition coefficients, representing the affinity of different particle types for this isotope. It was also used to estimate the errors associated with some common simplifications made in 234Th-based BCP studies

L’objectif principal de cette thèse est de mieux comprendre les différents facteurs contrôlant la pompe biologique de carbone en Atlantique Nord et dans l’Océan Austral, à proximité des îles Kerguelen, en utilisant notamment deux approches: le Thorium-234 (234Th) et le baryum biogénique (Baxs).En Atlantique Nord, les flux d’export de carbone organique particulaire (POC) augmentent lorsqu’ils sont associés à des minéraux biogéniques (silice biogénique et carbonate de calcium) et lithogènes, capable de lester les particules. L’efficacité d’export, généralement plus faible que précédemment supposé (< 10%), est inversement corrélée à la production, soulignant un décalage temporel entre production et export. La plus forte efficacité de transfert, i.e. la fraction de POC atteignant 400m, est reliée à des particules lestées par du carbonate de calcium ou des minéraux lithogènes.Les flux de reminéralisation mésopélagique sont similaires ou parfois supérieurs aux flux d’exports et dépendent de l’intensité du développement phytoplanctonique, de la structure en taille, des communautés phytoplanctoniques et des processus physiques (advection verticale).Comme observé pour le POC, l’export des éléments traces est influencé par les particules lithogènes provenant des marges océaniques, mais aussi des différentes espèces phytoplanctoniques.Dans l’Océan Austral, la zone à proximité de l’île de Kerguelen est naturellement fertilisée en fer, augmentant les flux d’export de fer, d’azote et de silice biogénique. Il a été démontré que la variabilité des flux dépendait des communautés phytoplanctoniques dans la zone fertilisée
The main objective of this thesis is to improve our understanding of the different controls that affect the oceanic biological carbon pump. Particulate export and remineralization fluxes were investigated using the thorium-234 (234Th) and biogenic barium (Baxs) proxies.In the North Atlantic, the highest particulate organic carbon (POC) export fluxes were associated to biogenic (biogenic silica or calcium carbonate) and lithogenic minerals, ballasting the particles.Export efficiency was generally low (< 10%) and inversely related to primary production, highlighting a phase lag between production and export. The highest transfer efficiencies, i.e. the fraction of POC that reached 400m, were driven by sinking particles ballasted by calcite or lithogenic minerals.The regional variation of mesopelagic remineralization was attributed to changes in bloom intensity, phytoplankton cell size, community structure and physical forcing (downwelling). Carbon remineralization balanced, or even exceeded, POC export, highlighting the impact of mesopelagic remineralization on the biological pump with a near-zero, deep carbon sequestration for spring 2014.Export of trace metals appeared strongly influenced by lithogenic material advected from the margins. However, at open ocean stations not influenced by lithogenic matter, trace metal export rather depended on phytoplankton activity and biomass.A last part of this work focused on export of biogenic silica, particulate nitrogen and iron near the Kerguelen Island. This area is characterized by a natural iron-fertilization that increases export fluxes. Inside the fertilized area, flux variability is related to phytoplankton community composition

La pompe biologique de carbone transfère le CO2 de l’atmosphère vers l’océan profond sous forme de matière organique particulaire. En formant des agrégats, les diatomées contribuent fortement au flux de particules. Les copépodes, en terme d’abondance et de diversité, dominent le zooplancton, sont les principaux consommateurs des diatomées et jouent un rôle important dans l’export de carbone via l’émission de pelotes fécales. Les limitations en sels nutritifs surviennent majoritairement en fin d’efflorescence phytoplanctonique, mais sont également une conséquence attendue du réchauffement global. L’objectif de la thèse vise à évaluer le rôle des interactions copépodes/diatomées sur l’export de carbone, dans un contexte de changement climatique. Les résultats obtenus démontrent que les limitations en affectant la composition biochimique des diatomées, influencent l’activité alimentaire des copépodes, ainsi que l’efficacité d’export par les pelotes fécales. J’ai également démontré que les traits fonctionnels des copépodes peuvent influencer à la fois la formation d’agrégats et leurs dynamiques. Enfin, via l’utilisation de données d’une campagne océanographique réalisée au cours de l’efflorescence printanière phytoplanctonique en Arctique, j’ai observé que la limitation en silicium après le retrait de la glace de mer contribue à la formation d’agrégats. Les copépodes en fin d’efflorescence migrent sous la couche de mélange là où les agrégats sont les plus abondants, ce qui peut suggérer que les agrégats soient utilisés comme source de nourriture
The biological carbon pump transfers CO2 from the atmosphere to the deep ocean as particulate organic matter. By forming aggregates, diatoms contribute strongly to the particle flux.Copepods, in terms of abundance and diversity, dominate zooplankton assemblages, are the main consumers of diatoms and play and key role in the carbon export via faecal pellets egestion. Nutrient limitations mainly occur at the end of phytoplankton blooms, but are also an expected consequence of global warming. The aim of the thesis is to evaluate the role of copepod/diatom interactions on carbon export in a context of climate change.The results obtained show that nutrient limitations affecting diatoms biochemical composition, that influences copepods feeding activity and the export efficiency of faecal pellets. I have also shown that the functional traits of copepods can influence both the aggregates formation and their dynamics. Finally, using data from an oceanographic campaign carried out during the Arctic phytoplankton spring bloom, I observed that silicon limitation after sea ice retreat contributes to the aggregates formation. Copepods, at the end of the bloom migrate under the mixing layer where the aggregates are most abundant, which may suggest that the aggregates could be used as a food

A travers les époques géologiques, l'océan Austral a joué un rôle majeur dans la régulation du climat à la surface de la Terre et en particulier dans la réduction de la concentration en CO2 atmosphérique. Cette région océanique est la plus importante pompe biologique de carbone et à travers la photosynthèse du phytoplancton permet la séquestration du carbone dans les profondeurs océaniques. Cette diminution aurait été causée par les dépôts de poussières qui par apportant des éléments comme le fer dans les régions limitées en nutriments, fertilise la surface des océans et permet l'activation de la pompe biologique de carbone. Aujourd'hui, l'entrée dans l'ère de l'Anthropocène a été marqué par l'impact que l'activité humaine exerce sur son environnement. L'activité anthropique génère et largue du dioxyde de carbone dans l'atmosphère provoquant un effet de serre sur la Terre altérant l'équilibre environnemental. Cette étude explore l'océan Austral qui est une zone de paradoxe biogéochimique avec de fortes concentrations en macronutriments, mais avec une faible productivité biologique. En 1990, John Martin a élaboré la « Iron Hypothesis » ou le fer (micronutriment) restreint la croissance phytoplanctonique. La poussière est une source majeure de métaux pour l'océan de surface. Dans l'océan Austral, les poussières ont une origine majoritairement d'Amérique du Sud (poussière patagonienne). Les apports d'Amérique du Sud contribuent pour 58% de la poussière totale dans l'océan Austral et seront multipliés par deux avec les futurs changements environnementaux. Pendant le dernier maximum glaciaire dans l'océan Austral, les apports de poussières auraient diminué la concentration en CO2 dans l'atmosphère. A de plus petites échelles de temps, des tests de fertilisation artificielle de fer ont été réalisés dans l'océan Austral et ont montré une forte productivité biologique. L'objectif de ce travail est de mieux caractériser et de quantifier la fraction de métaux qui se solubilise de la poussière patagonienne dans l'eau de mer sous des conditions actuelles et futures (2100) et d'améliorer les prédictions de l'évolution du phytoplancton dans la réponse à l'intensification de l'apport de poussières patagoniennes et des autres changements environnementaux dans l'océan Austral dans le but d'évaluer les impacts sur la production de carbone
Throughout geological time, the Southern Ocean has played a major role in regulating the Earth's surface climate and in particular in the reduction of atmospheric CO2. This oceanic region is the most important biological pump of carbon and through the photosynthesis of phytoplankton allows the sequestration of carbon in the deep ocean. This decrease would have been caused by dust deposits which, by bringing elements such as iron in areas limited in micronutrients, fertilize the ocean surface and allow the activation of the biological carbon pump. Nowadays, the entering into the Anthropocene era has been marked by the impact that human activity has exerted on its environment. Anthropogenic activity that generates the release of carbon dioxide into the atmosphere causes a greenhouse effect on the surface of the Earth and upsets the environmental balance. This study investigates the Southern Ocean which is biogeochemical paradox zone with high concentration of macronutrients but low biological productivity. In 1990 John Martin elaborated the "Iron hypothesis" hence iron (micronutrients) restricts phytoplankton growth. Dust is major source of metals in the surface ocean. In the Southern Ocean, dust have mainly a South America (Patagonian dust) origin. Input from South America contributed to 58% of the total dust into the Southern Ocean and will increase by two fold higher with the future environmental changes. During the last glacial maximal in the Southern Ocean, dust input would have decreased the CO2 concentration in the atmosphere. Moreover, in the small timescale there are tests of artificial iron fertilization performed in Southern Ocean have demonstrated high biological productivity. The overall aim of this work is to better characterize and quantify the fraction of metals that solubilizes from Patagonian dust in seawater under actual and future conditions (2100) and to improve predictions of the phytoplankton evolution in response to intensification of Patagonian dust input and other multi-stressor changes in the Southern Ocean in order to evaluate the impacts on carbon production

Ce travail s'inscrit dans le cadre du projet SIMED fédérant les activités de modélisation à l'échelle méditerranéenne, et plus globalement dans le programme MERMEX qui vise à étudier les cycles biogéochimiques en mer Méditerranée et leurs évolutions futures. L'étape préliminaire a été de coupler la plateforme de modélisation hydrodynamique (NEMO) à celle de modélisation biogéochimique mécaniste (Eco3M), afin de réaliser une simulation (2000-2012) utilisant les sorties hydrodynamiques de la configuration NEMO-MED12 pour forcer le modèle biogéochimique Eco3M-MED. Les nombreuses comparaisons menées dans cette thèse (chlorophylle, sels nutritifs, production primaire, etc.) ont aidé à s'assurer de la capacité du modèle à reproduire les principales caractéristiques biogéochimiques de la Méditerranée. Ce travail a permis de généraliser le rôle majeur joué par le carbone organique dissous dans la pompe biologique à l'échelle de la mer Méditerranée. Les résultats montrent que la production de carbone organique particulaire est restreinte aux régions de forte dynamique physique, tandis que l'accumulation de carbone organique dissous dans les eaux de surface est commune à la plupart des régions du bassin. Ce dernier processus s'est avéré dépendant des contenus cellulaires du phytoplancton et des bactéries hétérotrophes. Finalement d'après le modèle, la fraction dissoute du carbone organique contribuerait à hauteur d'environ 64 % à l'exportation dans le bassin Ouest, et de 90 % dans le bassin Est. Le bassin Est -en dépit de sa plus forte oligotrophie- s'avère participer à près de 60 % à l'exportation de carbone organique en mer Méditerranée
This work is part of the SIMED project which is dedicated to basin-scale modeling of the Mediterranean Sea. It also belongs to the MERMEX program which aims at studying biogeochemical cycles in the Mediterranean Sea and their evolution. The first step of this work was to couple the hydrodynamic modeling platform (NEMO) to the mechanistic biogeochemical modeling platform (Eco3M). We ran a simulation (2000-2012) using the hydrodynamic outputs from NEMO-MED12 configuration to force the biogeochamical model Eco3M-MED. The model evaluation was conducted using numerous field measurements (chlorophyll, nutrients, primary production, etc.). The simulation strengthens and extends to the whole basin the prominent role of dissolved organic carbon in the biological carbon pump in the whole Mediterranean Sea. A comprehensive analysis of organic carbon (particulate and dissolved) production processes production was performed. Results reveal that particulate organic carbon production is restricted to the highly dynamic areas, whereas dissolved organic carbon accumulation in the surface layers is a common process in much areas of the basin. This latter process appeared to dependant on the cellular contents of phytoplancton and heterotrophic bacteria, themselved being controled by low phosphate availability. Finally, the dissolved organic carbon contribution to carbon export is around 64 % in the Western basin, and up to 90 % in the Eastern basin. When taking into account the dissolved fraction, total organic carbon export in the Eastern basin -despite its higher oligotrophy- exceeds the one in the Western basin (60% against 40 %)

The project examines the possibilities to develop a local and sustainable model for food production in Uppsala with focus on diet, farming methods and different types of greenhouse installations. With the simulation software VIP energy 3.1.1 the energy balance and temperature development of greenhouses of different materials were calculated for different operating cases. The results were also compared when the greenhouse was installed stand-alone or integrated to the wall of a small standard or passive house. With a starch based diet and biological farming methods research suggests it is possible to produce food efficiently without compromising the environment or our health. The yearly food needs for a family of four that follows the suggested diet was estimated to 4362 kg and the outdoor land required to produce it was calculated to 4676 m2 through organic yield statistics. The area could however be reduced to 2813 m2 if the only starch staple in production was potatoes. The tender growing season in a greenhouse constructed with a covering of 5 mm glass or 5-16Ar-5 mm was calculated to 85 and 148 days respectively. The energy use required for year round production of mushrooms in the respective greenhouses was calculated to 53 or 16 kWh/m2,year. Half hardy plants required 399 or 173 kWh/m2,year and tender plants 953 or 358 kWh/m2,year. When the greenhouses were connected to the wall of a small house the heating demand could be reduced by up to 22 % depending on the operating case.

Ce travail de thèse porte sur la quantification de la diazotrophie et son influence sur les cycles biogéochimiques dans l'océan de surface Pacifique tropical sud-ouest, une région particulièrement sous-échantillonnée à ce jour. Les objectifs de ce travail étaient (1) de quantifier la fixation de N2 et identifier les principaux acteurs de la diazotrophie dans cette région, (2) d’évaluer l'influence de la fixation de N2 sur la production primaire et sur l'export de carbone, (3) d’identifier les voies de transfert de l’azote fixé dans la chaine trophique planctonique.Il a été mis en évidence que la région du Pacifique tropical sud-ouest était un hot spot de fixation de N2. A l'ouest, les eaux oligotrophes des archipels Mélanésiens présentaient des taux de fixation de N2 élevés et la communauté diazotrophe était dominée par Trichodesmium. A l'est, les eaux ultra-oligotrophes de la gyre du Pacifique sud présentaient des taux de fixation de N2 plus faibles et la communauté diazotrophe était dominée par les UCYN-B.Des bilans d'azote montrent que la fixation de N2 contribuait à plus de 90 % des apports d'azote nouveau dans la couche euphotique, et soutenait donc la quasi intégralité de la production primaire nouvelle. L'étude des voies de transfert de l'azote fixé montre qu’entre 7 et 15 % de la fixation de N2 totale était transféré vers les organismes non-diazotrophes.Ces travaux de thèse démontrent que la diazotrophie soutient la pompe biologique dans l'océan Pacifique tropical sud-ouest, et qu'elle peut jouer un rôle déterminant dans la structure des communautés planctoniques et les cycles biogéochimiques du carbone et de l'azote dans les régions oligotrophes
This PhD thesis focuses on the quantification of diazotrophy and its influence on biogeochemical cycles in the western tropical South Pacific Ocean, a critically under-sampled region so far. The aim of this work is to (1) quantify N2 fixation and identify the main contributors of diazotrophy in this region, (2) assess the influence of N2 fixation on primary production and carbon export, (3) identify transfer pathways of the fixed nitrogen in the planktonic food web.We have found that the western tropical South Pacific Ocean was a hotspot of N2 fixation. In the western part, the oligotrophic waters of the Melanesian archipelago presented high N2 fixation rates and diazotrophes were dominated by Trichodesmium. In the eastern part, the ultra-oligotrophic waters of the South Pacific gyre presented lower N2 fixation rates, and diazotrophs were dominated by UCYN-B.The nitrogen budgets show that N2 fixation contributed to more than 90 % of the of new nitrogen input in the photic layer. The study of the transfer pathways of the fixed nitrogen has shown that 7 to 15 % of total N2 fixation was transferred to non-diazotrophs.This PhD thesis indicates that diazotrophy sustains the biological pump in the western tropical South Pacific Ocean, and can have a critical influence in the planktonic community structure and in biogeochemical cycles of carbon and nitrogen in oligotrophic regions

Initiatives to study the impact of climate change on carbon sequestration in the subantarctic Southern Ocean have led to regular research voyages and the establishment of long-term moorings at the Southern Ocean Time Series site (47oS, 140oE) in the region. The subantarctic zone plays an important role in the physical uptake and sequestration of carbon dioxide due to the formation and subduction of water masses. However, while extensively studied in other parts of the world's ocean, the biological production, transformation, and transport of particulate material is not well documented for the subantarctic zone. In particular, the role of zooplankton in the biological gravitational, mesopelagic-migrant, and seasonal lipid pumps has received less attention. Current knowledge gaps extend across zooplankton species composition in subsurface waters and its seasonal development, zooplankton mortality that leads to downward carbon ux by carcasses and quanti _cation of zooplankton respiration in the water column. This thesis synthesises information on zooplankton and biogeochemistry in the subantarctic Southern Ocean to study the zooplankton-mediated carbon pump, including data from samples collected by deep-sea sediment traps, on _eld campaigns and from laboratory measurements. The thesis is composed of a general introduction (Chapter 1), a literature review (Chapter 2), three analysis chapters (Chapter 3-5) and a discussion, containing synthesis and future research priorities (Chapter 6). The second chapter reviews the role of zooplankton in establishing characteristic carbon export regimes in the Southern Ocean. Two case studies, the Kerguelen Plateau (high productivity, relatively low export) and the High-Nutrient Low-Chlorophyll waters south of Australia (low primary productivity, relatively high downward export), illustrate the importance of the zooplankton community composition, biomass and grazing for downward carbon export. The third chapter presents a long-term time-series (>20 years) of deep-sea zooplankton community composition data, collected as swimmers in sediment traps. Results indicate a decrease of abundance and diversity with increasing depth, low seasonality in zooplankton abundances and the absence of a long-term trend in the zooplankton community. The fourth chapter shows the importance of zooplankton carcasses for downward biological carbon export in the subantarctic zone. Estimations of the carcass ux are sensitive to alteration of mortality rates and sinking speed, but less sensitive to a change in microbial decomposition rates. Finally, a newly developed research instrument to measure zooplankton respiration in the _eld is presented in Chapter 5. The light trap attracts zooplankton into the main chamber of the ZOORESPIRE, which closes after a pre-set time period. During the incubation phase their respiration in-situ as a decline in oxygen concentration over time, which will enable better quanti_cation of respiration throughout the water column and especially in the under-studied mesopelagic zone.

In the ocean, the perpetual 'snowfall' of biogenic marine particles exports organic carbon from the well-lit surface layer to the deep sediments, promoting its sequestration. The efficiency of this 'biological carbon pump' (BCP), presents strong spatio-temporal variations that are not yet fully explained. Changes in surface plankton communities and trophic interactions appear important because they lead to modifications of sinking particle characteristics (e.g. composition, structure, sinking velocity). These controls are explored here via the characterization of sinking particles originating from varying planktonic community structures and evaluation of their ability to export carbon. During the second KErguelen Ocean and Plateau compared Study (KEOPS2) conducted in Oct.-Nov. 2011, six sites were sampled over and downstream of the Kerguelen Plateau (Southern Ocean), where a mosaic of phytoplankton blooms of changing communities forms in response to natural iron fertilisation. Sinking particles were collected with free-drifting sediment traps at four mesopelagic depths to examine their form and composition, including optical characterization using polyacrylamide gel filled traps. Concurrently, aggregates were formed in roller tanks from surface water phytoplankton assemblages, to explore the intricate influences of particle size, structure and composition on the sinking velocity. At each site, carbon export efficiencies were calculated as the ratio of carbon flux to net primary productivity (e-ratio). High productivity was associated with the lowest carbon export efficiency (e-ratio ~0.02) while maximum export efficiency (e-ratio ~0.2) was found at low-productivity sites. Two explanations were identified. Firstly, at high-biomass sites, strong zooplankton grazing generated large fecal pellets sustaining high carbon fluxes at 100-200 m (180 mg C m⁻² d⁻¹). This export pathway represented a 'dead end' due to rapid attenuation of the fecal pellet flux at 200-400 m, releasing most of the carbon (48±21 % carbon flux decrease). Secondly, based on the roller tank results, the morphology of dominant diatom species appeared to be an important control on aggregate sinking velocities, possibly via species-specific coagulation efficiency affecting particle structure and density. At high-biomass sites, dominant small spine-forming species formed loose slow-sinking aggregates (~10 m d⁻¹), whereas chain-forming diatoms without spines, at low-productivity sites, produced compact fast-sinking aggregates (~250 m d⁻¹). The similarity of aggregate morphology and structure from roller tank and gel traps (2-D fractal number = 1.8 and 1.9 respectively), increased confidence in applying these results to in situ conditions. A generic 3-D physical-biogeochemical (BGC) model was modified to investigate conceptually the influence of planktonic community variations on carbon export efficiency through their control on detritus composition and sinking velocity. This was achieved by introducing in the model a variable detritus sinking velocity based on phytoplankton and zooplankton detrital fractions (using experimental results). Changes from a constant (100 m d⁻¹) to a variable sinking velocity induced a significant increase of the annual integrated carbon flux at 100 m (45±23 %) highlighting the importance of sinking velocity parameterisation in BGC models. Simulations indicate that export efficiency could depend upon subtle trophic interactions between phyto- and zooplankton communities influencing the relative rates of productivity and associated carbon flux and determining the conditions of biomass retention or export. The insights and tools developed here improve our understanding of how a climate-mediated shift of surface plankton communities can alter the efficiency of the BCP.

Planktonic ecosystems provide a key mechanism for the transfer of CO2 from the atmosphere to the deep ocean via the so-called "biological pump". Mathematical models of these ecosystems have been used to predict CO2 uptake in surface waters, and more recently have been embedded in global climate models. While the equilibrium properties of these models are well studied, less attention has been paid to their response to external perturbations, despite the fact that as a result of the variability of environmental forcing such ecosystems are rarely, if ever, in equilibrium. Human induced perturbations to these ecosystems, namely the addition of limiting nutrients (e.g. iron) to areas where nitrate is plentiful to accelerate the biological pump, have been proposed as a solution to reduce atmospheric CO2. Linear theory is used to determine the structure of "unit-norm" perturbations (size in mmol N m^-3) to state variables of an ecosystem model in steady state, describing Ocean Station P (50N 145W) in summer, that optimize either instantaneous export flux of organic matter at fixed times or integrated export as the ecosystem relaxes towards equilibrium. For all perturbations, the flux to higher trophic levels is the primary contributor to export flux, the contribution of aggregation is negligible, and (sinking) detritus increases significantly in the transient dynamics. Two perturbations considered optimize instantaneous export flux; both perturbations synchronize P1 and Z1 relative to their predator prey cycle, resulting in a maximum instantaneous export flux of 4.4 mmol N m^-2 d^-1, and also increased integrated export above that at steady state (6 g C m^-2 over 150 days). An increase in larger phytoplankton (P2), representing diatoms, results in the highest integrated export (7 g C m^-2). The perturbations in which P2 persist the longest give the highest integrated export, and these perturbations are primarily increases in P2. The additional integrated export in response to a proportional increase to steady state concentrations of both large and small phytoplankton is positive, but much lower than the optimal perturbations. However, the additional integrated export in response to an increase in only P1 is negligible. The linear and nonlinear ecosystem and export responses to two perturbations are compared; for perturbations of magnitude 0.5 mmol N m^-3, the linearization of the ecosystem dynamics, rather than of the export flux, is the primary cause for differences between the fully linear and fully nonlinear cases.