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32 pages, 14 figures, 3 tables, 2 appendixes, supporting Information https://doi.org/10.1029/2018JC014668.-- The source code of NEMO is available on the NEMO website (http://www. nemo-ocean.eu). The GlobColour data (http://globcolour.info) used in this study has been developed, validated, and distributed by ACRI-ST, France. The data used in this study, together with the studies they come from, are listed in the supporting information, Thorium‐234 (234Th), an insoluble radioisotope scavenged by marine particles, can be used as a proxy of the biological carbon pump. Thorium‐234 observations can constrain biogeochemical models, but a necessary first step is to estimate the poorly known partition coefficients between particulate and dissolved phases. In this study, the 234Th partition coefficients for five particle types, differing in size and chemical composition, are estimated by fitting a global 3‐D 234Th model based on the coupled ocean general circulation‐biogeochemistry model NEMO‐PISCES (at a resolution of 2°) to a global 234Th data set (including GEOTRACES data). Surface partition coefficients are estimated between 0.79 and 16.7×106. Biogenic silica has the smallest partition coefficients. Small particulate organic carbon and lithogenic dust have the largest. Thorium‐234 observations at depth cannot be recovered without allowing partition coefficients to increase by one order of magnitude from surface to 1,000 m deep. In our time‐dependent global 3‐D model, the biases introduced by three common assumptions made in biological carbon pump studies can be quantified. First, using the C:234Th ratio of large particles alone leads to an overestimation of carbon export at the base of the euphotic layer, by up to a factor 2. Furthermore, assuming steady state and neglecting transport by advection and diffusion can bias fluxes by as much as 50%, especially at high latitudes and in upwellings, with a sign and intensity depending on the season, This work is part of the first author's PhD, supported by the “Laboratoire d'Excellence” LabexMER (ANR-10-LABX-19) and cofunded by a grant from the French government under the program “Investissements d'Avenir”, by a grant from the Regional Council of Brittany and by project ANR CIGOEF

International audience; Within the marine field, zooplankton grazing may contribute to carbon export through faecal pellets emission or delay vertical sinking flux sinking phytoplankton aggregates. To assess this process, artificial monospecific aggregates of two diatom species (Chaetoceros neogracile and Skeletonema marinoi) and natural aggregates of Melosira sp. were incubated with different copepod species (Acartia clausi, Temora longicornis, Calanus helgolandicus, Euterpina acutifrons and Calanus hyperboreus). We measured a direct grazing on aggregates with ingestion rates ranging from 0.39 to 6.71 µg pigment ind-1 d-1. The relation between aggregates equivalent spherical diameters and sinking velocities have not changed, showing that copepods grazing do not affect their densities. Regarding the particle flux, we observed three main trends: 1) Fragmentation: copepods activities increase the number of particles and decrease sinking velocities, the case of incubation with T. longicornis, the number of aggregates per litter increased with significant decrease of aggregates sinking velocities; 2) Re-aggregation: copepods activities increase aggregates size spectra and consequently the sinking velocities, the average size spectra of C. neogracile aggregates significantly increased during incubation with A. clausi but not with E. acutifrons; 3) No impact, when S. marinoi aggregates were incubated with E. acutifrons or C. helgolandicus. Our results showed that copepod grazing could modulate biological pump of carbon through fragmenting or re-aggregating but not through change of aggregate density.

In the deep ocean, fluxes of particulate organic carbon (POC) and calcium carbonate are positively correlated, suggesting that CaCO3 could increase sinking particle densities and/or protect the organic matter from degradation by prokaryotes, the so called "ballast effect". Here, we used the PArticle Sinking Simulator (PASS) system to investigate the effect of increasing pressure on the biodegradation of calcifying Emiliania huxleyi aggregates. Incubations were carried out over a period of 10 days, simulating the changes in temperature and pressure in the water column of the NW Mediterranean Sea. Aggregates sinking from a depth of 200 m to 1700 m (assuming an average sinking velocity of 150 m d(-1)) were exposed to a natural mesopelagic prokaryotic community collected from 200 m. In contrast to previous studies, where silicifying diatom aggregates were used, the calcifying E. huxleyi aggregates were found to be more sensitive to degradation with increasing hydrostatic pressure (relative to constant atmospheric pressure). This was confirmed by changes in lipid composition which suggested increased cell lysis. Changes in particulate inorganic carbon and total alkalinity indicated that CaCO3 dissolution might have been faster under pressure. Increased hydrostatic pressure also had a positive effect on particle aggregation, which may compensate for the effect of increased cell lysis. Our results imply that in coccolithophorid-dominated sinking aggregates, the ballasting and protection effects of coccoliths may collapse throughout the water column. The increased aggregation potential with pressure observed in these controlled conditions, may balance the loss of mineral ballast to a certain extent, although this needs to be confirmed in situ.

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., 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 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.; 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.; 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.

International audience; The effect of cobalt (Co), zinc (Zn) or cadmium (Cd) availability on the growth and particulate inorganic (PIC) to organic (POC) carbon ratio of the cosmopolitan coccolithophore Emiliania huxleyi was examined using batch cultures. Growth co-limitation by Co and Zn occurred at low free metal ion concentrations below 10–12 pM. The two metals could replace one another in biochemical functions: full replacement of Zn by Co was possible, but the 20% higher growth rate observed with high Co levels in the absence of Zn than observed in the presence of high Zn but no added Co suggested that there was an absolute growth requirement of Co that could only partly be met by Zn. In contrast, Cd had no effect on growth in the absence of Co and Zn, indicating that this strain cannot use Cd under these conditions. The co-limitation by inorganic Co and Zn led to highly calcified cells containing a large quota of nitrogen, but diminished organic carbon content, likely due to a lower photosynthetic production rate. Deficiency of Zn and Co cofactors could have dramatically decreased the activity of carbonic anhydrase, lowering CO2 availability for photosynthesis. In contrast to the large decreases in carbon fixation rates at low Zn and Co ion concentrations, calcification rates were unaffected at low Zn levels and were only minimally decreased by low Co. As a result the PIC:POC ratios in E. huxleyi increased by up to 8-fold under Zn limitation and 3–5-fold under Co limitation to values where coccolithophores act as a source of atmospheric CO2. As a result, low Co and Zn availability in seawater could affect the efficiency of the biological carbon pump, and atmospheric CO2 levels. Thus, the impact of Co and Zn limitation may need to be considered to improve assessments of the impact of E. huxleyi and other biogenic calcifiers on oceanic sequestration of CO2.

Nitrogen is a key limiting nutrient that influences marine productivity and carbon sequestration in the ocean via the biological pump. In this study, we present the first estimates of nitrogen cycling in a coupled 3D ocean-biogeochemistry-isotope model forced with realistic boundary conditions from the Last Glacial Maximum (LGM) ~21,000 years before present constrained by nitrogen isotopes. The model predicts a large decrease in nitrogen loss rates due to higher oxygen concentrations in the thermocline and sea level drop, and, as a response, reduced nitrogen fixation. Model experiments are performed to evaluate effects of hypothesized increases of atmospheric iron fluxes and oceanic phosphorus inventory relative to present-day conditions. Enhanced atmospheric iron deposition, which is required to reproduce observations, fuels export production in the Southern Ocean causing increased deep ocean nutrient storage. This reduces transport of preformed nutrients to the tropics via mode waters, thereby decreasing productivity, oxygen deficient zones, and water column N-loss there. A larger global phosphorus inventory up to 15% cannot be excluded from the currently available nitrogen isotope data. It stimulates additional nitrogen fixation that increases the global oceanic nitrogen inventory, productivity, and water column N-loss. Among our sensitivity simulations, the best agreements with nitrogen isotope data from LGM sediments indicate that water column and sedimentary N-loss were reduced by 17–62% and 35–69%, respectively, relative to preindustrial values. Our model demonstrates that multiple processes alter the nitrogen isotopic signal in most locations, which creates large uncertainties when quantitatively constraining individual nitrogen cycling processes. One key uncertainty is nitrogen fixation, which decreases by 25–65% in the model during the LGM mainly in response to reduced N-loss, due to the lack of observations in the open ocean most notably in the tropical and subtropical southern hemisphere. Nevertheless, the model estimated large increase to the global nitrate inventory of 6.5–22% suggests it may play an important role enhancing the biological carbon pump that contributes to lower atmospheric CO2 during the LGM.

Enhanced vertical carbon transport (gravitational sinking and subduction) at mesoscale ocean fronts may explain the demonstrated imbalance of new production and sinking particle export in coastal upwelling ecosystems. Based on flux assessments from 238U:234Th disequilibrium and sediment traps, we found 2 to 3 times higher rates of gravitational particle export near a deep-water front (305 mg C⋅m-2⋅d-1) compared with adjacent water or to mean (nonfrontal) regional conditions. Elevated particle flux at the front was mechanistically linked to Fe-stressed diatoms and high mesozooplankton fecal pellet production. Using a data assimilative regional ocean model fit to measured conditions, we estimate that an additional ∼225 mg C⋅m-2⋅d-1 was exported as subduction of particle-rich water at the front, highlighting a transport mechanism that is not captured by sediment traps and is poorly quantified by most models and in situ measurements. Mesoscale fronts may be responsible for over a quarter of total organic carbon sequestration in the California Current and other coastal upwelling ecosystems.

On geological time-scales, the production and degree of recycling of biogenic carbon in the marine realm and ultimately its removal to sediments, exerts a dominant control on atmospheric CO2 and hence variability in climate. This is a highly complex system involving a myriad of inter-connected biological, chemical, and physical processes. For this reason alone, linking observations, often highly abstracted in the form of proxies, to the primary processes involved and ultimately to explanatory hypotheses for specific geological events and transitions, is challenging. The past few decades have seen a progressive improvement in theoretical and process-based understanding of the various components that make up the marine carbon cycle and, hand-in-hand with this, the development of numerical model representations of the complete system. Models have also been designed and/or adapted with paleoclimate questions in mind and applied to quantitatively explore the role of the marine carbon cycle in both perturbations and long-term geologic evolutionary trends in global climate, and possible feedbacks between them. However, we must ask whether paleoclimate models incorporate sufficiently appropriate representations of the dynamics and sensitivities of the marine carbon cycle, and indeed, whether in the geological context, we really know what these dynamics are. Here we provide a comprehensive overview of how marine carbon cycling and the biological carbon pump is treated in available paleoclimate models, with the aim of critically evaluating their ability to help interpret past marine carbon cycle and climate dynamics. To this end, we first provide an overview of commonly used paleoclimate models and some of their associated paleo-applications, drawing from a wide range of global carbon cycle box models and Earth system Models of Intermediate Complexity (EMICs). Secondly, we review and evaluate the three dominant processes involved in the cycling of organic and inorganic carbon in the marine system and how they are represented in models, namely: biological productivity at the ocean surface, remineralisation/dissolution of particulate carbon within the water column, and the benthic-pelagic coupling at the seafloor. We generate and employ illustrative examples using the model GENIE to show how different parameterisations of water-column and sediment processes can lead to significantly different model projections. Our compilation reveals the prevalence of static parameterisations of marine carbon cycling among existing paleoclimate models, which are commonly empirically derived from present-day observations. Although such approaches tend to represent carbon transfer in the modern ocean well, they are potentially compromised in their ability to reflect the true degree of freedom and strength of feedbacks with respect to past climate events, particularly those characterised by environmental boundary conditions that differ fundamentally from today. Finally, we discuss the importance of using models of different complexities and how questions of model uncertainty may start to be addressed.

The biological carbon pump (BCP) is a complex suite of processes responsible for transporting organic matter produced in the surface ocean to depth. As such, it is an important mechanism in controlling the sequestration of atmospheric carbon dioxide (CO2) and its storage on time scales of decades to centuries. This receives special attention in light of the rising anthropogenic CO2 emissions, which are unprecedented in the recent geological history of this planet. Despite its importance, we are still lacking a mechanistic understanding of the processes controlling the efficiency of the BCP. Over the past decade, the focus has increasingly shifted towards illuminating the effect of differences in ecosystem structure on organic matter export. This doctoral dissertation thus aimed and succeeded to reveal patterns in the relation between food-web structure changes and the efficiency of the BCP and circumstantiated recent concepts in this field of research. Furthermore, this work exemplifies that the methodological approach of utilizing in situ mesocosms can make a significant contribution to BCP research, for it allows answering questions that conventional methods have not been able to address. Die biologische Kohlenstoffpumpe (BKP) ist ein komplexes Zusammenspiel aus Prozessen, welche in ihrer Gesamtheit für den Transport von organischer Materie aus dem Oberflächenozean in die Tiefe verantwortlich ist. Als solches spielt sie gleichzeitig eine wichtige Rolle in der Sequestrierung von atmosphärischem Kohlenstoffdioxid (CO2) und seiner Speicherung in der Tiefe über Zeiträume von Jahrzehnten bis Jahrtausenden. Dies hat besondere Bewandtnis im Anbetracht der steigenden anthropogenen CO2 Emissionen, welche beispiellos sind in der jüngsten geologischen Geschichte dieses Planeten. Trotz ihrer zweifelslosen Bedeutung sind wir noch immer in Ermangelung eines mechanistischen Verständnisses der Prozesse, welche die Effizienz der BKP kontrollieren. Im Laufe der letzten zehn Jahre hat sich der Fokus zunehmend auf das Verständnis des Zusammenhangs zwischen Ökosystem-Strukturen und Export von organischer Materie verlagert. Zusammenfassend hat die vorliegende Doktorarbeit Muster in dem Verhältnis zwischen Nahrungsnetz-Struktur und der Effizienz der BKP aufgezeigt, jüngste Konzepte bestätigt und erweitert. Außerdem verdeutlicht diese Arbeit, dass der methodische Ansatz von in situ Mesokosmenexperimenten einen wichtigen Beitrag in der Erforschung der BKP leisten kann und die Beantwortung von Fragen ermöglicht, welche mit herkömmlichen Methoden bisher nicht ohne weitere Annahmen möglich war.

International audience; Transparent Exopolymer Particles (TEP) have received considerable attention since they were first described in the ocean more than 20 years ago. This is because of their carbon-rich composition, their high concentrations in ocean’s surface waters, and especially because of their ability to promote aggregation due to their high stickiness (i.e. biological glue). As large aggregates contribute significantly to vertical carbon flux, TEP are commonly seen as a key factor that drives the downward flux of particulate organic carbon (POC). However, the density of TEP is lower than that of seawater, which causes them to remain in surface waters and even move upwards if not ballasted by other particles, which often leads to their accumulation in the sea surface microlayer. Hence we question here the generally accepted view that TEP always increase the downward flux of POC via gravitational settling. In the present reassessment of the role of TEP, we examine how the presence of a pool of non-sinking carbon-rich particulate organic matter in surface waters influences the cycling of organic carbon in the upper ocean at daily to decadal time scales. In particular, we focus on the role of TEP in the retention of organic carbon in surface waters versus downward export, and discuss the potential consequences of climate change on this process and on the efficiency of the biological carbon pump. We show that TEP sink only when ballasted with enough high-density particles to compensate their low density, and hence that their role in vertical POC export is not solely linked to their ability to promote aggregation, but also to their contribution to the buoyancy of POC. It follows that the TEP fraction of POC determines the degree of retention and remineralization of POC in surface waters versus its downward export. A high TEP concentration may temporally decouple primary production and downward export. We identify two main parameters that affect the contribution of TEP to POC cycling; TEP stickiness, and the balance between TEP production and degradation rates. Because stickiness, production and degradation of TEP vary with environmental conditions, the role of TEP in controlling the balance between retention versus export, and hence the drawdown of atmospheric CO2 by the biological carbon pump, can be highly variable, and is likely to be affected by climate change.

The ocean’s biological carbon pump plays a central role in regulating atmospheric CO2 levels. In particular, the depth at which sinking organic carbon is broken down and respired in the mesopelagic zone is critical, with deeper remineralisation resulting in greater carbon storage. Until recently, however, a balanced budget of the supply and consumption of organic carbon in the mesopelagic had not been constructed in any region of the ocean, and the processes controlling organic carbon turnover are still poorly understood. Large-scale data syntheses suggest that a wide range of factors can influence remineralisation depth including upper-ocean ecological interactions, and interior dissolved oxygen concentration and temperature. However these analyses do not provide a mechanistic understanding of remineralisation, which increases the challenge of appropriately modelling the mesopelagic carbon dynamics. In light of this, the UK Natural Environment Research Council has funded a programme with this mechanistic understanding as its aim, drawing targeted fieldwork right through to implementation of a new parameterisation for mesopelagic remineralisation within an IPCC class global biogeochemical model. The Controls over Ocean Mesopelagic Interior Carbon Storage (COMICS) programme will deliver new insights into the processes of carbon cycling in the mesopelagic zone and how these influence ocean carbon storage. Here we outline the programme’s rationale, its goals, planned fieldwork and modelling activities, with the aim of stimulating international collaboration.

The elemental composition of particulate organic matter in the surface ocean significantly affects the efficiency of the ocean's store of carbon. Though the elemental composition of primary producers is an important factor, recent observations from the western North Atlantic Ocean revealed that carbon-to-nitrogen ratios (C:N) of phytoplankton were significantly higher than the relatively homeostatic ratio of the total particulate pool (particulate organic carbon:particulate organic nitrogen; POC:PON). Here we use an idealized ecosystem model to show how interactions between primary and secondary producers maintain the mean composition of surface particulates and the difference between primary producers and bulk material. Idealized physiological models of phytoplankton and microzooplankton, constrained by laboratory data, reveal contrasting autotrophic and heterotrophic responses to nitrogen limitation: under nitrogen limitation, phytoplankton accumulate carbon in carbohydrates and lipids while microzooplankton deplete internal C reserves to fuel respiration. Global ecosystem simulations yield hypothetical global distributions of phytoplankton and microzooplankton C:N ratio predicting elevated phytoplankton C:N ratios in the high-light, low-nutrient regions of the ocean despite a lower, homeostatic POC:PON ratio due to respiration of excess carbon in systems subject to top-down control. The model qualitatively captures and provides a simple interpretation for, a global compilation of surface ocean POC:PON data.

The world’s oceans are a major sink for atmospheric carbon dioxide (CO2). The biological carbon pump plays a vital role in the net transfer of CO2 from the atmosphere to the oceans and then to the sediments, subsequently maintaining atmospheric CO2 at significantly lower levels than would be the case if it did not exist. The efficiency of the biological pump is a function of phytoplankton physiology and community structure, which are in turn governed by the physical and chemical conditions of the ocean. However, only a few studies have focused on the importance of phytoplankton community structure to the biological pump. Because global change is expected to influence carbon and nutrient availability, temperature and light (via stratification), an improved understanding of how phytoplankton community size structure will respond in the future is required to gain insight into the biological pump and the ability of the ocean to act as a long-term sink for atmospheric CO2. This review article aims to explore the potential impacts of predicted changes in global temperature and the carbonate system on phytoplankton cell size, species and elemental composition, so as to shed light on the ability of the biological pump to sequester carbon in the future ocean.

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 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 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.

To improve the understanding of population dynamics of organisms, it is necessary to examine organisms under natural conditions. Only at such conditions, knowledge about their in situ use of resources, predator-prey interactions and loss rates can be obtained. It is possible to examine and understand these processes with controlled ocean iron fertilization experiments, which stimulate the growth of unicellular algae. This thesis provides a comprehensive description of the reactions and vertical distribution of the main components of the pelagic ecosystem and highlights the food-web interactions of individual organisms, which characterize this habitat. The response of the plankton community to iron addition was successfully observed during the Indo-German iron fertilisation experiment LOHAFEX (LOHA is hindi and means iron, FEX stands for fertilisation experiment) carried out in the Southern Ocean from January to March in 2009 lasting for 38 days. The iron-induced bloom was achieved in the closed core of a mesoscale eddy. The aim of the experiment was to study the growth and demise of the phytoplankton bloom and to examine whether the biomass is retained in the surface layers through recycling processes or whether biomass sinks out to the deep ocean. The fertilized patch was characterized by low silicic acid concentrations, which is an essential nutrient for diatoms, hence a flagellate-bloom developed with cells < 20 µm in size. The bloom remained stable over the course of the experiment. This was verified by microscopic analysis and molecular methods. The main reason for the lack of large scale biomass increase, was the strong grazing pressure by the large copepod population, consisting primarily of Calanus simillimus and Oithona similis. Incubation experiments proved that copepods increased their grazing rates and fecal pellet production within the patch. Neutrally buoyant PELAGRA traps were deployed to quantify the export fluxes. These contained a few diatoms and fecal pellets and were dominated by unicellular plankton like dinoflagellates, flagellates and coccoid cells. Hence fertilizing this type of plankton community did not increase the vertical flux. This lead to the hypothesis that the system was influenced by recycling processes in surface layers. The protozoan community and its vertical distribution was an important part of this work and was studied by focussing on key heterotrophic organisms. These included thekate dinoflagellates, loricate and aloricate ciliates, foraminifera, radiolarians, and juvenile and adult copepods. Again, the high grazing pressure by the copepods controlled the development of the protozoan community, and the copepod fecal pellets contained large amounts of damaged and empty loricae, but also foraminifera, which are usually not a preferred food item for copepods. This indicated that the copepods were food limited and resorted to large, armoured protozoans which they might have otherwise avoided. Dinoflagellates were mainly abundant at depths below 100 m, possibly this distribution pattern was caused by an escape response in order to avoid predators and to feed on the flux of larger particles which generally peaks at those depths. In conclusion, the plankton community during LOHAFEX was top-down controlled whereby a highly efficient retention type system prevailed, which resulted in low particle export fluxes

Planktic foraminifers (PF) are heterotrophic mesozooplankton of global marine abundance, being ubiquitous proxy in paleoceanography, and climate reconstruction. In turn, the individual and biomass (Corg) of PF was largely unknown due to methodological problems. To quantitatively understand the trophic position of PF within the regional and global plankton, we have developed a new analytical method, and quantified the individual biomass of 952 specimens of 26 PF species. The new non-destructive protocol is derived from the bicinchoninic acid (BCA) method, and a nano-photospectrometer is used to measure protein biomass. We tested the method on the benthic foraminifer Ammonia tepida, from fresh and frozen samples, and from culture experiments. We then applied the new method to measure PF protein-biomass of specimens from oligotrophic and eutrophic regions, including the subtropical to temperate ocean. The average individual PF biomass amounts to 0.845 μg. Our results indicate neither inter-specific differences nor any influence of the shape of test on the individual biomass. In turn, Individual PF biomass is highly correlated with test size and mass, and independent of ecologic conditions (i.e., e.g., trophic state, water depth, and temperature). Following our new method, the PF assemblage biomass was calculated from 1128 locations and water depth from the North Atlantic, Arabian Sea, Red Sea, and Caribbean, and literature data from off Japan and Oregon. A first-order estimate of the average global PF biomass production amounts to 25-100 Tg C yr−1 including juvenile individuals. The organic to inorganic carbon (Corg : Cinorg) ratio of PF populations between the surface and subsurface water column down to 2500 m water depth seems to stay constant at ~2/3, as indicated by a case study from the Azores region. Those results show an export of both Corg and Cinorg to the deep ocean, making PF part of the biological carbon pump. The results obtained in this thesis make PF a potential proxy to quantify the biomass of paleo-assemblages, and to improve our understanding of past carbon cycle and biological carbon pump.; Les foraminifères planctoniques (FP) sont des organismes hétérotrophes appartenant au mésozooplancton, abondants dans tous les domaines marins et communément utilisés dans les reconstitutions paléoenvironnementales. Pour quantifier la position des FP dans le cycle du carbone au sein du plancton à des échelles régionales et globales, il est nécessaire de connaitre leur production en biomasse (Corg), jusque là très peu connue car très difficilement mesurable. Dans ce travail, nous avons développé une nouvelle méthode analytique non destructive développée à partir de la méthode bicinchoninic acid (BCA), et mesuré la biomasse individuelle de 952 spécimens de 26 espèces de FP provenant de régions tempérées à subtropicales. Nos résultats indiquent que la biomasse moyenne d'un FP s'élève à 0,845 μg. Le protocole a été calibré sur l'espèce benthique Ammonia tepida, et au cours d'expériences en culture. L'analyse statistique des données ne fait ressortir aucune différence interspécifique, ni des conditions écologiques (niveau trophique, profondeur ou température). En revanche, nous avons démontré que la biomasse des FP est fortement corrélée avec la masse et la taille de leur test calcitique. Grâce à cette corrélation, les biomasses des populations de FP ont été calculées pour 1128 sites et profondeurs d'échantillonnage de l'Atlantique Nord, la mer d'Arabie, la mer Rouge, les Caraïbes, le Japon et l'Oregon. La production actuelle de biomasse par les FP a pu être estimée entre 25 et 100 Tg.C.an−1, en incluant les individus juvéniles. Le ratio carbone organique sur inorganique (Corg : Cinorg) des populations de FP entre la surface et 2500 m de profondeur semble rester constant à ~2/3, tel que montré dans la zone des Açores. Ces résultats prouvent qu'il y a un export de carbone à la fois organique et inorganique, et que les FP contribuent incontestablement à la pompe biologique de carbone. Les résultats obtenus au cours de cette thèse font des FP de potentiels outils pour quantifier la biomasse initiale de paléo-assemblages, et améliorer notre compréhension du cycle du carbone et de la pompe biologique de carbone dans le passé.

The mesopelagic (200 – 1000 m) micronekton (2 to 20 cm) community, formed mainly of small fish, cephalopods, crustacean and gelatinous zooplankton, hide in near darkness during the daytime to reduce the risk of being preyed on by visual predators. A proportion of this community migrates daily to the surface at night to feed (diel vertical migration, DVM). DVM provides a biological pathway for carbon to be transported to the surface from the deep ocean. The impact of this active component (as opposed to passively sinking matter) of the so called ‘biological carbon pump’ (BCP) on our climate, will be related to total migrant biomass, its metabolic activity at various depths, predator-prey interactions, and DVM dynamics. Recently, studies have shown that global biomass of mesopelagic fish could be more than 10 timesan historic estimate of c. 1 gigaton: should these new estimates be proven correct, our view of the importance of the mesopelagic community in the carbon-cycle, will shift to a new paradigm.

In situ imaging of particles in the ocean are rapidly establishing themselves as powerful tools to investigate the ocean carbon cycle, including the role of sinking particles for carbon sequestration via the biological carbon pump. A big challenge when analysing particles in camera images is determining the size of the particle, which is required to calculate carbon content, sinking velocity and flux. A key image processing decision is the algorithm used to decide which part of the image forms the particle and which is the background. However, this critical analysis step is often unmentioned and its effect rarely explored. Here we show that final flux estimates can easily vary by an order of magnitude when selecting different algorithms for a single dataset. We applied a range of static threshold values and 11 different algorithms (seven threshold and four edge detection algorithms) to particle profiles collected by the LISST-Holo system in two contrasting environments. Our results demonstrate that the particle detection method does not only affect estimated particle size but also particle shape. Uncertainties are likely exacerbated when different particle detection methods are mixed, e.g., when datasets from different studies or devices are merged. We conclude that there is a clear need for more transparent method descriptions and justification for particle detection algorithms, as well as for a calibration standard that allows intercomparison between different devices.

The mesopelagic (200 – 1000 m) micronekton (2 to 20 cm) community, formed mainly of small fish, cephalopods, crustacean and gelatinous zooplankton, hide in near darkness during the daytime to reduce the risk of being preyed on by visual predators. A proportion of this community migrates daily to the surface at night to feed (diel vertical migration, DVM). DVM provides a biological pathway for carbon to be transported to the surface from the deep ocean. The impact of this active component (as opposed to passively sinking matter) of the so called ‘biological carbon pump’ (BCP) on our climate, will be related to total migrant biomass, its metabolic activity at various depths, predator-prey interactions, and DVM dynamics. Recently, studies have shown that global biomass of mesopelagic fish could be more than 10 times an historic estimate of c. 1 gigaton: should these new estimates be proven correct, our view of the importance of the mesopelagic community in the carbon-cycle, will shift to a new paradigm.