Suspension-feeding bivalves produce biodeposits (faeces and pseudofaeces) that have much higher sinking velocities than their constituent particles. Consequently they cause sedimentation of material that might otherwise not be deposited. The benthic remineralisation of biodeposits increases sediment oxygen demand and nutrient regeneration, thus enhancing the benthic-pelagic coupling of nearshore ecosystems. In New Zealand the mussel Perna canaliculus has a high natural abundance and is also intensively cultured. This thesis examines the dispersal and remineralisation characteristics of mussel P. canaliculus biodeposits and the impacts of sedimentation from a mussel farm in the Firth of Thames on sediment biogeochemistry by combining laboratory, field and modelling studies. Dispersal characteristics were examined in the laboratory by measuring sinking velocities and erosion thresholds of biodeposits produced by mussels of a wide size range fed three experimental diets. The results show that biodeposit dispersal is a function of mussel diet and size and thus could differ significantly between locations and seasons. Estimates of dispersal distances based on these results demonstrated that the initial dispersal of biodeposits produced by cultured mussels is not far. Depending on the hydrodynamic conditions, secondary dispersal via resuspension potentially plays a more important role in the dispersal of biodeposits from mussel farms than initial dispersal and almost certainly serves as the major means of transport of biodeposits from natural mussel beds. Biodeposit mineralisation was studied by incubating coastal sediments with added biodeposits and measuring oxygen and nutrient fluxes as well as sediment characteristics over an 11 d period. Sediment oxygen consumption and ammonium release increased immediately after biodeposit addition and remained elevated compared to control cores without additions for the incubation period. A biodeposit decay rate (0.16 d-1) was calculated by fitting a first-order G model to the observed increase in oxygen consumption. This rate is 1 - 2 orders of magnitude higher than published decay rates of coastal sediments without organic enrichment or plant material. Nutrient fluxes during the incubation period illustrated that biodeposit remineralisation alters the stoichiometry of the nutrients released from the sediments which may potentially be more significant than the changes of the individual fluxes. To determine the impact of a mussel farm in the Firth of Thames I measured sediment oxygen and nutrient fluxes by deploying benthic chambers, sediment characteristics by collecting sediment cores and sedimentation rates by deploying sediment traps in four seasons. Oxygen consumption and sediment nutrient release rates were generally higher under the farm compared to a reference site, demonstrating the typical response to increased organic input. Unusually low nitrogen release rates measured in summer may indicate enhanced denitrification under the farm. A simple budget demonstrated the importance of benthic nutrient regeneration in maintaining primary production in this region and that mussel culture can lead to a redistribution of nutrients. This study showed that site-specific hydrodynamic and biogeochemical conditions have to be taken into account when planning new mussel farms to prevent excessive modifications of nutrient dynamics. Results of the laboratory and field studies conducted in this thesis were used to parameterise, calibrate and validate models of mussel biodeposit dispersal and remineralisation. A particle tracking model showed that the maximum initial dispersal of faecal pellets from the mussel farm is approximately 300 m and that pellets can be transported several times this distance via resuspension. The remineralisation model was able to simulate the increased nitrogen fluxes from the sediments well and highlighted the need for thorough calibration and parameterisation of the model. This thesis contributed to the current understanding of the ecosystem impacts of mussel culture and provided numerical models and model parameters that will assist in the assessment of mussel culture sustainability and the contribution of mussels to the nutrient cycling in nearshore ecosystems.

Os sedimentos costeiros são importantes globalmente, pois atuam como receptores de grandes quantidades de material orgânico alóctone e autóctone, sendo responsáveis por cerca de 90% do enterramento de carbono no oceano global. Dentro dos ecossistemas de plataforma continental, a fauna bêntica desempenha papel vital tanto como receptora de energia proveniente do pelagial, quanto como fornecedora de energia para os organismos demersais e de nutrientes para o fitoplâncton. O objetivo principal do presente trabalho foi investigar a variação temporal da dinâmica da macrofauna bêntica na plataforma interna de Ubatuba. A dinâmica bêntica foi analisada pela abundância, biomassa, descritores da comunidade (riqueza, diversidade, equitatividade) e análise trófica dos grupos mais abundantes, em função da origem e composição da matéria orgânica sedimentar. As coletas foram realizadas mensalmente em uma estação fixa, com início em outubro de 2006, por um período de um ano. A estação fixa possui uma profundidade de 40 m e um regime oceanográfico de transição entre águas costeiras e de plataforma continental. A composição da matéria orgânica em termos de MOT, fitopigmentos, fitodetritos e biomarcadores lipídicos apresentou uma complexidade típica de ambientes de plataforma interna, relacionados à dinâmica oceanográfica que rege os principais eventos de acúmulo ou remoção da matéria orgânica lábil na região de Ubatuba. A composição dos biomarcadores lipídicos presentes no sedimento evidenciou que a matéria orgânica particulada na região de plataforma interna de Ubatuba possui uma origem principalmente autóctone, e que está constituída por uma combinação de material derivado do plâncton vivo ou detrítico, da produção bacteriana e da fauna associada ao sedimento, havendo uma contribuição terrestre relativamente pequena. O presente estudo indicou que a dinâmica bêntica na região da plataforma interna de Ubatuba é moldada por forçantes ambientais, como a intrusão de massas dágua (e.g. ACAS) trazendo nutrientes para a zona fótica e estimulando a produção primária fitoplanctônica nova, induzindo o aumento na densidade e biomassa bêntica. A chegada de frentes frias, com ventos fortes, mistura da coluna dágua e revolvimento do fundo também possui fundamental importância, através do decréscimo nos valores dos parâmetros da comunidade bêntica. Esse padrão de acúmulo e remoção sugere que a biota bêntica da plataforma interna de Ubatuba esteja numa constante dinâmica de colonização e recolonização, que pode ser chave na manutenção de altos níveis de riqueza e equitatividade na região. Os resultados obtidos no presente estudo sugerem um íntimo e complexo acoplamento bentopelágico dependente, por um lado, de eventos oceanográficos de mesoescala (i.e. centenas de km; intrusão da ACAS) e, por outro, de eventos atmosféricos que influenciam o sistema bêntico em escala local, através da ressuspensão de sedimentos. / Coastal sediments are globally important for their role in the carbon cycle, being responsible for about 90% of the carbon burial in the global ocean. In continental shelf ecosystems, benthic communities play a vital role receiving energy from the pelagic system, serving as food source for demersal organisms, recycling nutrients back to the water column and sequestering part of the carbon into deeper layers of marine sediments. The present study aimed to investigate the variation on the dynamics of the benthic macrofauna on the inner shelf off Ubatuba-SP. Benthic macrofauna abundance, biomass, species richness, diversity, equitability and polychaete trophic groups were compared with the origin and composition of sedimentary organic matter. Sampling was carried out on a monthly basis starting in October 2006 for a year in a permanent station at 40 meters depth. The area is characterized by a transition between coastal and oceanic regimens. Sedimentary organic matter composition in terms of total organic matter, lipid biomarkers and phytopigments and phytodetritus showed a complexity typical from inner shelves and was driven by oceanic and atmospheric dynamics. Lipid biomarker composition revealed that particulated organic matter was mainly derived from autochthonous sources, composed of a combination of material derived from live plankton and detritic remains, bacterial production and from the benthic metazoan fauna. Terrestrial contribution to the sediment organic matter was small. The present study indicated that the benthic dynamics in the inner shelf off Ubatuba is molded by environmental forcing, especially the intrusion of water masses onto the shelf (e.g. ACAS), which brings nutrients to the euphotic zone stimulating new phytoplanktonic primary production. This enhances the flux of organic matter to the bottom increasing the benthic biota density and biomass. The arrival of cold fronts, with strong S-SW winds promoting water column mixing and sediment resuspension, was also fundamental in decreasing benthic community parameters (i.e. abundance and biomass). The dynamics of organic matter accumulation and removal suggest that the benthic biota in the inner shelf of Ubatuba is subjected to a constant pattern of settling and recolonization, which can be a key factor in the maintenance of high levels of species richness and equitability. The results obtained in the present study suggest a strong and complex benthic-pelagic coupling, influenced by mesoescale oceanographic events (i.e. hundreds of km; intrusion of ACAS) on the one hand and, on the other, by atmospheric events influencing the benthic system on a local scale, through the remobilization of sediments.

Os sedimentos costeiros são importantes globalmente, pois atuam como receptores de grandes quantidades de material orgânico alóctone e autóctone, sendo responsáveis por cerca de 90% do enterramento de carbono no oceano global. Dentro dos ecossistemas de plataforma continental, a fauna bêntica desempenha papel vital tanto como receptora de energia proveniente do pelagial, quanto como fornecedora de energia para os organismos demersais e de nutrientes para o fitoplâncton. O objetivo principal do presente trabalho foi investigar a variação temporal da dinâmica da macrofauna bêntica na plataforma interna de Ubatuba. A dinâmica bêntica foi analisada pela abundância, biomassa, descritores da comunidade (riqueza, diversidade, equitatividade) e análise trófica dos grupos mais abundantes, em função da origem e composição da matéria orgânica sedimentar. As coletas foram realizadas mensalmente em uma estação fixa, com início em outubro de 2006, por um período de um ano. A estação fixa possui uma profundidade de 40 m e um regime oceanográfico de transição entre águas costeiras e de plataforma continental. A composição da matéria orgânica em termos de MOT, fitopigmentos, fitodetritos e biomarcadores lipídicos apresentou uma complexidade típica de ambientes de plataforma interna, relacionados à dinâmica oceanográfica que rege os principais eventos de acúmulo ou remoção da matéria orgânica lábil na região de Ubatuba. A composição dos biomarcadores lipídicos presentes no sedimento evidenciou que a matéria orgânica particulada na região de plataforma interna de Ubatuba possui uma origem principalmente autóctone, e que está constituída por uma combinação de material derivado do plâncton vivo ou detrítico, da produção bacteriana e da fauna associada ao sedimento, havendo uma contribuição terrestre relativamente pequena. O presente estudo indicou que a dinâmica bêntica na região da plataforma interna de Ubatuba é moldada por forçantes ambientais, como a intrusão de massas dágua (e.g. ACAS) trazendo nutrientes para a zona fótica e estimulando a produção primária fitoplanctônica nova, induzindo o aumento na densidade e biomassa bêntica. A chegada de frentes frias, com ventos fortes, mistura da coluna dágua e revolvimento do fundo também possui fundamental importância, através do decréscimo nos valores dos parâmetros da comunidade bêntica. Esse padrão de acúmulo e remoção sugere que a biota bêntica da plataforma interna de Ubatuba esteja numa constante dinâmica de colonização e recolonização, que pode ser chave na manutenção de altos níveis de riqueza e equitatividade na região. Os resultados obtidos no presente estudo sugerem um íntimo e complexo acoplamento bentopelágico dependente, por um lado, de eventos oceanográficos de mesoescala (i.e. centenas de km; intrusão da ACAS) e, por outro, de eventos atmosféricos que influenciam o sistema bêntico em escala local, através da ressuspensão de sedimentos. / Coastal sediments are globally important for their role in the carbon cycle, being responsible for about 90% of the carbon burial in the global ocean. In continental shelf ecosystems, benthic communities play a vital role receiving energy from the pelagic system, serving as food source for demersal organisms, recycling nutrients back to the water column and sequestering part of the carbon into deeper layers of marine sediments. The present study aimed to investigate the variation on the dynamics of the benthic macrofauna on the inner shelf off Ubatuba-SP. Benthic macrofauna abundance, biomass, species richness, diversity, equitability and polychaete trophic groups were compared with the origin and composition of sedimentary organic matter. Sampling was carried out on a monthly basis starting in October 2006 for a year in a permanent station at 40 meters depth. The area is characterized by a transition between coastal and oceanic regimens. Sedimentary organic matter composition in terms of total organic matter, lipid biomarkers and phytopigments and phytodetritus showed a complexity typical from inner shelves and was driven by oceanic and atmospheric dynamics. Lipid biomarker composition revealed that particulated organic matter was mainly derived from autochthonous sources, composed of a combination of material derived from live plankton and detritic remains, bacterial production and from the benthic metazoan fauna. Terrestrial contribution to the sediment organic matter was small. The present study indicated that the benthic dynamics in the inner shelf off Ubatuba is molded by environmental forcing, especially the intrusion of water masses onto the shelf (e.g. ACAS), which brings nutrients to the euphotic zone stimulating new phytoplanktonic primary production. This enhances the flux of organic matter to the bottom increasing the benthic biota density and biomass. The arrival of cold fronts, with strong S-SW winds promoting water column mixing and sediment resuspension, was also fundamental in decreasing benthic community parameters (i.e. abundance and biomass). The dynamics of organic matter accumulation and removal suggest that the benthic biota in the inner shelf of Ubatuba is subjected to a constant pattern of settling and recolonization, which can be a key factor in the maintenance of high levels of species richness and equitability. The results obtained in the present study suggest a strong and complex benthic-pelagic coupling, influenced by mesoescale oceanographic events (i.e. hundreds of km; intrusion of ACAS) on the one hand and, on the other, by atmospheric events influencing the benthic system on a local scale, through the remobilization of sediments.

There is large natural variation in light and nutrient conditions across lakes. In the boreal-subarctic region most lakes are small, shallow and nutrient poor. In such lakes there is often sufficient light to support primary production at the lake bottom. An expectation for the future is that colored dissolved organic matter (cDOM) of terrestrial origin will increase in these lakes. cDOM depresses the underwater light climate but is often associated with elevated pelagic nutrient concentrations. A dynamical model of a coupled benthic-pelagic food web was explored for how lake ecosystems might respond to altered light and nutrient regimes. The model predicts that mobile carnivores (fish) control grazers and release primary producers from grazing pressure. Primary producers are therefore limited by their resources and cross-habitat interactions are dominated by spatially asymmetric competition for light and nutrients. At high light and low nutrient supply benthic algae out-compete pelagic algae for nutrients diffusing from the sediment, whereas pelagic algae shade out benthic algae at lower light and/or higher nutrient supply. Biomass patterns of benthic and pelagic consumers follow the patterns of primary production. In contrast, habitat coupling through carnivore movement has only a weak impact on biomass patterns in the model food web. Model predictions were compared with data from boreal-subarctic lakes covering a broad range of cDOM concentrations. In agreement with model expectations the following relationships with increasing light attenuation were observed: benthic primary and secondary production decreased, pelagic primary production showed a unimodal trend, and pelagic nutrient concentrations as well as the proportion of fish feeding in the pelagic habitat increased. As a consequence, both primary and fish production were negatively related to pelagic nutrient concentrations across lakes. In a comparative study of boreal-subarctic lakes covering a broad range of cDOM concentrations, a similar negative relationship was found between pelagic total nutrient concentrations and the biomass of epilithic algae. This was surprising, because epilithon cannot access nutrients from the sediment. Patterns in epilithon biomass were largely driven by nitrogen fixing cyanobacteria, which in turn were positively related to light supply. The data suggest that nitrogen fixing autotrophs may have a competitive advantage over other epilithic primary producers in low-cDOM, low-nutrient, high-light environments, and that patterns in epilithic biomass, nutrient sequestration and elemental stoichiometry depend upon which functional group is dominant in the epilithic biofilm.

Animals living in marine sediments (the second largest habitat on earth) play a major role in global biogeochemical cycling. By feeding on organic matter from settled phytoplankton blooms they produce food for higher trophic levels and nutrients that can fuel primary production. In the Baltic Sea, anthropogenic stresses, such as eutrophication and introductions of invasive species, have altered phytoplankton dynamics and benthic communities. This thesis discusses the effects of different types of phytoplankton on the deposit-feeding community and the importance of benthic biodiversity for fate of the phytoplankton bloom-derived organic matter. Deposit-feeders survived and fed on settled cyanobacterial bloom material and in doing so accumulated the cyanobacterial toxin nodularin. Their growth after feeding on cyanobacteria was much slower than on a diet of spring bloom diatoms. The results show that settling blooms of cyanobacteria are used as food without obvious toxic effects, although they do not sustain rapid growth of the fauna. Since all tested species accumulated the cyanotoxin, negative effects higher up in the food web can not be ruled out. Both species composition and richness of deposit-feeding macrofauna influenced how much of the phytoplankton bloom material that was incorporated in fauna or retained in the sediment. The mechanism behind the positive effect of species richness was mainly niche differentiation among functionally different species, resulting in a more efficient utilization of resources at greater biodiversity. This was observed even after addition of an invasive polychaete species. Hence, species loss can be expected to affect benthic productivity negatively. In conclusion, efficiency in organic matter processing depends both on pelagic phytoplankton quality and benthic community composition and species richness. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: In press. Paper 5: Manuscript.</p>

Mysid shrimps (Mysidacea, Crustacea) are efficient zooplanktivores in both marine and freshwater systems as well as lipid rich prey for many species of fish.  Although some efforts have been made to study the role of mysids in the Baltic Sea, very few studies have been carried out in recent time and there are still knowledge gaps regarding various aspects of mysid ecology. This thesis aims to explore some of these gaps by covering a mixture of topics. Using multifrequency hydroacoustics we explored the possibility to separate mysids from fish echoes and successfully established a promising and effective method for obtaining mysid abundance/biomass estimates (paper I). An investigation of the current mysid community in a coastal area of the northern Baltic proper (paper II) demonstrated that the formerly dominant, pelagic mysid Mysis mixta had decreased substantially (~50%) in favor for phytoplanktivorous, juvenile Neomysis integer and Mysis relicta sp. By examining different aspects of mysid behavior, we studied the vertical size distribution of mysids in the field and found that size increased with depth/declining light, irrespective of temperature; indicating that their vertical size distribution primarily is a response to predation (paper II). In paper III, a combination of ecological and genetic markers was used to investigate intraspecific differences in migratory tendency. Both marker types indicated that some part of the Mysis salemaai population is sedentary on the bottom and that this strategy is a phenotypically plastic but persistent trait, analogous to the partial migrations seen in many birds and fishes. In paper IV a temperature and weight specific respiration model was developed for the littoral Praunus flexuosus. Routine respiration was moreover elevated by post-prandial effects (specific dynamic action) for longer times than previously suggested. Consequently, ignoring such effects could significantly bias respiration measurements. / At the time of doctoral defence the following papers were unpublished and had a status as follows: Paper  2: Accepted; Paper 3: Submitted; Paper  4: Accepted

Aquatic sediments are, by surface, the largest habitat on Earth. A wide diversity of organisms inhabit these sediments and by their actions they have a large influence on and also mediate many ecosystem processes. Several of these processes, such as decomposition and remineralisation of organic matter are important on a global scale and are essential to sustain life on Earth. The main aim of this thesis was to use an experimental ecosystem ecology approach in order to study some of these ecosystem processes in marine sediments and how they are linked to biodiversity. Paper I and II found that an increased species richness of sediment deposit feeders increases the processing of organic matter from phytoplankton settled on the sea-floor, and that species-rich communities have a more efficient resource utilization of deposited organic matter. The results in paper IV and V also suggest that there is a link between microbial diversity in sediments and the degradation of organic contaminants. Paper V also shows that antibiotic pollution is a potential threat to natural microbial diversity and microbially mediated ecosystem services. The introduction of invasive species to ecosystems is another major threat to biodiversity and was studied in Paper II and III, by investigating the ecology of Marenzelleria arctia, a polychaete worm recently introduced in the Baltic Sea. Paper II suggests that M. arctia mainly utilize food resources not used by native deposit feeders, thus potentially increasing the benthic production in the Baltic Sea by increasing resource use efficiency. Paper III, however, show that M. arctia is protected from predation by the native benthic invertebrate predators, due to its ability to burrow deep in the sediment, suggesting that predation on M. arctia by higher trophic levels is restricted, thereby limiting trophic transfer. In conclusion, this thesis gives some examples of the importance of marine biodiversity for the generation of a few key ecosystem processes, such as organic matter processing and the degradation of harmful contaminants. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: In press.

Marine sediments are a key component of the global carbon cycle and climate system. They host one of the largest carbon reservoirs on Earth, provide the only long-term sink for atmospheric CO2, recycle nutrients and represent the most important climate archive. Early diagenetic pro- cesses in marine sediments are thus central to our understanding of past, present and future biogeochemical cycling and climate. Because all early diagenetic processes can be directly or indirectly linked back to the degradation of organic matter (OM), advancing this understand- ing requires disentangling the different factors that control the fate of OM (sedimentation, degradation and burial) on different spatial and temporal scales. In general, the heterotrophic degradation of OM in marine sediments is controlled by the quantity and, in particular, by the ap- parent reactivity of OM that settles onto marine sediments. While the potential ((micro)biological, chemical and physical) controls on OM reactivity are increasingly well understood, their relative significance remains difficult to quantify. Traditionally, integrated data-model approaches are used to quantify apparent OM reactivity (i.e. OM degradation rate constants) at well-studied drill-sites. These approaches rely on Reaction-Transport Models (RTMs) that typically account for transport (advection, molecular diffusion, bioturbation, and bioirrigation) and reaction (pro- duction, consumption, equilibrium) processes, but vary in complexity. Apparent OM reactivity (i.e. the OM degradation rate constant) is generally considered as a free parameter that is used to fit observed depth-profiles, reaction rates or benthic-pelagic exchange fluxes. Currently, no quantitative framework exists to predict apparent OM reactivity in areas where comprehensive benthic data sets are not available.To evaluate the impact of this knowledge gap, the sensitivity of benthic biogeochemical reaction rates, as well as benthic-pelagic exchange fluxes to variations in apparent OM reactivity (i.e. reactive continuum model parameters a and ν) is explored by means of a complex, numerical diagenetic model for shelf, slope and deep sea depositional environments. Model results show that apparent OM reactivity exerts a dominant control on the magnitude of biogeochemical reaction rates and benthic-pelagic exchange fluxes across different environments. The lack of a general framework to quantify OM reactivity thus complicates the parametrization of regional and global scale diagenetic models and, thus, compromises our ability to quantify global benthic-pelagic coupling in general and OM degradation dynamics in particular.To make a first step towards an improved systematic and quantitative knowledge of OM reac- tivity, apparent OM reactivity (i.e. reactive continuum model parameters a and ν) is quantified by inverse modelling of organic carbon, sulfate (and methane) sediment profiles, as well as the location of the sulfate-methane transition zone using a complex, numerical diagenetic model for 14 individual sites across different depositional environments. Model results highlight again the dominant control of OM reactivity on biogeochemical reaction rates and benthic exchange fluxes. In addition, results show that, inversely determined ν-values fall within a narrow range (0.1 < ν < 0.2). In contrast, determined a-values span ten orders of magnitude (1 · 10−3 < a < 1·107) and are, thus, the main driver of the global variability in OM reactivity. Exploring these trends in their environmental context reveals that apparent OM reactivity is determined by a dynamic set of environmental controls rather than traditionally proposed single environmental controls (e.g. water depth, sedimentation rate, OM fluxes). However, the high computational demand associated with such a multi-species inverse model approach, as well as the limited availability of comprehensive pore water data, limits the number of apparent OM reactivity estimates. Therefore, while providing important primers for a quantification of OM reactivity on the global scale, inverse model results fall short of providing a predictive framework.To overcome the computational limitations and expand the inverse modelling of apparent OM reactivity to the global scale, the analytical model OMEN-SED is extended by integrating a nG- approximation of the reactive continuum model that is fully consistent with the general structure of OMEN-SED. The new version OMEN-SED-RCM thus provides the computational efficiency required for the inverse determination of apparent OM reactivity (i.e. reactive continuum model parameters a and ν) on the global scale. The abilities of the new model OMEN-SED-RCM in capturing observed local, as well as global patterns of diagenetic dynamics are rigorously tested by model-data, as well as model-model comparison.OMEN-SED-RCM is then used to inversely determine apparent OM reactivity by inverse modelling of 394 individual dissolved oxygen utilisation (DOU) rate measurements. DOU is commonly used as a proxy for OM reactivity, it is more widely available than comprehensive porewater data sets and global/regional benthic maps of dissolved oxygen utilisation rates (DOU) have been derived based on the growing DOU data set. Sensitivity test show that, while inverse modelling of DOU rates fails to provide a robust estimate of RCM parameter ν, it is a good indicator for RCM parameter a. Based on previous findings, parameter ν was thus assumed to be globally constant. Inversely determined a-values vary over order of magnitudes from a = 0.6 years in the South Polar region to a = 5.6 · 106 in the oligotrophic, central South Pacific. Despite a high intra- as well as interregional heterogeneity in apparent benthic OM reactivity, a number of clear regional patterns that broadly agree with previous observations emerge. High apparent OM reactivities are generally observed in regions dominated by marine OM sources and characterized by efficient sinking of OM and a limited degradation during sinking. In contrast, the lowest apparent OM reactivities are observed for regions characterized by low marine primary production rates, in combination with a great distance to the continental shelf and slope, as well as deep water columns. Yet, results also highlight the importance of lateral transport processes for apparent OM reactivity. In particular, deep sea sediments in the vicinity of dynamic continental margin environments or under the influence of strong ocean currents can receive comparably reactive OM inputs from more productive environments and, thus, reveal OM reactivities that are higher than traditionally expected. Finally, based on the observed strong link between apparent OM reactivity (i.e. RCM parameters a) and DOU rate, a transfer function that predicts the order of magnitude of RCM parameter a as a function of DOU is used to derive, to our knowledge, the first global map of apparent OM reactivity.Finally, we use the new global map of apparent OM reactivity to quantify biogeochemical dynamics and benthic-pelagic coupling across 22 benthic provinces that cover the entire global ocean. To this end, the numerical diagenetic model BRNS model is set-up for each province and forced with regionally averaged boundary conditions derived from global data sets, as well as apparent OM reactivities informed by the global OM reactivity map. The 22 regional model set-ups were then used to quantify biogeochemical process rates, as well as benthic carbon and nutrient fluxes in each province and on the global scale. Model results of regional and global fluxes and rates fall well within the range of observed values and also agree with general globally observed patterns. Results also highlight the role of the deeper ocean for benthic-pelagic cycling and indicate towards a large regional variability in benthic cycling at great depth. This is a first step towards a more refined global estimate of benthic biogeochemical cycling that accounts for the global heterogeneity of the seafloor environment. This aspect is critical to improve our understanding of benthic feedbacks on benthic-pelagic coupling and on the carbon-climate system, which can then be incorporated in benthic processes in Earth System Models. / Les sédiments marins sont un élément clé du cycle mondial du carbone et du système climatique. Ils abritent l’un des plus grands réservoirs de carbone sur Terre, fournissent le seul puits à long terme pour le CO2 atmosphérique, recyclent les nutriments et constituent les archives climatiques les plus importantes. Les processus de la diagénèse précoce dans les sédiments marins sont donc au cœur de notre compréhension des cycles et du climat biogéochimiques passés, présents et futurs. Étant donné que tous les processus diagénétiques précoces peuvent être directement ou indirectement liés à la dégradation de la matière organique (MO), faire progresser cette compréhension nécessite de démêler les différents facteurs qui contrôlent le devenir de la MO (sédimentation, dégradation et enfouissement) à différentes échelles spatiales et temporelles. En général, la dégradation hétérotrophique de la MO dans les sédiments marins est contrôlée par la quantité et, en particulier, la réactivité apparente de la MO qui se dépose sur les sédiments marins. Bien que les contrôles potentiels ((micro) biologiques, chimiques et physiques) de la réactivité de la MO soient de mieux en mieux compris, leur importance relative reste difficile à quantifier. Traditionnellement, des approches de modèle de données intégrées sont utilisées pour quantifier la réactivité apparente de la MO (c’est-à-dire les constantes de vitesse de dégradation de la MO) sur des sites de forage bien étudiés. Ces approches reposent sur des modèles de réaction-transport (RTM) qui tiennent généralement compte des processus de transport (advection, diffusion moléculaire, bioturbation et bio-irrigation) et de réaction (production, consommation, équilibre), mais leur complexité varie. La réactivité apparente de la MO est généralement considérée comme un paramètre libre qui est utilisé pour ajuster les profils de profondeur, les taux de réaction ou les flux d’échange benthique-pélagique observés. À l’heure actuelle, aucun cadre quantitatif n’existe pour prédire la réactivité apparente de la MO dans les zones où aucun ensemble complet de données benthiques n’est disponible.Pour évaluer l’impact de ce manque de connaissance, nous avons exploré la sensibilité des taux de réaction biogéochimiques benthiques, ainsi que des flux d’échange benthique-pélagique aux variations de la réactivité apparente de la MO (c.-à-d. les paramètres du modèle de con- tinuum réactif a et ν) au moyen d’un modèle diagénétique numérique complexe appliqué aux zones de dépôts sur les plateaux, les talus et en haute mer. Les résultats du modèle montrent que la réactivité apparente de la MO exerce un contrôle dominant sur l’ampleur des taux de réaction biogéochimiques et des flux d’échange benthique-pélagique dans différents environ- nements. L’absence d’un cadre général pour quantifier la réactivité de la MO complique donc la paramétrisation des modèles diagénétiques à l’échelle régionale et mondiale et, ainsi, compromet notre capacité à quantifier le couplage benthique-pélagique global en général et la dynamique de dégradation de la MO en particulier.Pour tendre à meilleure connaissance systématique et quantitative de la réactivité de la MO, la réactivité apparente OM (c.-à-d. les paramètres du modèle de continuum réactif a et ν) est quantifiée par modélisation inverse des profils de sédiments organiques de carbone, de sulfate (et de méthane), ainsi que localisation de la zone de transition sulfate-méthane à l’aide d’un modèle diagénétique numérique complexe pour 14 sites individuels à travers différents environnements de dépôt. Les résultats du modèle mettent à nouveau en évidence le contrôle dominant de la réactivité de l’OM sur les taux de réaction biogéochimiques et les flux d’échanges benthiques. De plus, les résultats montrent que les valeurs déterminées inversement déterminées se situent dans une plage étroite (0,1 <ν<0,2). En revanche, les valeurs déterminées s’étendent sur dix ordres de grandeur (1 ·10−3 <ν< 1·107) et sont donc le principal moteur de la variabilité globale de la réactivité OM. L’exploration de ces tendances dans leur contexte environnemental révèle que la réactivité apparente de l’OM est déterminée par un ensemble dynamique de contrôles environnementaux plutôt que par des contrôles environnementaux uniques traditionnellement proposés (par exemple, la profondeur de l’eau, le taux de sédimentation, les flux OM). Cependant, la forte demande de calcul associée à une telle approche de modèle inverse multi-espèces, ainsi que la disponibilité limitée de données complètes sur l’eau interstitielle, limitent le nombre d’estimations apparentes de la réactivité OM. Par conséquent, tout en fournissant des amorces importantes pour une quantification de la réactivité de l’OM à l’échelle mondiale, les résultats du modèle inverse sont loin de fournir un cadre prédictif.Pour surmonter les limites de calcul et étendre la modélisation inverse de la réactivité apparente de l’OM à l’échelle mondiale, le modèle analytique OMEN-SED est étendu en intégrant une approximation nG du modèle de continuum réactif qui est pleinement cohérente avec la structure générale d’OMEN-SED. La nouvelle version OMEN-SED-RCM fournit ainsi l’efficacité de calcul requise pour la détermination inverse de la réactivité apparente de l’OM (c’est-à-dire les paramètres du modèle de continuum réactif a et ν) à l’échelle mondiale. Les capacités du nouveau modèle OMEN-SED-RCM à capturer les modèles locaux et globaux de dynamique diagénétique observés sont rigoureusement testés par les données du modèle, ainsi que la comparaison modèle- modèle.OMEN-SED-RCM est ensuite utilisé pour déterminer inversement la réactivité apparente de l’OM par modélisation inverse de 394 mesures individuelles du taux d’utilisation de l’oxygène dissous (DOU). Le DOU est couramment utilisé comme indicateur de la réactivité de l’OM, il est plus largement disponible que les ensembles de données exhaustifs sur l’eau interstitielle et les cartes benthiques mondiales/régionales des taux d’utilisation de l’oxygène dissous (DOU) ont été dérivées sur la base de l’ensemble de données DOU croissant. Le test de sensibilité montre que, bien que la modélisation inverse des taux de DOU ne fournisse pas une estimation robuste du paramètre RCM ν, c’est un bon indicateur pour le paramètre RCM a. Sur la base des résultats précédents, le paramètre ν a donc été supposé être globalement constant. Les valeurs a déterminées à l’inverse varient selon l’ordre de grandeur, de a = 0,6 an dans la région polaire sud à a = 5, 6 · 106 dans le Pacifique sud oligotrophique central. Malgré une forte hétérogénéité intra et interrégionale dans la réactivité apparente de la MO benthique, un certain nombre de schémas régionaux clairs qui correspondent largement aux observations précédentes émergent. Des réactivités apparentes élevées de l’OM sont généralement observées dans les régions dominées par des sources marines de MO et caractérisées par un naufrage efficace de l’OM et une dégradation limitée pendant le naufrage. En revanche, les réactivités MO apparentes les plus faibles sont observées pour les régions caractérisées par de faibles taux de production primaire marine, en combinaison avec une grande distance du plateau continental et de la pente, ainsi que des colonnes d’eau profonde. Pourtant, les résultats mettent également en évidence l’importance des processus de transport latéral pour la réactivité apparente de l’OM.En particulier, les sédiments des mers profondes au voisinage d’environnements de marge continentale dynamiques ou sous l’influence de forts courants océaniques peuvent recevoir des apports OM de réactivité comparable provenant d’environnements plus productifs et, ainsi, révéler des réactivités OM plus élevées que ce qui était traditionnellement prévu. Enfin, sur la base du lien fort observé entre la réactivité apparente de l’OM (c’est-à-dire le paramètre RCM a) et le taux DOU, une fonction de transfert qui prédit l’ordre de grandeur du paramètre RCM a en fonction de DOU est utilisée pour dériver, pour nos connaissances, la première carte mondiale de la réactivité apparente de l’OM. Les résultats du modèle des flux et des taux régionaux et mondiaux se situent bien dans la gamme des valeurs observées et également d’accord avec les tendances générales observées au niveau mondial. Les résultats mettent également en évidence le rôle de l’océan profond pour le cycle benthique-pélagique et indiquent une grande variabilité régionale du cycle benthique à grande profondeur. Il s’agit d’une première étape vers une estimation mondiale plus précise du cycle biogéochimique benthique qui tient compte de l’hétérogénéité mondiale du milieu marin. Cet aspect est essentiel pour améliorer notre compréhension des rétroactions benthiques sur le couplage benthique-pélagique et sur le système carbone-climat, qui peuvent ensuite être incorporées aux processus benthiques dans les modèles du système terrestre. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished