Coastal ecosystems are faced with increasing pressures from human activities. Perhaps one of the most profound impacts is that of excess nitrogen loading which drives a series of negative consequences. Excess nitrogen fuels primary productivity and the subsequent enhanced microbial decomposition of organic matter, consumes oxygen and releases carbon dioxide, which causes large fluctuations in pH. Changes in organic matter availability, oxygen concentrations, and pH can have significant yet unconstrained implications for sediment recycling and removal of biologically important nutrients such as nitrogen and phosphorus. Such changes can also impact the production and consumption of two powerful greenhouse gases – nitrous oxide and methane. Here I use two temperate estuaries, Long Island Sound (New York, USA) and Waquoit Bay (Massachusetts, USA) to assess the role of human impacts on coastal sediment biogeochemical fluxes. In Chapter 1, I investigate the influence of organic matter loading on sediment nutrient cycling, excess nitrogen filtering, and greenhouse gas emissions in Long Island Sound, a heavily nutrient polluted estuary. To provide a comprehensive analysis of these benthic fluxes and their environmental drivers, I incubated sediment cores from five stations along a west to east transect representing a gradient of high to low nutrient inputs and organic matter deposition. I found sediments across the estuary removed only 9% of land-based nitrogen entering the system and had a nitrogen removal efficiency of 30%. Additionally, sediments were often a source of inorganic nitrogen and phosphorus as well as nitrous oxide and methane. This study provides the first directly measured rates of sediment nitrogen removal and production in Long Island Sound. In Chapters 2 and 3, I investigate the effect of coastal acidification on benthic fluxes of greenhouse gases and nutrients across the sediment-water interface in Waquoit Bay. I collected sediment cores from two sites experiencing different rates of nutrient loading and experimentally altered the overlying water pH through a series of incubations representing moderate (pH 7.3) and extreme (pH 6.3) pH conditions. My results show low pH conditions have a strong effect on greenhouse gas and nutrient fluxes and responses vary by site. Specifically, in the high nutrient impacted site, nitrous oxide flux increased and methane flux decreased under acidification. In the low nutrient impacted site acidification drove reduced nitrous oxide flux, while methane flux decreased in the moderate treatment and increased in the extreme treatment. Acidification also affected benthic nutrient fluxes and drove the high nutrient impacted site to become phosphorus limited. Furthermore, the relationships and drivers between nutrient availability and nutrient fluxes shifted under acidification. This dissertation provides additional insight into how coastal ecosystems respond to human impacts. In Chapter 1, I present a critical missing piece of the nitrogen budget of a heavily impacted estuary. In Chapters 2 and 3, I begin to elucidate how low pH conditions can impact sediment biogeochemistry in estuarine ecosystems. Efforts to improve our understanding of human impacts on sediment biogeochemical fluxes will create better informed coastal management practices for these dynamic systems under a changing climate. / 2025-10-23T00:00:00Z

A acidificação dos oceanos, resultado do aumento das emissões de gás carbônico (CO2), por atividades antrópicas, vem causando uma mudança no equilíbrio químico do sistema carbonato e uma consequente diminuição do pH nos oceanos mundiais. Cerca de 30% das emissões antropogênicas de CO2 é absorvida pelo oceano, o que já reduziu o PH em 0,1 unidade em águas superficiais e são esperadas ainda maiores reduções. A escala de mudanças \"toleráveis\" de pH ainda é incerta para muitos organismos e pouco conhecida para muitos processos biológicos, particularmente no sedimento. Este trabalho teve como objetivo quantificar tanto as taxas atuais de remineralização da matéria orgânica e fluxos de nutrientes na interface água-sedimento, como as alterações nessas taxas em resposta a diferentes cenários de acidificação do oceano, usando câmaras de incubação bêntica tanto in situ como em laboratório. Os experimentos in situ e coleta de material para montagem dos experimentos em laboratório foram realizados através de mergulho autônomo, na área rasa de Ubatuba-SP (6-8 m de profundidade). As incubações mostraram alto consumo de O2, variando entre -17 mmol m-2 d-1 em Julho de 2012 e -112 mmol m-2 d-1 em Abril e Junho de 2013. Houve uma dominância da nitrificação, com fluxos entre 0.2 and 0,4 µmol m-2 d-1 (sem variação temporal). As incubações também mostraram fluxos positivos de amônio, sendo os mais altos (1.0 - 1.5 µmol m-2 d-1) observados em Março, Abril e Junho de 2013. No geral, os processos de heterotrofia líquida prevaleceram sobre os processos autotróficos na região de estudo. Esses resultados indicam que os processos que ocorrem nos sedimentos costeiros de Ubatuba são: (1) remineralização aeróbica bêntica, (2) processos de nitrificação maiores que denitrificação e (3) provável excreção de organismos bênticos. O experimento de acidificação in situ indicou um aumento nos fluxos de O2 (de 0.02 para 45 mmol m-2 d-1). Os experimentos com acidificação mostraram efeitos similares: aumento do consumo médio de O2 e liberação de CO2, principalmente na areia. Houve diminuição nos processos de nitrificação em resposta à diminuição do pH. O estudo forneceu resultados importantes e inéditos sobre os processos biogeoquímicos em sedimentos costeiros da região de Ubatuba (SP), assim como os efeitos da acidificação dos oceanos nos processos biogeoquímicos em sedimentos costeiros. / Ocean acidification, a result of an increase in carbon dioxide (CO2) anthropic emissions, has caused a change in the chemical balance of the carbonate system and a consequent pH decrease in the world\'s oceans. Approximately 30% of anthropogenic CO2 is absorbed by the ocean, which has already reduced the pH by ∼0.1 units in surface waters (with further reductions expected). The scale of \"tolerable\" pH changes is still uncertain for many organisms and little-known for biological processes, particulary for the sediment. This work aimed to quantify both the current rates of organic matter remineralization and nutrient fluxes at the sediment-water interface and the changes in those rates in response to different ocean acidification scenarios, using benthic incubation chambers both in situ and in the laboratory. The in situ studies and sample collections for laboratory experiments were performed via SCUBA in a shallow area near Ubatuba-SP (6-8 m deep). Incubation experiments showed high oxygen (O2) consumption, ranging from -17 mmol m-2 d-1 in July 2012 to -112 µmol m-2 d-1 in April and June 2013. They also exhibited a dominance of nitrification, with fluxes between 0.2 and 0,4 µmol m-2 d-1 (with no temporal variation). Incubations also exhibited a release of ammonium, with the highest fluxes (1.0 - 1.5 µmol m-2 d-1) in March, April and June 2013. In general, net heterothrophic processes prevailed over autotrophic processes for the study region. The interstitial water parameters (ammonium, phosphate, dissolved iron and total sulfides) exhibited no significant difference between the two kinds of sediment analyzed, silt (station 1) and sand (station 2). These results suggested that the processes occurring in the coastal sediments of Ubatuba are: (1) benthic remineralization mediated by bacterial biota, (2) nitrification prevailed over denitrification and (3) probably excretion by benthic organisms. The experiment in situ indicated an increase in the fluxes of O2 (from -70 to -108 µmol m-2 d-1) and CO2 (from 0.02 to 45 µmol m-2 d-1). The acidification experiments showed a similar effect: a higher O2 average consumption and CO2 release, mostly in the sandy sediment. A decrease in nitrification processes occurred in response to decreased pH. This work has provided a baseline for the biogeochemical processes in coastal sediments in Ubatuba (SP), as well as demonstrated the effects of ocean acidification on biogeochemical processes in coastal sediments.

A acidificação dos oceanos, resultado do aumento das emissões de gás carbônico (CO2), por atividades antrópicas, vem causando uma mudança no equilíbrio químico do sistema carbonato e uma consequente diminuição do pH nos oceanos mundiais. Cerca de 30% das emissões antropogênicas de CO2 é absorvida pelo oceano, o que já reduziu o PH em 0,1 unidade em águas superficiais e são esperadas ainda maiores reduções. A escala de mudanças \"toleráveis\" de pH ainda é incerta para muitos organismos e pouco conhecida para muitos processos biológicos, particularmente no sedimento. Este trabalho teve como objetivo quantificar tanto as taxas atuais de remineralização da matéria orgânica e fluxos de nutrientes na interface água-sedimento, como as alterações nessas taxas em resposta a diferentes cenários de acidificação do oceano, usando câmaras de incubação bêntica tanto in situ como em laboratório. Os experimentos in situ e coleta de material para montagem dos experimentos em laboratório foram realizados através de mergulho autônomo, na área rasa de Ubatuba-SP (6-8 m de profundidade). As incubações mostraram alto consumo de O2, variando entre -17 mmol m-2 d-1 em Julho de 2012 e -112 mmol m-2 d-1 em Abril e Junho de 2013. Houve uma dominância da nitrificação, com fluxos entre 0.2 and 0,4 µmol m-2 d-1 (sem variação temporal). As incubações também mostraram fluxos positivos de amônio, sendo os mais altos (1.0 - 1.5 µmol m-2 d-1) observados em Março, Abril e Junho de 2013. No geral, os processos de heterotrofia líquida prevaleceram sobre os processos autotróficos na região de estudo. Esses resultados indicam que os processos que ocorrem nos sedimentos costeiros de Ubatuba são: (1) remineralização aeróbica bêntica, (2) processos de nitrificação maiores que denitrificação e (3) provável excreção de organismos bênticos. O experimento de acidificação in situ indicou um aumento nos fluxos de O2 (de 0.02 para 45 mmol m-2 d-1). Os experimentos com acidificação mostraram efeitos similares: aumento do consumo médio de O2 e liberação de CO2, principalmente na areia. Houve diminuição nos processos de nitrificação em resposta à diminuição do pH. O estudo forneceu resultados importantes e inéditos sobre os processos biogeoquímicos em sedimentos costeiros da região de Ubatuba (SP), assim como os efeitos da acidificação dos oceanos nos processos biogeoquímicos em sedimentos costeiros. / Ocean acidification, a result of an increase in carbon dioxide (CO2) anthropic emissions, has caused a change in the chemical balance of the carbonate system and a consequent pH decrease in the world\'s oceans. Approximately 30% of anthropogenic CO2 is absorbed by the ocean, which has already reduced the pH by ∼0.1 units in surface waters (with further reductions expected). The scale of \"tolerable\" pH changes is still uncertain for many organisms and little-known for biological processes, particulary for the sediment. This work aimed to quantify both the current rates of organic matter remineralization and nutrient fluxes at the sediment-water interface and the changes in those rates in response to different ocean acidification scenarios, using benthic incubation chambers both in situ and in the laboratory. The in situ studies and sample collections for laboratory experiments were performed via SCUBA in a shallow area near Ubatuba-SP (6-8 m deep). Incubation experiments showed high oxygen (O2) consumption, ranging from -17 mmol m-2 d-1 in July 2012 to -112 µmol m-2 d-1 in April and June 2013. They also exhibited a dominance of nitrification, with fluxes between 0.2 and 0,4 µmol m-2 d-1 (with no temporal variation). Incubations also exhibited a release of ammonium, with the highest fluxes (1.0 - 1.5 µmol m-2 d-1) in March, April and June 2013. In general, net heterothrophic processes prevailed over autotrophic processes for the study region. The interstitial water parameters (ammonium, phosphate, dissolved iron and total sulfides) exhibited no significant difference between the two kinds of sediment analyzed, silt (station 1) and sand (station 2). These results suggested that the processes occurring in the coastal sediments of Ubatuba are: (1) benthic remineralization mediated by bacterial biota, (2) nitrification prevailed over denitrification and (3) probably excretion by benthic organisms. The experiment in situ indicated an increase in the fluxes of O2 (from -70 to -108 µmol m-2 d-1) and CO2 (from 0.02 to 45 µmol m-2 d-1). The acidification experiments showed a similar effect: a higher O2 average consumption and CO2 release, mostly in the sandy sediment. A decrease in nitrification processes occurred in response to decreased pH. This work has provided a baseline for the biogeochemical processes in coastal sediments in Ubatuba (SP), as well as demonstrated the effects of ocean acidification on biogeochemical processes in coastal sediments.

Dans le bassin d’Arcachon, le crustacé thalassinidé Upogebia pusilla habite préférentiellement les vasières intertidales colonisées par les zostères naines (Zostera noltei) où il trouve la stabilité sédimentaire indispensable à l’établissement durable de son terrier. Du fait de la profondeur de ce dernier (> 30 cm) et de sa grande mobilité, cette espèce ingénieure a souvent été négligée dans les études antérieures ayant pour objectif de mieux comprendre le rôle des communautés macro-benthiques dans le fonctionnement des herbiers de phanérogames et les conséquences de leur régression rapide. Ce manuscrit présente une étude intégrée du rôle d’U. pusilla dans le fonctionnement de son écosystème en s’attachant particulièrement à caractériser et quantifier les relations entre (1) ses différentes activités (fouissage, ventilation, locomotion, …), (2) les modes de bioturbation qui en résultent et (3)leurs impacts respectifs sur la dynamique biogéochimique sédimentaire. Ce travail montre qu’U. pusilla engendre un remaniement et une bioirrigation intenses de la matrice sédimentaire qui l’entoure. Sa présence stimule ainsi fortement la reminéralisation de la matière organique sédimentée et les échanges de solutés à travers l’interface eau-sédiment.Bien que l’influence d’U. pusilla sur ces processus écologiques et biogéochimiques soit très dépendante des conditions environnementales (e.g., saisonnalité, prévalence parasitaire),l’ensemble de mes résultats suggère que le déclin progressif de ses populations, conséquence directe de la dégradation de son habitat, est susceptible de fortement altérer le fonctionnement global des écosystèmes du bassin d’Arcachon. / In Arcachon bay, the endobenthic thalassinid crustacean Upogebia pusilla is tightly associated with the intertidal dwarf grass Zostera noltei providing the sediment stability required for the construction of (semi-)permanent burrows. Because of the depth and complex architecture of their burrow (> 30 cm), this high mobile engineer species have been largely ignored in previous studies aiming at better understanding the role of macrobenthic communities in the functioning of seagrass ecosystems and the consequences of their rapid decline. This manuscript presents an integrated study regarding the role played by U. pusillain the functioning of its ecosystem, with particular emphasis on the characterisation and quantification of the relationships between (1) its different activities (burrowing, ventilating,walking…), (2) both bioturbation modes and rates and (3) their respective impacts on the sedimentary biogeochemical dynamics. This work shows that mud shrimp activity leads tohigh mixing and bioirrigation of the surrounding sediment matrix, thus strongly enhancing organic matter mineralisation processes and solute exchanges across the sediment-water interface. Although the influence of U. pusilla on ecological and biogeochemical processes largely depends on environmental conditions (e.g., seasonality and parasitism), altogether my results suggest that the gradual decline of its population in Arcachon bay, as a direct consequence of benthic habitat degradation, may greatly alter the overall functioning of this vulnerable marine ecosystem.

L’industrialisation de l’étang de Berre au cours du 20ème siècle s’est accompagnée d’importants rejets en éléments traces métalliques (ETM) qui ont été en partie accumulés dans les sédiments et sont aujourd’hui susceptibles d’être remobilisés vers la colonne d’eau ou d’être intégrés dans le réseau trophique et d’entrainer un risque écotoxicologique.La reconstitution de l’évolution temporelle et spatiale de la contamination des sédiments montre que les niveaux de contaminations actuels des sédiments de surface sont les plus bas depuis plusieurs décennies en lien avec l’efficacité des réglementations sur les rejets industriels mises en place dans les années 1970. Ces niveaux sont faibles à modérés en surface mais de très fortes contaminations existent quelques centimètres sous la surface des sédiments.Le rôle des oxy-hydroxydes de Fe ou de Mn et des sulfures dans le contrôle de la mobilité des ETM dans le sédiment et leurs flux à l’interface eau/sédiment a pu être démontré grâce à la modélisation du transport et des réactions des composés chimiques et des ETM dans les eaux interstitielles, de leurs profils de concentrations dans la fraction réactive de la phase particulaire et d’expérimentations en conditions contrôlées au laboratoire. L’oxygénation de la colonne d’eau constitue le principal paramètre influençant cette mobilité et ces flux, et l’influence d’une réoxygénation des fonds dans le Grand Etang est discutée.Enfin, la biodisponibilité des ETM et le stress (géno)toxicologique qu’ils peuvent constituer pour un organisme benthique cible, le polychète Nereis succinea, ont été évalués par l’estimation des fractions potentiellement biodisponibles dans les sédiments (extractions chimiques et Diffusive Gradient in Thin-films), par la mesure des concentrations bioaccumulées et par l’utilisation de biomarqueurs de défense (métallothionéines) et de dommages (tests de génotoxicité). Certains ETM qui sont fortement bioaccumulés représentent un risque potentiel et pourraient être impliqués dans la dégradation de la macrofaune benthique. / The industrialization of the Berre lagoon in the 20th century was accompanied by large releases trace metals, which were partially accumulated in sediments and are now likely to be remobilized to the water column or be integrated into the food chain and cause an ecotoxicological risk.The reconstruction of the temporal and spatial trends of sediment contamination shows that current levels of contamination of surface sediments have been the lowest for decades in agreement with the effectiveness of regulations on industrial releases set up in the years 1970. These levels are low to moderate in surface but very high contamination exist a few centimeters below the sediment surface.The role of Fe and Mn oxy-hydroxides and sulfides in controlling the mobility of ETM in the sediment and fluxes at the water/sediment interface has been demonstrated through the modeling of transport and reactions of chemical compounds and trace metals in the pore waters, their concentration profiles in the reactive fraction of the particulate phase and experiments under controlled laboratory conditions. The oxygenation of the water column is the main parameter influencing the mobility and fluxes and the influence of reoxygenation of bottom water column in the Grand Etang is discussed.Finally, the bioavailability of trace metals and adverse effects they may constitute for a target benthic organism, the polychaete Nereis succinea, were evaluated by estimating the potentially bioavailable fraction in sediments (chemical extractions and Diffusive Gradient in Thin-films), by measuring bioaccumulated concentrations and by the use of biomarkers (metallothioneins and genotoxicity assays). Some highly bioaccumulated trace metals pose a potential risk and might be involved in the degradation of the benthic macrofauna.