Dissertations / Theses on the topic 'Marine organic matter'

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2013.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Marine phytoplankton are the principal producers of oceanic dissolved organic matter (DOM), the organic substrate responsible for secondary production by heterotrophic microbes in the sea. Despite the importance of DOM in marine food webs, details regarding how marine microbes cycle DOM are limited, and few definitive connections have been made between specific producers and consumers. Consumption is thought to depend on the source of the DOM as well as the identity of the consumer; however, it remains unclear how phytoplankton diversity and DOM composition are related, and the metabolic pathways involved in the turnover of DOM by different microbial taxa are largely unknown. The motivation for this thesis is to examine the role of microbial diversity in determining the composition, lability, and physiological consumption of marine DOM. The chemical composition of DOM produced by marine phytoplankton was investigated at the molecular level using mass spectrometry. Results demonstrate that individual phytoplankton strains release a unique suite of organic compounds. Connections between DOM composition and the phylogenetic identity of the producing organism were identified on multiple levels, revealing a direct relationship between phytoplankton diversity and DOM composition. Phytoplankton-derived DOM was also employed in growth assays with oligotrophic bacterioplankton strains to examine effects on heterotrophic growth dynamics. Reproducible responses ranged from suppressed to enhanced growth rates and cell yields, and depended both on the identity of the heterotroph and the source of the DOM. Novel relationships between specific bacterioplankton types and DOM from known biological sources were found, and targets for additional studies on reactive DOM components were identified. The physiology of DOM consumption by a marine Oceanospirillales strain was studied using a combined transcriptomic and untargeted metabolomic approach. The transcriptional response of this bacterium to Prochlorococcus-derived DOM revealed an increase in anabolic processes related to metabolism of carboxylic acids and glucosides, increased gene expression related to proteorhodopsin-based phototrophy, and decreased gene expression related to motility. Putative identification of compounds present in Prochlorococcus-derived DOM supported these responses. Collectively, these findings highlight the potential for linking detailed chemical analyses of labile DOM from a known biological source with bacterioplankton diversity and physiology.
by Jamie William Becker.
Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) - a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean.
by Oscar Abraham Sosa.
Ph. D.

The Global Ocean is the largest Earth compartment holding carbon and nutrients that reaches the upper-ocean at temporal scales ranging from months to 10 kyr. The availability of these nutrients is fundamental to sustain primary production and the concentration of dissolved inorganic carbon (DIC) in surface waters controls the glacial-interglacial changes in atmospheric CO2. One process that influences both nutrients and carbon availability is the Microbial Carbon Pump (MCP), which refers to the production of refractory dissolved organic carbon (RDOC) compounds via heterotrophic microbial activity. Variations in the RDOC pool affect long-term carbon storage in the ocean, hence influencing the carbon cycle and climate. The general objective of this thesis is to expand our understanding of the connections between RDOC production by MCP and the ocean metabolism (understood as the upper-ocean net autotrophic community production), paying special attention to the role of the marine microbial processes in the glacial-interglacial transitions of the Earth system. The RDOC production by MCP is inferred through the lineal dependence of fluorescent dissolved organic matter (FDOM) with apparent oxygen utilization (AOU) and nutrients. This relationship, however, depends on the preformed content in the water masses. In this thesis, a valuable dataset, obtained from a high-resolution spatial sampling along 7.5ºN in the equatorial Atlantic Ocean, is used to distinguish the variability of FDOM distribution associated with in situ production from that related to the water properties at origin. A simple objective nonlinear-global methodology for resolving the non-conservative fraction of biogeochemical variables distribution is presented. The approach focuses on fitting high-order polynomial models over the entire temperature-salinity space. The differences between the modelled values and the observations are identified as biogeochemical anomalies. The goodness of the method is compared, for each water stratum, with the traditional approach, which is based on the local linear mixing of a maximum of three source water masses. The new methodology has good skill at distinguishing between the conservative and non-conservative contributions to biogeochemical variables, lending information about biogeochemical processes, stoichiometric ratios and patterns of connectivity within a certain region. For the first time, a general relationship between humic-like FDOM and AOU in the dark equatorial Atlantic Ocean is formulated, irrespective of the water masses. The results endorse the idea that FDOM is mostly produced in situ in the dark ocean. In the second part of the thesis, the role of RDOC pool in quaternary climate transitions is explored. The glacial-interglacial transitions are considered as functional states of the complex Earth system, with different energetic conditions in terms of solar energy conversion through marine photosynthesis. The oceanic system capacity to capture and transform the incident solar radiation depends on the availability of DIC and nutrients to the productive upper ocean. The supply of DIC and nutrients by the Meridional Overturning Circulation (MOC) and the DOM pool are evaluated through a simple two-box and two-state relaxation-type model for the DIC and nutrients in the upper ocean. The model, inspired on physiological concepts, considers the upper ocean to switch between basal (glacial) and enhanced (interglacial) metabolic states. The model reproduces well the atmospheric CO2 time series for the last 420 kyr, providing a solution for the size and temporal dependence of the MOC and setting global constraints on primary production and remineralization in the upper ocean. The RDOC accumulates during the glacial period and its availability at the end of this cycle sets the metabolic intensity of the subsequent interglacial, in what constitutes a central component of the Earth’s pulsating homeostatic organization.
El Océano Global es el mayor reservorio de carbono y nutrientes que llegan al océano superior en escalas temporales de meses hasta 10.000 años. La disponibilidad de nutrientes es fundamental para la producción primaria y la concentración de carbono inorgánico dis suelto (DIC en inglés) en las aguas superficiales controla los cambios glacial-interglacial del CO2 atmosférico. La bomba de carbono microbiana (MCP en inglés) se refiere a la producción de compuestos refractarios de carbono orgánico disuelto (RDOC en inglés) a través de la actividad microbiana heterotrófica siendo un proceso que influye tanto en los nutrientes como en la disponibilidad de carbono. Las variaciones en el reservorio de RDOC afectan al almacenamiento de carbono a largo plazo en el océano, influyendo en el ciclo del carbono y el clima. El objetivo general de esta tesis es ampliar la comprensión de las conexiones entre la producción de RDOC por la MCP y el metabolismo oceánico (entendido como la producción comunitaria autótrofa neta del océano superior), prestando especial atención al papel de los procesos microbianos en las transiciones glacial - interglacial del sistema terrestre. La producción de RDOC por la MCP se infiere a través de la dependencia lineal de la materia orgánica disuelta fluorescente (FDOM, en inglés) con la utilización aparente de oxígeno (AOU, en inglés) y los nutrientes. Dicha relación depende del contenido preformado en las masas de agua. A partir de datos obtenidos a lo largo de 7.50N en el Océano Atlántico ecuatorial, se evalúa que variabilidad de la distribución de FDOM corresponde con producción in situ y cual a las propiedades del agua en origen. Se presenta una metodología objetiva y simple, no lineal y global para resolver la fracción no conservativa de la distribución de variables biogeoquímicas mediante el ajuste de modelos polinomiales en todo el espacio de temperatura y salinidad. Se evalúa la bondad del método para cada estrato de agua comparándolo con el enfoque tradicional, basado en la mezcla lineal y local de un máximo de tres masas de agua fuente. La nueva metodología distingue entre las contribuciones conservativas y no conservativas de las variables biogeoquímicas, proporciona información de procesos biogeoquímicos, relaciones estequiométricas y patrones de conectividad dentro de una región. Por primera vez, se formula una relación general entre FDOM tipo húmico y AOU en el Océano Atlántico ecuatorial, independiente de las masas de agua. Los resultados respaldan la idea de que el FDOM se produce principalmente in situ en el océano profundo. En la segunda parte de la tesis, se explora el papel del RDOC en las transiciones climáticas del cuaternario. Las transiciones glacial-interglacial se consideran estados funcionales del sistema terrestre, con diferentes condiciones energéticas en términos de conversión de la energía solar a través de la fotosíntesis. La capacidad del sistema oceánico para capturar y transformar la radiación solar incidente depende de la disponibilidad de DIC/nutrientes en el océano superior. El aporte de DIC/nutrientes por el Bucle Latitudinal (MOC, en inglés) y el reservorio de materia orgánica disuelta se evalúan a través de un modelo simple de dos cajas y de relajación de dos estados para el DIC/nutrientes en el océano superior. El modelo, inspirado en conceptos fisiológicos, considera que el océano superior cambia entre dos estados metabólicos diferentes, basal (glacial) y excitado (interglacial). El modelo reproduce la serie temporal de 𝐶���𝐶���𝐶���𝐶���2 atmosférico de los últimos 420 kyr, proporcionando la magnitud y dependencia temporal de la MOC y estableciendo restricciones en la producción primaria y la remineralización en el océano superior. El RDOC acumulado en el período glacial y su disponibilidad al final de este ciclo establece la intensidad metabólica del interglacial subsiguiente, constituyendo por tanto un componente central de la organización homeostática pulsante de la Tierra.

Thesis: Ph. D., Joint Program in Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017.
Cataloged from PDF version of thesis.
Includes bibliographical references.
While aerobic respiration is typically invoked as the dominant mass-balance sink for organic matter in the upper ocean, many other biological and abiotic processes can degrade particulate and dissolved substrates on globally significant scales. The relative strengths of these other remineralization processes - including mechanical mechanisms such as dissolution and disaggregation of sinking particles, and abiotic processes such as photooxidation - remain poorly constrained. In this thesis, I examine the biogeochemical significance of various alternative pathways of organic matter remineralization using a combination of field experiments, modeling approaches, geochemical analyses, and a new, high-throughput lipidomics method for identification of lipid biomarkers. I first assess the relative importance of particle-attached microbial respiration compared to other processes that can degrade sinking marine particles. A hybrid methodological approach - comparison of substrate-specific respiration rates from across the North Atlantic basin with Monte Carlo-style sensitivity analyses of a simple mechanistic model - suggested sinking particle material was transferred to the water column by various biological and mechanical processes nearly 3.5 times as fast as it was directly respired, questioning the conventional assumption that direct respiration dominates remineralization. I next present and demonstrate a new lipidomics method and open-source software package for discovery and identification of molecular biomarkers for organic matter degradation in large, high-mass-accuracy HPLC-ESI-MS datasets. I use the software to unambiguously identify more than 1,100 unique lipids, oxidized lipids, and oxylipins in data from cultures of the marine diatom Phaeodactylum tricornutum that were subjected to oxidative stress. Finally, I present the results of photooxidation experiments conducted with liposomes - nonliving aggregations of lipids - in natural waters of the Southern Ocean. A broadband polychromatic apparent quantum yield (AQY) is applied to estimate rates of lipid photooxidation in surface waters of the West Antarctic Peninsula, which receive seasonally elevated doses of ultraviolet radiation as a consequence of anthropogenic ozone depletion in the stratosphere. The mean daily rate of lipid photooxidation (50 ± 11 pmol IP-DAG L⁻¹ d⁻¹, equivalent to 31 ± 7 [mu]g C m⁻³ d⁻¹) represented between 2 and 8 % of the total bacterial production observed in surface waters immediately following the retreat of the sea ice.
by James R. Collins.
Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric and Planetary Sciences and the Woods Hole Oceanographic Institution, 1986.
Microfiche copy available in Archives and Science.
Vita.
Bibliography: leaves 271-297.
by Bruce J. Brownawell.
Ph.D.

Thesis (M.S.)--Joint Program in Oceanography and Oceanographic Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), June 1996.
"May 1996."
Includes bibliographical references (leaves 66-68).
This thesis details two years of research conducted with the guidance and support of three advisors: Dr. J. K. Whelan, Dr. J. S. Seewald and Dr. T. I. Eglinton. Each of the three chapters represents a different, self-contained research project. All of the projects are related to the organic geochemistry of marine sediments, however, this is a fairly encompassing area of study. Chapters 1 and 2 stem from the same experimental study -- the use of hydrous-pyrolysis to investigate mechanisms leading to the production of petroleum-related products during kerogen maturation. Chapter 3, on the other hand, utilizes a recently developed technique of isolating and AMS-14C dating individual compounds from complex sedimentary organic mixtures. The samples used in each investigation came from all over the world. The first two chapters utilize ancient marine sediment samples obtained from an outcrop in California (Chpts. 1 and 2) and from a well in Alabama (Chpt. 2). In contrast, recent marine sediment samples were obtained from the Arabian and Black Seas for the third chapter. Several preparative and analytical methods are common to all three studies. Nevertheless, each employ techniques totally unique from one another and from previous investigations. In Chapter 1, for example, X-ray absorption spectroscopy (XANES) is used to determine the speciation of organic sulfur present in kerogen, bitumen, and bulk sediment samples. While Chapter 3 represents the first study in which the "4C ages of individual, known hydrocarbon biomarkers are determined after isolation by Preparative Capillary Gas Chromatography (PCGC). The insights gained by these investigations are discussed in detail in the following chapters. The common thread between the three chapters is that the source of organic matter, the rate at which it is delivered to marine sediments and the depositional environment, all set the stage for kerogen formation and eventual petroleum generation.
by Bryan C. Benitez-Nelson.
M.S.

A study of the organic matter (OM) sources and biogeochemical and physicochemical sinks was undertaken in the York River estuary, Virginia. The reactivity of dissolved organic carbon (DOC) was enhanced from ∼25--68% by the combined effects of exposure to natural sunlight and bacterial decomposition. In contrast, sunlight exposure decreased the bioreactivity of DOC in the higher salinity lower York by a factor of five. The combined effects of photochemical and bacterial processing were found to modify both the bioavailability and metabolic fate of OM (e.g. respiration vs. biomass). Stable isotopic (delta13C, delta15N) and radiocarbon (Delta14C) values of bacterial nucleic acids were used to estimate the sources and ages of OM assimilated by bacteria in the York and Hudson River estuaries. Bacterial production in freshwater regions of the York was fueled by OM of young, terrigenous origin which accounted for 42--89% of OM assimilated. The remainder (11--58%) of OM assimilated was derived from freshwater algae. In the mid-salinity York, bacterial production was supported by phytoplankton-derived OM in the spring and summer (93--100%) and marsh-derived OM in the fall (73--100%). Isotopic values of bacteria in the lower York suggested production was supported by phytoplankton-derived OM (86--100%) in July and November and algal and marine-like OM (50--69%) in October. In contrast to the young (10--20 yr) OM assimilated by bacteria in the York, production in the Hudson River was subsidized by old (∼1200 BP) terrigenous OM. Higher C:N ratios, lower delta13C and delta 15N values and depletions of total lipid and lipid compound classes in high molecular weight dissolved organic matter (HMW DOM (≥3kDa)) relative to particulate organic matter (POM), suggested differences in the reactivity and cycling of these two OM fractions. Within the dissolved pool, polyunsaturated fatty acids (FA) were a strong predictor of DOC decomposition in bioassays. FA and sterol distributions suggest that POM is derived from phytoplankton/zooplankton sources, while HMW DOM has a bacterial and vascular plant signature. Thus, the physical form of OM (particulate vs dissolved) may affect both the distribution and biogeochemical processing of OM such that terrigenous DOM may be exported, while POM is retained within the estuary.

Climate change scenarios predict that seawater temperature and precipitation will increase in the Baltic Sea region during the next century. In the northern part of the Baltic Sea, increasing inflows of the terrestrial allochthonous dissolved organic matter (ADOM) are expected to be a major consequence of elevated rainfall, which can alter light and nutrient availability for phytoplankton. The aim of my thesis was to elucidate effects of ADOM on phytoplankton production, community, size-structure and nutritional strategy along offshore south-north gradients in the Baltic Sea, as well as in estuarine systems exposed to seasonal variation in river discharge. Field studies, a mesocosm experiment and a modeling study were used to explore these issues. Results from the field studies and mesocosm experiment illustrated that the nutritional strategy, size-structure and cellular pigment content of the phytoplankton were governed by changes in ADOM, and thus in light and nutrient availability. A summer study along an offshore south-north gradient showed that the proportion of mixotrophic phytoplankton increased towards the north. In this area the concentrations humic substances (proxy for ADOM) were high, while the light availability and phosphorus concentrations were relatively low. The phytoplankton cells responded to reduced light availability by increasing their chlorophyll a: carbon ratio. Additionally, the levels of photoprotective pigments decreased from south to north, as a result of acclimation to a low-light environment and reduced exposure to ultraviolet radiation. According to ecological assumptions picophytoplankton should be favored in light- and nutrient-limited environments. However, the results did not follow that pattern, the proportion of picophytoplankton being highest in the relatively nutrient rich Baltic Proper. The study was performed during the decline of an extensive bloom of filamentous cyanobacteria, a successional phase in which picophytoplankton often dominate the phytoplankton community. The estuarine studies performed in the Bothnian Bay (Råne estuary) and in the Bothnian Sea (Öre estuary) showed different successions. In the Råne estuary no spring phytoplankton bloom occurred and highest primary production was observed during the summer. This absence of a spring bloom was explained by low phosphorus and high ADOM concentrations, while the summer maximum could be explained by higher temperature and nutrient concentrations. In the Öre estuary a marked phytoplankton spring bloom was observed as well as an ADOM sustained bacterial production phase. The later secondary peak of bacterial production observed in summer, concomitant with an extended secondary primary production peak, suggests that autochthonous dissolved organic matter supported the bacterial growth Furthermore, the photosynthetic efficiency (i.e. phytoplankton growth rates) was lower during spring, indicating that high ADOM, and thus lower light and phosphorus availability, disfavored phytoplankton growth. Our modeling study showed that climate change can impact the food web; however effects will be different between basins. In the southern Baltic Sea elevated temperature and nutrient discharge may promote nutrient recycling and oxygen consumption, potentially extending anoxic areas, sediment nutrient release and cyanobacteria blooms. In the north, increased inflow of ADOM may promote heterotrophic bacterial production and decrease primary production due to light attenuation and lower phosphorus availability. This will favor the heterotrophic microbial food web and consequently lead to lower food web efficiency of the ecosystem.

Thesis (Ph. D.)--Florida State University, 2009.
Advisor: William T. Cooper III, Florida State University, College of Arts and Sciences, Dept. of Chemistry and Biochemistry. Title and description from dissertation home page (viewed Nov. 8, 2009). Document formatted into pages; contains xviii, 119 pages. Includes bibliographical references.

Zooplankton play a key role in the cycling of dissolved organic matter (DOM) and inorganic nutrients. The factors that affect these processes, however, are not fully understood. I measured the effects of various diets on DOM and inorganic nutrient production by the copepod Acartia tonsa and the heterotrophic dinoflagellate Oxyrrhis marina, and explored the mechanisms of nutrient release from copepods. Copepods feeding on a mixed diet, the preferred diet of most copepods, had significantly lower dissolved organic carbon (DOC), ammonium (NH4+), and total dissolved nitrogen (TDN) release rates compared to feeding on a carnivorous or herbivorous diet. Thus, copepod feeding strategy can control the magnitude and composition of regenerated nutrients supplied to bacteria and phytoplankton. Secondly. I determined the effects of non-bloom and bloom concentrations of non-toxic and toxic cultures of harmful algal bloom (HAB) species Prorocentrum minimum and Karlodinium veneficum on grazing and production of DOM and inorganic nutrients by A. tonsa and O. marina. All algal diets deterred grazing, which likely resulted in starvation and subsequent catabolism of grazer body tissue. Additionally, DOM was typically a higher proportion of total dissolved nutrients released by zooplankton while feeding on the toxic algal culture, suggesting algal nutrient quality or direct toxic effects played a role in the differential nutrient release. Low ingestion rates coupled with high nutrient release rates could lead to feedback mechanisms that could intensify HABs. Finally, the various mechanisms of A. tonsa nutrient release, including sloppy feeding, excretion, and fecal pellet leaching, were isolated. Excretion and sloppy feeding were the dominant modes of DOC and NH4+ release, while sloppy feeding and fecal pellet leaching were dominant modes of urea release. A large proportion of ingested PON was lost as dissolved NH4+ and urea from copepods via all release mechanisms. These results have implications for the rapidity and location at which the regenerated nutrients are recycled in the water column. My dissertation results emphasize the importance of diet and release mechanism on the production of nutrients, particularly DOM, by zooplankton, which are important in understanding the recycling and transfer of nutrients and organic matter in marine food webs.

Complexities associated with dissolved organic matter (DOM) isolation from seawater have hampered compositional characterization of this key component of global carbon and nutrient cycles. Two techniques, Electrodialysis (ED) and Solid Phase Extraction (SPE), were combined to more effectively isolate DOM from salt-containing waters. Sample recovery was optimized and evaluated on a range of samples including coastal ocean seawater, open ocean seawater, artificial seawater from cultures of marine phytoplankton, and artificial seawater samples containing standard compounds of different molecular sizes and charge. ED was performed with a system optimized for processing 2 to 10 L sample volumes and SPE was performed using Bond Elut PPL exchange resin. With the combination of ED and PPL techniques an average recovery of 76.7 ± 2.6% was obtained for natural coastal seawater. Comparison of C/N ratios and fluorescence excitation emission matrices (EEMs) taken at the beginning and end of the recovery process indicated that the final recovered material was representative of the DOM present in the original samples.

Dissolved and suspended particulate organic carbon (DOC, POC), nitrogen (DON, PON), phosphorus (DOP, POP) and inorganic nutrient distributions and elemental ratios were measured and evaluated for the Atlantic, Southern, and Pacific Oceans. Results indicate that DOC is remineralized during mean deep-water transport from the North Atlantic to the North Pacific. Elemental ratios for both dissolved organic matter (DOM) and particulate organic matter (POM) indicate that organic N is preferentially remineralized compared with organic C, while organic P is preferentialy remineralized relative to both organic C and N. Comparison between the DOM and POM pools further suggests that surface POM may be less refractory than concurrently sampled DOM. Major compound class compositions of ultrafiltered DOM (UDOM) in the North Atlantic, North Pacific and Chesapeake Bay indicate that the majority of UDOM was comprised mainly of a molecularly-uncharacterized fraction, followed by carbohydrates, proteins and lipids. Delta14C and delta 13C results of UDOM compound classes suggest that UDOM in Bay mouth and surface open ocean waters were similarly dominated by old, marine sources, while UDOM from the freshwater endmember was influenced by much younger terrestrial sources. Results indicate that DOM is comprised of different aged organic fractions and provide evidence for a potential organic "size"-age continuum; from low-molecular weight DOM (oldest) to UDOM (intermediate age) to POM (youngest). Lipid biomarker results indicate that North Atlantic and Pacific UDOM and POM were relatively more reactive at the surface compared with greater depths, coinciding with elemental C:P and N:P ratios greater than Redfield. Factor analyses suggest that there exists a "lability continuum" spanning from surface ocean POM to riverine and deep ocean UDOM. Terrigenous organic material was found at all Bay sites although autochthonous sources of organic matter were also important. Dark microbial incubations of DOM from the Pacific Subtropical Front and South Atlantic Bight indicate that open ocean DOM is relatively refractory over short time scales (less than 2 months). Experiments with plankton leachate DOM show that this sub-pool of DOM is relatively labile and is converted to refractory DOM within days. DOP is preferentially remineralized in all experiments compared with DOC or DON.

Large gelatinous zooplankton (GZ) blooms of lobate ctenophores, Mnemiopsis leidyi, and scyphomedusae, Chrysaora quinquecirrha , occur throughout Chesapeake Bay and its tributaries. The mechanisms of GZ bloom formation, and the roles GZ blooms play in dissolved organic matter (DOM) and carbon (C) cycling are not fully understood. During 2003--2006, I conducted laboratory experiments and field surveys in the lower York River to determine factors controlling timing and magnitude of GZ blooms, and to evaluate their effects on C cycling. Highest biomass of M. leidyi occurred in early summer (May-June) and in late winter. Peaks in ctenophore biomass in the mesohaline region occurred one-month earlier than in downriver, polyhaline regions, due to higher ctenophore reproduction and larval dispersal upriver. High predation by C. quinquecirrha scyphomedusae on M. leidyi appears to cause the rapid decline in summer ctenophore blooms, and we hypothesize that subsequently medusae become C-limited. High GZ biomass coincides with peaks in microbial biomass, and as DOM is released by zooplankton but consumed by bacteria, these disparate trophic levels may be linked. I measured DOM production by GZ and the response of free-living bacterioplankton to GZ DOM, quantified in terms of bacterial metabolism, and bacteria phylogenetic community composition. Release rate of DOC by both GZ species was high relative to simultaneous release of DON and DOP, and for M. leidyi DOM metabolites were C-rich due to high mucus production in ctenophores. Furthermore, bacterioplankton abundance and production rapidly increased (within 6 hours) in response to uptake of GZ metabolites; however, decreases in bacterial growth efficiencies indicated that increases in bacterial C respiration were greater relative to changes in bacterial biomass. Enumeration of microbial assemblages using the fluorescence in situ hybridization (FISH) technique showed specific bacterial groups, namely gamma-proteobacteria, are responsible for increased metabolism of GZ DOM metabolites. In the context of worldwide increases in GZ, my results have significant implications for C transfer in marine food webs, with the potential for more C to be shunted to the microbial loop away from higher trophic levels.

Microbes, including Bacteria, are globally important mediators of elemental transformations in the marine water column, but not until recently has their biomass been suggested to contribute significantly to carbon export flux. Here I characterize lipid and carbon isotopic signatures in marine particulate organic matter (POM) explicitly at microbial size scales, and I quantitatively explore how these signatures are transferred down the water column. In the North Pacific Subtropical Gyre (NPSG) an isotopically-enriched pool of submicron POM appears to dominate export to mesopelagic depths, supporting recent observations that bacterioplankton communities contribute to export flux in proportion to their biological abundance. In the Eastern Tropical North Pacific (ETNP) complex pathways emerge for the flux of POM to the deep ocean. I use the largest data set to date for natural \(^{13}C\) signatures of individual water column lipids to reveal that submicron and larger-size suspended POM size classes are isotopically distinct. Results point to de novo production of lipids above and within the oxygen minimum zone. I develop quantitative models to deconvolve the signatures of sinking and in situ sources of these lipids. Results converge on a best-fit model for downward flux in the ETNP that includes both surface-derived and sub-photic zone lipids. Overall results from the modern ocean suggest that approximately half of total suspended POM is submicron in size, much of it is bacterial in origin, and despite the small size of this material, it participates dynamically in water column export flux. These results also suggest some revised interpretations of organic matter signatures in the geologic record. I formulate a quantitative model of marine microbial production and degradation, and reproduce "inverse" isotopic signatures found in lipids and organic matter preserved in Proterozoic sedimentary rocks. Results suggest that the disappearance of this inverse \(^{13}C\) pattern was a consequence of the shift from Bacteria to Eukarya as dominant producers of marine autotrophic biomass. Together, results of this thesis reveal that heterogeneity in the isotopic signatures of marine suspended POM is associated with particle size, and by extension, must be a function of the composition of the total planktonic community.
Earth and Planetary Sciences

In the coming decades, global warming will affect the biogeochemical cycles evolution, particularly the carbon cycle. In this context, it is necessary to gain knowledge on the Earth natural mechanisms to relieve the atmosphere of the greenhouse gases excess. The "biological pump" is one of the main mechanisms employed by the oceans to "sequester" the CO2 accumulated in the atmosphere. Thereby, the organic carbon produced by the biological activity is transferred from surface to deep waters where part of this pool is accumulated in the seafloor. Another mechanism involving the accumulation of carbon in the ocean, called the "microbial carbon pump" (MCP), has been described recently. It is composed by an intricate set of microbial processes that enable the formation of highly recalcitrant dissolved material and therefore facilitate the accumulation of carbon in the deep waters. The oceans store about 660 Pg C in the form of dissolved organic matter (DOM), a quantity comparable to the atmospheric CO2. Understanding the processes that control the dynamics, recycling and exportation of the DOM is crucial to evaluate the oceans capability to gather the excess of atmospheric CO2. On its course down throughout the water column, microorganisms degraded the DOM produced at the surface layers. Concentrations decrease from ~90 µmol C L-1 down to 40-50 µmol C L-1, values homogeneously distributed in the deep oceans throughout the planet. The fact that below 1000 m and deeper the DOM is degraded at lower speed is still unknown, and the processes that can affect this DOM degradation have been studied in this thesis. In this regard, we performed experiments with deep Atlantic Ocean microbial communities. These communities were exposed to DOM of different quality. The results revealed that the presence of humic-like allocthonous compounds favored the generation of new humic-like compounds in situ. Consequently, we proved that the composition of the DOM that reach the deep ocean conditions its ease-to-degrade nature. In this thesis we also evaluated the effect of global change (acidification and eutrophication) on the quality of the DOM. With this purpose in mind, we developed mesocosms experiments in tanks of 200 L in which we enclosed coastal planktonic communities from the NW Mediterranean Sea. The planktonic populations were exposed to different treatments of pH and eutrophication (addition of inorganic nutrients). The results of these experiments demonstrated that low pH levels favored the increase of the planktonic organisms' growth rates, while the input of nutrients promoted the transformation to complex DOM. Finally, a monthly monitoring sampling of several biogeochemical variables was carried out at the Estartit Oceanographic Station (EOS). One of the principal aims consisted in identify the DOM sources and its inter-annual variability. The results revealed the importance of the winds in transporting oceanic DOM inputs to the system, which contrasted with previous results observed in nearby sampling stations (e.g. Blanes Bay, Bay of Banyuls-sur-mer), where the major DOM contributions were terrestrial inputs.
En las próximas décadas el cambio climático afectará globalmente a la evolución de los ciclos biogeoquímicos en general, y al ciclo del carbono en particular. En este contexto, es necesario adquirir conocimiento sobre los mecanismos naturales de los que dispone el planeta para eliminar de la atmósfera el exceso de gases de efecto invernadero. La ‘bomba biológica’ es uno de los principales mecanismos que presentan los océanos para "secuestrar" el CO2 acumulado en la atmósfera. De este modo, el carbono orgánico producido por la acción biológica es transferido desde la superficie a las capas profundas del océano hasta su parcial almacenamiento en los fondos marinos. Recientemente se ha descrito otro mecanismo que facilita la acumulación de carbono, la “bomba microbiana de carbono” (MCP). Está compuesta por un conjunto de complejos mecanismos microbianos que posibilitan la formación de material disuelto altamente recalcitrante y por tanto conllevan a la acumulación de carbono en las aguas profundas. Los océanos albergan alrededor de 660 Pg C en forma de materia orgánica disuelta (DOM), cantidad equiparable al CO2 atmosférico. Entender los procesos que controlan la dinámica, el reciclado y la exportación de la DOM es crucial para evaluar la capacidad de los océanos en acumular el exceso de carbono atmosférico. A su paso a través de la columna de agua, la DOM generada en superficie es degradada por los microorganismos. Su concentración disminuye desde ~90 μmol C L-1 en las aguas superficiales hasta 40-50 μmol C L-1, rango uniforme de valores presentes en las aguas profundas de los océanos de todo el planeta. A partir de 1000 m de profundidad, la DOM se descompone a una tasa mucho más lenta y aparentemente imperceptible. Las causas de esta dilación en la descomposición a día de hoy son todavía inciertas y han sido objeto de estudio en esta tesis. En este sentido, se realizaron experimentos con comunidades microbianas del Océano Atlántico profundo, las cuales fueron sometidas a varios tratamientos de enriquecimiento con compuestos orgánicos. Los resultados revelaron que la presencia de precursores húmicos alóctonos favorecía la generación de nuevos compuestos húmicos dentro del sistema. Consecuentemente, la composición de la DOM que llega al océano profundo condiciona su facilidad para ser degradada. Por otro lado, en esta tesis también se ha examinado experimentalmente el efecto del cambio global (acidificación y eutrofización) sobre la calidad de la DOM. En este caso los experimentos se realizaron con comunidades planctónicas costeras del Mediterráneo noroccidental incubadas en mesocosmos de 200 litros. Las comunidades se sometieron a distintas condiciones de pH y eutrofización. El seguimiento de la respuesta de los microorganismos y la dinámica de la DOM demostraron por un lado que las tasas de reproducción de los organismos planctónicos se aceleraron con la disminución de los niveles de pH, y, por otro lado, que el aumento de nutrientes inorgánicos favoreció la generación de compuestos orgánicos de estructura compleja. Por último, se realizó un seguimiento mensual de medición de diferentes variables biogeoquímicas en el punto de muestreo de l’Estartit (EOS) con el objetivo de identificar la variabilidad interanual de la DOM así como identificar la procedencia de los aportes. Los resultados obtenidos muestran la importancia de factores ambientales como el viento, que en este caso acentúa la presencia de inputs de origen oceánico, contrastando con lo descrito previamente en otros puntos de muestreo cercanos (Bahía de Blanes, Bahía de Banyuls-sur-mer), donde el principal origen de los aportes orgánicos fue atribuido a una influencia terrestre
En les properes dècades el canvi climàtic afectarà globalment a l'evolució dels cicles biogeoquímics en general, i al cicle del carboni en particular. En aquest context, és necessari adquirir coneixement sobre els mecanismes naturals dels quals disposa el planeta per eliminar de l'atmosfera l'excés de gasos d'efecte hivernacle. La ‘bomba biològica’ és un dels principals mecanismes que presenten els oceans per "segrestar" el CO2 acumulat en l'atmosfera. D'aquesta manera, el carboni orgànic produït per l'acció biològica és transferit des de la superfície a les capes profundes de l'oceà fins al seu parcial emmagatzematge en els fons marins. Recentment s'ha descrit un altre mecanisme que facilita l'acumulació de carboni, la “bomba microbiana de carboni” (MCP). Està composta per un conjunt de complexos mecanismes microbians que possibiliten la formació de material dissolt altament recalcitrant i, per tant, comporten a l'acumulació de carboni en les aigües profundes. Els oceans alberguen al voltant de 660 Pg C en forma de matèria orgànica dissolta (DOM), quantitat equiparable al CO2 atmosfèric. Entendre els processos que controlen la dinàmica, el reciclat i l'exportació de la DOM és crucial per avaluar la capacitat dels oceans a acumular l'excés de carboni atmosfèric. Al seu pas a través de la columna d'aigua, la DOM generada en superfície és degradada pels microorganismes. La seva concentració disminueix des de ~90 μmol C L-1 en les aigües superficials fins a 40-50 μmol C L-1, rang uniforme de valors presents en les aigües profundes dels oceans de tot el planeta. A partir de 1000 m de profunditat, la DOM es descompon a una taxa molt més lenta i aparentment imperceptible. Les causes d'aquesta dilació en la descomposició a dia d'avui són encara incertes i han estat objecte d'estudi en aquesta tesi. En aquest sentit, es van realitzar experiments amb comunitats microbianes de l'Oceà Atlàntic profund, les quals van ser sotmeses a diversos tractaments d'enriquiment amb compostos orgànics. Els resultats van revelar que la presència de precursors húmics al·lòctons afavoria la generació de nous compostos húmics dins del sistema. Conseqüentment, la composició de la DOM que arriba a l'oceà profund condiciona la seva facilitat per ser degradada. D'altra banda, en aquesta tesi també s'ha examinat experimentalment l'efecte del canvi global (acidificació i eutrofització) sobre la qualitat de la DOM. En aquest cas els experiments es van realitzar amb comunitats planctòniques costaneres del Mediterrani nord-occidental incubades en mesocosmos de 200 litres. Les comunitats es van sotmetre a diferents condicions de pH i eutrofització. El seguiment de la resposta dels microorganismes i la dinàmica de la DOM van demostrar d'una banda que les taxes de reproducció dels organismes planctònics es van accelerar amb la disminució dels nivells de pH, i d'altra banda, que l'augment de nutrients inorgànics va afavorir la generació de compostos orgànics d'estructura complexa. Finalment, es va realitzar un seguiment mensual de mesurament de diferents variables biogeoquímiques en el punt de mostreig de l’Estartit (EOS) amb l'objectiu d'identificar la variabilitat interanual de la DOM així com identificar la procedència de les aportacions. Els resultats obtinguts mostren la importància de factors ambientals com el vent que, en aquest cas, accentua la presència d’aportacions d'origen oceànic, contrastant amb el descrit prèviament en altres punts de mostreig propers (Badia de Blanes Badia de Banyuls-sud-mer), on el principal origen de les aportacions orgàniques va ser atribuït a una influència terrestre.
Nas próximas décadas o cambio climático afectará globalmente á evolución dos ciclos bioxeoquímicos en xeral, e ó ciclo do cabono en particular. Neste contexto, é necesario adquirir coñecemento sobre os mecanismos naturais dos que dispón o planeta para eliminar da atmósfera o exceso de gases de efecto invernadeiro. A "bomba biolóxica" é un dos principais mecanismos que presentan os océanos para "secuestrar" o CO2 acumulado na atmósfera. Desta forma, o carbono orgánico producido pola acción biolóxica é transferido dende a superficie das capas profundas do océano hasta o seu parcial almacenamento nos fondos mariños. Recentemente describiuse outro mecanismo que facilita a acumulación de carbono, a "bomba microbiana de carbono" (MCP). Está composta por un conxunto de complexos mecanismos microbianos que posibilitan a formación de material disolto altamente recalcitrante e por tanto levan á acumulación de carbono nas augas profundas. Os océanos albergan ó redor de 660 Pg C na forma de materia orgánica disolta (DOM), cantidade equiparable ó CO2 atmosférico. Entender os procesos que controlan a dinámica, o reciclado e a exportación da DOM é crucial para evaluar a capacidade dos océanos en acumular o exceso de carbono atmosférico. Ó seu paso a través da columna de auga, a DOM producida na superficie é degradada polos microorganismos. A súa concentración disminúe dende ~90 μmol C L-1 nas augas superficiais ate 40-50 μmol C L-1, rango uniforme de valores presentes nas augas profundas dos océanos de todo o planeta. A partir dos 1000 m de profundidade, a DOM descomponse a unha tasa moito máis lenta e aparentemente imperceptible. As causas desta dilación na descomposición son todavía incertas na actualidade e foron obxeto de estudio nesta tesis. Neste sentido realizáronse experimentos con comunidades microbianas do Océano Atlántico profundo, as cales foron sometidas a varios tratamentos de enriquecemento con compostos orgánicos. Os resultados revelaron ca presencia de precursores húmicos alóctonos favorecía a produción de novos compostos húmicos dentro do sistema. Consecuentemente, a composión da DOM que chega ó océano profundo condiciona a súa facilidade de ser degradada. Por outro lado, nesta tesis tamén se examinou experimentalmente o efecto do cambio global (acidificación e eutrofización) sobre a calidade da DOM. Neste caso os experimentos realizaronse con comunidades planctónicas costeiras do Mediterráneo noroccidental, incubadas en mesocosmos de 200 litros. As comunidades someteronse a distintas condicións de pH e eutrofización. O seguemento da resposta dos microorganimos e a dinámica da DOM demostraron que as tasas de reproducción dos organismos planctónicos aceleráronse coa disminución dos niveis de pH, e tamén que o aumento de nutrintes inorgánicos favoreceu a produción de compostos orgánicos de estrutura complexa. Ademáis realizouse un seguemento mensual de varias variables bioxeoquímicas no punto na estación oceanográfica de l'Estartit (EOS) co obxetivo de identificar a variabilidade interanual da DOM, ademáis de identificar a procedencia dos aportes. Os resultados obtidos mostran a importancia de factores ambientais como o vento, que neste caso acentúa a presencia de inputs de orixe oceánica, contrastando co descrito previamente noutras estacións oceanográficas cercanas (Bahía de Blanes, Bahía de Banyuls-sur-mer), onde a principal orixe dos aportes orgánicos foi atribuido a unha influencia terrestre.

Terrestrial organic matter (TOM) constitutes an important source of energy in many aquatic environments (streams, lakes, wetlands). This is the first study to examine the role of TOM in food webs of the rocky intertidal zone. We compared the consumption of red alder leaves (Alnus rubra) to common marine sources of drifting detritus along the southern Oregon coast (Nereocystis luetkeana, Phyllospadix spp., and Fucus gardneri). We used short term (hours to days) and long term (months) feeding experiments to compare the rate of consumption among each plant species during the Spring and Fall of 2014 and 2015. In addition, we quantified the amount of TOM in beach wrack and in the drift of two streams that flowed directly to the rocky intertidal zone. We also measured the food quality of each plant species (C:N and polyphenolic concentrations). On average, the two small streams in this study transported 1,113.6 kg AFDM/m3 of TOM per day during Fall leaf abscission to the rocky intertidal zone. Also, the biomass of terrestrial leaves in beach wrack varied from negligible (2.1 g AFDM) to the dominant source of detritus (60.7 g AFDM) depending on if it was the dominant riparian plant growing along the edges of the shore. Consistent with previous research, N. luetkeana was a high quality food (C:N = 15:1; polyphenolics = 418 mg/ml), whereas F. gardneri (C:N = 22:1; polyphenolics = 8098 mg/ml) was more recalcitrant. Phyllospadix spp. was puzzling because it had low concentrations of polyphenolics (800 mg/ml) but was not consumed. Alnus rubra had a high concentration of structural compounds (C:N = 33:1) and intermediate levels of polyphenolics (3,415 mg/ml after leaching). Both short term and long term experiments showed that the rates of consumption of Spring-shed, green leaves and freshly fallen brown leaves of A. rubra were intermediate between N. luetkeana and the less palatable marine species (F. gardneri and Phyllospadix spp.). Thus, A. rubra was eaten by common intertidal consumers and may constitute an important source of energy between brief inputs of more nutritious marine resources (e.g. N. luetkeana).

The bathyal continental margins (200 – 3000 m) account for 7 % of global sea floor area, but are responsible for recycling 30 % of sedimentary organic matter (OM) within the oceans. Climate-change driven expansion of oxygen minimum zones and increasing frequency of extreme weather events (storms) may have implications for OM processing at the continental margins, resulting in decreased oxygen availability and increases in terrigenous OM inputs. The present thesis tests how changes in oxygen availability influence sea floor community structure and OM processing across the OMZ-impacted Indian continental margin. Megafaunal and macrofaunal assemblages exhibit a distinct zonation, with faunal distributions controlled by changes in oxygen availability and sediment OM content. In situ stable-isotope pulse-chase experiments reveal that, following phytodetritus deposition, macrofaunal feeding responses were influenced by oxygen availability through changes in macrofaunal assemblage structure. Macrofaunal feeding was governed at the organismal level, with fauna maximising organic nitrogen assimilation against an internal carbon-nitrogen budget. Bacterial feeding responses were not directly influenced by changes in oxygen availability and instead were regulated by the macrofaunal assemblage. This thesis proposes that the macrofauna may control the availability of labile organic matter in OMZ-sediments, limiting bacterial activity. The thesis also investigates the differential fates of marine and terrigenous phytodetritus in the sediments of the Whittard canyon (NE Atlantic). In situ pulse-chase experiments reveal nitrogen demand to control macrofaunal feeding responses, inhibiting the utilisation of the nitrogen-poor terrigenous phytodetritus. Bacteria exhibit similar feeding responses to the fauna, whilst bacterial biomass was negatively correlated to increasing faunal activity. This demonstrates that increased inputs of terrigenous organic matter may alter ecosystem-scale carbon cycling pathways and trophic interactions within continental margin sediments.

To evaluate the effects of anthropogenic alteration of the Chesapeake Bay (CB) watershed since European settlement, the historical progression of eutrophication and anoxia in the mesohaline region of CB was reconstructed. Lipid biomarker and carbon and nitrogen stable isotopic and elemental composition of CB surficial sediments were examined seasonally in order to identify the present sources of organic matter to CB sediments and the processes controlling their distribution. Temporal variability in surficial sediment composition could be linked to seasonal changes in phytoplankton community composition and biomass while spatial variation was dominated by the delivery of alloclithonous versus autochthonous sources of organic matter. Three cores (3 to 4.5 m in length) collected from the mesohaline region of Chesapeake Bay were dated using a combination of tools including 210Pb and 137Cs radioisotopes, anthropogenic Pb and pollen indices. Enrichments in the carbon and nitrogen isotopic signature of sediments of all three cores deposited between 1790 and 1915 indicated enhanced primary productivity and nitrogen recycling, respectively. at the same time, increases in the flux of total organic carbon (TOC) and episodic enrichments (relative to TOC) of algal and bacterially-derived lipid biomarker compounds signaled a change in the sources of OM to the sediments. More extreme change occurred after the 1915's with further isotopic enrichments, a 1.5 to 2.5-fold increase in TOC deposition and 2 to 5-fold enrichments in algal and bacterially-derived lipid biomarker compounds. No change in the contribution of terrestrially-derived OM was indicated in any of the cores. Changes in sulfur speciation identified the initial occurrence of anoxia/hypoxia in 1790 at the deepest site (26 m) and in 1929 at a 15 m depth site. An examination of both qualitative evidence and quantitative models of degradation indicates that diagenesis cannot account for the observed increases in the total amount and labile quality of OM deposited during the 19th and 20th century in CB. Using diagenetic models, it is estimated that both algal and bacterial production has increased by 100 to 200% relative to pre-Colonial times with a temporal progression similar to the history of anthropogenic alteration of the watershed.

Oceans store 685 Pg of organic carbon of which 662 Pg are in a dissolved form. The diversity of compounds that make up the dissolved organic matter (DOM) pool and the low concentration of each compound make the chemical characterization of this material a difficult task. For that reason, less than 11% of the oceanic DOM has been identified. A variable fraction of the DOM ¿between 20% in the open ocean and 70% in coastal areas- absorbs UV and visible radiation and it is known as coloured DOM (CDOM). A sub-fraction of the CDOM emits the absorbed radiation as fluorescence, although with a low quantum yield (around 1%), and this is called fluorescent DOM (FDOM). The study of the CDOM and FDOM pools, combining the spectroscopy of absorption and fluorescence, allows us to obtain knowledge about (i) the molecular structure of the DOM (i.e., aromaticity and average molecular weigh) and (ii) its biological and photochemical reactivity in a relatively simple, fast and economic way. This can be done through the study of the production, utilization and/or chemical alteration of the different chromophores and fluorophores in response to the activity of the microorganisms and the solar radiation in the ocean. The work that has resulted in this thesis has involved both laboratory experiments and field studies. Some experiments have deepened our knowledge of (or focused on??) the microbiological sources of the CDOM and FDOM. For example, our work has shown that marine phytoplankton produces a fluorophore at Ex/Em 320/410 nm which is consumed by marine bacteria which at the same time produce another absorbing fluorophore at Ex/Em 340/440. These ¿humic-like¿ fluorophores, known in the literature as ¿pico-M¿ and ¿pico-C¿, are considered to be characteristic of marine and continental ecosystems, respectively. This work suggests that differentiation is mostly due to the type of cells that produce them: eukaryotic and prokaryotic cells. Furthermore, DOM isolated by tangential ultrafiltration (> 1 KDa) from different aquatic environments has also been characterized. Significant changes were observed in the aromaticity and average molecular weigh of the samples depending on whether they were of continental or marine origin and also on the exposition to the sunlight before sampling. Moreover, controlled experiments were performed in order to study the response of these materials to natural radiation. These experiments showed degradation of the humic-like fluorophores ¿peak-M¿ and ¿peak-C¿ and the formation of another protein-like fluorophores, known in literature as ¿pico-T¿. When the marine bacteria were cultivated using the irradiated materials as substrate a rapid recovery of the humic-like fluorophores was observed. This recovery was proportional to the initial fluorescence of the materials before irradiation. Finally, we have also studied the relative importance of the processes that involve the mixing between water masses of continental and marine origin, microbial production and photochemical degradation on the CDOM and FDOM distribution of two distinct coastal ecosystem: the ¿Ría de Vigo¿ and the Blanes Bay. The Ría de Vigo, enclosed in the Iberian upwelling system, is periodically affected by downwelling and upwelling events. Microbial production was the dominant process during the donwelling period while the photochemical decomposition predominated during upwellings. On the other hand, Blanes Bay, in the oligotrophic Northwest Mediterranean Sea, possesses a seasonal cycle determined by natural radiation. This is characterized by the accumulation of chromophores and fluorophores absorbing at < 300 nm and the photochemical decomposition of those absorbing at > 300nm during the summer season.
Los océanos albergan 685 Pg de carbono orgánico, de los que 662 Pg están en forma disuelta. La enorme diversidad de compuestos que constituyen la materia orgánica disuelta (DOM) y la baja concentración en que se encuentra cada uno de ellos, hace de la caracterización química y estructural de este material una ardua tarea. Es por eso que menos del < 11% de la DOM está identificado en la actualidad. Una fracción variable de la DOM –entre el 20% en océano abierto y el 70% en zonas costeras– absorbe luz UV y visible, por lo que se conoce como DOM coloreada (CDOM). Parte de la CDOM, emite la radiación absorbida en forma de fluorescencia, si bien con un rendimiento cuántico bajo (en torno al 1%) y es conocida como DOM fluorescente (FDOM). El estudio simultaneo de la CDOM y FDOM combinando espectroscopia de absorción y fluorescencia permite –de forma relativamente simple, rápida y barata– ahondar en el conocimiento de (i) la estructura molecular de la DOM, en aspectos tales como su aromaticidad y peso molecular medio; y (ii) su reactividad biológica y fotoquímica, a través del estudio de la producción, consumo y/o alteración química de diferentes grupos cromóforos y fluoróforos en respuesta a la actividad de los microorganismos y la radiación solar en los océanos. En esta Tesis se han realizado tanto experimentos de laboratorio como estudios de campo. En una serie de experimentos se ha profundizado en las fuentes microbiológicas de la CDOM y FDOM en condiciones controladas, demostrando que el fitoplancton marino produce un fluoróforo a Ex/Em = 320 nm/410 nm que es consumido por las bacterias marinas, que a su vez producen otro fluoróforo a Ex/Em = 340 nm/440 nm. Estos fluoróforos de naturaleza húmica, conocidos en la literatura especializada como “pico-M” y “pico-C”, se consideraban característicos de ecosistemas marinos y continentales, respectivamente. Este trabajo sugiere que la diferenciación tiene más que ver con el tipo de células que las producen: eucariotas o procariotas. Se ha caracterizado ópticamente DOM aislada por filtración tangencial (> 1 KDa) de diversas aguas naturales, observándose cambios significativos en la aromaticidad y peso molecular medio de las muestras en función de su origen continental o marino y de su exposición a la luz natural antes de ser colectadas. Igualmente, se realizaron experimentos controlados para estudiar la respuesta de estos materiales a la radiación natural, observándose degradación de los fluoróforos de naturaleza húmica “pico-M” y “pico-C” y generación de un fluoróforo de naturaleza protéica, conocido en la literatura como “pico-T”. Al cultivar bacterias marinas usando los materiales irradiados como substrato se observa una rápida recuperación de los fluoróforos de naturaleza húmica, proporcional a la fluorescencia inicial de los materiales antes de ser irradiados. Finalmente, se ha estudiado la importancia relativa de los procesos de mezcla de masas de agua de origen continental y marino, producción microbiana y degradación fotoquímica sobre la distribución de CDOM y FDOM en dos ecosistemas costeros con distintas condiciones: la Ría de Vigo y la Bahía de Blanes. La Ría de Vigo, sistema eutrófico enclavado en el afloramiento ibérico, se ve afectada periódicamente por episodios de afloramiento y hundimiento, resultando la producción microbiana el proceso dominante en condiciones de afloramiento y la descomposición fotoquímica en condiciones de hundimiento. Por otro lado, la Bahía de Blanes, en el oligotrófico Mediterráneo Nororiental, describe un marcado ciclo estacional dictado por la radiación natural incidente caracterizado por la acumulación estival de cromóforos y fluoróforos que absorben a <300 nm y la descomposición fotoquímica de los que lo hacen a > 300 nm.
Els oceans alberguen 685 Pg de carboni orgànic, dels quals 662 Pg estan en forma dissolta. L’enorme diversitat de compostos que constitueixen la matèria orgànica dissolta (DOM) i la baixa concentració en què es troba cadascun d’ells, fa de la caracterització química i estructural d’aquest material una àrdua tasca. És per això que menys del < 11% de la DOM està identificat a dia d’avui. Una fracció variable de la DOM –entre el 20% a l’oceà obert i el 70% a zones costaneres– absorbeix llum UV i visible, per la qual cosa es coneix com DOM acolorida (CDOM). Part de la CDOM, emet la radiació absorbida en forma de fluorescència, si bé amb un rendiment quàntic baix (entorn del 1%) i és coneguda com DOM fluorescent (FDOM). L’estudi simultanei de la CDOM i la FDOM combinant espectroscòpia d’absorció i fluorescència permet –de forma relativament simple, ràpida i barata– aprofundir en el coneixement de (i) l’estructura molecular de la DOM, en aspectes tals com la seva aromaticitat i el pes molecular mitjà; i (ii) la seva reactivitat biològica i fotoquímica, a través de l’estudi de la producció, consum i/o alteració química de diferents grups cromòfors i fluoròfors en resposta a l’activitat dels microorganismes i la radiació solar en els oceans. En aquesta Tesi s’han realitzat tant experiments de laboratori com estudis de camp. En una sèrie d’experiments s’ha aprofundit en les fonts microbiològiques de la CDOM i FDOM en condicions controlades, demostrant que el fitoplàncton marí produeix un fluoròfors a Ex/Em = 320 nm/410 nm que és consumit pels bacteris marins, que al seu torn produeixen un altre fluoròfors a Ex/Em = 340 nm/440 nm. Aquests fluoròfors de naturalesa húmica, coneguts en la literatura especialitzada com “pic-M” i “pic-C”, es consideraven característics d’ecosistemes marins i continentals, respectivament. Aquest treball suggereix que la diferenciació té més a veure amb el tipus de cèl·lules que les produeixen: eucariotes o procariotes. S’ha caracteritzat òpticament DOM aïllada per filtració tangencial (> 1 KDa) de diverses aigües naturals, observant-se canvis significatius en la aromaticitat i pes molecular mitjà de les mostres en funció del seu origen continental o marí i de la seva exposició a la llum natural abans de ser mostrejadas. Igualment, es van realitzar experiments controlats per estudiar la resposta d’aquests materials a la radiació natural, observant-se degradació dels fluoròfors de naturalesa húmica “pic-M” i “pic-C” i generació d’un fluoròfors de naturalesa protéica, conegut en la literatura com “pic-T”. En cultivar bacteris marins utilizant els materials irradiats com a substrat s’observa una ràpida recuperació dels fluoròfors de naturalesa húmica, proporcional a la fluorescència inicial dels materials abans de ser irradiats. Finalment, s’ha estudiat la importància relativa dels processos de barreja de masses d’aigua d’origen continental i marí, producció microbiana i degradació fotoquímica sobre la distribució de CDOM i FDOM en dos ecosistemes costaners diferents: la Ria de Vigo i la Badia de Blanes. La Ria de Vigo, sistema eutròfic enclavat en l’aflorament ibèric, es veu afectada periòdicament per episodis d’aflorament i enfonsament, resultant la producció microbiana el procés dominant en condicions d’aflorament i la descomposició fotoquímica en condicions d’enfonsament. D’altra banda, la Badia de Blanes, en el oligotròfic Mediterrani Nord-oriental, descriu un marcat cicle estacional dictat per la radiació natural incident caracteritzat per l’acumulació estival de cromòfors i fluoròfors que absorbeixen a <300 nm i la descomposició fotoquímica dels quals que ho fan a > 300 nm.

Global records of temperature show a warming trend both in the atmosphere and in the oceans. Current climate change scenarios indicate that global temperature will continue to increase in the future. The effects will however be very different in different geographic regions. In northern Europe precipitation is projected to increase along with temperature. Increased precipitation will lead to higher river discharge to the Baltic Sea, which will be accompanied by higher inflow of allochthonous organic matter (ADOM) from the terrestrial system. Both changes in temperature and ADOM may affect community composition, altering the ratio between heterotrophic and autotrophic organisms. Climate changes may thus have severe and complex effects in the Baltic Sea, which has low species diversity and is highly vulnerable to environmental change. The aim of my thesis was to acquire a conceptual understanding of aquatic food web responses to increased temperature and inputs of ADOM. These factors were chosen to reflect plausible climate change scenarios. I performed microcosm and mesocosm experiments as well as a theoretical modeling study. My studies had a holistic approach as they covered entire food webs, from bacteria and phytoplankton to planktivorous fish. The results indicate a strong positive effect of increased temperature and ADOM input on the bacterial community and the microbial food web. However, at the prevailing naturally low nutrient concentrations in the Baltic Sea, the effect of increased temperature may be hampered by nutrient deficiency. In general my results show that inputs of ADOM will cause an increase of the bacterial production. This in turn can negatively affect the production at higher trophic levels, due to establishment of an intermediate trophic level, consisting of protozoa. However, the described effects can be counteracted by a number of factors, as for example the relatively high temperature optimum of fish, which will lead to a more efficient exploitation of the system. Furthermore, the length of the food web was observed to be a strong regulating factor for food web responses and ecosystem functioning. Hence, the effect of environmental changes may differ quite drastically depending on the number of trophic levels and community composition of the system. The results of my thesis are of importance as they predict possible ecological consequences of climate change, and as they also demonstrate that variables cannot be examined separately.

This thesis was supported by grants from the Swedish Research Council FORMAS to AA and SL (217-2006-674), the Centre for Environmental Research in Umeå (CMF) to UB, AA and SL, and by the Swedish strategic research program ECOCHANGE to Umeå University.

Thesis (Ph. D.)--Earth and Atmospheric Sciences, Georgia Institute of Technology, 2006.
Taillefert, Martial, Committee Member ; Weber, Rodney, Committee Member ; Stack, Andrew, Committee Member ; Benner, Ronald, Committee Member ; Ingall, Ellery, Committee Chair. Includes bibliographical references.

Marine sediments are key components of the Earth system. They represent one of the largest active pools of organic matter and provide long-term sink for CO2 and CH4. Thus, the biogeochemical processes that take place in those sediments are crucial for the global carbon cycle and Earth climate. Organic matter reactivity plays a key role on organic matter degradation and burial, and thus on biogeochemical processes. Despite of its importance, the environmental controls on reactivity are poorly understood on global-scale. The lack of comprehensive, multidisciplinary approaches investigating the controls on reactivity limits our ability to further understand biogeochemical processes on global and different time-scales. Here, this problem is tackled in coupled quantitative investigation of the relationships between organic matter reactivity and sources. A large-scale compilation of contrasting depositional environments is systematically probed through consistent model parametrization for quantifying reactivity and laboratory protocols for determining lipid biomarker compositions. On global-scale, organic matter reactivity exhibits weak correlations with single characteristics of depositional environments, albeit on regional-scales a few patterns emerge. Similarly, the organic matter compositions show a broad global pattern with a terrestrial-to-marine shift in sources with increase of water depth, although different lipid proxies behaved differently across this spectrum. The environmental controls on reactivity are complex, and lipid biomarker compositions only offer robust information when considered in the broad environmental context of each depositional regime. With this holistic view, the controls on organic matter reactivity are better understood on global-scale. Those findings challenge the classical view of simple mechanisms and single characteristics control on reactivity. Yet, those findings have direct impact on model parametrization since they help to identify reasonable intervals of reactivity parameters in different depositional regimes. Ultimately, this results in better predictive capability and helps to better constrain perturbations on the past, present, and future carbon cycle and climate.

Organic matter which is insoluble in common solvents and non-oxidising acids often comprises the quantitatively most important fraction of organic matter in sediments. This operationally defined material is usually simply termed 'insoluble organic matter' (IOM) or 'kerogen' when it is isolated from ancient sediments. Indeed, kerogen is regarded as the most abundant form of carbon on the planet. The molecular character of this generic material has not been fully elucidated, principally because of its insolubility which limits instrumental methods of analysis to those applicable to solid substrates. This thesis describes the quantitative isolation of IOM from lacustrine and marine sediments and two species of methanogenic bacteria using a sequential isolation procedure. A range of synthetic IOMs (melanoidins) was also prepared. The dissolution of IOM and melanoidins obtained in this manner was then attempted using the acidic ionic liquid l-ethyl-3- methylimidazolium chloride-aluminium (III) chloride. Two synthetic dendrimers containing similar functional groups to those observed in sedimentary IOM were used to try and assess the mode of action of the ionic liquid. Ionic liquid treatment of the DCM soluble dendrimers resulted in the formation of 7 - 62 % of material that was no longer soluble in DCM, whilst the soluble components had been substantially altered. The ionic liquid was found to non-quantitatively promote ether cleavage, protonation and rearrangement reactions. IOM was isolated from lacustrine Rostherne Mere, UK, sediments (7 - 3 0 % dry weight), Kimmeridge Clay, Dorset (11 - 12 %) and methanogenic bacteria (Methanococcus jannaschii, 3 %; Methanobacterium thermoaiitotrophicum, 0.1 %) using a time-consuming isolation procedure involving over forty separate chemical manipulations. Monitoring of the sequential isolation of IOM and characterisation of the final isolates was carried out using solid-state NMR, IR, elemental analysis, pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS), scanning electron microscopy, and the newer surface sensitive technique of time of flight-secondary ion mass spectrometry (ToF-SIMS). Less than 1 % of sedimentary IOM and 5 % of Kimmeridge Clay IOM was soluble in DCM following ionic liquid treatment, whilst alkyl chains were lost from the insoluble portion which also increased in aromaticity. The poor yield recovered following ionic liquid treatment of M. jannaschii IOM (5 %) was attributed to loss of volatile material during hydrolysis. Following ionic liquid treatment 93 - 96 % of the melanoidins remained insoluble in DCM although their character had been altered, becoming more condensed. This ionic liquid dissolution procedure has not provided the substantial progress in elucidating the molecular character of IOM promised by earlier reports.

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
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Permafrost soils in the Arctic store large quantities of organic matter, roughly twice the amount of carbon that was present in the atmosphere before the industrial revolution. This freeze-locked carbon pool is susceptible to thawing caused by amplified global warming at high latitudes. The remobilization of old permafrost carbon facilitates its degradation to carbon dioxide and methane, thereby providing a positive feedback to climate change. Accelerating coastal erosion in addition to projected rising river discharge with enhancing sediment loads are anticipated to transport increasing amounts of land-derived organic carbon (OC) to the Arctic Ocean. On its shallow continental shelves, this material may be remineralized in the water column or in the sediments, transported without being altered off shelf towards the deep sea of the Arctic Interior or buried in marine sediments and hence sequestered from the contemporary carbon cycle. The fate of terrigenous material in the marine environment, though offering potentially important mechanisms to either strengthen or attenuate the permafrost-carbon climate feedback, is so far insufficiently understood. In this doctoral thesis, sediments from the wide East Siberian Arctic Shelf, the world’s largest shelf-sea system, were used to investigate some of the key processes for OC cycling. A range of bulk sediment properties, carbon isotopes and molecular markers were employed to elucidate the relative importance of different organic matter sources, the role of cross-shelf transport and the relevance of degradation during transport and after burial. Overall, OC released from thawing permafrost constitutes a significant proportion of the sedimentary organic matter on the East Siberian Arctic Shelf. Two sediment cores from the inner and outer East Siberian Sea recorded no substantial changes in source material or clear trends in degradation status for the last century. With increasing distance from the coast, however, strong gradients were detected towards lower concentrations of increasingly reworked land-derived OC. The time spent during cross-shelf transport was consequently found to exert first-order control on degradation. Compound-specific radiocarbon dating on terrigenous biomarkers revealed a net transport time of ~4 000 years across the 600 km wide Laptev Sea shelf, yielding degradation rate constants for bulk terrigenous OC and specific biomarkers on the order of 2-4 kyr-1. From these results, the carbon flux released by degradation of terrigenous OC in surface sediments was estimated to be ~1.7 Gg yr-1, several orders of magnitude lower than what had been quantified earlier for dissolved and particulate OC in the water column. Lower oxygen availability and close associations with the mineral matrix may protect sedimentary OC from remineralization and thereby weaken the permafrost-carbon feedback to present climate change.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Manuscript.

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

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

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

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

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

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

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

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

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

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

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

Doctorat en Sciences agronomiques et ingénierie biologique
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Dans le cadre du dragage de Port-Camargue (projet national ECODREDGE-MED), l'objectif principal des travaux de thèse a été d'étudier la re-sédimentation des sédiments ré-immergés et d'appréhender les transferts de matière (particulaires et moléculaires) associés. Une approche expérimentale de caractérisation a été réalisée pour appréhender ces phénomènes, aux échelles macroscopiques (mécanismes de sédimentation), mésoscopiques (transferts de matière particulaires) et moléculaires (phénomènes de sorption). Les travaux ont porté sur l'étude de cinq sédiments et de leurs fractions granulométriques. Une méthode de séparation granulaire a donc été développée et optimisée en ce sens, soulignant l'importance de vérifier la qualité de la séparation lorsque les développements portent sur les fractions granulaires. L'approche morpho-granulaire utilisée dans la caractérisation de ces systèmes a permis, dans un premier temps, de mettre en évidence le comportement cohésif des sédiments et d'identifier différents types d'agglomérats. Elle a ensuite été utilisée pour proposer une méthode de classification simple et rapide des sédiments, basée essentiellement sur la détermination, par granulométrie laser, du rapport volumique limon/sable.En second lieu, le comportement à la re-sédimentation a été appréhendé en étudiant la stabilité physico-chimique des particules dans la colonne de sédimentation grâce à un analyseur de suspensions concentrées, le Turbiscan MA2000. Cette stratégie apporte de nouvelles connaissances, notamment sur les mécanismes de sédimentation et l'impact de certains paramètres comme le rapport limon/sable, la salinité ou la fraction volumique sur ces mécanismes. Combinée à l'analyse du Carbone Organique Total (COT), des transferts de matière ont été identifiés dans la colonne de sédimentation, via les phénomènes interparticulaires (agglomération/dispersion) et les phénomènes de sorption (adsorption/désorption)
In the framework of Port-Camargue dredge (ECODREDGE-MED project), the main objective was to study the dredged sediment re-sedimentation and matter transfers (particular and molecular matter). An experimental characterization approach was realized in order to study these phenomena working at different scales : macroscopic (sedimentation mechanisms), mesoscopic (particular matter mobilization) and molecular (sorption phenomena). These research works focused on study of five sediments and their granular fractions. A dispersion granular method was developed and highlighted the importance to verify dispersion quality of processes concerning study of granular fractions. Morpho-granular approach used in theses works permitted to highlight cohesive aspect of sediments and to identify different agglomerate types. This approach was also used to propose a classification method of sediments, based on limon/sand ratio determination by laser granulometry.Secondly, re-sedimentation behavior was investigated studying physico-chemical stability of particles in the water column with a suspension analyszer (Turbiscan MA2000). The results contributed knowledge on sedimentation mechanisms and parameter (limon/sand ratio, salinity and volume fraction) influence. With the use of TOC analyze (Total Organic Carbone), matter transfers were identified in water column, via interparticular phenomena (agglomeration/dispersion) and sorption phenomena (adsorption/désorption)

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.

La marge ibérique est un milieu biologiquement productif régit par l'influence d'un upwelling saisonnier et des apports continentaux. Les foraminifères benthiques sont des protistes matins qui présentent une grande sensibilité aux conditions environnementales. Ils apparaissent ainsi comme des bio-indicateurs particulièrement efficaces dans ce type de contexte. Dans le cadre de cette thèse, les faunes de foraminifères benthiques, vivants, morts et fossiles prélevées sur un total de 23 carottes interfaces et deux carottes et deux carottes piston, essentiellement situées au débouché de quatre feluves ouest-ibériques majeurs (Douro, Mondego, Tage et Sado) ont été étudiés.Cette analyse faunistique, conjointe à des mesures sédimentaires et géochimiques a permis d'identifier l'impact de la qualité de la matière organique, et donc des apports fluviatiles sur la distribution des faunes vivantes en période hivernale. La comparaison des faunes mortes et vivantes sur les premiers centimètres de sédiments illustre la variation saisonnière de la réponse faunistique à l'upwelling et aux apports continentaux. Elle met également en évidence l'impact des processus taphonomiques sur la conservation de ces bio-indicateurs en vue de permettre une meilleure compréhension du signal fossile de ces faunes. L'application paléoenvironnementale de ces bio-indicateurs a été menée sur une carotte longue prélevée au large du Tage qui permet une reconstruction des derniers 5700 ans cal. BP. Elle a permis de mettre en évidence des périodes caractérisées par des apports importants de matière organique issus du fleuve ainsi que des variations de l'intensité de l'upwelling
The Iberian Margin is a highly productive system driven by coastal upwelling and river inputs. Benthic foraminifera are marine protists particularly sensitive to environmental conditions. Hence they appear well suited bio-indicators for such environment. In the framework of this thesis, living, dead and fossil benthic foraminifera were analized on 23 surface sediment cores and two piston cores essentially from locations off the major rivers of the Portuguese Coast (Douro, Mondego, Tagus and Sado). This faunal analysis, combined with sedimentary and geochemical measurements allow thhe identification of the impact of fluvial exports and organic matter quality during the late winter period. The comparison of dead and living communities, on the first few centimeters of the sediment, shows the seasonal variation of faunas controlled by upwelling activity and riverine discharges intensity. The impact of taphonomical processes on the preservation of these bio-indicators is also investigated in the perspective of a better understanding ofthe fossil signal of these faunas. The paleoenvironmental application of these bio-indicators was then conducted on a 10 m long core from the Tagus shelf that allows paleoreconstruction for the last 5,700 cal. yr BP. The fossil benthic foraminifera record shows that some periods were characterized by intense river runoff and others by variable intensity of the seasonal upwelling

La matière organique dissoute (MOD) est un des principaux vecteurs de carbone à l’océan.Cependant, elle est profondément altérée lors de son transit dans les eaux estuariennes et son séjour en milieu côtier. L’objectif de cette thèse est d’apporter de nouveaux éléments sur la composition, le rôle dans les cycles biogéochimiques le long du transfert terre-mer et le devenir dans l’océan côtier de la MOD.L’analyse de la MOD a été réalisée à l’aide d’une technique d’analyse globale et semi-spécifique : la chromatographie d’exclusion stérique multi-détection (SEC-mDEC), qui permet de séparer la MOD en six fractions de tailles aux propriétés diverses. La dynamique de ces composés a été étudiée de manière saisonnière dans l’estuaire de l’Aulne et la rade de Brest. Dans l’estuaire, le couplage de la SECmDEC avec la fluorescence 3D a aussi été étudié.Initialement conçue pour l’analyse des eaux douces, la SEC-mDEC adaptée à l’analyse des milieux à salinité variable a permis de démontrer que la MOD est impliquée dans de nombreux processus biogéochimiques. Dans l’estuaire de l’Aulne, elle permet de tracer les apports terrigènes et marins.Des modifications substantielles sont apportées à la MOD par le développement des microorganismes et les processus de flocculation en amont du gradient halin. Dans la rade de Brest, l’ensemble des fractions de taille permet de dessiner un continuum de réactivité autour de la dégradation bactérienne du bloom phytoplanctonique. Ces résultats démontrent que l’utilisation du seul carbone organique dissous global des échantillons n’est pas suffisante pour contraindre la dynamique de la MOD dans le continuum terre-mer
Dissolved organic matter (DOM) is one of the most important vector of carbon to the ocean.However, DOM is deeply altered during its transit through estuarine waters and its residence time in Coastal waters. The purpose of this thesis is to bring new insights on the DOM composition, role in biogeochemical cycles during land-sea transfer and fate in Coastal areas. DOM analysis was performed with a global and semi-specific tool: size-exclusion chromatography multi-detection (SEC-mDEC), which allow the separation of DOM into six size fractions of different nature. Dynamics of these compounds are studied seasonally in the Aulne estuary and the bay of Brest. The coupling between SEC-mDEC and 3D fluorescence was studied in the estuary.Initially design for freshwater analysis, the adapted SEC-mDEC for estuarine and marine water analyses permitted the demonstration that DOM is involved in several biogeochemical processes. In the Aulne estuary, DOM tracks the contribution of both riverine and marine sources. Substantial changes are made to the DOM by microorganisms and flocculation processes upstream. In the Bay of Brest, ail fractions enable to design a reactivity continuum from the bacterial degradation of the phytoplanktonic bloom.Results demonstrate that the single use of the global dissolved organic carbon is not enough to constrain DOM dynamic in the land-sea continuum