This dissertation includes theoretical and applied components that address the effect of coatings on rates of mineral reactions that occur in acid mine drainage (AMD) environments. The two major projects investigated how diffusion-limited transport of reactants through pore spaces in coatings on mineral grains affects the reaction rate of the underlying mineral. The first project considered the growth of gypsum coatings on the surface of dissolving limestone in anoxic limestone drains (ALD), which reduces the neutralization rate of the dissolving limestone and the subsequent effectiveness of this treatment. The second project investigated the conditions where iron oxyhydroxide coatings form on oxidizing pyrite and the potential strategies to prevent "runaway" AMD by reducing the rate of acid production to the point that the acid can be neutralized by the surrounding rocks. In both studies, experiments were conducted to measure reaction rates for the underlying minerals, as coatings grew thicker. These experimental data were fit to a diffusion model to estimate diffusion coefficients of reactants through pore spaces in coatings. These models are extrapolated to longer times to predict the behavior of the coated grains under field conditions. The experimental results indicate that management practices can be improved for ALDs and mine waste piles. For example, supersaturation with respect to gypsum, leading to coating formation, can be avoided by diluting the ALD feed solution or by replacing limestone with dolomite. AMD can be prevented if the rate of alkalinity addition to mine waste piles is faster than acid is produced by pyrite oxidation. The diffusion model developed in this study predicts when iron oxyhydroxide coatings will become thick enough that alkalinity from the surroundings is sufficient to neutralize acid produced by coated pyrite oxidation and additional alkalinity is no longer required. / Ph. D.

The high productivity of Eastern Boundary Upwelling Ecosystems (EBUE), some of the most productive ecosystems in the globe, is attributed to the nutrient rich waters brought up through upwelling. Climate change scenarios for coastal upwelling systems, predict an intensification of coastal upwelling winds. Associated with intensification in upwelling are biogeochemical changes such as ocean hypoxia and ocean acidification. In recent years, the California Current System (CCS) has experienced the occurrence of nearshore hypoxia and the novel rise of anoxia. This has been attributed to changes in the intensity of upwelling wind stress. The effects of some of the more severe hypoxia and anoxia events in the CCS have been mass mortality of fish and benthic invertebrates. However, the impacts on zooplankton in this system are not known. Meroplankton, those organisms which have a planktonic stage for only part of their life cycle, are an important component of zooplankton communities. The larval stage of benthic invertebrates forms an important link between benthic adult communities and planktonic communities. Larvae serve to disperse individuals to new locations and to link populations. They are also food for fish and planktonic invertebrates. This important life stage can spend long periods in the plankton (from days to months) where environmental conditions can affect larval health, subsequent settlement and recruitment success, and juvenile health. This research assesses the role of hypoxia and larval survivorship, and the relationship between individual abundance and community structure of larvae to environmental factors in the field. In laboratory experiments (Chapter 2), a suite of 10 rocky intertidal invertebrate species from four phyla were exposed to low oxygen conditions representative of the nearshore environment of the Oregon coast. Results revealed a wide range in tolerances from species with little tolerance (e.g. the shore crab Hemigrapsus oregonensis) to species with high tolerance (e.g. the California mussel Mytilus californianus). The differential responses across larvae to chronic hypoxia and anoxia potentially could affect their recruitment success and consequently, the structure and species composition of intertidal communities. Field studies (Chapter 3 & 4) explore the relationship between environmental variables and larval abundance and community structure. Chapter 3 focuses on broad taxonomic groups, while Chapter 4 focuses on larval decapods in particular. Fine focus was devoted to decapod larvae, due to laboratory findings of heightened sensitivity to hypoxia of decapod crabs. A finding that is also supported in the literature. The goal of field studies was to identify the environmental parameters that structure meroplankton and larval decapod communities and identify which of these parameters play a significant role in influencing larval abundance. A number of environmental variables contributed to meroplankton assemblage structure and larval decapod assemblage structure. These included distance from shore, depth, date, upwelling intensity, dissolved oxygen, and cumulative wind stress. Some of these factors occurred frequently in larval abundance models. In Chapter 3, individual abundance across broad taxonomic groups was most commonly explained by upwelling intensity while in Chapter 4, individual abundance of different decapod species was explained by cumulative wind stress, which is a proxy for upwelling intensity. The prominent role of upwelling related factors in explaining individual abundance is important considering climate change projections of an increased intensification of upwelling winds in EBUE. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Jan. 6, 2012 - Jan. 6, 2013

Les écosystèmes côtiers sont des milieux complexes au sein desquels les communautés microbiennes, jouant un rôle majeur dans leur fonctionnement et leur maintien, s’adaptent et sont tolérantes à des conditions environnementales fluctuantes. En effet, au rythme des marées et de l'activité de la macrofaune, des oscillations oxie/anoxie influencent la composition et la dynamique des communautés microbiennes et par conséquent leur implication métabolique. Afin d’appréhender le devenir du pétrole dans ces écosystèmes, il est donc indispensable d’apporter des connaissances sur l’écologie des microorganismes intervenant dans son élimination, notamment dans des conditions oscillantes anoxie/oxie. Ainsi, ce travail de thèse a eu pour objectif de décrypter l’assemblage de communautés microbiennes hydrocarbonoclastesde sédiments intertidaux soumises à des oscillations anoxie/oxie en présence de pétrole lors d’une expérience en bioréacteurs. Les réponses écologiques des communautés bactériennes globales et de micro-organismes sulfato-réducteurs en conditions oscillantes ont pu être décrites en comparaison avec celles obtenues en conditions d’oxie ou d’anoxie permanentes, par l’analyse des données obtenues par séquençage haut-débit des gènes de l’ARN 16S et dsrB au niveau transcriptionnel. Ces études comparatives ont mis en évidence des profils écologiques en réponseaux conditions oscillantes, pouvant être répandus dans différents environnements marins côtiers. En réponse à ces conditions particulières, de nombreux microorganismes semblent avoir le potentiel à tolérer et/ou s’adapter aux différentes conditions d'oxygénation. Cette capacité d’acclimatation rapide des communautés bactériennes aux conditions oscillantes se sont accompagnées de capacités de dégradation équivalentes ou supérieures dans ces conditions par rapport à la condition d’oxie permanente montrant l’influence des oscillations anoxie/oxie sur le devenir du polluant dans les environnements pollués soumis à ces conditions. / Coastal ecosystems are complex environments in which microbial communities, playing a major role in their functioning and maintain, are tolerant and adapt to changing environmental conditions. Indeed, the tides and the macrofauna’s activity generate oxic/anoxic oscillations which influence the composition and dynamics of microbial communities and consequently their metabolic in volvement. To understand the fate of oil in these ecosystems, it is essential to provide knowledge on the ecology of microorganisms involved in these systems, taking into account anoxic/oxicoscillating conditions. Thus, this thesis aimed to decipher the organization of hydrocarbonoclastic microbial communities inhabiting intertidal sediments, when they are subjected to anoxic/oxic oscillations in an experiment in bioreactors with oil addition. Ecological responses of bacterial communities and sulfate-reducing microorganisms in oscillating conditions have been described comparing with those obtained with permanent oxic or anoxic conditions, using high-throughputsequencing analyses of the 16S rRNA and dsrB genes at the transcriptional level. These comparatives studies have highlighted ecological profiles in response to the oscillating conditions, which can be prevalent in different coastal marine environments. In response to these particular conditions, many organisms seem to have the potential to tolerate and / or adapt to the different conditions of oxygenation. This rapid acclimation capacity of bacterial communities tothese changing conditions have been accompanied by equivalent or greater degradation capacity under these conditions compared to the permanent oxic condition, showing the influence of the anoxic/oxic oscillations on the fate of pollutant in environments subjected tothese conditions.

Le géothermomètre Δ47 est basé sur la relation entre l’abondance des liaisons 13C–18O des carbonates et la température de calcification. Ce proxy contourne potentiellement les limites des autres thermomètres (δ18O, Mg/Ca) pour reconstruire les paléo-températures des océans, expliquant son développement exponentiel depuis dix ans. Cette thèse teste pour la première fois le potentiel et les limites de la thermométrie Δ47 sur les coccolithes, des nannofossiles calcaires produits par des organismes calcifiants dans la zone photique. Ces biominéraux calcitiques et ubiquistes constituent une part importante de l’archive sédimentaire. Des cultures in vitro nous ont permis d’établir que trois espèces de coccolithes actuelles enregistrent la même relation Δ47 – T que la calcite inorganique, alors qu'elles présentent de très larges effets vitaux en δ18O (±5‰). Nous concluons que ces espèces de coccolithes d'importance géologique ne présentent pas d’effets vitaux en Δ47. Nous avons ensuite appliqué le Δ47 à l’étude des sédiments enregistrant l’événement d’anoxie océanique du Toarcien (–183 Ma) au cours duquel les reconstructions de températures restent encore ambigües, notamment du fait de la méconnaissance de la composition isotopique en oxygène de l’eau de mer. Sur la base des données Δ47 acquises, nous proposons des températures élevées (de l’ordre de 36°C), mais restant relativement stables sur l'intervalle d'étude. En couplant ces températures aux données de δ18O des carbonates, nous suggérons une variation importante du δ18O de l'eau de mer dans le Bassin de Paris lors de la mise en place des faciès black shales. Enfin, sur des sédiments pélagiques subactuels, l’une des espèces étudiées présente des déséquilibres isotopiques en Δ47 non observés en culture et explicables par d’autres paramètres environnementaux comme l’intensité lumineuse. Cette thèse illustre le potentiel du thermomètre Δ47 des coccolithes en différents contextes, ouvrant un vaste champ d’application de reconstruction des paléo-environnements sur le Méso-Cénozoïque / The Δ47 geothermometer relies on the relationship between the 13C–18O abundance in carbonateand temperature of calcification. This proxy has the potential to overcome limitations of other thermometers(δ18O, Mg/Ca) to reconstruct oceanic paleotemperatures. This thesis evaluates for the first time the potentialand the limitations of the Δ47 thermometry of the coccoliths, the calcareous nannofossils produced byorganisms calcifying in the photic zone. These calcitic and ubiquitous biominerals represent an importantpart of the sedimentary archive. In vitro cultures allow us to establish that three modern coccoliths speciesrecord the same Δ47–T relation than inorganic calcite, although exhibiting substantial δ18O vital effects(±5‰). We conclude that these coccoliths species do not present any Δ47 vital effect. We subsequentlyapplied the Δ47 proxy to sediments from the Toarcian oceanic anoxic events (–183 Ma) during which thetemperatures reconstructions are still elusive, mainly due to the unknown oxygen isotopic composition ofseawater. On the basis of our Δ47 data, we infer relatively high, yet steady temperatures (around 36°C) duringthe examined interval. By combining these Δ47-derived temperatures to carbonate δ18O data, we can suggestdrastic change in the seawater δ18O composition in the Paris Basin at the onset of black shale deposition. Acore top calibration of Δ47 of coccoliths revealed that one of the studied cultured species exhibits Δ47disequilibrium that is accountable by other environmental parameters, such as light irradiance in the naturalenvironment. Thus, this thesis illustrates the potential of the coccolith Δ47 thermometer in different settings,opening a wide range of application to reconstruct the palaeoenvironments over the Meso-Cenozoic Eras

In Australia, significant effort goes into reducing the amount of nitrogen and phosphorus entering inland waters from point sources. However, little is known of the extent to which riparian organic matter may act as a source of these nutrients. Also, whilst the relationships between the nitrogen, phosphorus and carbon cycles are broadly known, there is little quantitative data regarding the release of these elements from Australian riparian organic matter and their subsequent microbial mineralisation within aquatic environments. In particular, comparatively little is known of their comparative role in nutrient and organic matter cycling within anoxic zones, and the influence that different riparian organic matter may have on stream water quality. This lack of such data presently hampers the ability of water managers to make educated decisions regarding the management of riparian zones in Australia. In order to improve understanding in this area, a combination of laboratory and in situ experiments were carried out in order to compare the abiotic release and aerobic/ anaerobic mineralisation of leaf derived dissolved organic carbon (DOC), dissolved nitrate/nitrite (NOx) and soluble reactive phosphorus (SRP) under different environmental conditions. Four plants common to Australian riparian zones were investigated: two native species, Eucalyptus camaldulensis (gum) and Phragmites australis (common reed), and two exotic species, Salix babylonica (willow) and Lolium multiflorum (rye grass). After 30 days, formaldehyde inhibited 1g willow and rye grass extracts contained the most SRP (0.7 mg/L), whilst gum extracts contained 0.3 mg/L and common reed 0.1 mg/L of SRP.Willow and rye grass abiotically released twice as much NOx than gum and common reed, although concentrations were only between 0.05-0.1 mg/L. Gum and common reed released the most DOC per gram of leaf matter (14 and 12 mmol/g of leaf matter respectively), but based on the initial carbon content of each leaf type, the largest percentage contributor of DOC under abiotic conditions was common reed and rye grass (both 38% mass/mass), with gum (33% mass/mass) and willow (30% mass/mass) being smaller contributors. The most bioavailable DOC was released by rye grass and common reed, with between 83 and 94% of this DOC microbially mineralised after 30 days in oxic conditions. When conditions were not inhibited, microbial growth was evident almost immediately in willow, rye grass and common reed leaf extracts. However, microbial growth was suppressed for the first 48 hours in gum leaf extracts. After this suppression period, the rate of DOC mineralisation was equal in willow and gum leaf extracts (0.1 day-1). Under anoxic conditions, the rate and extent of DOC mineralisation of willow and gum leaves depended on the type of electron acceptor provided. Added nitrate and iron III enhanced the mineralisation of both willow and gum leaves relative to no terminal electron acceptors (from zero to 0.01-0.04 and 0.002- 0.004 moles/day respectively), but added sulphate only enhanced the mineralisation of gum leaves (0.04 moles/day). When no additional electron acceptors were provided, particulate leaf mineralisation was more extensive under oxic than anoxic conditions. However, the mineralisation of leaf derived DOC were the same regardless of oxygen availability, and after 35 days in either condition the percentage of leaf DOC mineralised for each leaf type was of the order common reed > rye grass > willow > gum. All the leaf types tested were able to sustain the caddis fly larvae Triplectides australis under controlled laboratory conditions, and survival rates were high using all four leaf types as a food source. Triplectides australis did not significantly increase the amount of DOC released from each type of leaf matter, but they did consistently increase the proportion of simple carbohydrates present within the DOC fraction. The results of these experiments suggest that changes to riparian vegetation, particularly from the native to exotic species used in this study, will inherently alter in-stream concentrations of dissolved carbon and nutrients (particularly SRP). This potentially will affect in-stream, hyporheic and subsurface processes, particularly in areas where surface water flow is low and riparian leaf inputs are high.

Continental shelves located along eastern boundary currents occupy relatively small volumes of the world’s oceans, yet are responsible for a large proportion of global primary production. The Oregon coast is among these ecosystems. Recent analyses of dissolved oxygen at shallow depths in the water column has suggested increasing episodes of hypoxia and anoxia, events that are detrimental to larger macro-faunal species. Microbial communities, however, are metabolically diverse, capable of utilizing alternative electron donors and acceptors, and can withstand transient periods of low dissolved oxygen. Understanding the phylogenetic and metabolic diversity of microorganisms in these environments is important for assessing the impact hypoxic events have on local and global biogeochemistry. Several molecular ecology tools were used to answer questions about the distribution patterns and activities of microorganisms residing along the coast of Oregon in this dissertation. Ribosomal rRNA fingerprinting and sequence analyses of samples collected during 2007-2008 suggested that bacterial community structure was not substantially influenced by changes in dissolved oxygen. However, substantial depth dependent changes were observed, with samples collected in the bottom boundary layer (BBL) displaying significant differences from those collected in the surface layer. Phylogenetic analyses of bacterial rRNA genes revealed novel phylotypes associated with this area of the water column, including groups with close evolutionary relationships to putative or characterized sulfur oxidizing bacteria (SOB). Analysis of metagenomes and metatranscriptomes collected during 2009 suggested increasing abundances of chemolithoautrophic organisms and their activities in the BBL. Thaumarchaea displayed significant depth dependent increases during the summer, and were detected at maximal frequencies during periods of hypoxia, suggesting that nitrification maybe influenced by local changes in dissolved oxygen. Metagenomic analysis of samples collected from 2010 revealed substantial variability in the metabolic potential of the microbial communities from different water masses. Samples collected during the spring, prior to upwelling clustered independently of those collected during the summer, during a period of upwelling, and did not display any clear stratification. Samples collected during the summer did cluster based on depth, consistent with previous observations, and increases in the relative abundances of chemolithotrophic gene suites were observed in the BBL during stratified conditions, suggesting that the metabolic potential for these processes is a repeatable feature along the Oregon coast. Overall, these observations suggest that depth impacts microbial community diversity, metabolic potential, and transcriptional activity in shallow areas of the Northeast Pacific Ocean. The increase in lithotrophic genes and transcripts in the BBL suggests that this microbial community includes many organisms that are able to use inorganic electron donors for respiration. We speculate that the dissolved organic material in the BBL is semi-labile and not available for immediate oxidation, favoring the growth for microorganisms that are able to use alternative electron donors. / Graduation date: 2012

Carbonate platforms contain a wealth of information regarding the changing biota, sea level, ocean-chemistry, and climate of the Cretaceous Period. The Comanche platform of the northern Gulf of Mexico represents a vast, long-lived carbonate system that extended from west Texas through the Florida panhandle. In central and south Texas, excellent outcrops and an extensive suite of subsurface data provide an opportunity to document the evolution of this system, from the shoreline to the shelf-margin and slope. This study examines the changing facies, platform morphologies, and shelf-margin architectures of the mixed carbonate-siliciclastic, middle-Hauterivian to lower-Campanian interval. Stratigraphic results are integrated with stable-isotope geochemistry to document the detrimental effects of oceanic anoxic events on the carbonate platform. Seven second-order, transgressive-regressive supersequences of 3-14 Myr duration are defined in south Texas using sequence stratigraphic analysis of shelf-interior facies successions. Second-order supersequences are subdivided into several third-order depositional sequences of 1-3 Myr duration. In these sequences, facies proportions and stratal geometries of the shelf-interior are found to be the result of changing platform morphology and temporal evolution from distally-steepened ramp to rimmed-shelf depositional profiles. Shelf-margin trajectories, stratigraphic architectures, and facies proportions are a function of long-term accommodation trends expressed in second-order supersequences. These characteristics are modified by lateral variability in the underlying structural/tectonic setting and localized syndepositional faulting. The stratigraphic equivalents of oceanic anoxic events 1a, 1b, 1d, 2, and 3 are documented in the Cretaceous section of south Texas. These oceanic anoxic events coincided with maximum flooding zones of supersequences and are linked to carbonate platform drowning events on four separate occasions. The occurrence of oceanic anoxic events is found to be a fundamental driver of carbonate platform morphology, faunal composition, and facies evolution in transgressive-regressive supersequences of the northern Gulf of Mexico. / text

Η ΒΥΠ διαθέτει αντίτυπο της διατριβής σε έντυπη μορφή στο βιβλιοστάσιο διδακτορικών διατριβών που βρίσκεται στο ισόγειο του κτιρίου της. / Η βιολογική απομάκρυνση του αζώτου μέσω της νιτροποίησης και της απονιτροποίησης είναι οι διεργασίες οι οποίες χρησιμοποιούνται για την επεξεργασία των αστικών και των βιομηχανικών υγρών αποβλήτων καθώς και για την προεπεξεργασία του πόσιμου νερού. Η νιτροποίηση (βιολογική οξείδωση της αμμωνίας) υλοποιείται από δύο διαφορετικές κατηγορίες αυτότροφων βακτηριών. Η πρώτη ομάδα (νιτρωδοποιητές) μετατρέπει την αμμωνία ( + 4 NH ) σε νιτρώδη ( − 2 NO ) και στη συνέχεια η δεύτερη ομάδα, οι νιτρικοποιητές, οξειδώνει περαιτέρω το ενδιάμεσο προϊόν σε νιτρικά. Η απονιτροποίηση είναι η βιολογική διεργασία, η οποία ευθύνεται για την απομάκρυνση του αζώτου με τη μορφή των νιτρικών και/ή νιτρωδών από τα απόβλητα με μετατροπή σε αέριο άζωτο. Τα τελευταία χρόνια, γίνεται σημαντική ερευνητική προσπάθεια για να παρακαμφθεί το στάδιο της νιτρικοποίησης. Είναι επιθυμητό η αμμωνία να οξειδώνεται σε νιτρώδη και μετά απευθείας να λαμβάνει χώρα η απονιτροποίηση, παρά να γίνεται πρώτα η μετατροπή σε νιτρικά στα συστήματα απομάκρυνσης αζώτου. Θεωρητικά εξοικονομείται περίπου 25% σε δέκτη ηλεκτρονίων (οξυγόνο) και 40% σε δότη ηλεκτρονίων, ενώ επίσης ο ρυθμός απονιτροποίησης αυξάνεται κατά 63% με μικρότερη παραγωγή βιομάζας για κάθε μονάδα αζώτου που απομακρύνεται, πράγμα το οποίο είναι πολύ ελκυστικό από οικονομικής πλευράς, καθώς μειώνεται αρκετά το κόστος λειτουργίας της διεργασίας. Η παράκαμψη αυτή συνήθως επιτυγχάνεται ρυθμίζοντας κατάλληλα τη συγκέντρωση του διαλυμένου οξυγόνου, το pH και τη θερμοκρασία. Ο σκοπός της παρούσας εργασίας ήταν να εξεταστεί το φαινόμενο «υστέρησης» που παρουσιάζουν οι νιτρικοποιητικοί μικροοργανισμοί εξαιτίας της μετάβασης από ανοξικές σε αερόβιες συνθήκες. Επίσης το συγκεκριμένο φαινόμενο μοντελοποιήθηκε για τη διεργασία της νιτροποίησης για (α) ένα αντιδραστήρα συνεχούς λειτουργίας (CSTR) στον οποίο λάμβανε χώρα ανάπτυξη βιομάζας τόσο στον υγρό όγκο όσο και στα τοιχώματα του αντιδραστήρα (προσκολλημένη) και (β) σε αντιδραστήρες διαλείποντος έργου. Με σκοπό να παρακαμφθεί η νιτρικοποίηση χρησιμοποιήθηκε ένας αντιδραστήρας διαλείποντος έργου (SBR) για να προσομοιωθεί η διεργασία της νιτροποίησης λαμβάνοντας υπόψη το φαινόμενο υστέρησης των νιτρικοποιητικών βακτηρίων. Η προσομοίωση αυτή έδειξε ότι είναι δυνατό να παρακαμφθεί η νιτρικοποίηση χρησιμοποιώντας 3 ζεύγη αερόβιας – ανοξικής φάσης, με συνολική διάρκεια κάθε φάσης 4.5 και 5.5 ωρών αντίστοιχα, επιτυγχάνοντας ταυτόχρονα σχεδόν πλήρη απομάκρυνση του αζώτου. Οι μονάδες βιολογικής επεξεργασίας των υγρών αποβλήτων γίνονται συχνά δέκτες αρκετών ξενοβιοτικών ουσιών, τα οποία πρέπει να επεξεργαστούν ταυτόχρονα με τα αστικά απόβλητα προτού εναποτεθούν στους υδάτινους αποδέκτες. Η παρουσία αυτών των ουσιών στις εισροές των βιολογικών καθαρισμών είναι πιθανόν παρεμποδιστικός παράγοντας για ευαίσθητες βιολογικές διεργασίες όπως η νιτροποίηση. Παρεμπόδιση αυτής της διεργασίας, μπορεί κάτω από ανεξέλεγκτες συνθήκες να οδηγήσει σε αποτυχία της βιολογικής απομάκρυνση αζώτου. Στην παρούσα διατριβή εξετάστηκε η τυχόν παρεμπόδιση 12 ξενοβιοτικών ουσιών σε (α) νιτρωδοποιητικά βακτήρια και (β) νιτρικοποιητικά βακτήρια τα οποία είχαν απομονωθεί από την ενεργό ιλύ. Από τα πειράματα αυτά προέκυψαν αξιοσημείωτα φαινόμενα παρεμπόδισης για κάποιες από τις εξεταζόμενες ουσίες. Η συγκεκριμένη παρεμπόδιση μοντελοποιήθηκε χρησιμοποιώντας το μη – ανταγωνιστικό μοντέλο παρεμπόδισης. / In the recent years significant research effort has been spent in bypassing the nitrification process. It is beneficial if ammonium is oxidized to nitrite and is thereafter directly denitrified rather than first being converted to nitrate in biological nitrogen removal systems. the bypass is often accimplished by changing the concentration of the dissolved oxygen, the pH and the temperature. The aim of this work was to examine the \"delay\" effect exhibited by nitrite oxidezers during the transition from anoxic to aerobic conditions. Furthermore, this effect was modeled for the nitrification process that took place in a)a continuously stirred tank reactor (CSTR) and b)in batch reactors. In order to bypass nitrification, a system called Sequencing Batch Reactor (SBR) was used to simulate the nitrification process by taking into account the delay effect of nitrite oxidizers. Sewage Treatment Plants (STPs) are usual receptors of xenobiotic compounds which may inhibit biological processes such as nitrification irrevesibly. This work also examined the possible inhibitory effect of twelve xenobiotic compounds an a)a mixed culture of autotrophic ammonium-oxidizing bacteria and b)nitrite-oxidizing bacteria isolated from activated sludge.

The Black Sea, with its oxic, suboxic and anoxic layers, provides a unique environment for studying how biological and geochemical processes affect the composition of particulate matter. The elemental composition of particles in the Black Sea is controlled by their origin and sources. Particles from rivers are dominated by aluminosilicate material that has compositions similar to the earth&rsquo / s crust. In general this material is relatively unreactive. Biological processes in the upper oxic and suboxic layers of the water column result in enrichments of elements which used as nutrients. Cu, Ba and Mo have been proposed as tracers for planktonic material and new production. Geochemical processes like manganese and iron recycling between oxidized and reduced forms, metal sulfide formation, and biogenic matter decomposition can have a large impact on the composition of particles in the suboxic and anoxic zones. The aim of this thesis was to study the composition of particles suspended in the water column of the Black Sea, in regional rivers draining into the Black Sea, and of particles deposited in these rivers and Black Sea sediments. The objectives were to determine the chemical composition and distribution of particles supplied by rivers and produced in the Black Sea, and compare with those particles buried in the sediments. The chemical distributions can help us to understand the biogeochemical processes taking place. The ultimate goal is to understand if there is a chemical signature that characterizes sediments deposited in anoxic basins that can be used to determine if ancient sedimentary rocks were deposited under such conditions. Water column filter samples were collected from the central western basin and along transects to the SW shelf regions during several research cruises of R/V Bilim and R/V Knorr in the Black Sea. Samples were taken by using both in situ large volume filtration systems and on deck vacuum filtration of discrete samples. River samples were collected by hand from the bank of four Turkish rivers and the Danube River. Sediment samples were obtained from 0 - 25 cm interval of a box core from the deep western basin. All samples were digested and analyzed by inductively coupled plasma - mass spectrometry and combination of atomic absorption (flame &amp / graphite furnace) instruments. The elements analyzed included Al, Ti, V, Cr, Mn, Fe, Ni, Co, Cu, Zn, Mo, Ag, Cd, Ba, Pb, and U. Great care was taken to avoid contamination and to obtain the highest level of precision and accuracy. The precision was typically about 5% for most elements. The accuracy, determined using standard reference materials, was also usually better than 5%. Another goal of this research was to determine the metal concentrations and best digestion methods using different types of filter materials. Blank filters were digested and analyzed and the analyses of various filter blanks are presented in the thesis. The analyses showed that the particulate matter data from Turkish Rivers were very similar to the composition of global average riverine particulate material and global average crust. The Danube River had elevated concentrations for some elements that were probably due to anthropogenic contamination. The Turkish river samples were closer to (but still higher than) the averages for the world&rsquo / s rivers but many elements in the Danube were much higher. These high values determined for major elements in the Danube samples strongly suggest considerable contamination of the Danube as compared to the Turkish Rivers. The Danube River samples were especially enriched in Pb, Zn, Ag, Cu, Cd, and Mn and slightly enriched with Cr and Ni. The first five elements, in particular, are well known indicators of pollution. The particulate matter in the water column of the Black Sea was influenced by lithogenic input from rivers, biological processes and geochemical processes. In order to examine the biogeochemical processes extensively, all the data were plotted as Metal/Al (Me/Al) ratios and compared with the ratios of the average crust and Turkish Rivers. Deviations were used to examine the anomalies due to biological and geochemical processes. In addition, the Al content of individual sample and the Me/Al ratio of crust or rivers were used to subtract the lithogenic component from the total composition. Enrichments due to biological processes were observed for Ba &gt / Fe &gt / Cr &gt / Mn &gt / Zn &gt / Ni &gt / Cu &gt / Mo &gt / V &gt / Co &gt / Cd &gt / U for the overall biogenic composition. Enrichments due to biology are most evident for Ba, Fe, Cr and Mn. This is a unique data set as there have been few previous analyses of biological enrichment for most of these elements. The results of particulate matter analyses showed that some elements including U, V, Cr, Ni, Cu, Co, Zn, Ba and Mo were enriched in the set of samples from the euphotic zone. Redox cycling in the suboxic zone was observed, as expected, for Mn and Fe, whose oxides play an important role in scavenging processes. The redox dependent processes in the suboxic &ndash / anoxic interface influence the vertical distribution of U, Ni, Co, Cu, Zn, Ba and possibly Mo, Cr and V. Elements influenced by sulfide formation in the anoxic layer are Fe, Cr, Ni, Co, Mo, and presumably Ag. The sediment data were also examined based on the same approaches. The elements Zn, Pb, U and Cd decreased with sediment depth over the top 5 cm suggesting that they were remobilized out of the sediments. In general the sediments from the Black Sea have Me/Al ratios very similar to local Turkish Rivers and average crust. There is no unique sediment signature (except possibly for Mo) indicating that these sediments were deposited under sulphidic conditions. This study does not support the hypothesis that the composition of ancient rocks can be used to characterize the environment of deposition.

Les écosystèmes marins côtiers sont constament soumis à des pollutions, notamment aux hydrocarbures, du fait de leur localisation et de leurs caractéristiques environnementales. Le rôle clé des microorganismes dans la dégradation de ces polluants est aujourd’hui très bien décrit. Toutefois, les conditions d’oxygénation fluctuantes dans ces environnements côtiers, dues aux marées et aux activités de bioturbation de la macrofaune, influencent les communautés microbiennes.Ainsi, ce travail de thèse a eu pour objectif de caractériser, l’assemblage de communautés microbiennes hydrocarbonoclastes de sédiments marins côtiers soumises à des oscillations oxie/anoxie en présence de pétrole lors d’une expérience en bioréacteurs. L’adaptation des bactéries marines hydrocarbonoclastes notamment des genres Alcanivorax et Cycloclasticus vis-à-vis de ces variations d’oxygène a pu être investiguée par oligotypage. Des écotypes ont été identifiés en fonction des conditions d’oxygénation démontrant ainsi les capacités d’adaptation aux conditions oscillantes d’oxygène de ces deux genres. La structure des communautés archéennes (séquençage des transcrits du gène de l’ARNr 16S) n’a pas montré de modification évidente liée aux conditions d’oxygénation démontrant ainsi des capacités d’adaptation et/ou de résistance plus importantes chez ces microorganismes comparées aux communautés bactériennes. Enfin, les analyses métagénomiques ont mis en évidence une réponse fonctionnelle spécifique aux oscillations oxie/anoxie. Ainsi, ces travaux de thèse apportent de nouvelles connaissances sur l’influence des variations d’oxygénation sur les communautés microbiennes et par conséquent sur la dégradation des hydrocarbures au sein des écosystèmes marins côtiers. / Coastal marine ecosystems are constantly subject to pollution, particularly hydrocarbons, because of their location and their environmental characteristics. The key role of microorganisms in the degradation of these pollutants is now well described. However, fluctuating oxygenation conditions in these coastal environments, due to tides and macrofauna bioturbation activities influence microbial communities.Thus, this thesis work aimed to characterize the assembly of microbial hydrocarbonoclastic communities of coastal marine sediments subjected to oxic/anoxic oscillations in the presence of oil during a bioreactor experiment. The adaptation of MOHCB, particularly of Alcanivorax and Cycloclasticus genera, to these oxygen variations has been investigated by oligotyping. Ecotypes were identified according to the oxygenation conditions demonstrating adaptation capacities of these two genera to the oscillating oxygen conditions. The structure of archaeal communities (16S rRNA transcript sequencing) did not show any modification related to the oxygenation conditions thus demonstrating greater adaptation and/or resistance capacities in these microorganisms compared to the bacterial communities. Finally, metagenomics analyses revealed a specific functional response to oxic/anoxic oscillations. Thus, this thesis provides new insights into the influence of oxygenation variations on microbial communities and consequently on the degradation of hydrocarbons in coastal marine ecosystems.