Previous studies have come to contrasting conclusions regarding nutrient limitation of hydrocarbon biodegradation in the Gulf of Mexico, and rate measurements are needed to support oil plume modeling. Thus, this study investigates the rates and controls of biodegradation in seawater and sediments, largely in the deepsea. Sediment and seawater samples were collected on research cruises in the northern Gulf from 2012 to 2014, where the seafloor was impacted by the Deepwater Horizon (DWH) oil spill. Biodegradation was clearly limited by both nitrogen and phosphorus availability in surface waters with significant rates of CO₂ production (100 μmol CO₂ l⁻¹ d⁻¹) only observed in treatments amended with ammonium and phosphate. In deepsea sediments, nutrient amendments resulted in an average of 6 fold higher degradation rates (0.49 μmol CO₂ g sed⁻¹ d⁻¹) compared to unamended controls. Microbial communities responded to oil contamination rapidly in a series of enrichment cultures, and selection was observed for populations of native hydrocarbon-degrading bacteria. Temperature was shown to be a major factor in controlling microbial community composition in the enrichments. At room temperature, community diversity in the enrichments was significantly reduced in the presence of oil, while under 4 °C, the community diversity and evenness remained relatively high upon oil amendment. From the same deepsea sediments, 30 strains of known oil-degrading bacteria (Rhodococcus and Halomonas) were enriched and isolated with hexadecane, phenanthrene, and Macondo oil as the sole carbon and energy source. Detection of these strains in sequence libraries indicates that they may have contributed to the degradation of oil deposited onto the sediments. Rhodococccus strain PC20 degraded approximately one-third of total petroleum hydrocarbons amended into cultures within 7 days. This work elucidates the controls of biodegradation and we provide model pure cultures to further elucidate the ecophysiology of hydrocarbon degradation, focusing on deepsea sediments of the northern Gulf of Mexico.

archives@tulane.edu / During the Deepwater Horizon (DWH) oil spill in 2010, approximately 0.5 billion liters (3.1 million barrels) of oil were released into the northern Gulf of Mexico during the largest marine oil spill in history . A significant portion of the released oil was weathered into residues by physical, photochemical, and biological processes prior to landing on 1773 km of coastline, including 754 km of marsh shoreline in Louisiana. Researchers endeavored to describe effects of oil residues in the soil on salt marsh organisms and communities. Many studies focused on two pillars of salt marsh ecology: the microbial communities through which a large portion of the salt marsh food web is connected and Spartina alterniflora, a foundational species of Gulf Coast salt marshes. In this dissertation I describe how cryptic, or difficult to observe, elements of salt marsh ecology, like microbial communities and plant genetics, respond to oil residues in the environment. Using a suite of field, growth chamber, and greenhouse experiments I show that these microbial communities are difficult to characterize and may respond to other factors more strongly than they do to oil residues. I present evidence that the plant is resilient to oil in the environment, and changes in its microbiome, but exerts a measurable influence on the biodegradation of oil residues and the microbiome in the soil. This dissertation provides a greater understanding of the complexity of the salt marsh response to an oil spill. / 1 / Stephen K. Formel

The Deepwater Horizon (DWH) blowout, in the Gulf of Mexico, heavily contaminated miles of sandy beaches. Previous experience of petroleum contamination has shown that oil residues can persist in the sediments for decades. Biodegradation is the major mechanism of remediation regarding petroleum hydrocarbons. There is an urgent need to evaluate the competent indigenous microbial biomass in contaminated sediments if the risks posed by toxic oil residues, for the coastal ecosystem, are to be minimized. We report a field investigation during December 2010 and January 2011 regarding measurement of microbial activity in a sandy beach at the Bon Secour National Wildlife Refuge in Alabama. One transect of wells for sampling was installed in the beach; starting with multiport one, being most landward and thought to be least exposed to oil residue and ending with multiport four being the most seaward and exposed to the open waters of the Gulf of Mexico. Sediment samples were collected from different depths purposely chosen from above, inside, and below the oil layers for microbial analysis. Dissolved oxygen (DO) measurements were obtained and temperature was recorded while collecting the oxygen measurements. Pore water samples were collected for nutrient content and were monitored using the multiport sampling wells. Moisture content was analyzed from the sediments extracted at various depths at each well. pH and salinity were also analyzed for their contributing affect on the microbial community. Grain size distribution analyses were conducted on samples collected at all wells and at multiple depths to characterize the field study location. Results show that the bacterial biomass, as measured by Adenosine-5-triphosphate (ATP) and numbers of alkane and polycyclic aromatic hydrocarbon (PAH) degraders determined by Most Probable Number (MPN), are consistently higher in the sediment layers where oil had been detected. A very good correlation was observed among the relative abundance of bacteria in the different samples using MPN and ATP measurements. As expected, ATP based estimates of the microbial populations were two orders of magnitude higher than the alkane and PAH numbers determined by MPN, which reflect the non-cultivability of most environmental bacteria. The lower concentrations of PAH degraders than alkane degraders that were observed in this study are consistent with other studies, even though both populations are lower than in studies involving fresh oil trapped in beach or wetland sediments. PAHs (aromatics) are notoriously more resistant to biodegradation than alkanes, therefore allowing a lower number of biomass to grow using them. The overall smaller size of the bacterial numbers could be explained by the naturally occurring low-organic content of beach sand. On the other hand, this may be due to the highly weathered nature of the oil or it could reflect some other limitation. / Civil Engineering

This dissertation explores the discursive production of, and response to, environmental disaster. The project is contextualized through the case of the 2010 Deepwater Horizon disaster in the Gulf of Mexico. By interrupting traditional perceptions of environmental disaster, this project frames socio-environmental disasters as a normal and increasingly experienced part of global hydrocarbon capitalism. The project purports that disaster is embedded within the current global economy and the high-]modernist ideologies that underlie it. As such, the strategies and techniques employed to respond to environmental disaster are intimately bound up within the same systemic processes that have created them in the first place. Moreover, because instrumentalist responses are quickly employed to mitigate disaster, the systemic factors productive of disaster remain concealed. Environmental disaster is thus a process of hydrocarbon capitalism rather than a product of it; as such it can, among other categories, be understood as manageable, profitable, and litigable. This research also highlights the normalization of chronic socio-environmental disaster though sensationalistic perspectives on acute disaster. This project explores the potential for resistance through artistic endeavors, highlighting how the discursive processes that construct traditional power/knowledge formations of environmental disaster might be subverted through non-traditional means. While the framework of eco-governmentality is especially useful in highlighting the problematic social relationships to nature, the project nonetheless acknowledges that counter-discourses for are likely to be appropriated by industry for the purpose of new enterprise and profit. / Ph. D.

Le forage de données, méthode et moyens développés dans cette thèse, redéfinit le processus d’extraction de données, de la formalisation de la connaissance et de son enrichissement notamment dans le cadre de l’élucidation d’évènements qui n’ont pas ou peu été documentés. L’accident de la plateforme de forage Deepwater Horizon, opérée pour le compte de BP dans le Golfe du Mexique et victime d’un blowout le 20 avril 2010, sera notre étude de cas pour la mise en place de notre preuve de concept de forage de données. Cet accident est le résultat d’un décalage inédit entre l’état de l’art des heuristiques des ingénieurs de forage et celui des ingénieurs antipollution. La perte de contrôle du puits MC 252-1 est donc une faillite d’ingénierie et il faudra quatre-vingt-sept jours à l’équipe d’intervention pour reprendre le contrôle du puits devenu sauvage et stopper ainsi la pollution. Deepwater Horizon est en ce sens un cas d’ingénierie en situation extrême, tel que défini par Guarnieri et Travadel.Nous proposons d’abord de revenir sur le concept général d’accident au moyen d’une analyse linguistique poussée présentant les espaces sémantiques dans lesquels se situe l’accident. Cela permet d’enrichir son « noyau de sens » et l’élargissement de l’acception commune de sa définition.Puis, nous amenons que la revue de littérature doit être systématiquement appuyée par une assistance algorithmique pour traiter les données compte tenu du volume disponible, de l’hétérogénéité des sources et des impératifs d’exigences de qualité et de pertinence. En effet, plus de huit cent articles scientifiques mentionnant cet accident ont été publiés à ce jour et une vingtaine de rapports d’enquêtes, constituant notre matériau de recherche, ont été produits. Notre méthode montre les limites des modèles d’accidents face à un cas comme Deepwater Horizon et l’impérieuse nécessité de rechercher un moyen de formalisation adéquat de la connaissance.De ce constat, l’utilisation des ontologies de haut niveau doit être encouragée. L’ontologie DOLCE a montré son grand intérêt dans la formalisation des connaissances à propos de cet accident et a permis notamment d’élucider très précisément une prise de décision à un moment critique de l’intervention. La population, la création d’instances, est le coeur de l’exploitation de l’ontologie et son principal intérêt mais le processus est encore très largement manuel et non exempts d’erreurs. Cette thèse propose une réponse partielle à ce problème par un algorithme NER original de population automatique d’une ontologie.Enfin, l’étude des accidents n’échappe pas à la détermination des causes et à la réflexion sur les « faits socialement construits ». Cette thèse propose les plans originaux d’un « pipeline sémantique » construit à l’aide d’une série d’algorithmes qui permet d’extraire la causalité exprimée dans un document et de produire un graphe représentant ainsi le « cheminement causal » sous-jacent au document. On comprend l’intérêt pour la recherche scientifique ou industrielle de la mise en lumière ainsi créée du raisonnement afférent de l’équipe d’enquête. Pour cela, ces travaux exploitent les avancées en Machine Learning et Question Answering et en particulier les outils Natural Language Processing.Cette thèse est un travail d’assembleur, d’architecte, qui amène à la fois un regard premier sur le cas Deepwater Horizon et propose le forage des données, une méthode et des moyens originaux pour aborder un évènement, afin de faire émerger du matériau de recherche des réponses à des questionnements qui échappaient jusqu’alors à la compréhension. / Data drilling, the method and means developed in this thesis, redefines the process of data extraction, the formalization of knowledge and its enrichment, particularly in the context of the elucidation of events that have not or only slightly been documented. The Deepwater Horizon disaster, the drilling platform operated for BP in the Gulf of Mexico that suffered a blowout on April 20, 2010, will be our case study for the implementation of our proof of concept for data drilling. This accident is the result of an unprecedented discrepancy between the state of the art of drilling engineers' heuristics and that of pollution response engineers. The loss of control of the MC 252-1 well is therefore an engineering failure and it will take the response party eighty-seven days to regain control of the wild well and halt the pollution. Deepwater Horizon is in this sense a case of engineering facing extreme situation, as defined by Guarnieri and Travadel.First, we propose to return to the overall concept of accident by means of an in-depth linguistic analysis presenting the semantic spaces in which the accident takes place. This makes it possible to enrich its "core meaning" and broaden the shared acceptance of its definition.Then, we bring that the literature review must be systematically supported by algorithmic assistance to process the data taking into account the available volume, the heterogeneity of the sources and the requirements of quality and relevance standards. In fact, more than eight hundred scientific articles mentioning this accident have been published to date and some twenty investigation reports, constituting our research material, have been produced. Our method demonstrates the limitations of accident models when dealing with a case like Deepwater Horizon and the urgent need to look for an appropriate way to formalize knowledge.As a result, the use of upper-level ontologies should be encouraged. The DOLCE ontology has shown its great interest in formalizing knowledge about this accident and especially in elucidating very accurately a decision-making process at a critical moment of the intervention. The population, the creation of instances, is the heart of the exploitation of ontology and its main interest, but the process is still largely manual and not without mistakes. This thesis proposes a partial answer to this problem by an original NER algorithm for the automatic population of an ontology.Finally, the study of accidents involves determining the causes and examining "socially constructed facts". This thesis presents the original plans of a "semantic pipeline" built with a series of algorithms that extract the expressed causality in a document and produce a graph that represents the "causal path" underlying the document. It is significant for scientific or industrial research to highlight the reasoning behind the findings of the investigation team. To do this, this work leverages developments in Machine Learning and Question Answering and especially the Natural Language Processing tools.As a conclusion, this thesis is a work of a fitter, an architect, which offers both a prime insight into the Deepwater Horizon case and proposes the data drilling, an original method and means to address an event, in order to uncover answers from the research material for questions that had previously escaped understanding.

L’explosion du forage et de la plate-forme pétrolière Deepwater Horizon (DWH) le 20 Avril 2010 a entrainé la plus importante catastrophe pétrolière de l’histoire des Etats-Unis, avec des quantités sans précédent de pétrole (779,000 T) et de gaz relâchées continuellement dans le Golfe du Mexique durant près de 3 mois. En retour et comme moyen de réponse, 8 million L de dispersant chimique (principalement Corexit 9500A®) furent utilisés pour disperser les nappes, dont 2.9 million L furent injectés directement à la tête du puits à 1500 m de profondeur. La marée noire coïncida avec la saison de ponte et de recrutement de l’huitre américaine Crassostrea virginica, une espèce à haute valeur écologique et commerciale dans le Golfe. En raison de ces caractéristiques biologiques (sédentaire, espèce filtreuse, répartition géographique, ponte et fécondation externe), les huitres ont été utilisées comme organisme modèle en écotoxicologie. Néanmoins, il existe très peu de données disponibles sur la toxicité du pétrole brute (HEWAF), du pétrole dispersé (CEWAF) ou du dispersant sur les jeunes stades de vie de C. virginica. L’objectif de ce travail de thèse fut 1) de déterminer les effets létaux et sublétaux d’expositions aigües et chroniques à du pétrole DWH et/ou du Corexit 9500A® sur différents stades de développement des jeunes huitres, 2) d’examiner les mécanismes de toxicité des HAP (dissouts ou particulaires) issus du pétrole et du dispersant sur des processus physiologiques sensibles, et 3) d’établir si les résultats obtenus en laboratoire correspondent aux valeurs recueillies sur le terrain lors du programme NRDA. Nos résultats ont démontré que le pétrole et/ou le dispersant pouvaient affecter la reproduction et le développement embryonnaire et larvaire de C. virginica, et que le pétrole dispersé et le dispersant induisaient en général le plus d’impact. En outre, des effets sublétaux tels que des inhibitions de croissance larvaire, de fixation ou de filtration furent observés à des niveaux d’HAP et de DOSS mesurés dans l’environnement. Ces résultats suggèrent que le pétrole et l’utilisation de dispersant, en particulier lors de la saison de ponte de l’huître, pourraient affecter son recrutement et impacter la ressource de façon délétère dans des régions touchées par une marée noire. Par ailleurs, des critères biologiques plus sensibles que la mortalité devraient être choisis et inclus dans une approche intégrative, afin d’estimer plus précisément l’impact environnemental des hydrocarbures et le devenir de ses constituants. / The explosion of the Deepwater Horizon (DWH) oil drilling rig on 20th April 2010 resulted in the largest oil-related environmental disaster in U.S history with an unprecedented amount of oil (779,000 t) and gas discharged continuously in the Gulf of Mexico, over a period of 3 months. As a response, 8 million L of chemical dispersants (mainly Corexit 9500A®) were applied on surface to dissipate the slicks, and injected directly at the well head (3 million L) at 1500 m depths. The oil spill coincided with the spawning and recruitment season of the ecologically and commercially important Eastern oyster, Crassostrea virginica. Due to its biological characteristics (sessile, filter-feeding, ubiquity, “free” spawner), oysters have been employed as a model species in ecotoxicology and for monitoring the environment. However, information on the toxicity of crude oil (HEWAF), dispersed oil (CEWAF) and dispersant alone (Corexit 9500A®) on early developmental stages of C. virginica are limited. The aim of this study was to i) determine the lethal and sublethal effects of acute and chronic exposure to surface-collected DWH oil and/or Corexit 9500A® on various life stages of oysters, ii) examine the mode of toxicity of oil-associated PAHs (dissolved or particulate) and dispersant on sensitive physiological processes, and iii) establish whether there is a relationship between results collected in the laboratory and field data collected during the NRDA sampling program. Our results indicated that oil and/or dispersant adversely affected reproduction and early development of C. virginica, with dispersed oil and dispersant having generally the highest impacts. Furthermore, sublethal effects such as inhibition of larval growth, settlement success or filtration rates were observed at environmentally realistic concentrations of tPAHs or DOSS. These results suggest that oil spills and the use of dispersant as a spill response, especially at the time of oyster spawning season, could affect oyster recruitment and ultimately oyster populations in affected regions. Besides, in order to assess more precisely the environmental impact of an oil spill and the fate of its constituents, meaningful endpoints other than lethality should be selected

The behavior of Deepwater Horizon crude oil and other sources of oil were investigated when exposed to sunlight in aquatic systems under environmentally relevant conditions. This research decoupled the abiotic and biotic weathering modifications of oil by focusing solely on the photochemical transformations of oil in aquatic systems. Photochemical rates and mechanisms were measured through the determination of reactive transients. Total hydroxyl radical formation was studied using high benzoic acid concentrations and varying exposure time. Titanium dioxide (TiO2) nanomaterials were added to the system in an effort to determine if the photocatalyst would enhance oil photodegradation. Photochemical production of singlet oxygen from thin oil films over seawater and pure water was measured with furfuryl alcohol as a selective chemical probe. The loss of furfuryl alcohol and the formation of 6-hydroxy(2H)pyran-3(6H)-one were monitored. Photochemical production of organic triplets from 6 different compositions of petroleum was measured through the cis-trans isomerization of 1,3 pentadiene in Gulf water. The data correlate very well with previously measured singlet oxygen concentrations. The energies were measured in the range of 280-300 kJ/mol. Macondo Well Oil from the Deepwater Horizon (DWH) rig was mixed with pure water and seawater and irradiated with simulated sunlight. After irradiation, the water-soluble organics (WSO) from the dark and irradiated samples were extracted and characterized by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Liquid-liquid extraction yielded two fractions from dark and irradiated water/oil mixtures: acidic WSOs (negative-ion electrospray (ESI)), and base/neutral WSOs (positive-ion ESI). These fractions were analyzed by FT-ICR MS to catalogue molecular-level transformations that occurred to oil-derived WSOs after solar irradiation. The increased abundance of higher-order oxygen classes in the irradiated samples relative to the dark samples indicates that photooxidized components of the Macondo crude oil become water-soluble after irradiation. Time series studies were performed to observe the changes in WSO composition. The predominance of higher-order oxygen classes indicates that multiple photochemical pathways exist that result in oxidation of petroleum compounds. More oxygenated compounds were observed in the WSO acid fraction of oils with higher API gravity.

Simulated oil spills were created in S. alterniflora sediment-water microcosms to determine the effects of applied crude oil on S.alterniflora during two 90-day studies. In the first experiment, oil dosage was varied at 0-250 mg crude oil/g wet soil to determine the lethal dosage level. In the second experiment, oil type, dosage, and soil type were varied to determine the effects of oil under multiple scales of resolution. A light, medium, and heavy crude oil at dosages ranging from 0-150 mg crude oil/g wet soil were used in addition to an oiled and non-oiled soil. Following the completion of the 90-day experiment, several key findings were observed: (1) The lethal dosage limit was reached at 250 mg crude oil/g wet soil during the first experiment but not the second, by design; (2) At initial dosages of 10 and 50 mg crude oil/g wet soil, the oiled soil (acclimated for 4 months) was more influential in decreasing cumulative biomass growth rates compared to oil applied at the oil-water interface; (3) At the heaviest dosages applied as a simulated oil slick, concentrations of 150 mg crude oil/g wet soil, evapotranspiration rates were negatively affected by the oil (significant at p=0.05 in a one-tailed t-test); (4) Light, heavy, and then medium crude oil showed the lowest biomass growths, in that order, indicating that light crude oil was the most toxic in these microcosm experiments with S. alterniflora; (5) The 10 mg oil/g wet soil out-performed the 0 mg oil/g wet soil in transpiration and biomass growth.

The goal of the research conducted in this dissertation was to define and test methods to incorporate oil spill effects into an ecosystem-based assessment model. It was instigated by the Deepwater Horizon oil spill, an unprecedented oil spill in the United States for both depth and volume, with unknown implications for the health of the region. Using an ecosystem-based assessment model like Atlantis, with integrated oil spill dynamics, was the ideal candidate to predict long-term impacts such as decreased abundance or population recovery time. However no previous methodology existed for doing so in any ecosystem-based assessment model. Therefore, first I conducted a literature review to gather data across fish species on lesion frequency and fish body growth impacts from oil exposure. The two data sets were then fitted to four different dose-response models, and an effect threshold log-linear “hockey-stick” model was selected as the best fit and most parsimonious for both lesions and growth. Next, I conducted a similar analysis comparing macrofaunal and meiofaunal abundances to oil exposure concentrations in the Gulf of Mexico collected after Deepwater Horizon. I confirmed that these data had the domed relationship between invertebrate abundances and oil concentration observed in previous invertebrate oil studies. This domed relationship indicates that abundance increases at low to moderate oil levels, and declines at high oil levels. To drive this relationship in an Atlantis ecosystem model, three scenarios were tested in combination with oil toxicity: 1) Mississippi nutrient loading, 2) increased detritus from marine oil snow sedimentation and flocculent accumulation, and 3) predators altering their behavior to avoid oil exposure. At the Atlantis polygon resolution, only scenario 2, increased detritus from marine oil snow sedimentation and flocculent accumulation, generated the domed relationship for invertebrate abundances. Lastly, the “hockey-stick” model for fish mortality and growth was applied to both fishes and invertebrates in combination with scenario 2 for an integrated long-term assessment of the Gulf of Mexico. Newly available fish exposure data were used to generate an uptake-depuration model for this assessment. The combined effect forcings on vertebrates and invertebrates proved to have more severe long-term implications on population size and recovery than simulations with only fish forcings. Large demersal fishes, including elasmobranchs, were the most severely impacted by large biomass declines in the model spill region. Sensitivity analyses indicated that there was the potential for no recovery during 50 years of simulation in the spill region for many functional groups. Analysis of the synergy between fishing mortality F and toxicity from an oil spill identified that some guilds are more sensitive in an oil spill simulation to varied F than others. Snappers are the most sensitive to increased fishing mortality, while groupers respond the most to a reduction in fishing mortality. The invertebrate guild and small pelagic fishes responded the least to different values of F. Changing F also had implications for guild recovery – some guilds only fully recovered to control scenario biomass when F was reduced. A few functional groups were unable to survive with the combined effects of oil toxicity and increased F, and went extinct before the end of the 50-year simulation. Overall, this work provided the first framework for initial integrated modeling of oil spill impacts in an ecosystem-based assessment model, a potentially important component to future ecosystem-based fisheries management. The “hockey-stick” dose response model is applicable beyond Atlantis modeling, and can be tuned to fit specific events based on available data. I have also identified the importance of including marine oil snow sedimentation and flocculent accumulation to accurately drive the response of benthic invertebrates. Findings from the combined vertebrate and invertebrate simulations should help inform research efforts in the Gulf of Mexico and future oil spill response efforts.

Cytokines are pleiotropic and redundant signaling molecules that govern the inflammatory response and immunity, a critical ecological parameter for organism success and population growth. Produced at the site of injury or pathogen intrusion by a variety of cell types, cytokines mediate cell-signaling in either an autocrine or paracrine manner. The type and magnitude of the cytokine milieu produced subsequently dictates the strength and form of immune response. As the most diverse vertebrate group, with a high sensitivity to contaminants, fish represent an important foci for the evaluation of immune system evolution, function, and alteration upon toxicant exposure. While many cytokines have been identified in teleosts, primary study has been limited to model species (e.g. zebrafish and fugu). However, evidence exists for several variations of cytokine genes within taxa, underscoring the need for species-specific evaluation. In this study, two pro-inflammatory cytokines (IL-1β and TNFα ), one chemokine (IL-8), and one anti-inflammatory cytokine (IL-10) were cloned, sequenced, and characterized for the first time in two commercially relevant Perciformes in the Gulf of Mexico, golden tilefish (Lopholatilus chamaeleonticeps) and red snapper (Lutjanus campechanus). The complete amino acid sequence was obtained and confirmed for IL-β and IL-8 from golden tilefish and for IL-8, IL-10, and TNFα from red snapper, with partial sequences obtained for the remaining proteins. The results indicate high homology among Perciformes for all cytokines studied, but divergence with other teleost orders, and low conservation when compared to birds, amphibians, and mammals. The sequences will be used to create a multi-plexed antibody-based assay for the routine detection of cytokines in teleost serum. This would allow the biochemical response to fish health challenges, such as oil spills and other contamination events, to be monitored at the protein level, building upon the current regime of genetic biomarkers. Thus, this work will aid in the understanding of how oil spills and other contamination events may alter the immune response in fishes.