published_or_final_version / Zoology / Master / Master of Philosophy

Fractures can increase the permeability and producability of reservoirs by acting as fluid and gas conduits to wells. Networks of fractures are most important in reservoirs where little to no matrix permeability exists such as tight gas sandstones. Two significant variables, fracture length and the abundance of fractures, are not readily measurable from subsurface observations such as those obtained from cores or well logs. Numerical models suggest natural fracture apertures and lengths follow systematic power-law (Marrett, 1996; Olson, 2007) and negative exponential distributions (Olson, 2004); fracture trace lengths are interrogated. This study tests those propositions through study of fractures in outcrop. Outcrops of the Cretaceous Frontier Formation at Oyster Ridge in southwest Wyoming and Oil Mountain near Casper, in central Wyoming provide evidence of reservoir scale fracture networks in sandstones. In the subsurface the Frontier Formation sandstones are reservoirs that produce gas and oil in several Wyoming basins. I mapped fracture patterns at twenty locations at Oyster Ridge and Oil Mountain and measured fracture trace length distributions and abundance (intensity). Fracture cumulative length distribution plots illustrate systematic length distributions. Trace length distributions of every fracture network follow negative exponential distributions regardless of the number of fractures (N = 39 to N = 394) or the size of the outcrop (1.3 to 710 m²). Results show that the fractures follow a negative exponential distribution over a range of lengths of a few centimeters to tens of meters. These trace length distributions are consistent with geomechanical model fracture pattern simulation results by Olson (2004) that suggests negative exponential trace length distribution result from fracture to fracture interaction during fracture formation. Length distributions from my field study are inconsistent with pattern simulation results by Marrett (1996) and Olson (2007) and others that produce power-law length distributions. This inconsistency suggests that the model assumptions of Olson (2004) best account for the patterns I observed. Two dimensional fracture intensity, defined as the total fracture trace length divided by the map area, was measured for each outcrop to determine how structural position affects fracture abundance patterns. Two-dimensional fracture intensity measurements collected at thirteen structural locations around Oil Mountain show higher values of fracture intensity near the fold-axial-trace compared to fold limbs. The difference is as much as 7.4 fractures per meter near fold hinges compared to 0.63 fractures per meter in fold limbs. Outcrops near small faults, with displacement of a few meters, show an increase in fracture intensity from background values around 4.8 fractures per meter to values nearly three times as high (13 fractures per meter) near faults. Values of fracture intensity that are more elevated near small tear faults imply that faulting has a greater influence on fracture intensity than folding. / text

Native oysters have been promoted as a means to improve water quality in Chesapeake Bay. This project added important insights into the potential of oyster aquaculture to process and remove nutrients from Bay waters. Results clarified that nutrient removal of nitrogen (N), phosphorous (P), and carbon (C) through harvest of cultivated oyster biomass can be quantified and modeled with high levels of statistical confidence. A simple, yet accurate, method is now available for estimating the amount of nutrients removed via harvesting aquacultured oysters. Based on model estimates, 106 harvest sized oysters (76 mm TL) remove 132 kg TN, 19 kg TP, and 3,823 kg TC. Previous work suggested that potentially substantial quantities of N may be removed through enhancement of the coupled nitrification-denitrification pathway in sediments as a result of oyster biodeposition. Using 15N and N2/Ar methods to measure N2 production in sediments, encompassing direct denitrification (DNF), coupled nitrification- denitrification, and anaerobic ammonium oxidation (anammox) pathways, at two oyster aquaculture sites and two reference sites (no aquaculture), we found that oyster biodeposition did not accelerate sediment N removal. We estimate sediment N removal rates via N2 production at an oyster cultivation site producing 5 x 105 oysters (1750 m2) to range from 0.49-12.60 kg N yr-1, compared to 2.27-16.72 kg N yr-1 at a reference site of the same area; making the contribution of oyster cultivation to N removal via sediment N2 production inconsequential as a policy initiative for Chesapeake Bay eutrophication mitigation. Molecular approaches and direct abundance measures have improved our understanding of the sediment microbial community response to oyster biodeposition. Overall, sediments impacted by oyster biodeposition had a significantly different denitrifying community composition than sediments a few meters away or at the non-aquaculture reference sites. Bacterial abundance in sediments was determined by site rather than by oyster biodeposition. No apparent effects of oyster biodeposition were evident in nitrifying bacterial abundance patterns at either site, indicating that oyster biodeposition does not enhance coupled nitrification-denitrification by increasing the abundance of nitrifiers in sediments.

Les huîtres présentent un cycle de vie en deux phases : les larves pélagiques s’adhérent avant de se métamorphoser pour une vie benthique.L’adhésion larvaire se fait au stade pédivéligère par sécrétion d’un bioadhésif produit par un organe spécialisé : le pied. Bien que l’huître Crassostrea gigas soit un organisme d’importance économique et écologique, et un modèle d’étude en biologie marine, le phénomène d’adhésion chez la larve pédivéligère est peu documenté. Une étude morphologique des larves pédivéligères par histologie et microscopie électronique a été réalisée, afin de décrire les glandes responsables de la sécrétion de l’adhésif. Une composition majoritairement protéique de l’adhésif a été révélée par histochimie et spectroscopie FTIR.Une analyse in silico des données transcriptomiques disponibles chez C. gigas a permis d’identifier des gènes probablement impliqués dans l’adhésion.Deux analyses protéomiques, menées sur les larves entières et l’adhésif sécrété ont permis de caractériser des protéines en lien avec la biosynthèse et la structure de l’adhésif. Une protéine de type collagène apparaît impliquée dans la structure de l’adhésif de C. gigas. Cette première approche de l’étude de l’adhésion de C. gigas, permet d’envisager la valorisation biotechnologique des molécules identifiées. Le développement d’adhésifs biomimétiques, élaborés sur le principe des bioadhésifs marins, autoriserait le collage en milieu humide, et serait une alternative aux adhésifs synthétiques qui malgré leur toxicité, dominent le marché mondial. / Oysters show a two-phase life cycle: pelagic larvae adhere before metamorphosis into benthic life. Larval adhesion occurs at the pediveliger stage by secretion of a bioadhesive produced by a specialized organ: the foot. The oyster Crassostrea gigas is an organism of economic and ecological importance, and a model for study in marine biology, but the phenomenon of adhesion in the pediveliger larvae is poorly documented. A morphological description of the pediveliger larvae by histology and electron microscopy was performed to describe the glands responsible for the secretion of the adhesive.A predominantly proteinaceous composition of the adhesive was revealed by histochemistry and FTIR spectroscopy. An in silico analysis of available transcriptomic data from C. gigas was made to identify genes probably involved in adhesion. Two proteomic analyses, performed on whole larvae and on the secreted adhesive, characterizing proteins related to biosynthesis and adhesive structure. A collagen-like protein appears to be involved in the adhesive structure of C. gigas. This first approach to the study of the adhesion of C. gigas makes it possible to consider the biotechnological enhancement of the identified molecules. Despite their toxicity, synthetic adhesives dominate the world market. The development of biomimetic adhesives, based on marine bioadhesive strategies could be an alternative, and allowing furthermore bonding in wet condition.

Le virus ostreid herpesvirus type 1 (OsHV-1), peut être considéré comme un des agents infectieux majeur affectant les élevages d’huîtres creuses, Crassostrea gigas, en France. Des différences de sensibilité à l’infection ont également été observées au sein de cette espèce. Des travaux précédents suggèrent un lien entre la base génétique et la survie des animaux face à l’infection. Dans ce contexte, l’objectif principal du travail de thèse était de mieux comprendre les interactions entre l’huître creuse et OsHV-1, et plus particulièrement, les bases moléculaires du cycle viral. Nos résultats montre que le virus est capable de se répliquer chez l’hôte quel que soit son stade de développement, et sa sensibilité. Cependant, la cinétique de multiplication est plus rapide chez des individus sensibles comparés aux moins sensibles. Il apparaît également que chez les individus survivants, le virus ne soit plus détectable après une phase de réplication active. Cette observation laisse suspecter (i) une rémission avec une élimination du virus ou (ii) une persistance du virus sans symptômes détectables. Ces résultats mettent en lumière la possibilité du virus de circuler au sein des individus survivants. Ces individus peuvent excréter des particules virales et intervenir ainsi dans le processus d’infection en milieu naturel. L’ensemble de ces résultats représentent une premier contribution à la compréhension du cycle d’ OsHV-1 chez l’huître creuse, plus particulièrement au niveau moléculaire. / In France, Ostreid herpesvirus type 1 (OsHV-1), can be considered one of the major infectious agents in Pacific oysters, Crassostrea gigas. Susceptibility differences to infection were observed in this species. Previous work suggested that the genetic basis and the survival animals to infection were related. In this context, the main objective of this thesis was to understand the interactions between oysters and OsHV-1, in particular, the molecular basis of the viral cycle. Our results shows that the virus is able to replicate in the host regardless of its stage of development or its susceptible. However, multiplication kinetic is faster in susceptible individuals compared to less susceptible individuals. After a active replication, it would appear that the virus is no detectable in survival individuals. This observation suggests (i) a remission with elimination of the virus or (ii) a virus persistence without detectable symptoms. These results highlight the ability of the virus circulating in the host without causing mortality. These individuals can excrete viral particles and interfere with the infection process in field. All these results represent a first contribution to the understanding of OsHV-1 cycle in Pacific oysters, particularly at the molecular level.

A partir do diagnóstico da viabilidade e ordenamento da ostreicultura na região de Cananéia-SP, estruturou-se o projeto "Ostra de Cananéia". Este projeto teve como principais estratégias: a introdução da criação de ostra, a regularização sanitária do produto, com a criação de uma Estação Depuradora e, principalmente, a organização da comunidade com a criação de uma entidade comunitária, a COOPEROSTRA. Apesar do projeto já apresentar resultados dentro da comunidade atingida, faltava realizar um diagnóstico sócio-econômico e com isso a caracterização do público pós-projeto. Esta dissertação pretende contribuir com informações sobre a transformação da realidade e condições de vida do grupo-alvo, o que vem a ser o objetivo maior da proposta inicial de ordenamento. Para tanto, foram realizadas entrevistas com os cooperados e com o corpo técnico que assessoram a cooperativa. Em seguida, os cooperados foram submetidos a um questionário fechado que buscou avaliar os impactos das novas tecnologias de produção de ostras e na geração de renda. Os cooperados apresentaram dificuldade na participação em atividades de gestão da cooperativa, no entanto, aqueles que participavam, obtiveram incremento de renda ou conseguiram mantê-la. Foi observado um aumento de auto-estima, dignidade, visão de mundo e reconhecimento da profissão, no entanto, ainda é necessário incorporar princípios democráticos em sua prática associativista. As técnicas de engorda em viveiros são amplamente utilizadas e a desmariscagem deixou de ser uma prática constante. O Estado desempenha um papel fundamental na criação e manutenção deste empreendimento, até que conquiste autonomia. A metodologia utilizada para atendimento dos objetivos propostos se mostrou eficiente. A COOPEROSTRA constitui modelo interessante para outras iniciativas comunitárias do mesmo tipo / A diagnostic study on the viability and organizational aspects of oyster aquaculture in the region of Cananéia, São Paulo, led to the development of the project "Oysters from Cananéia". This project’s main goals were to introduce oyster rearing, regulate the sanitary quality of the product by creating a depuration station, and, principally, organize the community through the creation of communitarian entity, COOPEROSTRA. Although the project had already shown results within the community it has reached, a socio-economic diagnosis had not been conducted nor a post-project analysis of the cooperative members. This dissertation intends to contribute with information on the transformation of reality and livelihood conditions of the target group, which is the major objective since the initial proposal for ordering. Consequently, interviews were conducted with the cooperative members and technical experts that assist the cooperative. Afterwards, the cooperative members were submitted to a closed questionnaire to help evaluate the impacts of new technology for oyster production and income generation. The cooperative members, did not seem comfortable whit the participate management activities of the cooperative, however, those who participated, were able to rise their income to keep it. Positive increases were observed in the cooperative members, notably with their self-esteem, dignity, world vision and recognition for their profession, however, it still is necessary to incorporate democratic principals to their association practices. The techniques for growing oysters in rearing beds are widely used and the practice of shelling oysters is no longer used. The State plays and important role in the creation and maintenance of this enterprise, until it attains autonomy. The methodology used to reach the proposed objectives proved to be efficient. COOPEROSTRA serves as an interesting model for other, similar community-based initiatives

Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2015-07-29T01:17:18Z No. of bitstreams: 1 Disserta??o Final_Sofia Aline Santos.pdf: 1372683 bytes, checksum: 1913347c4bf754b4de49bf2916dbb519 (MD5) / Made available in DSpace on 2015-07-29T01:17:18Z (GMT). No. of bitstreams: 1 Disserta??o Final_Sofia Aline Santos.pdf: 1372683 bytes, checksum: 1913347c4bf754b4de49bf2916dbb519 (MD5) Previous issue date: 2014-03-27 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / The presence of oocysts of pathogenic protozoa in coastal waters resulting from the introduction of humans and animals contaminated feces has been recorded in different regions of the world. Bivalve molluscs such oysters can filter and retain in their tissues encysted protozoa and so act as potential transmitter of parasitic forms capable of causing diseases like toxoplasmosis and cryptosporidiosis. The aim of this study was to detect natural contamination in oysters of the species Crassostrea rhizophorae, grown in areas at the influence of de Todos os Santos Bay, Apicomplexa protozoan (Cryptosporidium and Toxoplasma gondii). A total of 615 oysters were collected from five points in two municipalities in the period from January to April 2013. Gills and digestive glands were dissected and grouped in pools of 3 animals, then resulted in 205 samples of gills and 205 samples of glands. For the molecular detection in tissue samples, DNA was extracted, then a nested-PCR was performed for the detection of genetic material of Cryptosporidium and another for detection of Sarcocystidae in order to amplify fragments of 600 and 290 base pairs, respectively. There was no DNA detection of Cryptosporidium in samples analysed. Genetic material compatible to T. gondii was amplified in 32 (7,8%) oyster tissue samples, and there are significant differences in the presence of positivity at two points of collecting. One of the factors that may be related with this finding is the proximity of these points to a location of soils washing containing feces of animals from farms. With these results we can infer that there is contamination of the aquatic environment and a risk of transmission of oocysts through consumption of oysters produced in these regions, which is an alert to the public health system. / A presen?a de oocistos de protozo?rios patog?nicos nas ?guas costeiras, resultantes da introdu??o de fezes contaminadas de humanos e de animais, tem sido registrada em diferentes regi?es do mundo. Moluscos bivalves como ostras podem filtrar e reter em seus tecidos protozo?rios encistados e assim atuar como potenciais transmissores de formas parasit?rias capazes de provocar doen?as como a criptosporidiose e a toxoplasmose. O objetivo deste trabalho foi detectar contamina??o natural de ostras da esp?cie Crassostrea rhizophorae cultivadas em ?reas de influ?ncia da baia de Todos os Santos por protozo?rios Apicomplexa (Cryptosporidium e Toxoplasma gondii). Um total de 615 ostras foi coletado em cinco pontos de dois munic?pios no per?odo de janeiro a abril de 2013. Br?nquias e gl?ndulas digestivas foram dissecadas e agrupadas em pools de 3 animais, resultando em 205 amostras de br?nquias e 205 amostras de gl?ndulas. Para a detec??o molecular, o DNA das amostras teciduais foi extra?do, em seguida foi realizada uma nested-PCR para a detec??o do material gen?tico do Cryptosporidium e uma outra para detec??o do DNA do Sarcocystidae, afim de amplificar fragmentos de 600 e 290 pares de base, respectivamente. N?o houve detec??o de DNA de Cryptosporidium nas amostras analisadas. Material gen?tico de T. gondii, determinado pela PCR-RFLP, foi amplificado em 32 (7,8%) amostras teciduais de ostras, havendo diferen?a significativa de positividade em dois pontos de coleta. Um dos fatores que pode estar relacionado com esse achado ? a proximidade destes pontos a locais de lichiviamento de solos contendo fezes de animais provenientes de fazendas. Com esses resultados podemos inferir que h? contamina??o do ambiente aqu?tico e um risco de transmiss?o de oocistos atrav?s do consumo das ostras produzidas nestas regi?es, o que ? uma alerta para o sistema de sa?de p?blica.

The heterogeneity provided by structured habitats is important in supporting diverse and dense fish communities. The biogenic reefs created by the native Eastern Oyster, Crassostrea virginica, were once the dominant structural habitat in Chesapeake Bay, and have since declined to less than 1% of historic estimates. Conflicting results on the effects of oyster reef restoration on pelagic fish assemblages make further investigation necessary. Incorporating multiple sampling strategies may help elucidate oyster reef habitat influence on fish assemblages. This study used multi-panel gillnets, hydroacoustic technology, and day-night sampling to describe pelagic fish assemblages on and off oyster reef habitat in the lower Piankatank River, VA. Data from oyster reef habitat, adjacent sandy-mud bottom habitat, and unstructured sandy habitat outside of a reef restoration area compared fish diversity, species composition, and density among habitat types. A multivariate analysis using day of the year, day or night, and habitat type as model terms found temporal factors explained variation in fish distribution more than habitat. Fish diversity varied significantly with day or night and habitat type. Diversity and density were significantly higher at night, demonstrating the necessity of nocturnal sampling in fish assemblage research. Results from this study conclude that fish assemblages were not significantly more diverse or denser on reef than non-reef habitat. We suggest that future work should concentrate on studying areas where oyster reef habitat comprises a larger proportion of the study area.

Les acteurs neuroendocriniens régulant la physiologie des Lophotrochozoaires, groupe frère des Ecdysozoaires parmi les Protostomiens, demeurent peu connus. Grâce à l’émergence récente de ressources génomiques, transcriptomiques et peptidomiques chez l’huître creuse Crassostrea gigas, l’étude des couples ligand(s)/récepteur(s) régulant les fonctions physiologiques est désormais facilitée. Ainsi, par une approche d’endocrinologie inverse consistant à éprouver l’activité d’un panel de ligands potentiels, plusieurs récepteurs couplés aux protéines G (RCPGs), jusqu’alors orphelins ont pu être caractérisés sur le plan fonctionnel. Trois voies de signalisation ont été étudiées : la voie de type cholécystokinine/sulfakinine (CCK/SK) la voie de type calcitonine (CT) et la voie de type dopamine (DA). Grâce à des tests fonctionnels, deux neuropeptides et deux récepteurs de type CCK/SK ont pu être caractérisés. Des tests d’activité biologique in vitro et des expériences de conditionnement alimentaire ont montré la potentielle implication de ces couples dans la régulation de la digestion et de la satiété chez l’huître. Par ailleurs, deux couples neuropeptide/récepteur de type CT ont été caractérisés montrant, à l’image de leurs homologues chez les vertébrés, leur possible rôle dans la régulation hydrique ou ionique. D’autre part, un récepteur activé de manière spécifique par la dopamine et la tyramine a été caractérisé. Ce système de signalisation semble être impliqué dans la médiation du stress et intervenir dans les processus régulateurs de la reproduction au niveau de la gonade. Ainsi, les différents résultats obtenus au cours de ces travaux ont permis d’identifier des couples ligands/récepteurs d’huître homologues de systèmes de signalisation présents chez les Ecdysozoaires et les vertébrés confirmant l’origine de ces systèmes neuroendocriniens depuis l’ancêtre commun des Bilatériens. Les résultats obtenus ont également permis de mieux comprendre comment l’huître intègre les paramètres du milieu et donc s’acclimate aux différentes contraintes environnementales. / The neuroendocrine regulators of the physiology of Lophotrochozoa, the sister clade of Ecdysozoa among Protostoma, remain poorly understood. Thanks to the recent emergence of genomic, transcriptomic and peptidomic resources in the Pacific oyster Crassostrea gigas, the functional characterization of ligand/receptor pairs regulating a diversity of physiological functions has been facilitated. Using a reverse endocrinology approach, a number of orphan G Protein-Coupled Receptors (GPCRs) have been functionally characterized. Three signalling systems have been studied in the oyster: The cholecystokinin/sulfakinin (CCK/SK), the calcitonin (CT) and the dopamine (DA) signalling systems. Two CCK/SK receptors and ligands have been characterized. In vitro bioassays and feeding conditions suggested the potential involvement of this signalling system in the regulation of digestion and satiety. Besides, two couples of CT-type peptides and receptors have been characterized showing, as for their vertebrate counterparts, their possible role in the regulation of water and ion balance. A receptor specifically activated by dopamine and by tyramine has also been characterized. This signalling system appeared to be implicated in the mediation of stress and to play a role in the regulatory processes of reproduction in the gonads. This study allowed the characterization in the oyster of ligand receptor pairs homolog to known signalling systems present in Ecdysozoa and vertebrates, thus confirming the origin of these neuroendocrine systems in the common ancestor of Bilateria. The results of this study also contributed to understand how the oyster integrates external parameters and adapts to various environmental constrains.

There has been a continuous decline in both the production and general performance of the SRO in NSW estuaries over the past three decades. The relationship of this decline to both environmental and oyster-density related factors are assessed in this thesis. This question has been examined at different scales: a large scale that compares two different estuaries (Clyde and Shoalhaven Rivers, southern NSW); a regional scale that encompasses variations within an estuary and, at a lease scale that examines processes pertaining to individual or small groups of oysters. Levels of inorganic nutrients were in general very low potentially limiting primary production. The limiting nutrient was nitrogen or phosphorus depending on whether long term conditions were dry or wet, respectively. Only during rain events, through the input of terrestrial material, were conditions favourable for fast rates of primary production. Carbon and nitrogen isotope analysis has demonstrated that both external material and local resuspension of the benthos constitute a major proportion of the SRO diet. The uptake of the various food sources also varied considerably depending on local environmental conditions. Increases in SRO growth were strongly correlated to increases in temperature with a low temperature cut-off at ~13°C. Growth also appeared to reduce considerably when salinities lower than ~15ppt persisted for the order of a month. These factors may alter growth through changes in filtration rates. These processes were modelled in a coupled hydrodynamic-NPO (Nitrogen-Phytoplankton-Oyster) model of the Clyde River. This demonstrated that primary production was more affected by estuarine dynamics and nutrient concentrations than oyster uptake. At the current levels of oyster densities, primary production by itself could not account for the observed oyster growth, however growth became realistic with observed levels of POC added to the model. A set of environmental indices were used to complement the model and to assess the sustainability of the culture system. The combined indices indicated that while the ecological carrying capacity of the Clyde was exceeded the production capacity at an estuarine scale was not. On the lease scale, density experiments showed that while growth was not reduced as a result of current stocking densities, the condition index was significantly affected.