Restoration of the oyster reefs has become increasingly crucial due to great population declines around the globe. Intertidal oyster reefs provide essential foraging and loafing grounds to many faunal species, including several threatened/endangered wading bird species. Biodegradable oyster reef restoration materials have been introduced to avoid potential plastic pollution from traditional materials. Studies have shown success regarding oyster recruitment rates to these materials. However, their impacts on fauna using restored oyster reefs are unknown. This project aims to evaluate oyster reef restoration using biodegradable materials to increase faunal diversity, abundance, and foraging behaviors. Camera traps were deployed to observe fauna on reefs of the eastern oyster (Crassostrea virginica) in summer 2021, winter 2022, and summer 2022 in Mosquito Lagoon, FL. Treatments included Biodegradable EcoSystem Engineering Elements (BESE) shell mats, cement-jute tiles, and cement-jute rings. Unrestored, live reefs were used as positive controls, and unrestored, dead reefs (piles of disarticulated shell) were used as negative controls with three replicates of each treatment. A total of 11,458 vertebrates were observed out of 82,261 video clips. These comprised 44 species, including seven species of birds listed as threatened in the state of FL. There was a significant interaction between timeframe and treatment for non-foraging behaviors, such as loafing, grooming, and walking. Restoration materials did not decrease counts of foraging. However, foraging counts significantly varied over time, based on bird migratory patterns and time since restoration. This research provides essential information on the faunal use of restored and unrestored oyster reefs and highlights the importance of a mosaic of oyster reef types in estuarine systems.

Les rythmes biologiques constituent une propriété fondamentale de la vie, permettant aux organismes d’appréhender leur environnement et d’en anticiper les changements. Ces rythmes possèdent une double origine : une horloge moléculaire génère ces rythmes, qui sont ensuite synchronisés par des facteurs environnementaux. Si les organismes terrestres sont essentiellement soumis au rythme d’alternance jour/nuit, les espèces marines côtières et estuariennes occupent un biotope plus changeant encore : ils sont en effet également confrontés au rythme des marées. Pourtant, leurs rythmes biologiques sont à ce jour encore mal connus et les mécanismes moléculaires de(s) (l’) horloge(s) sous-jacente(s) ne sont pas caractérisés. Parallèlement, les efflorescences d’algues toxiques, en constante augmentation depuis 1970, constituent un problème écologique majeur, tant local qu’international. Les objectifs du présent travail consistaient à caractériser les rythmes de référence de l’huître Crassostrea gigas et d’en déterminer l’origine (moléculaire, zeitgebers). Il s’agissait ensuite d’étudier les perturbations potentielles de ces rythmes par l’algue toxique Alexandrium minutum, qui produit des toxines paralytiques et est régulièrement présente dans de nombreuses mers du globe. Les travaux réalisés ont permis de mettre en évidence l’existence d’un rythme d’activité valvaire circadien, faible et dual, et n’a pas permis de supporter l’hypothèse de l’existence d’une horloge circatidale. Nous avons formulé l’hypothèse que, chez C. gigas, le rythme tidal est soit d’origine exogène, soit produit par l’horloge circadienne synchronisée par les marées. Les analyses moléculaires réalisées sur le gène circadien cryptochrome dans le muscle adducteur - effecteur du mouvement des valves - ont montré que ce gène oscille à une fréquence tidale dans le muscle strié, favorisant notre seconde hypothèse. Par ailleurs, au-delà des gènes de l’horloge, l’algue A. minutum réprime l’expression de gènes impliqués dans différentes voies métaboliques importantes : la lutte contre le stress oxydant (cat, gpx), la respiration mitochondriale (cox1), l’immunité (ilk), la détoxification (mdr). Finalement nos analyses ont permis de mettre en évidence un impact génotoxique d’A. minutum chez C. gigas. / Biological rhythms constitute a fundamental property of life, allowing organisms to anticipate and adapt to their changing environment. These rhythms present a double origin: they are generated by a molecular clock and synchronized by environmental cues. Whereas terrestrial organisms are mainly subjected to day/night alternation, coastal and estuarine marine species inhabit an even more cycling biotope. They are indeed also submitted to tides. Nevertheless, biological rhythms in marine species are still unrecognized and molecular mechanisms of the underlying oscillator(s) are to date not determined. At the same time, toxic algae blooms are increasing since the 1970s and represent a major ecological concern, both at local and international levels. An objective of the present work was the characterization of biological rhythms in the oyster Crassotrea gigas and of their origin (molecular mechanism, zeitgebers). Furthermore, the work was designed to study the potential disruption of these rhythms by the toxic algal of worldwide distribution Alexandrium minutum, which produces paralytic toxins. The present results show the existence of a weak and dual circadian rhythm of valve activity in the oyster, and do not provide evidence for the existence of any circatidal clock. We suggested that, in the oyster C. gigas, the tidal rhythm could either be generated exogenously or endogenously by the tidally-synchronized circadian clock. Molecular analyses performed on the circadian gene cryptochrome in the adductor muscle of oyster, the effector of valve movements, revealed that Cgcry oscillates at tidal frequency in the striated muscle. This result supports our second hypothesis. Furthermore, A. minutum represses the expression of genes involved in key metabolic pathways: struggle against oxidative stress (cat, gpx), mitochondrial respiration (cox1), immunity (ilk), detoxification (mdr). Moreover, A. minutum impacts C. gigas at DNA level, being thus genotoxic.

Le bassin d’Arcachon est une lagune semi-fermée qui concentre de forts enjeux économiques grâce à la pratique de l’ostréiculture. Cette activité est affectée depuis une trentaine d’années par des phénomènes de mortalités estivales, et plus récemment par des surmortalités du naissain. Ces travaux se sont intéressés au rôle des polluants majeurs du bassin d’Arcachon dans ce contexte de crise en étudiant leurs effets sur la biologie de Crassostrea gigas. Une approche in situ a d’abord été adoptée afin d’identifier les contaminants les plus présents dans le milieu naturel. Des opérations de transplantation d’huîtres et des prélèvements de sédiments ont permis de quantifier divers contaminants et d’associer leur présence à des réponses biologiques. Les polluants ainsi identifiés ont ensuite été employés en conditions contrôlées au laboratoire. Trois expérimentations ont été réalisées : la première concerne l’étude des voies de contamination par le tributylétain ; la seconde concerne les effets des pesticides et du cuivre ; la troisième concerne l’effet des HAP sur des huîtres diploïdes et triploïdes. Nos résultats indiquent que les organismes transplantés au coeur de la lagune sont plus exposés aux polluants, en lien avec les caractéristiques hydrodynamiques du système. La plupart des paramètres biologiques étudiés sur le terrain ont par ailleurs montré une saisonnalité liée aux processus de gamétogenèse. Au laboratoire, la plupart des contaminants testés ont induit une réponse adaptative chez les huîtres exposées. Notre étude souligne l’importance de coupler approche de terrain et approche expérimentale pour comprendre le fonctionnement des écosystèmes côtiers. / The Arcachon Bay is a semi-enclosed lagoon and represents the core of strong economic stakes through the practice of oyster-farming. This activity has been affected for around thirty years by summer mortality events, and more recently by abnormally high death rates of juveniles. This work focused on the role of the Arcachon Bay’s main contaminants in this crisis, by studying their effects on the cupped oyster’s biology. Firstly, an in situ approach was adopted in order to identify the major pollutants of the bay: caged oysters were transplanted and sediments were sampled. The presence of contaminants in the samples was associated to biological responses. Secondly, the contaminants identified in situ were used in controlled conditions at the laboratory. Three experimentations were performed; the first dealt with the contamination pathways of tributyltin; the second focused on the biological effects of pesticides and copper; the third concerned the effects of PAH towards diploid and triploid oysters. Our results indicate that the inner stations present higher accumulation of metals and PAH, in accordance with the hydrodynamic features of the bay. The bioindicators used in situ exhibited seasonal trends related to the oysters’ gametogenesis. In the laboratory, most of the contaminants used at environmental levels induced an adaptive response of the exposed oysters. Our study highlights the importance of coupling in situ and laboratory approaches in order to understand the functioning of coastal ecosystems.

L’ostréiculture constitue l'une des principales composantes de l’aquaculture. Cependant, ce secteur est confronté à des épisodes de mortalités anormales survenant aussi bien en écloseries que dans le milieu naturel, affectant les huîtres diploïdes et triploïdes et à différents stades de leur vie. Pendant les épisodes de mortalité des mollusques bivalves en France, des bactéries, initialement classées dans le groupe de V. harveyi, ont été régulièrement isolées à coté des virus de type herpès, V. splendidus ou de V. aestuarianus. Afin d'affiner l’affiliation taxonomique de ces isolats, une caractérisation génotypique et phénotypique a été réalisée. Les isolats bactériens, initialement classés dans le groupe de V. harveyi, se sont révélés génétiquement plus proches de souches du groupe V. tubiashii, reconnues comme agents pathogènes affectant larves et juvéniles de mollusques aux Etats-Unis et en Angleterre. Des outils de diagnostic ont été élaborés pour évaluer la propagation de cette espèce lors des périodes de mortalité depuis 2007, supportant cette première description de V. tubiashii en France. La virulence des isolats et la toxicité de leurs produits extracellulaires (ECPs) ont été confirmés par infections expérimentales sur des larves et des juvéniles de C. gigas. Les essais in vitro ont révélé la capacité des ECPs de V. tubiashii à perturber des fonctions immunitaires hémocytaires probablement via la dégradation de certaines protéines structurales. Finalement, des analyses protéomiques et transcriptomiques ont révélé la conjonction de multiples facteurs de virulence, y compris les métalloprotéases dans la virulence des souches françaises de V. tubiashii. / The oyster farming constitutes one of the major components of the global aquaculture. However, this sector is facing abnormal mortalities outbreaks that affect diploid and triploid oyster at their different life stages, in the hatcheries and in the field. During bivalve molluscs mortality events in France, bacteria initially classified into Harveyi group, were regularly isolated along with herpes virus, V. splendidus or V. aestuarianus. In order to fine tune the taxonomic affiliation of those isolates, a genotypic and phenotypic approach was used. The bacterial isolates, initially misclassified into the Harveyi clade, were shown to be genetically closed to V. tubiashii strains already recognized as the main causative agents of larvae and juvenile mollusc mortalities in America and in England. A diagnostic tool was developed to evaluate its spread in mortality events since 2007, supporting this first description of V. tubiashii in France. Moreover, the virulence of isolates and the toxicity of their extracellular products (ECPs) were confirmed on C. gigas larvae and juveniles by experimental infections. Using in vitro assays, French V. tubiashii ECPs revealed their ability to alter some hemocytes immune defense probably through the degradation of matrix structural proteins. Finally, proteomic and transcriptomic analyses revealed the conjunction of multiples virulence factors including metalloproteases in the virulence of the French V. tubiashii strains.

Tout d’abord considérés comme simples composants d’une barrière imperméable, il a été démontré que les lipides membranaires auraient en fait un rôle biologique bien plus important, pouvant modifier l’environnement des enzymes membranaires et moduler l’activité de ces dernières. Dans la thèse présentée ici, ces relations ont été étudiées dans les mitochondries de l’huître creuse Crassostrea gigas. Les bivalves subissent d’importants changements environnementaux et l’adaptation à ces changements peut passer par un remodelage des membranes, ce qui fait de ces animaux des modèles intéressants pour les études des relations entre la structure des membranes et les activités d’enzymes associées. Des huîtres ont été nourries en écloserie avec deux régimes d’algues monospécifiques, T-Iso et Chaetoceros gracilis, et un mélange équilibré de ces deux algues. Malgré d’importantes modifications de composition en acides gras induites par les différents régimes alimentaires, une grande stabilité des processus membranaires mitochondriaux a été observée. D’un autre côté, la comparaison entre des huîtres élevées en écloserie et des huîtres élevées dans leur milieu naturel a révélé d’importantes modifications de capacités mitochondriales, qui pourraient être liées à une modulation des classes de phospholipides et de leur insaturation. Ces différences ne peuvent pas s’expliquer par une influence des cycles tidaux dans la mesure où, malgré un changement de production d’ATP, l’activité des mitochondries a été montrée comme étant similaire chez les huîtres collectées en émersion et en immersion. L’homéostasie mitochondriale observée dans cette étude pourrait être un moyen pour les huîtres de faire face aux variations biotiques (disponibilité en nourriture) et abiotiques (disponibilité en oxygène) de l’environnement naturel de C. gigas, et de maintenir leurs fonctions physiologiques malgré ces variations. / First considered as simple components of an impermeable barrier, it has been shown that membrane lipids would have a more important biological role. These lipids could modify the environment of membrane enzymes and modulate their activity. In this thesis, these relationships have been studied in mitochondria of the oyster Crassostrea gigas. Bivalves undergo major environmental changes and adaptation to these changes may require a membrane remodelling, which makes these animals interesting models to study the relationship between membrane structure and membrane processes. In this study oysters were fed in hatchery with two monospecific algal diets, T-Iso and Chaetoceros gracilis, and an equilibrated mix of both algae. Despite significant changes in fatty acid composition induced by these diets, mitochondrial capacities remained stable. On the other hand, the comparison between hatchery-reared oysters and oysters reared in their natural environment revealed significant changes in mitochondrial capacity, which could be related to modulation of phospholipid class composition and unsaturation. These differences can not be explained by the influence of tidal cycles. Indeed, despite a change in ATP production, mitochondrial activity was shown to be similar in oysters collected during emersion and immersion.Mitochondrial homeostasis observed in this study could be a way for oysters to cope with biotic (food availability) and abiotic (oxygen availability) variations in the natural environment of C. gigas, and to maintain their physiological functions despite these variations.

Predation may be a key component of the unsuccessful restoration of the Eastern Oyster (Crassostrea virginica), a former keystone species in Chesapeake Bay. Here, I examine the polyclad flatworm Stylochus ellipticus and its potential role as an important predator of C. virginica. Using small-fragment size C. virginica specific DNA primers, oyster DNA was successfully detected in whole organisms homogenates of wild-caught S. ellipticus individuals. Of the 1,575 individuals tested, 68.1% tested positive, thus predation occurred. Predation did not appear to be affected by salinity or temperature; however, season did appear to have an effect on both predation and S. ellipticus abundance (p-value: <0.05). The findings also imply that S. ellipticus are highly mobile, entering the water column to reach hard substrate at various depths, whereas previous studies suggest otherwise. These findings are useful in the planning and management of oyster cultivation and restoration. Furthermore, this study outlines a method of diet study that may be more sensitive than traditional DNA-based techniques.

A simulation algorithm based on biological references points proposed by Powell and Klink (2007) is implemented for predicting the total allowable catch of eastern oysters (Crassostrea virginica) from Louisiana’s coast. The model accepts initial per-square-meter shell mass and oyster size distributions as input. Fishing effort is provided as fractions removed of each resource for each month of the season. The model outputs the expected remaining shell mass and harvests of sack and seed oysters after discrete fishing months. Oyster mortality credits the shell budget, while fishing fractions debit oyster and shell resources. Surviving oysters grow larger along a time-dependent von Bertalanffy growth curve. Fishing fractions are chosen heuristically with the goal of minimizing shell loss. Input data is collected by the Louisiana Department of Wildlife and Fisheries in their annual stock assessment. The model is available as a public web resource at www.oystersentinel.org.

<p>Curiosity is a powerful tool, and combined with the ability to observe the natural world, grants humankind an unique opportunity, the opportunity to wonder why. Why do things exist?, why do they do the things they do?, why is this even possible?</p> <p>Research in our lab is focused on the basic understanding and potential application of biological materials, in particular, biological adhesives produced by marine organisms such as oysters. Oysters produce a cement-like material that is able to withstand the dynamic conditions found in coastal environments. The focus of this dissertation is to lay the basis of the characterization of new biological materials by observing and analyzing its physical properties, to measure the performance of the material in natural conditions and finally to identify the basic components that give the material the properties that we observe. The end goal of this project is to understand the properties of this material so we are able to develop a synthetic system that is able to imitate, as close as possible, what we find in nature. These results, and more importantly, the new questions that emerge from this research, provide a first look at the adhesive system of oysters leading the way to new discoveries in the future.</p>

Mollusc shells are unique adaptations that serve to protect the organisms that make them, and are a defining feature of the phylum. However the molecular underpinnings of shell forming processes are still largely unexplored. To further understand mollusc shell formation, I studied three bivalve species in this project: the blue mussel Mytilus edulis, the Pacific oyster Crassostrea gigas, and the king scallop Pecten maximus. While previous analyses of the shell proteomes showed species specificity, transcriptomes of the mantle tissues revealed more commonalities. To reconcile these differences, I studied differential gene expression in shell damage-repair experiments and during the formation of the first larval shell, to produce a comprehensive overview of shell formation processes. Expression data showed large biological variability between individuals, requiring matched-pair experimental designs to detect differential gene expression during shell repair. Loci differentially expressed during shell repair and in the larvae encoded shell matrix proteins, transmembrane transporters, and novel transcripts. A large number of shell matrix proteins, encoded in differentially expressed loci, were common in all three species during shell formation, indicating that shell forming proteins between different species may be more common than previously thought. Differential expression of transmembrane transporters during shell repair indicated that the animals may be regulating bicarbonate ions during shell formation. Finally, the experiments revealed novel transcripts, with unknown annotations to public datasets, that may putatively be involved in shell formation.

Submitted by (edna.saturno@ufrpe.br) on 2017-02-14T14:32:41Z No. of bitstreams: 1 Izabel Cristina da Silva Almeida.pdf: 3784157 bytes, checksum: 9dd220764f324bfa5ddd8bbf00714adf (MD5) / Made available in DSpace on 2017-02-14T14:32:41Z (GMT). No. of bitstreams: 1 Izabel Cristina da Silva Almeida.pdf: 3784157 bytes, checksum: 9dd220764f324bfa5ddd8bbf00714adf (MD5) Previous issue date: 2006-10-09 / This work aimed to delimit collective aquaculture areas to the “native oyster” Crassostrea rhizophorae farming, as part of the Mariculture Development Local Plan in the Pernambuco’s north coast. Indicators were identified, selected and hierarquized to enable the elaboration of a conceptual model subsidizing the selection process of potential oyster farming areas. Depth measurements were realized in transversal sections of the estuarine channels using ecobathimeter linked to a GPS (Global Positioning System) and a Palmtop. In the of aquaculture area demarcation was used eight environmental indicators, seven socioeconomic and five of production/logistics to subsidize the selection process of the oyster farming potential areas. Three preferential areas were delimited, in which six collective aquaculture areas were demarcated, being three in the municipality of Goiana (estuary of the river Itapessoca), two in Igarassu (estuary of the river Timbó) and one in Itapissuma (Santa Cruz channel), where 263 individual aquaculture areas could be inserted, totalizing 77,2 ha of collective aquaculture areas. / O presente trabalho visa a delimitação parques aqüícolas para o cultivo da “ostra nativa” Crassostrea rhizophorae os quais integram o Plano Local de Desenvolvimento da Maricultura no litoral norte de Pernambuco. Foram identificados, selecionados e hierarquizados descritores que possibilitaram a elaboração de um modelo conceitual subsidiando o processo de seleção de áreas potenciais para fins de ostreicultura. Realizou-se a batimetria nas secções transversais dos canais estuarinos selecionados com o auxílio de um ecobatímetro acoplado a GPS (Global Positioning System) e Palmtop. Posteriormente, com um GPS geodésico foi realizada a demarcação dos parques aqüícolas. Identificaram-se oito descritores ambientais, sete sócio-econômicos e cinco de produção/logística capazes de subsidiar no processo de seleção das áreas potenciais ao cultivo de ostra. Foram delimitadas três faixas de preferência, nas quais demarcaram-se seis parques aqüícolas, sendo três pertencentes ao município de Goiana (estuário do rio Itapessoca), dois de Igarassu (estuário do rio Timbó) e um de Itapissuma (canal de Santa Cruz.), onde poderão ser inseridas 263 áreas aqüícolas, totalizando 77,2 ha de parques aqüícolas.