Salinization has been identified as an increasing threat to freshwater mussel diversity in recent years. Native mussels have been observed to display reduced salinity tolerance in comparison to some invasive bivalve species, but methods by which organismal tolerance is achieved are not well understood. This study was designed to compare the behavioral and physiological responses of the native Lampsilis ovata to that of the invasive Corbicula fluminea. Lampsilis were found to exhibit strong behavioral avoidance to salinity exposure, whereas Corbicula displayed very weak avoidance to comparable salinity concentrations followed by indications of osmotic conformation through physiological mechanisms. Prolonged valve closure in Lampsilis could translate to adverse consequences related to feeding, waste removal, and energetics. Alternatively, while physiological osmotic conformation in Corbicula is associated with increased energetic costs, it allows continued respiration and feeding. These differences could convey a competitive advantage with the increasing prevalence and severity of freshwater salinization events.

The Powell River is located in southwestern Virginia and northeastern Tennessee, USA and supports a diverse freshwater mussel assemblage of 29 extant species. Throughout the river major ion and trace element concentrations have increased over the last several decades due to extensive surface coal-mining in the headwaters in Virginia. As watershed area affected by mining has increased, mussel populations have declined, especially in Virginia where populations have been severely reduced or extirpated. The upper watershed now has been extensively mined for coal, causing widespread effects on water and sediment quality. To investigate how mining may be affecting mussel populations, I first conducted a laboratory bio-assay to assess the effects of elevated major ions and the trace element nickel (Ni) on growth and survival of juvenile mussels, including one common species (Villosa iris) and one endangered species (Epioblasma capsaeformis). No significant differences in overall survival between treatments and control were observed for either species over a 70 day test period. Total growth was not significantly different between treatments and control for either species. However, overall growth varied significantly (p=0.009) between species, with V. iris (2.49 mm) exhibiting greater growth compared to E. capsaeformis (1.97 mm). Results suggest that major ion chronic toxicity alone or in combination with Ni at or below my test concentration is not a likely source of toxicity to juvenile mussels in the Powell River. Secondly, I conducted a field study in the Powell River using two cohorts of juveniles of Villosa iris to assess the effects of trace elements and PAH contamination related to mining on mussel survival and growth. Specific conductance was elevated throughout the Powell River, where site means ranged from 450 to 900 µS/cm. While mortality was high at all eight sites it was not significantly different among these sites (p>0.28); however, growth of juvenile mussels was significantly higher (p<0.001) in the lower river in Tennessee. Regression analysis showed significant relationships (p<0.001) of river kilometer with temperature, specific conductance, and aqueous major ion concentrations. A principal component analysis (PC) was conducted on all trace element data. Growth of Cohort 1 on Day 106 was best explained by the PC dominated by aqueous major ion concentrations (p<0.0001, R2= 0.65) and growth of Cohort 2 on Day 106 was best explained by specific conductance (p<0.0001, R2= 0.68). Growth of Cohort 2 at Day 423 was best explained by tissue trace element concentration PC1 and PC2 (p<0.0001, R2= 0.73). This study suggests major ions and select trace elements (Ba, Ni, Fe, Se, and Sr) in the Powell River are negatively affecting the growth of freshwater mussels and that the source of these contaminants is primarily from mining in the headwaters. / Master of Science / The Powell River is located in southwestern Virginia and northeastern Tennessee, USA and supports a diverse freshwater mussel assemblage of 29 extant species. Throughout the river major ion and trace element concentrations have increased over the last several decades. As watershed area affected by coal mining has increased mussel populations have declined, especially in Virginia where populations have been severely reduced or extirpated. The upper Powell River watershed has been extensively mined for coal, causing widespread decline in the river’s water and sediment quality. My study consisted of a laboratory and field exposure to assess the toxicity of the mining related contaminants, such as major ions, trace elements, and polycyclic aromatic hydrocarbons (PAHs) to freshwater mussels. Further, the study investigated the concentrations of these contaminants in the river and their effects on the survival and growth of exposed juvenile mussels. In my laboratory study, mussels of a common species (Villosa iris) and an endangered species (Epioblasma capsaeformis) showed no effect when exposed to a suite of major ions and the trace element Ni similar to levels measured in the Powell River. When juvenile Villosa iris were exposed in the Powell River at eight sites in Virginia and Tennessee, high rates of mortality were observed at all eight sites and growth of juveniles showed a significant spatial trend, with higher growth observed downstream in Tennessee. Water quality analysis revealed increased concentrations of major ions at all sites but concentrations of trace elements were generally below EPA water quality criteria. Further, many of the major ions and trace elements trended spatially with higher concentrations measured in the headwaters in Virginia and lower concentrations observed downstream in Tennessee. Statistical analysis revealed that major ions and trace elements (Ba, Ni, Fe, Se, and Sr) may have negatively affected growth of exposed mussels. This study revealed that laboratory conditions may not adequately be representing river conditions and that in the river major ions and trace elements likely are negatively effecting growth and survival of freshwater mussels. This study revealed that conditions in the Powell River likely are not suitable for mussel reintroduction and that mining is the main source of the contaminants in the river.

Scour around important foundation elements for bridges and other coastal infrastructure is the leading cause of failure and instability of those structures. Traditional scour mitigation methods, such as the placement of riprap, the use of collars or slots, embedding foundations deeper, or a combination thereof can be costly, require long-term maintenance, and can potentially have detrimental environmental effects downstream. These difficulties with traditional methods are potentially alleviated with the implementation of self-sustaining bivalve (e.g., mussel, oyster, scallop) farms that could act as mats of interconnected living barriers, protecting the seabed from scour. The mats would help to attract larval settlement by making the substrate a more suitable habitat, contributing to the sustainability of the bivalve farms. Colonies of bivalves are already being used as living shorelines for retreatment mitigation, embankment stabilization, and supporting habitat for other marine life. These applications are accomplished, in part, by bivalves' strong attachment capabilities from the bioadhesives they secrete that act as a strong underwater glue, adhering their shells to granular substrate. Some species of mussels have been shown to withstand water flow velocities greater than 6 m/s without detaching. For reference, riprap with a median grain size of about 655 mm has been shown to require a flow velocity of at least 1.7 m/s for incipient motion of the boulder-sized riprap. In addition to the contiguous living bivalve mat offering scour protection, the whole or fragmented shells (i.e., shell hash) that are left behind from dead bivalves are hypothesized to reduce erosion potential. Shell hash-laden sediments should be able to better withstand shearing, thereby increasing the critical shear stress required to erode material, compared to sediment without shell hash. Habitat suitability for bivalve colonies is also an important consideration to evaluate what surface enhancements may be needed for a site to be selected for implementation of bivalve scour mats. Bed surfaces that consist of unconsolidated fine-grained sediment are unlikely to be able to support bivalve species as the organisms could sink into the sediment, not allowing solid anchoring points. In contrast, harder substrates typically found in granular sediments offer much more suitable habitats. Along with testing the influence of shell hash and bioadhesive on sediment behavior, this thesis aims to establish a methodology to evaluate whether a section of seafloor can support bivalves or enhancement materials (e.g., shell, shale, or slag fragments) without them sinking, thereby depriving them of oxygen. Together, the examining of geotechnical aspects of bivalve habitat enhancement through seabed soil alteration and the influence of shell hash and bioadhesives on sediment shear behavior are part of a novel multidisciplinary approach toward this proposed bioengineered scour solution. Consequently, the research objectives explored in this thesis are as follows: (1) characterize morphology of existing bivalve colonies through acoustic and direct field measurements; (2) evaluate the spatial variation of the sediment shear strength in terms of proximity to bivalve colonies; (3) expand the domain of confining pressures and shell hash weight fractions used in sediment strength testing; (4) quantify the changes in shear strength and erodibility from laboratory tests on sampled material with and without the presence of bioadhesives, as well as shell fragments mixed in with the sediment; and, (5) develop a methodology ranking system for the suitability of a surficial sediments to support seeding material to improve benthic life habitat substrates. Three exploratory field surveys were conducted where colonies of oysters and other benthic life were present: in the Piankatank River in Virginia, in the Northwest Arm of the Sydney Harbour in Nova Scotia, Canada, and at the Rachel Carson Reserve in North Carolina. Field sampling techniques included Ponar grab samples, hand-dug samples, X-ray rectangular prism cores, and cylindrical push cores, which were all pivotal to understanding sediment composition, size and shape of particle distributions, as well as in-situ depth profiles of shells. Remote sensing and intrusive instrumentation included a rotary scanning sonar, acoustic Doppler current profilers, CTD (Conductivity, Temperature, Depth) probes, underwater cameras, a portable free-fall penetrometer, and in-situ jet erosion testing which helped to characterize the morphology of the bivalve colonies and the spatial variability of sediment strength. Subsequent laboratory experiments included grain size distribution analyses, vacuum triaxial tests to measure changes in shear strength with and without shell hash, and miniature vane and pocket erodometer tests on bioadhesive-treated sediments. The results showed: (1) a significant increase in the standard deviation of the backscatter intensity where the oyster reef was located; (2) the in-situ sediment shear strength increased slightly closer to the oyster reef at the Piankatank River site; (3) samples with a higher oyster density exhibited less uniform particle size distributions; (4) the presence of less than approximately 4% (by weight) of shell fragments increased the secant friction angle by approximately 6° relative to samples with no shell fragments; and, (5) the harbor bed of the Northwest Arm of the Sydney Harbour is a suitable stiffness for enhancement with shell hash over about 23% of its area. Preliminary testing showed a subtle increase in the torsional shear resistance and a decrease in erodibility for bioadhesive-treated samples; however, further testing is needed for confidence to be achieved in the results due to bioadhesive supply issues. / Master of Science / Oysters and mussels are aquatic mollusks (i.e., bivalves) that are known to be able to withstand strong storm flows without detaching from rocks and other hard surfaces. Knowing this and the increasing need for environmental- and ecological-friendly solutions in engineering and construction further accelerated by climate change and sea level rise are the motivations for studying whether bivalves can be used in this capacity. Traditional methods to protect against bridge failures caused from individual piers that become unstable from sediment eroding away from their bases can be costly, require long-term maintenance efforts, and can potentially have detrimental environmental impacts. As an alternative to or supplement to traditional methods, bivalves could be laid down in mats near the base of piers to act as a protective interconnected layer, diverting strong water flows away from the otherwise exposed sediments susceptible to erosion while strengthening the seabed. Much is known and has been investigated on the biology of bivalves but understanding how these organisms influence the sediments near them has not been studied extensively from a geotechnical engineering perspective. Specifically, within geotechnical engineering, this study is focused primarily on the influence of oyster shell fractures, naturally found in the vicinity of bivalve colonies, and the organic glue that bivalves use to attach themselves to rocks on the engineering behavior of nearby sediments. Secondary to that main objective is to establish a methodology to evaluate whether a section of seafloor can support bivalves without them sinking, thereby suffocating them. In summary, this thesis investigates methods to evaluate whether the seafloor is suitable for supporting bivalves and if their presence changes the way sediments behave after various forces are applied. To accomplish these research goals, three exploratory field surveys were conducted for this thesis: in the Piankatank River in Virginia, in the Northwest Arm of the Sydney Harbour in Nova Scotia, Canada, and at the Rachel Carson Reserve in North Carolina where bivalves were present. Through field sediment sampling, underwater sonar imagery, penetrating probes, and subsequent geotechnical laboratory testing, shell-sediment interactions were characterized. The results showed: (1) an oyster reef in the Piankatank River could be observed in great detail with sonar imagery; (2) sediment strength increased slightly the closer to the oyster reef; samples with more oyster shells in them exhibited (3) a wider range of particle sizes and (4) an increase in sediment strength; and (5) less than a quarter of the harbor bed of the Northwest Arm of the Sydney Harbour is suitable for armoring the seafloor with pieces of shell, shale, and slag to support bivalve growth. Initial tests with the organic underwater glue from bivalves showed promising results with respect to improvements in sediment strength and decreased erodibility, however, further testing is needed as supply of the organic glue was limited.

O consumo de moluscos bivalves pode representar sérios riscos à saúde pública, pois refletem diretamente as condições do meio ambiente. Desta forma considera-se de extrema importância o consumo de mexilhões livres de contaminação. Esta pesquisa objetivou estudar a qualidade microbiológica das águas e mexilhões de três pontos de cultivo do município de Ubatuba, SP, a saber: Engenho da Almada, Barra Seca e Costão do Cedro em um período compreendido entre novembro de 2002 e março de 2003, totalizando 5 coletas mensais. Analisou-se na água: Bacillus cereus, Clostrídios Sulfito Redutores, Aeróbios Mesófilos, Staphylococcus aureus, Coliformes totais e fecais, Enterococos e Salmonella. Nos mexilhões foram analisados os mesmos microrganismos citados para água mais o Clostridium perfringens. Os resultados encontrados tanto para as análises de água como dos mexilhões foram satisfatórios, condizentes com a legislação brasileira em vigor, salvo a coleta do mês de março, do cultivo da Barra Seca, onde a média dos valores encontrados para coliformes fecais na água (5,7x101 NMP/100mL) foi superior ao recomendado pela legislação sendo detectado também neste mesmo cultivo e mês, presença de Salmonella em 25 g nas amostras de mexilhões. Mesmo que as contagens de S. aureus e B. cereus na carne estejam de acordo com a legislação em vigor, cuidados devem ser tomados quanto ao armazenamento e a forma de consumo. Averiguou-se a intensidade de interferências sazonais na contagem microbiana na água e constatou-se que a tábua de marés e o índice de insolação diária tiveram uma correlação negativa baixa, ao contrário do índice pluviométrico que apresentou correlação positiva alta. / The consumption of bivalve mollusks can represent serious risks to the public health, because they reflect the conditions of the environment directly. This way it is considered of extreme importance the consumption of mussels without contamination. This work aims of studing the water and mussels microbiology quality from three different seafood farms in Ubatuba, SP, to know: Engenho da Almada, Barra Seca and Costão do Cedro from November 2002 to March 2003, totaling five monthly. It was analyzed in the water: Bacillus cereus, Total Clostridia, Aerobic Mesophilic, Staphylococcus aureus, total and fecal coliforms, Enterococci and Salmonella. In the mussels the same microorganisms were analyzed mentioned for water more Clostridium perfringens. The results found in the water and in the mussels were satisfactory, suitable with the Brazilian legislation, except for the sample at Barra Seca’s beach, in March. The average of the values found at that place for fecal coliformes in the water was higher (5,7x101 MPN/100mL) than the recommended by the legislation. Even in this collection, it was also detected Salmonella in 25 g of mussels. Even if the counts of S. aureus and B. cereus in the mussesls are in agreement with the legislation in vigor cares they should be taken with relationship to the storage and the consumption form. The intensity of seasonal interferences was discovered in the microbial count in the water, in which was verified that the board of tides and the index of daily heatstroke had a low negative correlation unlike the index pluviometric it presented high positive correlation

La palourde grise européenne, Ruditapes decussatus est un coquillage d’importance socio-économique en Europe du Sud. Sa production est basée sur le recrutement naturel, qui est sujet à de fortes fluctuations annuelles. Au Portugal, les principales zones de production de cette espèce sont les lagunes de Ria de Aveiro et Ria Formosa. Ces populations présentent des réponses différentes à l'induction de la ponte, résultat d’intérêt dans un contexte d'amélioration de la production aquacole. L'objectif de cette thèse était d'améliorer les connaissances sur la reproduction de R. decussatus en utilisant des approches génomiques et cellulaires avec pour principales applications : le conditionnement de géniteurs et la qualité des gamètes.Le cycle de reproduction de ces populations a été caractérisé par histologie pour le développement gonadique, l’aire gonadique et le diamètre de l’ovocyte. À l'exception de la dynamique de la gamétogénèse, aucune différence significative n’a été identifiée entre populations. Grâce à un effort de séquençage (Illumina) de banque d’ADNc de différents tissus/stades pour enrichir en transcrits liés à la reproduction, une puce à ADN (oligoarray) représentant 51 678 contigs a été produite et utilisée afin de caractériser les bases transcriptomiques de la reproduction de R. decussatus. Des gènes différentiellement exprimés et la voie “N-Glycan biosynthesis”, impliquées dans l'interaction spermatozoïde – ovocyte, ont été soulignés, ce qui suggère que la reconnaissance entre gamètes puisse expliquer en partie les différences de succès d'induction de ponte entre ces populations. De plus, le transcriptome d’ovocytes collectés chez 15 femelles a été analysé par puce à ADN avec pour objectif d'identifier des potentiels marqueurs de la qualité des ovocytes. Des gènes codant pour des protéines chaperonnes, dont certains caractérisés comme des ARNm maternels essentiels pour le développement précoce, sont apparus différentiellement exprimés entre ovocytes de bonne et mauvaise qualité établie sur le taux de larves D obtenu. La présente étude fournit de nouvelles informations génomiques précieuses pour la compréhension de la reproduction de cette espèce et liste des gènes candidats codant la protéine disulforide isomerase (PDI), des calmodulines et la caspase 8 comme points de départ possibles pour des études fonctionnelles. Leur implication dans les phases importantes de la reproduction comme l’interaction spermatozoïde-ovocyte, la protection de l'ovocyte, la régulation du calcium et l'apoptose ont font des marqueurs potentiels de la qualité ovocytaire de cette espèce. / The European clam, Ruditapes decussatus is considered a high value seafood product in Southern Europe. Its production is almost based on natural recruitment, which is subject to annual fluctuations. In Portugal, two of the main production areas of this species are Ria de Aveiro and Ria Formosa Lagoons. These populations were characterized by different responses to spawning induction, which is of great interest in a context of improvement of aquaculture. The purpose of this thesis was to improve the cellular and genomic knowledge on the reproduction of R. decussatus with major applications: broodstock conditioning and gamete quality.The reproductive cycle of the two populations was histologically characterized by comparing the gonadal development, gonadal area and oocyte diameter. With the exception of the dynamics of gonadal development, which may originate in the environment, no differences concerning gametogenesis were found. cDNA libraries of oocytes, larvae and gonads were sequenced on Illumina platform, to enrich resources in reproductive Expressed Sequence Tags, and a custom oligoarray representing 51,678 assembled contigs was then designed. To characterize the transcriptomic bases of reproduction, microarray analyses were performed in four gonadal maturation stages of the two populations. Differentially expressed probes and the “N-Glycan biosynthesis” pathway, potentially involved in sperm-egg interaction, were identified, suggesting that gamete recognition can explain part of the differences in terms of spawning induction success between populations.Moreover, microarray analyses were also performed in oocytes, with the objective of identifying potential markers of oocyte quality in this species. Genes coding for chaperone proteins demonstrated to be important markers of oocyte quality, with some of them being maternal mRNAs essential for early development.The present study provides new highly valuable genomic information for the understanding of reproduction of R. decussatus and emphasizes some candidate genes like protein disulforide isomerase (PDI), Calmodulin family and caspase 8 as possible starting points for further functional studies.

FundaÃÃo de Amparo à Pesquisa do Estado do Cearà / Os moluscos bivalves sÃo alimentos de grande importÃncia nutricional sendo ususalmente consumidos nas regiÃes costeiras. Quando ingeridos in natura (crus) ou levemente cozidos, podem oferecer risco à saÃde pÃblica por serem filtradores e acumuladores de resÃduos quÃmicos e biolÃgicos, principalmente se a qualidade sanitÃria da Ãgua onde forem capturados estiverem comprometidas. A presente pesquisa tem como objetivo estudar a espÃcie Tagellus plebeius ("unha de velho") no estuÃrio do rio cearà em Fortaleza - Ce, considerando aspectos de seu ciclo reprodutivo, da sua biologia populacional e de suas condiÃÃes microbiolÃgicas. Para a anÃlise do ciclo reprodutivo os exemplares de T. plebeius foram coletados mensalmente no estuÃrio do rio cearà em Fortaleza - Ce (03, 42, 09.8 S; 35, 35, 49.0 W) no perÃodo de abril de 2006 a junho de 2007 em marÃs diurnas de sizÃgia. A cada mÃs as gÃnadas de 30 indivÃduos fram submetidas a exame histolÃgico. Para as amostragens microbiolÃgicas, as anÃlises foram feitas em dois meses da estaÃÃo seca )novembro e dezembro de 2006) e em dois meses da estaÃÃo chuvosa (marÃo e abril de 2007). Foram isoladas 22 cepas suspeitas de Salmonella spp., das quais 11 cepas foram confirmadas atravÃs do teste de sorologia com o antisoro polivalente O:H, sendo identificados 3 sorovares (S. Bredeney, S. London e S. Muenchen) e 1 (uma) cepa foi classificada atà subespÃcie: S. enterica subesp. enterica. Dentre os fatores ambientais observados neste estudo, a precipitaÃÃo pluviomÃtrica e a salinidade foram os que apresentaram as maiores amplitutes de variaÃÃo. O aumento da contaminaÃÃo por coliformes termotelorantes (45ÂC) na estaÃÃo chuvosa pode estar relacionado ao aporte de Ãgua doce no rio, como uma consequente diminuiÃÃo da salinidade associada a uma maior contaminaÃÃo bacteriologica. A correlaÃÃo significativa observada entre a salinidade e as fases "MaturaÃÃo/EliminaÃÃo Inicial" (M/E) e "Atresia Acular" (AC) mostra tambÃm a influÃncia desta variÃvel ambiental no desenvolvimento gonadal da espÃcie, prolongando ou reduzindo as fases do seu ciclo reprodutivo. / Bivalve molluscs are of great nutritional food ususalmente being consumed in the coastal regions. When ingested in nature (raw) or lightly cooked, can provide public health risk because filtrating and accumulators of chemical and biological waste, especially if the sanitary quality of water they are caught compromised. This research aims to study the species Tagellus plebeius ( "nail the old") on the estuary of the Rio Cearà in Fortaleza - Ce, considering aspects of their reproductive cycle, its population biology and their microbiological conditions. For the analysis of the reproductive cycle the specimens of T. plebeius were collected monthly in the estuary of the Rio Cearà in Fortaleza - Ce (03, 42, 09.8 S, 35, 35, 49.0 W) from April 2006 to June 2007 in the diurnal tides sizÃgia. Each month the gonads of 30 individuals subjected to histological examination FRAM. For microbiological samples, the tests were made in two months of dry season) in November and December 2006) and in two months of the rainy season (March and April 2007). We isolated 22 strains of suspected Salmonella spp., Of which 11 strains were confirmed by serology test with polyvalent antiserum O: H, and identified 3 serovars (S. Bredeney, S. London and S. Muenchen) and 1 (one ) strain was classified by subspecies: S. enterica subsp. enterica. Among the environmental factors observed in this study, rainfall and salinity were those who had the greatest amplitutes change. The increase of contamination by coliform termotelorantes (45 C) in the rainy season may be related to the intake of fresh water in the river, and a consequent decrease in salinity with increased bacterial contamination. The significant correlation observed between salinity and stages "Maturation / Initial Elimination" (M / E) and "incite atresia (CA) also shows the influence of the environmental variable in the gonadal development of the species, extending or reducing the phases of its cycle reproductive.

O consumo de moluscos bivalves pode representar sérios riscos à saúde pública, pois refletem diretamente as condições do meio ambiente. Desta forma considera-se de extrema importância o consumo de mexilhões livres de contaminação. Esta pesquisa objetivou estudar a qualidade microbiológica das águas e mexilhões de três pontos de cultivo do município de Ubatuba, SP, a saber: Engenho da Almada, Barra Seca e Costão do Cedro em um período compreendido entre novembro de 2002 e março de 2003, totalizando 5 coletas mensais. Analisou-se na água: Bacillus cereus, Clostrídios Sulfito Redutores, Aeróbios Mesófilos, Staphylococcus aureus, Coliformes totais e fecais, Enterococos e Salmonella. Nos mexilhões foram analisados os mesmos microrganismos citados para água mais o Clostridium perfringens. Os resultados encontrados tanto para as análises de água como dos mexilhões foram satisfatórios, condizentes com a legislação brasileira em vigor, salvo a coleta do mês de março, do cultivo da Barra Seca, onde a média dos valores encontrados para coliformes fecais na água (5,7x101 NMP/100mL) foi superior ao recomendado pela legislação sendo detectado também neste mesmo cultivo e mês, presença de Salmonella em 25 g nas amostras de mexilhões. Mesmo que as contagens de S. aureus e B. cereus na carne estejam de acordo com a legislação em vigor, cuidados devem ser tomados quanto ao armazenamento e a forma de consumo. Averiguou-se a intensidade de interferências sazonais na contagem microbiana na água e constatou-se que a tábua de marés e o índice de insolação diária tiveram uma correlação negativa baixa, ao contrário do índice pluviométrico que apresentou correlação positiva alta. / The consumption of bivalve mollusks can represent serious risks to the public health, because they reflect the conditions of the environment directly. This way it is considered of extreme importance the consumption of mussels without contamination. This work aims of studing the water and mussels microbiology quality from three different seafood farms in Ubatuba, SP, to know: Engenho da Almada, Barra Seca and Costão do Cedro from November 2002 to March 2003, totaling five monthly. It was analyzed in the water: Bacillus cereus, Total Clostridia, Aerobic Mesophilic, Staphylococcus aureus, total and fecal coliforms, Enterococci and Salmonella. In the mussels the same microorganisms were analyzed mentioned for water more Clostridium perfringens. The results found in the water and in the mussels were satisfactory, suitable with the Brazilian legislation, except for the sample at Barra Seca’s beach, in March. The average of the values found at that place for fecal coliformes in the water was higher (5,7x101 MPN/100mL) than the recommended by the legislation. Even in this collection, it was also detected Salmonella in 25 g of mussels. Even if the counts of S. aureus and B. cereus in the mussesls are in agreement with the legislation in vigor cares they should be taken with relationship to the storage and the consumption form. The intensity of seasonal interferences was discovered in the microbial count in the water, in which was verified that the board of tides and the index of daily heatstroke had a low negative correlation unlike the index pluviometric it presented high positive correlation

Le développement des approches robustes et non paramétriques pour l’analyse et le traitement statistique de gros volumes de données présentant une forte variabilité,comme dans les domaines de l’environnement et de la génétique, est fondamental.Nous modélisons ici des données complexes de biologie appliquées à l’étude du comportement de bivalves et à l’analyse de liaison génétique. L’application des mathématiques à l’analyse du comportement de mollusques bivalves nous a permis d’aller vers une quantification et une traduction mathématique de comportements d’animaux in-situ, en milieu proche ou lointain. Nous avons proposé un modèle de régression non paramétrique et comparé 3 estimateurs non paramétriques, récursifs ou non,de la fonction de régression pour optimiser le meilleur estimateur. Nous avons ensuite caractérisé des rythmes biologiques, formalisé l’évolution d’états d’ouvertures,proposé des méthodes de discrimination de comportements, utilisé la méthode des shot-noises pour caractériser différents états d’ouverture-fermetures transitoires et développé une méthode originale de mesure de croissance en ligne.En génétique, nous avons abordé un cadre plus général de statistiques robustes pour l’analyse de liaison génétique. Nous avons développé des estimateurs robustes aux hypothèses de normalités et à la présence de valeurs aberrantes, nous avons aussi utilisé une approche statistique, où nous avons abordé la dépendance entre variables aléatoires via la théorie des copules. Nos principaux résultats ont montré l’intérêt pratique de ces estimateurs sur des données réelles de QTL et eQTL. / The development of robust and nonparametric approaches for the analysis and statistical treatment of high-dimensional data sets exhibiting high variability, as seen in the environmental and genetic fields, is instrumental. Here, we model complex biological data with application to the analysis of bivalves’ behavior and to linkage analysis. The application of mathematics to the analysis of mollusk bivalves’behavior gave us the possibility to quantify and translate mathematically the animals’behavior in situ, in close or far field. We proposed a nonparametric regression model and compared three nonparametric estimators (recursive or not) of the regressionfunction to optimize the best estimator. We then characterized the biological rhythms, formalized the states of opening, proposed methods able to discriminate the behaviors, used shot-noise analysis to characterize various opening/closing transitory states and developed an original approach for measuring online growth.In genetics, we proposed a more general framework of robust statistics for linkage analysis. We developed estimators robust to distribution assumptions and the presence of outlier observations. We also used a statistical approach where the dependence between random variables is specified through copula theory. Our main results showed the practical interest of these estimators on real data for QTL and eQTL analysis.

Composante importante de l’écosystème marin benthique, les bivalves exploités sont surtout situés dans la zone littorale dont les caractéristiques spatiales et temporelles engendrent des fluctuations populationnelles naturelles et contribuent à de fortes variations de biomasse et de structure démographique s’ajoutant aux effets d’activités anthropiques. La compréhension des interactions entre l’espèce, son environnement et son exploitation est cruciale. Leur formalisation, y compris pour la gestion, passe par le développement de modèles mathématiques qui visent à décrire le fonctionnement du système, expliquer des phénomènes observés en termes de cause à effet ou prédire l’effets de nouvelles causes. Espèce introduite en France dans les années 1980, la palourde japonaise (Venerupis philippinarum) constitue une ressource économique importante pour des zones littorales. Pour le bassin d’Arcachon, les pêcheurs à pied professionnels capturent quelques 600 tonnes par an. Outre la réglementation européenne qui fixe une taille minimale de capture, des mesures de gestion complémentaires sont établies par les structures professionnelles locales de la pêche dans un cadre de cogestion impliquant ces structures, scientifiques et administration.Ce travail de thèse s’inscrit dans ce contexte en intégrant les traits d’histoire de vie de la population dans le modèle de simulation utilisé à des fins de gestion. A l’échelle locale, l’analyse de forme conventionnelle basée sur des mesures métriques et pondérales établit des relations d’allométrie entre des paires de descripteurs avec un changement significatif de morphologie à partir d’une longueur de 16-20 mm. La variabilité phénotypique intra-site s’articule en trois patrons morphologiques. Dans le bassin d’Arcachon, le caractère globuleux, décrit pour la première fois ici, est associé à de faibles densités et à de fortes proportions d’individus affectés par la maladie du muscle marron, maladie émergente sur le bassin. A l’échelle de la façade atlantique française, trois ratios morphométriques (indices d’élongation, de densité de la valve et de poids de la valve sur sa longueur) discriminent les populations des sites nord (Banc du Guer, golfe du Morbihan) de celles des sites sud (Bellevue, bassin d’Arcachon). Une corrélation significative entre ces ratios et les conditions trophiques approchées par la concentration en chlorophylle a ainsi qu’un lien entre l’indice de densité de la valve et le pourcentage de températures comprises entre 12 et 20°C sont démontrés. La complexité des facteurs intervenant sur la morphologie intra et inter-sites laisse supposer l’intervention d’autres facteurs comme la nature du substrat, ce qui est conforté par des premières analyses de contours. Les travaux ont confirmé l’importance de la température sur les variables d’état du stock notamment lors de la période de reproduction. Pour ces mêmes variables, un rôle majeur des ressources trophiques a aussi été démontré avec des réponses différant selon les stades. Une partie de ces résultats a contribué à des modifications dans le modèle de simulation. Elles ont surtout concerné l’intégration de l’effet des ressources trophiques sur le recrutement, la révision de la production de juvéniles et des taux de croissance par classe de taille, la précision de données de captures et l’ajout d’un effet prix sur les stratégies de pêche. En parallèle à la validation du modèle, l’analyse de sensibilité a mis en évidence la sensibilité du modèle aux paramètres environnementaux et aux variables relatives aux stades les plus jeunes. Dans un contexte de cogestion, l’outil a été utilisé pour réaliser des projections sur le devenir de la population selon différents scénarios de gestion. Les différences de tendances d’évolution de la biomasse en réponse à ces dispositifs d’action ont servi aux gestionnaires pour la définition des mesures de gestion actuellement en vigueur. Au final, le modèle renforce la démarche participative engagée. / Significant component of the marine benthic ecosystem, exploited bivalves are mainly located inside the coastal area, which temporal and spatial features generate natural population fluctuations and contribute to considerable biomass and demographic structure changes added to anthropogenic activities’ effects (fishing, pollution,…). Understanding of the relationships between the species, its environment and its exploitation is crucial and their formalization, including for management purposes, requires development of mathematical models that aim at describing the functioning of the system, to explain the observed phenomenon in terms of cause and effect or predict effects of new causes. Originating from venerid culture trials carried out in France in the 80s, Manila clam (Venerupis philippinarum) is an important economic resource for coastal areas. Inside the Arcachon Bay, professional fishermen catch about 600 tonnes annually. Whereas the minimum legal harvest size is set by European legislation, complementary management measures are established by regional and departmental professional organizations in the framework of a co-management approach involving professional, scientists and administration. This doctoral thesis is part of this objective of co-management by integrating life history traits of the population in a simulation model used for management purposes. At local scale, conventional shape analysis methods using metric weights and measures establish allometric relationships between pairs of descriptors with a significant morphological change detected from a length of ca. 16-20 mm. Intra-site phenotypic variability is structured in three morphological patterns. Occurrence of globular character inside the Arcachon Bay, described here for the first time, is associated to low densities and to high proportions of individuals affected by brown muscle disease, an emerging disease in the Bay. At the scale of the French Atlantic coast, three morphological ratios (elongation, valve density and weight related to length indices) discriminate populations from northern (Banc du Guer and Morbihan Gulf) and southern sites (Bellevue and Arcachon Bay). Significant relationships between those ratios and trophic conditions expressed by chlorophyll a concentrations, as well as a link between weight surface ratios and percentage of seawater temperature ranging from 12 to 20°C are demonstrated. Complexity of factors involved in intrasite and intersite morphology suggests intervention of other factors such as sediment characteristics, which is supported by a first outlines analysis. This work confirmed the importance of seawater temperature on stock state variables particularly during the reproduction period. For those same variables, a major role of trophic conditions has also been demonstrated with answers depending on development stages. Part of this result contributed to modifications within the simulation model dedicated to this population. The modifications mainly concerned integration of trophic resources effect on recruitment level, juveniles’ production and growth rates per length class revision, accuracy of catches by professional fishermen and addition of a price effect on the fishing strategies. In conjonction with the model validation, the sensitivity analysis undertaken highlighted the sensitivity of the model to environmental parameters and to variables related to the younger stages. In a co-management context, this tool was used to perform projections on the future of the population according to various management scenarios. The differences in the patterns of biomass evolution in response to those action schemes were used by the stakeholders to identify management measures currently in force. In the end the model reinforces the engaged participatory process.

Les structures des communautés procaryotes (diversité β) ont été caractérisées au sein de deux compartiments du benthos en milieu littoral: les sédiments et les bivalves fouisseurs.Dans les sédiments de surface, les communautés bactériennes et archéennes ont été ciblées par ARISA (Automated Ribosomal Intergenic Spacer Analysis) et T-RFLP (Terminal-Restriction Fragment Length Polymorphism) sur le gène codant pour l’ARN 16S respectivement. Sur 29 sites des zones intertidale et subtidale du Bassin d’Arcachon, les communautés procaryotes présentaient des patrons de distribution spatiale corrélés à ceux de la macrofaune benthique mais représentaient une faible diversité cumulée par habitat. L’extension à des écosystèmes proches (Vasière Ouest Gironde, Estuaire de la Gironde) a mis en évidence une forte proportion d’OTU (Operational Taxonomic Unit) rares et une diminution de la similarité entre les communautés avec l’éloignement géographique des écosystèmes. Chez les bivalves, les communautés bactériennes ont été caractérisées successivement à l’échelle de l’individu, de l’organe isolé et de l’espèce. Le suivi d’une cohorte de coques n’a pas montré d’influence de la présence du parasite Bucephalus minimus sur la structure de ces communautés à l’échelle de l’individu. En revanche, prises à l’échelle de l’organe en comparant la coque à la palourde, les communautés bactériennes associées aux bivalves se sont différenciées en fonction des organes (e.g branchies, tube digestif, reste des tissus), de l’habitat et/ou de l’espèce. / The structures of prokaryotic communities (β diversity) were characterized in sediments and burrowing bivalves.In the sediments, the bacterial and archaeal communities were analyzed by ARISA (Automated Ribosomal Intergenic Spacer Analysis) and 16S RNA gene T-RFLP (Terminal-Restriction Fragment Length Polymorphism) respectively. In 29 subtidal and intertidal sites of the Arcachon Bay, the spatial patterns of prokaryotic and benthic macrofaunal communities were correlated whereas prokaryotic community species exhibited a low cumulated diversity per habitat. Extending to neighboring ecosystems (West-Gironde mud patch, Gironde estuary) revealed the occurrence of a high proportion of rare OTU (Operational Taxonomic Unit) and a decrease of community similarities with geographic distance among ecosystems.For the bivalves, the whole individual, the organ-scale and the species-scale were successively considered. A cockle cohort monitoring indicated no influence of the parasite Bucephalus minimus occurrence on bacterial community structure at the individual-scale. Comparing cockle and clam at the organ level demonstrated that bivalve associated bacterial communities could differ among organs (e.g. gills, digestive gut, others tissues), among habitats and/or between species.