This thesis contributes to the development of dinoflagellate cysts as indicators of past environmental change in the Northeastern Pacific coastal ocean, and investigates past variations in sea-surface temperature, salinity and primary productivity encoded in dinoflagellate cyst sedimentary records from the Santa Barbara Basin (SBB, southern California) and Effingham Inlet (Vancouver Island, British Columbia) over the last millennium. The dinoflagellate cyst records extracted from the SBB and Effingham Inlet predominantly laminated sediments and analysed at sub-decadal resolutions, constitute some of the most detailed records of cyst-producing dinoflagellate populations in the world. A two year-long sediment trap study from the SBB documents the seasonality in dinoflagellate cyst production for the first time on the Pacific coast of the United States. The study shows that dinoflagellate cyst data can be used as indicators of changes in sea-surface temperature and primary productivity associated with seasonal upwelling in the SBB. In particular, several dinoflagellate cyst taxa such as Brigantedinium spp. and Lingulodinium machaerophorum are identified as indicators of “active upwelling” (typically occurring in spring and early summer) and “relaxed upwelling” conditions (fall and early winter) at the site, respectively. Analysis of a dinoflagellate cyst record from the SBB spanning the last ~260 years at biannual resolution documents the response of cyst-producing dinoflagellates to instrumentally-measured warming during the 20th century, and reveals decadal scale variations in primary productivity at the site that are coherent with phases of the Pacific Decadal Oscillation (PDO). The cyst assemblages are dominated by cysts produced by heterotrophic dinoflagellates (in particular Brigantedinium spp.), but the turn of the 20th century is marked by an abrupt increase in concentrations of L. machaerophorum and Spiniferites ramosus, two cyst taxa of autotrophic affinity. Their increasing abundances during the 20th century are interpreted to reflect warmer conditions and possibly stronger stratification during summer and fall. The dinoflagellate cyst data suggest a warming pulse in the early 1900s and provide further evidence that persistently warmer and/or more stratified conditions were established by the late 1920s. The dinoflagellate cyst record from Effingham Inlet, spanning the last millennium, is characterized by the proportionally equal contribution of cysts produced by autotrophic and heterotrophic dinoflagellates in most samples. The cyst data indicate variations in sea-surface temperature, salinity and primary productivity that are associated with local expressions of the Medieval Climate Anomaly (from the base of the record to ~1230), the Little Ice Age (from ~1230 to ~1900) and warming during the second half of the 20th century. Both dinoflagellate cyst records reveal that since the beginning (in the SBB) and mid-20th century (in Effingham Inlet), autotrophic dinoflagellates contribute to a greater portion of the primary production in the region, whereas heterotrophic dinoflagellates, as indicators of diatom populations, decline. Variability in the dinoflagellate cyst data is coherent at both sites and suggest a reduced expression of decadal scale variability associated with the PDO during the 19th century. / Graduate / 0416 / 0427 / mbringue@uvic.ca

Dans une ferme d'élevage de bar (Dicentrarchus labrax) du sud de la mer du Nord, de fortes mortalités de bar coïncident régulièrement avec l'efflorescence phytoplanctonique printanière. Le rôle du phytoplancton dans ces mortalités a donc été étudié : un suivi saisonnier (février-novembre 2012) a permis de définir les communautés phytoplanctoniques en présence et, la diversité et la toxicité du genre Pseudo-nitzschia. Ainsi, trois espèces potentiellement toxiques ont été identifiées (P. delicatissima, P. pungens, P. fraudulenta) en association avec des concentrations élevées d'acide domoïque (jusqu'à 229 pg. mL-¹). Au cours d'une expérience d'exposition (45 jours), les effets délétères de P. delicatissima sur les juvéniles de bar ont été étudiés. Si un stress d'exposition a été observé via la surproduction de mucus par l'épithélium branchial, cela n'a pas eu d'incidence sur la condition ni la physiologie des poissons. Les mortalités seraient donc davantage liées à un effet de communautés. Cette hypothèse a été testée en utilisant le pouvoir de filtration des moules (Mytilis edulis) en amont des bassins d'élevage. Cela a permis de limiter l'ampleur de l'efflorescence phytoplanctonique printanière. En conséquence, les poissons élevés dans l'eau filtrée avaient de meilleures conditions, croissance et rapport ARN:ADN que ceux élevés dans l'eau de mer non filtrée. Ce travail souligne la nécessité de généraliser le suivi des communautés phytoplanctoniques afin d'identifier les espèces délétères et leur dynamique et de développer des outils de mitigation permettant d'atténuer l'impact des efflorescences phytoplanctoniques sur l'aquaculture. / For several years, mass mortalities of farmed sea bass (Dicentrarchus labrax) have coincided with phytoplankton spring blooms in the southern North Sea. Since these mortalities could not be explained by classical finfish diseases, phytoplankton noxious effects have been suspected and investigated. A seasonal survey allowed the identification of potentially deleterious phytoplankton species giving particular attention to the Pseudo-nitzschia genus. Three potentially toxic Pseudo-nitzschia species were identified (P. delicatissima, P. pungens, P. fraudulenta) and their presence was related to both domoic acid concentrations and phytoplankton communities. P. delicatissima being dominant over spring and presenting toxic and physical features compatible with fish mortality, a laboratory exposure experiment was carried out. Although gills irritations (mucus overproduction) revealed an exposure stress, no effect on sea bass condition nor on physiological performances was demonstrated. This suggest that phytoplankton community as a whole rather than single species should be involved in fish mortalities. This third hypothesis was tested using mussels (Mytilus edulis) as seawater filters upstream from the rearing tanks to dampen the phytoplankton spring bloom and estimate its impact on fish. Indeed, fish had better condition , growth and RNA:DNA ratio when reared in filtered seawater than in natural seawater. This work highlights the need to develop phytoplankton monitoring in fish farms so as to identify potentially deleterious species and understand their dynamics. It also demonstrates that new mitigation tools should be developed to prevent phytoplankton impacts on farmed fish.

A brown tide bloom of the pelagophyte Aureoumbra lagunensis caused significant impacts to north Indian River Lagoon (IRL) in 2012-2013, including seagrass die-offs, fish kills, and reduced growth and grazing of ecologically important bivalves. There is potential for another pelagophyte, Aureococcus anophagefferens, to expand into this system. Filtration rates (FR) of the pleated tunicate Styela plicata exposed to Aureoumbra lagunensis and Aureococcus anophagefferens were measured against exposure to a control alga (Tisochrysis lutea) in order to determine its potential use as a bioremediator against these harmful algal blooms (HABs). In addition, whether S. plicata might serve as a vector of HABs was studied by culturing fecal deposits. Short-term exposure to HABs significantly reduced FR, whereas long-term exposure indicates comparable cell removal compared to the control. Vector potential of S. plicata was inconclusive. Results warrant further research to determine whether S. plicata can acclimate or respond to HAB conditions over time. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection

Les populations de bivalves exploités subissent régulièrement des épizooties qui affaiblissent voire déciment les stocks, et qui peuvent avoir des conséquences majeures pour l’aquaculture. Ces maladies, dues à des virus, bactéries, ou parasites, se développent particulièrement au printemps et en été. Ces périodes de l’année offrent également des conditions propices aux efflorescences de micro-algues toxiques, dont des dinoflagellés du genre Alexandrium. Ainsi, le risque de co-occurrence d’efflorescences d’Alexandrium sp. et de maladies infectieuses chez les bivalves est élevé. Or, ces micro-algues synthétisent et excrètent des neurotoxines et des composés cytotoxiques responsables d’altérations physiologiques chez les bivalves. L’objectif de cette thèse est d’évaluer les effets combinés d’une exposition à Alexandrium sp. et d’une infection par des agents pathogènes sur la physiologie des bivalves, à travers l’étude de différentes interactions tripartites bivalve – pathogène – Alexandrium sp. Les résultats de ce travail indiquent que différents profils de réponse existent en fonction des espèces impliquées dans ces interactions. Ainsi, une exposition à Alexandrium sp. peut augmenter le taux d’infection par des agents pathogènes chez des bivalves ou au contraire le diminuer. Les réponses hémocytaires associées peuvent traduire l’implication des défenses immunitaires dans ces modulations hôte-pathogène. De plus, l’exposition à des agents pathogènes peut interférer avec le processus d’accumulation de toxines algales dans les tissus des bivalves, illustrant la complexité de ces interactions. Ces résultats, associés à l’observation de lésions tissulaires chez les bivalves peuvent traduire l’altération des activités de nutrition (filtration, digestion…). Ce travail de thèse apporte une meilleure compréhension de l’implication des efflorescences toxiques dans le développement des maladies touchant les bivalves d’intérêt commercial, mais également de l’implication de l’environnement biotique des bivalves sur l’accumulation de phycotoxines réglementées. / Bivalve populations undergo regular epidemics that weaken or decimate exploited stocks and thus limit aquaculture. These diseases are caused mainly by viruses, bacteria or parasites, and occur primarily during spring and summer. This period of the year also provides favorable conditions for toxic dinoflagellate blooms, including species of the genus Alexandrium. Thus, the risk of Alexandrium sp. blooms and infectious diseases co-occurring in bivalves is high. However, these micro-algae synthesize and excrete toxins and cytotoxic compounds responsible for physiological changes in bivalves and could lead to an immuno-compromised status.The objective of this thesis is to evaluate the combined effects on bivalve physiology of exposure to the toxic dinoflagellate, Alexandrium sp., and infection by pathogens, through the study of different bivalve - pathogen - Alexandrium sp. tripartite interactions. The results of this work highlight the species-specific nature of these impacts.Thus, exposure to Alexandrium catenella reduces the herpesviruses infection in oyster Crassostrea gigas, whereas the dinoflagellate A. fundyense increases the susceptibility of C. virginica oyster to the parasite Perkinsus marinus, probably via immuno-suppression, as suggested by the partial inhibition of hemocyte responses. Additionally, the effect of a toxic algal bloom on oyster susceptibility to opportunistic diseases when exposed to a new microbial environment (simulating a transfer) was evaluated. Hemocyte responses to a changing microbial environment were suppressed by exposure to A. catenella, although no new bacterial infection was detected.Finally, exposure to pathogens or to a new microbial environment interferes with the processes by which oysters exposed to A. catenella accumulate algal toxins, illustrating the complexity of these interactions. These results provide a better understanding of the involvement of toxic algal blooms in the development of diseases affecting commercial bivalve species, but also of the involvement of the bivalve biotic environment in the accumulation of regulated toxins.

Relatively little published information on cyanoprokaryote (blue-green algal) blooms in the freshwater wetlands in Western Australia is available. There has been little research on the urban lakes and rivers, examining the relationship between environmental conditions and toxin-producing blooms. In this project the ecology, morphology and toxicity of cyanoprokaryota blooms in 27 metropolitan lakes and sumplands, as well as three major rivers, from 2000 to 2003, on the Swan Coastal Plain (SCP) in the southwest of Western Australia were investigated. / A total of 24 species were identified and described, of which nine species had not been previously documented in the area. This included the potentially toxic species Cylindrospermopsis raciborskii, Aphanizomenon ovalisporum and Anabaena bergii var. limnetica. An illustrated guide to the common bloom-forming species was generated using conventional taxonomic criteria. / Microcystis flos-aquae and Microcystis aeruginosa were the dominant bloom-forming cyanoprokaryotes, widespread in their distribution. Anabaena circinalis, A. bergii var. limnetica and Anabaenopsis elenkinii were the common filamentous species. Anabaena circinalis was common to certain freshwater sites, while A. bergii var. limnetica and A. elenkinii occurred in salinity ranging from fresh (< 1ppt) to hyposaline (3-10 ppt). Sites with similar species assemblages were identified using two-way indicator species analysis and clustering analysis. From this, a distinct distribution pattern emerged, which was defined by the main genera observed in the lakes – Microcystis, Anabaena, Aphanizomenon and Anabaenopsis. / The spatial and temporal distribution of the common bloom-forming cyanoprokaryote species was examined in conjunction with spring-summer physico-chemical data using principal component analysis. It was found that pH, water temperature and electrical conductivity/salinity accounted for variations among the lakes, with electrical conductivity the variable explaining the greatest variation. Lakes located on the coast, or further inland at the base of the Darling Scarp, were more hyposaline to saline, and the remaining lakes were fresh. Although the SCP lakes form consanguineous groups based on geochemistry and hydrology, no similarities among them were found in terms of water quality. / The relationship between nitrogen (N) and phosphorus (P) concentrations (total and dissolved inorganic) and cyanoprokaryote community structure (N-fixing versus non-N-fixing species) was investigated in five selected lakes; Yangebup Lake, Bibra Lake, Blue Gum Lake, Tomato Lake and Emu Lake. The lakes ranged from mesotrophic to eutrophic and supported spring-summer blooms containing multiple species. Overall an inverse relationship between cyanoprokaryote abundance and total ambient nutrient concentrations at the time of the blooms was evident. No transition in dominance in the community was observed in Yangebup Lake, Emu Lake and Bibra Lake, as they were dominated by non-heterocytic species (M. aeruginosa and M. flos-aquae) throughout spring and summer. For Yangebup Lake and Bibra Lake, the abundance of non-heterocytic species decreased concomitantly with decreasing dissolved inorganic N. In contrast, heterocytic species (A. circinalis) dominated the spring community in Tomato Lake, and summer community in Blue Gum Lake, when N and P concentrations were at their highest. / The presence of microcystins in Microcystis dominated blooms was examined using high performance chromatography. A total of 32 natural bloom samples, representing 13 lakes, were analysed for microcystin variants; -LR, -RR and -YR. Twenty-eight samples proved to be toxic with the highest total microcystin concentration from 1645 to 8428.6 µg L[superscript]-1, the lowest concentrations were less than 10 µg L[superscript]-1 with some below the detection limit. Microcystis aeruginosa and M. flos-aquae were associated with these microcystin-containing blooms, although M. flos-aquae appear to be less toxic. The presence of Nodularia spumigena in the Lake Yangebup was associated with high concentrations of nodularin (1664 µg L[superscript]-1). / Employing enzyme-linked immunosorbent assay for microcystins and the brine shrimp (Artemia) bioassays allowed a greater number of lake samples to be analysed and provided a rapid assessment of toxicity. The three methods for cyanotoxin detection verified Yangebup Lake, Herdsman Lake, Hyde Park, Jackadder Lake and Emu Lake as highly toxic sites. Low toxicity was demonstrated in samples from Lake Goollelal, Lake Joondalup, Lake Claremont, Blue Gum Lake and North Lake. These results provided the first evidence of cyanotoxin producing blooms in urban lakes of the SCP. / A comparative study on cyanoprokaryota blooms in Swan River estuary, upper Canning River and upper Serpentine River found that these sites, although hyposaline to saline, contained species that were common in the freshwater lakes. Sampling the river systems showed M. aeruginosa, M. flos-aquae, A. circinalis, A. elenkinii and Planktothrix planctonica to be cosmopolitan in distribution, present in SCP wetlands of varied salinity. Similarities between the upper Canning River and lakes in environmental conditions and species assemblage were demonstrated using multivariate analyses. / Toxin analysis of bloom samples from the Swan River and upper Canning River revealed microcystin concentrations were less than that of the surrounding lakes (1.05-124.16 µg L[superscript]-1). Similarly, nodularin concentrations were higher in Yangebup Lake than the upper Serpentine River. However, the dominance of Anabaena in Canning River samples, and the highly toxic result from the Artemia bioassay suggests microcystin is not the predominant cyanotoxin in this wetland. / This study has produced an overview of the distribution and morphology of cyanotoxin-producing cyanoprokaryotes in the SCP wetlands. The data presented provide the basis for further cyanoprokaryote research in Western Australia, in particular the molecular characterisation of bloom-forming toxic species.

Global change poses new threats for life in the oceans forcing marine organisms to respond through molecular acclimatory and adaptive strategies. Although bivalve molluscs are particularly tolerant and resilient to environmental stress, they must now face the challenge of more frequent and severe Harmful Algal Blooms (HABs) episodes. These massive outbreaks of microalgae produce toxins that accumulate in the tissues of these filter-feeder organisms, causing changes in their gene expression profiles, which in turn modify their phenotype in order to maintain homeostasis. Such modifications in gene expression are modulated by epigenetic mechanisms elicited by specific environmental stimuli, laying the foundations for long-term adaptations. The present work aims to examine the links between environmental stress in bivalve molluscs (with especial emphasis on Harmful Algal Blooms) and specific epigenetic marks triggering responses through modifications in gene expression patterns. Overall, a better understanding of the molecular strategies underlying the conspicuous stress tolerance observed in bivalve molluscs will provide a framework for developing a new generation of biomonitoring strategies. In addition, this strategy will represent a valuable contribution to our knowledge in acclimatization, adaptation and survival. With that goal in mind, the present work has generated transcriptomic data using RNA-Seq and microarray technologies, facilitating the characterization and investigation of the epigenetic mechanisms used by the Mediterranean mussel Mytilus galloprovincialis during responses to HAB exposure. That information was made publicly available through a specialized online resource (the Chromevaloa Database, chromevaloa.com) assessing the response of chromatin-associated transcripts to Okadaic Acid. Specific epigenetic marks have been assessed under lab-controlled exposure experiments simulating the natural development of the HAB Florida Red Tide (FRT). Results demonstrate a role for the phosphorylation of histone H2A.X and DNA methylation in the response to FRT in the Eastern oyster Crassostrea virginica. Lastly, the study of co-expression networks based on RNA-Seq data series from the Pacific oyster Crassostrea gigas reveals dynamic transcriptomic patterns that vary with time, stressor and tissue. However, consistent functional profiles support the existence of a core response to general conditions of environmental stress. Such response involves metabolic and transport processes, response to oxidative stress and protein repair or disposal, as well as the activation of immune mechanisms supporting a tightly intertwined neuroendocrine-immune regulatory system in bivalves.

Les estuaires et les zones côtières constituent des territoires à fort enjeux stratégiques économiquement et pour l'environnement. Ils assurent de nombreuses fonctions biologiques et écologiques dont celle de nourricerie et de frayère pour les poissons. Ces écosystèmes sont pourtant soumis à de multiples facteurs de stress, à la fois naturels et anthropogéniques, qui peuvent représenter une menace potentielle envers les organismes aquatiques, en particulier pour les espèces commerciales de poissons. Dans ce contexte, les effets de facteurs de stress environnementaux tels que la contamination chimique et les efflorescences algales nuisibles (HABs) ont été étudiés par des approches in situ et expérimentale (microcosme et mésocosme) sur deux espèces de poissons : le flet (Platichthys flesus) et le bar (Dicentrarchus labrax). Durant cette thèse, nous avons utilisé différents indicateurs pour déterminer les réponses des poissons aux stress environnementaux. Parmi ces outils, nous avons utilisés des indices de croissance et condition, des biomarqueurs moléculaires et des paramètres immunologiques. / Estuaries and coastal areas are essential fish habitat as nursery and spawning but characterized by the presence of multiple interacting stressors, both natural and anthropogenic, which can represent potential threat toward aquatic organisms, especially for commercial fish species. In this context, the impacts of environmental stressors such as chemical contamination and Harmful algal blooms (HABs) have been studied by in situ and experimentally (microcosm and mesocosm) approaches on two fish species : European flounder (Platichthys flesus) and European sea bass (Dicentrarchus labrax). During this thesis, we used various indicators to determine fish responses to environmental stressors. Among these tools, we used the growth and conditions indices, molecular biomarkers and immunological parameters. In situ approach has been realized in two different systems anthropogenically influenced : one is heavily impacted system (Seine estuary) and the others are less impacted and/or considered as "clean" systems (Canche, Authie and Somme estuaries). As juvenile flounders concentrate in estuaries, we have chosen this species as a biological indicator to evaluate the quality of these estuarine habitats. This in situ study emphasized the negative impact of contaminants on the nursery function of estuaries. The Seine estuary exhibited the highest metals and PAHs contents in sediment compared to other estuaries and metal concentration in juvenile flounder of this estuary were also significantly higher than ones collected in the less polluted estuaries. In the same way, fish growth and condition indices were significantly lower in individuals from this estuary in spite of the sufficient food availability. To control environmental parameters such as hydrological parameters and food availability, a microcosm experiment was carried out on sea bass juveniles exposed to fresh sediment from five sites with different chemical concentrations using multi-biomarker approaches. After 21 days exposure, no metal accumulation in fish gills and any significant differences on the physiological performances and immune system responses of fish juveniles could be observed. On the other hand, responses of molecular biomarkers, particularly, EROD, GST and CAT activities increase with the chemical contamination gradient after 7days of exposure in sediment. This microcosm study confirmed the sensibility and relativity of short term molecular biomarkers responses to the chemical contamination. These two studies highlighted the complexity of the fish responses to environmental stressor due to the many variable environmental factors in situ and due to the selection of fish species (pelagic or benthic) and the exposure duration in controlled laboratory assays. Beside the impact of pollution on fish, Harmful algal blooms (HABs) are widespread along the eastern English Channel and may alter ecological functions of coastal zones and thus affecting nursery ground and fish populations. Nevertheless, the effects of two recurrent harmful algal blooms : a) Phaegocystis globosa and its degraded form transparent exopolymeric particles (TEP) with foam accumulation and b) Pseudo-nitzschia pseudodelicatissima (exponential versus senescent phase) was investigated on the growth and condition of sea bass juveniles. Both mesocosm experiments exhibited any negative impact on juvenile sea bass physiological performance, hence, survival and recruitment success. In conclusion, the results of this thesis contributed to improve the fish responses with multi-biomarker approaches to monitor and assess the health of fish communities and fish habitat quality, as well as the general ecological status of coastal zones and estuaries against the various environmental stressors.

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