Made available in DSpace on 2015-04-17T14:55:25Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 7694336 bytes, checksum: 9e31ccfd75ef937c6222af7f15aff9a9 (MD5) Previous issue date: 2013-04-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The class Holothuroidea has approximately 1400 species existent, these nearly 50 are recorded to de Brazilian coast. Studies about this class are relatively few, particularly to the North and Northeast of Brasil. In front of the lack of information on the species of holothurians to the Brazilian coast the present study aimed to identify the species of the class Holothuroidea from the Northeast of Brasil to inventory and provide detailed taxonomic information as well as data on their distribution in the region. The Invertebrate Collection Paulo Young, of the Department of Systematics and Ecology (DSE), of Federal University of Paraíba (CIPY-DSE-UFPB) was the main the main material analyzed. Were also examined the collections of the museums of the Federal University of Bahia (MZUFBA), Museu Nacional do Rio de Janeiro (MNRJ) and University of São Paulo (MZUSP). The study of specimens includes analysis of external and internal morphological characters, beyond the pattern of calcareous ossicles, these latter are fundamental for determining the specific level. 32 species were identified, belonging to 3 orders, 8 families, 19 genera and 8 subgenera. Of the species recorded Thyone crassidisca Miller & Pawson, 1981, Euthyonidiella trita (Sluiter, 1910), Protankyra ramiurna Heding, 1928 and Holothuria (Holothuria) dakarenisis represent new records to Brazilian coast. The states with the highest diversity regarding Holothuroidea fauna was, respectively, Paraíba (n = 22 spp.), Bahia (n = 21 spp.), Alagoas (n = 14 spp.) and Pernambuco (n = 10). No species were recorded for states of Maranhão e Sergipe. The fauna of infralittoral requires better sampling. Moreover, in some species taxonomic problems were observed and discussed. The study provides the first annotated list of sea cucumbers from Northeastern Brazil. Reinforces the importance of scientific collections for systematic studies and increased knowledge of biodiversity. / A classe Holothuroidea possui aproximadamente 1400 espécies viventes, das quais 50 foram registradas para a costa brasileira. Estudos sobre a classe no Brasil são relativamente escassos, principalmente para as regiões Norte e Nordeste. Diante da carência de informações sobre as espécies de holotúrias do litoral brasileiro o presente estudo objetivou identificar as espécies da classe Holothuroidea proveniente da região Nordeste do Brasil, a fim de inventariar e fornecer informações taxonômicas detalhadas bem como dados sobre sua distribuição na região. O principal acervo analisado foi o da Coleção de Invertebrados Paulo Young, do Departamento de Sistemática e Ecologia (DSE), da Universidade Federal da Paraíba (CIPY-DSE-UFPB). Além deste, Foi examinado material do Museu de Zoologia da Universidade Federal da Bahia (MZUFBA), Museu Nacional (MNRJ) e Museu de Zoologia da Universidade de São Paulo (MZUSP). O estudo dos espécimes abrange a análise de caracteres morfológicos externos e internos, bem como do padrão dos ossículos calcários, estes últimos são fundamentais para a determinação a nível específico. Foram identificadas 32 espécies pertencentes a 3 ordens, 8 famílias, 19 gêneros e 8 subgêneros. Das espécies registradas Thyone crassidisca Miller & Pawson, 1981, Euthyonidiella trita (Sluiter, 1910), Protankyra ramiurna Heding, 1928 e Holothuria (Holothuria) dakarenisis representam novos registros para a costa brasileira. Os estados que apresentaram maior diversidade em relação à fauna de Holothuroidea foram respectivamente, Paraíba (n = 22 spp.), Bahia (n = 21 spp.), Alagoas (n = 14 spp.) e Pernambuco (n = 10). Com base nos acervos analisados, Maranhão e Sergipe foram os únicos estados em que nenhuma espécie da classe foi registrada. Nota-se que a fauna do infralitoral necessita de uma melhor amostragem. O estudo fornece a primeira lista comentada dos Holothuroidea do Nordeste. Fortalece ainda a importância das coleções científicas para estudos em sistemática e ampliação do conhecimento da biodiversidade.

This thesis deals with the topic of eocrinoid echinoderms from the Barrandian area (Příbram- Jince Basin, mid-Cambrian, Drumian). The thesis is presented as a compilation of five published papers and an introduction. The introduction is an overview of current knowledge about eocrinoid echinoderms. It also includes links to new information from the five included papers, and serves as a unifying element for these professional publications. The topic of the thesis is focused on a revision of selected specimens of eocrinoid echinoderms, and the study of their ontogeny, phylogeny, palaeoecology and systematic position. This thesis has also improved our understanding of early evolution of basal blastozoans. This is the first study of Cambrian ontogenetic development on eocrinoid material from the Czech Republic. Complete ontogeny was described on the genus Akadocrinus, and it was possible to establish two basic phases in the development of this genus: pre-epispire-bearing phase and epispire-bearing phase. The new primitive blastozoan Felbabkacystis is described from the Jince Formation - its unique body plan highlights evolution of the body wall among blastozoans. Palaeoecology and phylogeny of the genus Vyscystis was studied, and phylogenetic analysis suggests a basal position of lepidocystoids among...

Collecting sea cucumbers to supply the high value Chinese dried seafood market is a livelihood activity available to many people in the Western Indian Ocean (WIO), making it an important part of local economies. These fisheries are generally not successfully managed and tropical sea cucumber fisheries show continuing signs of decline. This thesis takes a social-ecological systems approach to guide better management of sea cucumber fisheries and aquaculture in the WIO. Papers 1 and 2 analyse the fishery situation in Zanzibar and find that in the absence of effective management institutions and income alternatives among fishers, leading to dependence, there are unsustainable expanding processes. Paper 3 compares the unmanaged fishery in Zanzibar to the highly controlled situation in Mayotte. In Mayotte, a protection effect is evident and the commercial value of stocks is significantly higher than in Zanzibar. The analysis of the situation in Mayotte demonstrates the importance of matching the fishery – management temporal scales through prepared and adaptive management to avoid processes that reinforce unsustainable expansion. Paper 4 analyses sea cucumber community spatial distribution patterns at a coastal seascape-scale in Mayotte establishing baseline patterns of habitat utilization and abundance, which can be used as reference in management. Paper 5 reviews the potential for sea cucumber aquaculture in the WIO. The review illustrates that this activity, which is currently gaining momentum, does so based on inflated promises and with significant social-ecological risks. Emphasis for improvements is, in this thesis, placed on the importance of prepared and adaptive institutions to govern and control expanding processes of the fishery. These institutional features may be achieved by increasing the level of knowledge and participation in governance and by integration of sea cucumber resources management into higher-level policy initiatives. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

microRNAs (miRNAs) are small (20-23 nt), non-coding single stranded RNA molecules that play an important role in post-transcriptional regulation of protein-coding genes. miRNAs have been found in all animal lineages, and have been implicated as critical regulators during development in multiple species. The echinoderms, Strongylocentrotus purpuratus (sea urchin) and Patiria miniata (sea star) are excellent model organisms for studying development due to their well-characterized transcriptional gene networks, ease of working with their embryos in the laboratory and phylogenetic position as invertebrate deuterostomes. Literature on miRNAs in echinoderm embryogenesis is limited. It has been shown that RNAi genes are developmentally expressed and regulated in sea urchin embryos, but no study in the sea urchin has examined the expression of miRNAs. The goal of my work has been to study miRNA regulation in echinoderm developmental gene networks. I have identified developmentally regulated miRNAs in sea urchin and sea star embryos, using a combination of computational and wet lab experimental techniques. I developed a probabilistic model (named HHMMiR) based on hierarchical hidden Markov models (HHMMs) to classify genomic hairpins into miRNA precursors and random stem-loop structures. I then extended this model to make an efficient decoder by introduction of explicit state duration densities. We used the Illumina Genome Analyzer to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of S. purpuratus and P. miniata. We developed a computational pipeline for analysis of these miRNAseq data to reveal the miRNA populations in both species, and study their differential expression. We also used northern blots and whole mount in situ hybridization experimental techniques to study the temporal and spatial expression patterns of some of these miRNAs in sea urchin embryos. By knocking down the major components of the miRNA biogenesis pathway, we studied the global effects of miRNAs on embryo morphology and differentiation genes. The biogenesis genes selected for this purpose are the RNAse III enzyme, Dicer and Argonaute. Dicer is necessary for the processing of mature miRNAs from hairpin structures while Ago is a necessary part of the RISC (RNA interference silencing complex) assembly, which is required for the miRNA to hybridize to its target mRNA site. Knocking down these genes hinders normal development of the sea urchin embryo and leads to loss of the larval skeleton, a novel phenotype not seen in sea stars, as well as abnormal gastrulation. Comparison of differentiation gene marker expression between control and Ago knocked down sea urchin embryos shows interesting patterns of expansion and suppression of adjoining some embryonic territories, while ingression of larval skeletogenesis progenitors does not occur.

The current increase in the atmospheric CO2 concentration results in two major consequences in the marine environment: an increase of the sea surface temperature (0.7 °C since pre-industrial times) and a decreased seawater pH. This decrease is being measured continuously in different parts of the world and ranges from -0.0017 to -0.04 units per year according to the location considered. Based on CO2 emissions models provided by the IPCC, it was predicted that the average open ocean pH would decrease further by 0.4 units by 2100 and 0.8 by 2300 (corresponding to about a three-fold and six-fold increase of the proton concentration). Also, saturation states of seawater for the different forms of calcium carbonate, such as calcite, magnesium calcite and aragonite which are produced by calcifying marine organisms, are decreasing and consequently the saturation horizons of these minerals are shoaling. Today, some environments are characterized by pH values lower than the average open ocean pH. These are intertidal rock pools, upwelling zones, the deep-sea and CO2 vents. In these environments, pH is either constantly low or fluctuates. Those changes are either due to biological activity, geological CO2 leakage, or water masses movements. Within these environments, it has been hypothesized that organisms could be adapted or acclimatized to low pH values such as those predicted for the near-future. <p><p>Tolerance to ocean acidification in metazoans is linked to their acid-base regulation capacities when facing environmental hypercapnia (i.e. increased CO2 concentration in the surrounding environment). The latter may result in a hypercapnia of the internal fluids and a concomitant acidosis (i.e. reduced pH of the internal fluids due to the dissociation of CO2 in this case). Organisms have two buffer systems allowing the compensation of this acidosis: the CO2-bicarbonate and the non-bicarbonate buffers. Homeostasis of the internal fluids thanks to these systems is essential for the proper functioning of enzymes and processes. As hypometabolic calcifying osmoconformers, three of the characteristics conferring a relative vulnerability to ocean acidification, echinoderms are considered “at risk” for the near-future conditions. Nonetheless, post-metamorphic (juveniles and adults) echinoderms inhabit all environments showing naturally low pH. Furthermore, sea urchins which are highly calcified (compared to sea stars or sea cucumbers) are also found in these environments. This suggests that echinoderms have strategies to adapt or acclimate to low pH environments. Recent studies indicated that while sea urchins are able to regulate their coelomic (extracellular) fluid by accumulation of bicarbonate, sea stars seem to tolerate the acidosis linked to environmental hypercapnia. However, this information was obtained on a reduced number of species and significant interspecific differences were evidenced. Some taxa have not been investigated at all. Furthermore, several aspects of the acid-base physiology were unexplored, like the buffering capacity of the extracellular fluid and the origin of carbon within these fluids.<p><p>Accordingly, the goal of this study was to characterize the acid-base physiology in post-metamorphic echinoderms of different taxa in order to understand their response to ocean acidification.<p><p>The acid-base regulation capacities within the different echinoderm taxa were compared. A method was designed to measure the total alkalinity in small volumes (500 µl) of the main extracellular fluid (the coelomic fluid). This study showed that regular euechinoids have an increased buffer capacity in their coelomic fluid compared to seawater and the other echinoderm groups. In sea urchins, bicarbonate and non-bicarbonate buffers come into play, the former playing the major role. This buffer capacity was increased in fed individuals compared to fasted ones and increased further when seawater pH was lowered.<p><p>The acid-base regulation capacities of sea urchins from different taxa were investigated. Regular euechinoids possess an increased buffer capacity of the coelomic fluid allowing them to maintain a higher pH compared to cidaroids at current seawater pH. This pattern was found for temperate, tropical and Antarctic sea urchins. Data was also obtained for irregular echinoids which also showed a particularly low extracellular pH and a buffer capacity close to seawater like cidaroids. When exposed to reduced seawater pH (8.0, 7.7, and 7.4) for 4-6 weeks, regular euechinoids showed an increasing buffer capacity of the coelomic fluid accompanied by a homeostasis of the pH. On the contrary, cidaroids showed no changes in their acid-base status whatever the seawater pH (8.0 to 7.4). The origin of coelomic fluid carbon, investigated by stable carbon isotope analysis, also differs according to taxa. The δ13CDIC of regular euechinoids evidenced a mixing between CO2 from metabolic origin and that from the surrounding seawater. This is further supported by the correlation between the seawater signal of reduced pH conditions (modified by the addition of industrial gas, changing the δ13C to more negative values) and that of the coelomic fluid. On the other hand, cidaroids exhibit a signal reflecting principally metabolic CO2 (very negative δ13C), and the δ13C did not change under varying pH conditions (i.e. did not adapt to the seawater δ13CDIC signature). For irregular echinoids, the carbon origin is unclear as some species show signals close to that of regular euechinoids whereas others are similar to cidaroids.<p><p>The impact of acid-base regulation was investigated by testing the effect of ocean acidification on the mechanical properties of the skeleton (test plates) in the sea urchin Paracentrotus lividus. Individuals from intertidal pools, CO2 vents and a one year acidification experiment (pH 8.0, 7.9 and 7.7) were compared. Only the intertidal pool individuals showed a difference of the Young’s modulus and fracture forces of their plates. Sea urchins from the tide pool with the largest pH fluctuations showed a lower stiffness and strengthened test. On the contrary, sea urchins from CO2 vents and experimental acidification did not display any differences in the several mechanical properties tested. We suggest that the different food qualities (calcified vs. uncalcified algae) in the different tide pools significantly contributed to the observed difference.<p><p>The acid-base regulation ability of sea cucumbers was assessed in two species from contrasted habitats (mangrove intertidal vs. coral reef species). These organisms underwent acidosis of the coelomic fluid when exposed to reduced seawater pH for a short time (6 to 12 days). The δ13C signal of the coelomic fluid mirrored that of the surrounding seawater in all conditions, indicating that the CO2 accumulated (cause of the acidosis) comes also from the seawater. This is still unexplained to date. However, metabolic processes such as respiration and ammonium excretion rates were not affected. No difference was evidenced between the two species.<p><p>The results obtained in this study compiled with data from the literature indicate that post-metamorphic echinoderms have contrasted acid-base physiology with most regular euechinoids compensating the coelomic fluid pH by accumulation of bicarbonate ions (and possibly ophiuroids also), cidaroids and at least one regular euechinoid (Arbacia lixula) having a naturally low coelomic fluid pH which is not affected by acidification, and sea stars and sea cucumbers which do not compensate their coelomic fluid pH when submitted to acidified seawater. In regular euechinoids, negative effects are linked to resource allocation with growth usually being reduced in favor of acid-base regulation mechanisms. Starfish and sea cucumbers appear as resilient to acidification, with very few functions being negatively impacted. In conclusion, it seems that post-metamorphic echinoderms studied so far will not be particularly at risk when facing ocean acidification levels expected by 2100. Furthermore, tolerance to ocean acidification does not seem linked to the present day ambient pH regime. Nevertheless, more studies need to be carried out on brittle stars and sea cucumbers to confirm preliminary results, as well as crinoids which have not been investigated to date. Long-term exposure experiments to estimate energy budget changes as well as more assessments of evolutionary potential in echinoderms are crucially needed./L’augmentation actuelle de la concentration en CO2 atmosphérique a deux conséquences majeures dans l’environnement marin :une augmentation de la température des eaux de surface (0.7°C depuis l’époque préindustrielle) et une diminution du pH de l’eau de mer. Cette diminution est mesurée continuellement dans différentes régions du monde et varie de -0.0017 à -0.04 unités de pH par an en fonction du site considéré. Basé sur des modèles d’émissions de CO2 du GIEC, il a été prédit que le pH moyen de l’océan diminuerait encore de 0.4 unités d’ici 2100 et 0.8 d’ici 2300 (correspondant à une augmentation de la concentration en protons d’environ 3 fois et 6 fois). De même, les états de saturation de l’eau de mer vis-à-vis des différentes formes de carbonate de calcium, telles que la calcite, la calcite magnésienne et l’aragonite produites par les organismes calcifiants, sont en train de diminuer et par conséquent, les horizons de saturation remontent vers les eaux de surface. Aujourd’hui, certains environnements sont caractérisés par des valeurs de pH plus basses que celle de l’océan. Ceux-ci sont les mares intertidales, les zones d’upwelling, l’océan profond et les évents volcaniques. Dans ces environnements, le pH est soit constamment bas ou fluctue. Ces changements sont soit dû à une activité biologique, une fuite de CO2 géologique, ou au mouvement des masses d’eau. Dans ces environnements, il a été suggéré que les organismes pourraient être adaptés ou acclimatés à des valeurs basses de pH, telles que celles prédites pour le futur proche.<p> <p>La tolérance à l’acidification des océans chez les métazoaires est liée à leur capacité de régulation acide-base lorsqu’ils sont exposés à une hypercapnie environnementale (c’est-à-dire, une augmentation de la concentration en CO2 dans l’environnement entourant l’organisme). Ce phénomène peut résulter en une hypercapnie des liquides internes et une acidose concomitante (c’est-à-dire, un pH des liquides internes réduit dû à la dissociation du CO2 dans ce cas précis). Les organismes ont deux systèmes tampons leur permettant de compenser l’acidose :les tampons CO2-bicarbonate et non-bicarbonate. L’homéostasie des liquides internes grâce à ces systèmes est essentielle pour le fonctionnement correct des enzymes et processus. En tant qu’osmoconformes calcifiant hypométaboliques, trois caractéristiques menant à une certaine vulnérabilité face à l’acidification des océans, les échinodermes sont considérés « à risque » pour les conditions du futur proche. Cependant, les échinodermes post-métamorphiques (juvéniles et adultes) occupent tous les environnements montrant un pH faible naturellement. De plus, les oursins qui sont hautement calcifiés (par rapport aux étoiles de mer ou aux concombres de mer) sont également retrouvés dans ces environnements. Ceci suggère que les échinodermes ont des stratégies d’adaptation ou d’acclimatation à ces environnements à bas pH. Alors que des études récentes montrent que les oursins sont capables de réguler le pH du liquide cœlomique (extracellulaire) par l’accumulation de bicarbonates, les étoiles semblent tolérer l’acidose liée à l’hypercapnie environnementale. Néanmoins, ces informations ont été obtenues sur un petit nombre d’espèces et des différences interspécifiques significatives ont été mises en évidence. Certains taxa n’ont pas été étudié du tout. Par ailleurs, différents aspects de la physiologie acide-base sont inexplorés, tels que la capacité tampon du liquide extracellulaire et l’origine du carbone dans ces liquides.<p><p>Par conséquent, le but de cette étude était de caractériser la physiologie acide-base chez les échinodermes post-métamorphiques de différents taxa afin de comprendre leur réponse à l’acidification des océans.<p><p>Les capacités de régulation acide-base au sein des différents groupes d’échinodermes ont été comparées. Une méthode a été mise au point afin de mesurer l’alcalinité totale dans de petits volumes (500 µl) de liquide extracellulaire (le liquide cœlomique). Cette étude démontra que la capacité tampon du liquide cœlomique des euéchinoïdes réguliers est accrue comparée à celle de l’eau de mer ainsi que celle des autres groupes d’échinodermes. Dans les oursins, les tampons bicarbonate et non-bicarbonate entrent en jeux, le premier étant majoritaire. Cette capacité tampon est augmentée chez les individus nourris par rapport à ceux à jeuns et est augmentée plus encore lorsque le pH de l’eau de mer est diminué.<p><p>Les capacités de régulation acide-base ont été étudiées plus spécifiquement dans les différents groupes d’oursins. Les euéchinoïdes réguliers possèdent une capacité tampon accrue du liquide cœlomique leur permettant de maintenir un pH élevé comparé aux oursins cidaroïdes, au pH de l’eau de mer actuel. Ce patron se retrouve dans les oursins tempérés, tropicaux et antarctiques. Des données ont également été obtenues pour les oursins irréguliers qui ont également un pH extracellulaire particulièrement bas et une capacité tampon proche de celle de l’eau de mer comme les cidaroïdes. Lorsqu’ils sont exposés à un pH de l’eau de mer réduit (7.7 et 7.4 par rapport à 8.0) pour 4 à 6 semaines, les euéchinoïdes réguliers ont montré une augmentation de la capacité tampon du liquide cœlomique accompagnée d’une homéostasie du pH de ce liquide. A l’inverse, les cidaroïdes n’ont montré aucune modification de leur statut acide-base quel que soit le pH (8.0 à 7.4). L’origine du carbone du liquide cœlomique, étudié par analyse des isotopes stables du carbone, diffère également en fonction du groupe. Le δ13CDIC des euéchinoïdes réguliers met en évidence un mélange entre du CO2 d’origine métabolique et celui de l’eau environnante. Ceci est également démontré par la corrélation entre le signal de l’eau de mer dont le pH est réduit (modifié par l’ajout de CO2 industriel, changent le δ13C vers des valeurs plus négatives) et celui du liquide cœlomique. En revanche, les cidaroïdes montrent un signal reflétant principalement celui du CO2 métabolique (δ13C très négatif), et le δ13C n’est pas influencé par des conditions de pH variées (c’est-à-dire, qu’il ne s’adapte pas à la signature du δ13CDIC de l’eau de mer). Pour les oursins irréguliers, l’origine du carbone est incertaine puisque certaines espèces montrent un signal proche de celui des euéchinoïdes réguliers et d’autres similaire à celui des cidaroïdes.<p><p>L’impact de la régulation acide-base a été étudié en testant l’effet de l’acidification des océans sur les propriétés mécaniques du squelette (plaques squelettiques) de l’oursin Paracentrotus lividus. Des individus de mares intertidales, d’évents volcaniques et d’une expérience d’acidification d’un an (pH 8.0, 7.9 et 7.7) ont été comparés. Seuls les individus des mares intertidales montrèrent une différence pour le module de Young et la force des fractures des plaques. Les oursins venant de la mare intertidale montrant les plus grandes variations de pH avaient une rigidité plus faible et un squelette renforcé. A l’inverse, les oursins des évents volcaniques et de l’expérience d’acidification n’ont montrés aucune différence dans les diverses propriétés mécaniques étudiées. Nous suggérons que les variations en termes de qualité de nourriture (algues calcifiées vs. non-calcifiées) dans les différentes mares intertidales ont contribués de manière significative à la différence observée.<p><p>L’habilité des concombres de mer à réguler leur balance acide-base a été évaluée dans deux espèces d’habitats contrastés (espèce intertidale des mangroves vs. subtidale des récifs coralliens). Ces organismes ont subis une acidose du liquide cœlomique lorsqu’ils ont été exposés à un pH réduit de l’eau de mer pour une courte durée (6 à 12 jours). Le signal δ13C du liquide cœlomique reflétait celui de l’eau environnante dans toutes les conditions, indiquant que le CO2 accumulé (cause de l’acidose) venait de l’eau. Ceci est encore inexpliqué à l’heure actuelle. Cependant, les processus métaboliques tels que la respiration ou l’excrétion d’ammonium n’ont pas été affecté. Aucune différence n’a été observée entre les deux espèces.<p><p>Les résultats obtenus dans cette étude compilés avec ceux de la littérature indiquent que les échinodermes post-métamorphiques ont une physiologie acide-base contrastée avec la plupart des euéchinoïdes réguliers qui compensent le pH du liquide cœlomique par l’accumulation d’ions bicarbonates (et peut-être les ophiures aussi), les cidaroïdes et au moins un euéchinoïde régulier (Arbacia lixula) qui ont naturellement un pH du liquide cœlomique bas et qui ne sont pas affectés par l’acidification, et les étoiles de mer et les concombres de mers qui ne compensent pas le pH du liquide cœlomique lorsqu’ils sont soumis à une eau acidifiée. Chez les euéchinoïdes réguliers, des effets négatifs sont liés à un changement de l’allocation des ressources avec souvent un taux de croissance réduit en faveur des mécanismes de régulation acide-base. Les étoiles de mer et les concombres de mer apparaissent plus tolérants à l’acidification, avec peu de fonctions négativement impactées. En conclusion, il semble que les échinodermes post-métamorphiques étudiés jusqu’à présent ne seront pas particulièrement à risque lorsqu’ils seront exposés au niveau d’acidification attendu pour 2100. De plus, la tolérance à l’acidification des océans ne semble pas liée au régime de pH subit actuellement. Cependant, plus d’études doivent être menées sur les ophiures et les concombres de mer afin de confirmer les résultats préliminaires, ainsi que sur les crinoïdes qui n’ont à l’heure actuelle pas encore été étudiés. Des expériences à long terme afin d’estimer le budget énergétique des organismes ainsi que plus d’évaluations du potentiel d’évolution chez les échinodermes sont absolument nécessaires.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Les spatangoïdes (échinides détritivores fouisseurs) possèdent un volumineux caecum qui s’ouvre au début de l’estomac, le caecum gastrique. Ce caecum est ‘distendu’ :il est toujours gorgé d’un liquide incolore dont la nature est inconnue. Les sédiments ingérés par ces oursins et qui occupent le reste du tube digestif, ne pénètrent jamais dans le caecum. La fonction du caecum gastrique n’est pas claire: il sécréterait des enzymes dans l’estomac, serait un site d’absorption, ou encore abriterait une microflore cellulolytique. En prenant pour modèle l’un des échinides fouisseurs les plus étudiés, Echinocardium cordatum, ce travail tente d’élucider le rôle du caecum gastrique, et s’intéresse plus particulièrement à l’étude de son contenu.<p>Les résultats indiquent que le caecum gastrique d’E. cordatum contient de l’eau de mer. L’entrée d’eau de mer dans le caecum a été visualisée en la colorant et des caractéristiques communes au liquide caecal et à l’eau de mer environnante ont été observées: une même osmolarité, les mêmes particules détritiques en suspension et les mêmes communautés bactériennes. Le caecum gastrique contient de la matière organique en suspension (détritus, bactéries transitoires); il est également absorbant. Ses capacités d’absorption ont été comparées à celles de l’estomac et de l’intestin grâce à un dispositif expérimental particulier :les chambres de Ussing. Les résultats ont montré que les entérocytes du caecum et de l’intestin participent davantage au transfert de glucose vers la cavité coelomique que ceux de l’estomac.<p>Un schéma de la circulation de l’eau de mer dans le tube digestif est proposé. L’eau de mer qui circule à la surface du corps de l’oursin et qui provient de la surface des sédiments atteint la cavité buccale, une circulation entretenue par la ciliature des clavules (piquants ciliés). Le péristaltisme de l’œsophage et celui du siphon assurent l’entrée d’eau de mer dans le tube digestif. Une partie de cette eau entre dans le siphon qui l’amène dans l’intestin d’où elle est entraînée à l’extérieur avec le bol alimentaire. L’eau de mer qui n’est pas prélevée par le siphon peut atteindre l’entrée du caecum gastrique. Un système de gouttières a été mis en évidence à l’entrée du caecum. Il s’étend de l’estomac au début du caecum où les gouttières sont flagellées, et acheminerait l’eau de mer dans la lumière caecale. Les différences de pression osmotique entre le liquide caecal et le liquide cœlomique permettraient le transfert d’eau depuis le caecum vers la cavité cœlomique. Une quantité d’eau similaire devrait alors être éliminée de la cavité coelomique. Cette élimination semble se faire dans le caecum intestinal, l’eau serait ensuite éliminée par l’anus. <p>D’après nos observations, le caecum gastrique pourrait être le site d’une digestion et d’une absorption de la matière organique détritique de l’eau de mer. Si cette hypothèse est exacte, E. cordatum serait alors un détritivore particulièrement ‘complet’, digérant non seulement la fraction détritique des sédiments mais aussi celle en suspension dans l’eau de mer. Ce modèle pourrait correspondre à tous les échinides atélostomes (spatangoïdes & holastéroïdes) qui, outre la présence d’un caecum gastrique bien développé et rempli de liquide, ont en commun d’être fouisseurs, et d’entretenir une circulation d’eau dans leur terrier grâce à des clavules groupés en fascioles.<p><p>Spatangoids (burrowed deposit-feeding echinoids) have a large caecum, which opens at the beginning of the stomach, the gastric caecum. It is always swollen, filled with a colorless liquid whose nature is unknown; sediments ingested by sea urchins fill the rest of the digestive tract but never enter in the caecum. The function of the gastric caecum is unclear: it would secrete enzymes in the stomach, would be a site of absorption, and/or would harbor a cellulolytic microflora. By taking as model one of the most studied burrowing echinoids, Echinocardium cordatum, this study attempts to highlight the role of the gastric caecum by examining its contents.<p>Results indicate that the gastric caecum of E. cordatum contains seawater. Seawater inflow into the caecum was visualized using dye. The caecal liquid and the surrounding seawater were demonstrated to have similar characteristics: the same osmolarity, the same suspended particles and the same bacterial communities. The gastric caecum contains suspended organic matter (detritus, transient bacteria) and is also involved in absorption. Absorption and transfer of glucose were compared between the gastric caecum, the stomach and the intestine, using a particular experimental device: the Ussing chamber. The results showed that the enterocytes of the caecum and of the intestine were more involved in glucose transfer to the coelomic cavity than those of the stomach.<p>Seawater circulation in the digestive tube is tentatively described. Seawater currents along the body of the sea urchin originate from the sediment surface and reach the mouth; this circulation is generated by ciliae of specialized spines, the clavules. Peristalsis of the esophagus and of the siphon induces seawater to enter the mouth and to move along the digestive tube. Part of this water enters the siphon, being then transported to the intestine, and driven outside via the anus. Seawater that has not been taken by the siphon can reach the opening of the gastric caecum. A system of grooves occurring at the entrance of the caecum extends from the anterior stomach to the proximal part of the caecum where it is flagellated; these grooves could transport seawater in the caecal lumen. Differences in osmotic pressures between the caecal liquid and the coelomic liquid could transfer water from the caecum to the coelomic cavity. A similar uptake of water could then be removed from the coelom through the wall of the intestinal caecum, and water be eliminated from the digestive tube via the anus.<p>According to our observations, the gastric caecum could be specialized in digestion and absorption of detrital organic matter occurring in seawater. If this hypothesis is correct, E. cordatum would be a deposit-feeder feeding both on the detritus fraction of the sediments and on that of seawater. This model could fit all Atelostomata echinoids (spatangoids & holasteroids) which, besides the presence of a well-developed gastric caecum filled with liquid, have in common the burrowing behaviour, and the maintenance of seawater currents in their burrows owing to the action of clavules grouped into fascioles.<p><p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

<p>Sea urchins are fascinating marine creatures belonging to the phylum Echinodermata that serve as an essential ecological component and hold promise as a prospective source of therapeutics. However, sudden environmental changes, such as global warming and marine pollution, are placing significant stress on these organisms. To maintain natural resources and exploit sea urchins commercially, researchers are investigating aquaculture as a solution.</p> <p>This investigation discloses the physiological and immunological effects of physical and chemical stressors on one of the most common edible species of sea urchin, <em>Arbacia punctulata</em>. The study employed an elevated temperature as a physical stressor (1°C/day), lipopolysaccharides (LPS) inoculation as a chemical stressor (4µg/ml/day), and a combination of both LPS and elevated temperature as combined stressors. The results demonstrated a significant alteration in the total and differential coelomocyte count in the LPS-stressed group (p<0.05) and combined stressed group (p<0.05) followed by abnormal behavioral activity compared to those of control. Additionally, exposure to acute LPS exposure (at day 1 and day 3) and combined stressors led to an increase in phagocytic capacity (p<0.05) and lysozyme activity (p<0.05). Chronic exposure to LPS and combined stressors resulted in a decrease in gonadosomatic index (p<0.05, at day 10) and lysozyme activity (at day 7). A significant increase in coelomic fluid (CF) protein (p<0.05)was observed in the temperature-stressed group on days 5 and 10, while the combined stressed group had significantly more CF protein on days 1, 5, 7, and 10. An upregulation of Nf-kB gene expression was also observed (p>0.05) in temperature stressed group.  </p> <p>The study also revealed that sea urchins contain bioactive compounds that protect against external and internal injury, cell death, and body wall extract of sea urchin exhibited high antioxidant activity(p<0.05). Furthermore, it confirmed the antibacterial activity (p<0.05) of sea urchin (<em>Arbacia punctulata </em>and<em> Lytechinus variegatus</em>) body wall and coelomic fluid (cell-free plasma) extracts against ten pathogenic bacteria. The ethyl acetate body wall extract of both sea urchin species demonstrated higher inhibitory activity against the pathogenic bacteria tested. Overall sea urchin has potentials to meet the demand of food and medicine. </p>

L’évolution spatio-temporelle des populations d’Ophiocomina nigra et d’Ophiothrix fragilis (Ophiuridés, Echinodermes) a été étudiée dans deux écosystèmes contrastés de la pointe de Bretagne (France); la rade de Brest et la baie de Douarnenez. Entre la fin des années 80 et 2011, la population d’O. nigra s’est très largement étendue sur l’ensemble des zones d’études et a vu sa densité augmenter d’un facteur 5 en rade de Brest. Dans ce site, l’expansion d’O. nigra a généré de profonds changements qui se sont progressivement traduits entre autre par une exclusion spatiale d’O. fragilis du bassin central vers la partie sud de la zone d’étude où l’espèce colonise des coquilles vides de crépidules; Crepidula fornicata. L’expansion d’O. nigra a été mise en relation avec la combinaison de possible changements globaux du milieu et les traits biologiques de l’espèce. Les isotopes stables naturels (δ13C & δ15N) et les marqueurs d’acides gras ont été utilisés pour décrire l’écologie trophique des deux ophiures par un suivi in situ, sur des stations sélectionnées en raison de leurs situations contrastées (influence continentale vs influence océanique). Les facteurs de discrimination (∆δ13C et ∆δ15N) ont été calculés en expérimentation pour les deux espèces avec trois types de sources et ont montré principalement un effet de la qualité de la nourriture et de l’état reproducteur des espèces sur ces facteurs et des différences interspécifiques. Le suivi in situ a principalement révélé des différences interspécifiques dans l’alimentation des espèces. Le phytoplancton (diatomées) apparait en été comme une source majeure pour les deux espèces et plus importante pour O. fragilis. Des valeurs en δ15N plus élevées chez O. nigra par rapport à O. fragilis associées à une plus forte contribution de bactéries, de détritus et de matériel d’origine animal, indiquent que l’espèce exploite une grande diversité de sources de nourriture expliquant en partie son succès. Les macroalgues (Ulva sp) et les apports terrigènes semblent jouer un rôle trophique mineur pour les deux espèces, malgré une augmentation significative dans les sites plus confinés en fin d’étude. / The temporal and spatial changes in the densities and biomass of two co-occurring ophiuroid populations Ophiocomina nigra and Ophiothrix fragilis (Ophiuroidea, Echinodermata) were studied in two contrasted coastal systems at the tip of Brittany (France); the Bay of Brest and the Bay of Douarnenez. Ophiocomina nigra increased about 5 times in density in the Bay of Brest. The current distribution pattern in this site revealed a spatial exclusion of O. fragilis from the central part toward the southern part of the study area and now overlapped dead slimper-limpet Crepidula fornicata beds. The success of O. nigra colonization is linked to its biological and functional traits, as well as deep changes in food supply over the studied period. Stable isotopes (δ13C and δ15N) and fatty acids were used as complementary tools to characterize the trophic ecology of these 2 ophiuroids. Preliminary, the tissue-diet discrimination factors (Δδ13C and Δδ15N) were studied and revealed differences between species but appeared to be mainly driven by the diet and to a lesser extent the physiological state of the organisms. We designed a field survey and used the dual stable isotope and fatty acid biomarkers approach to explore the contribution of oceanic vs continental inputs to the diet of ophiurids, according to seasons. In our study, spatiotemporal variations in stable isotopes and fatty acid profiles of ophiurids were generally low compared to interspecific differences. Both ophiurids rely mainly on phytoplankton (diatoms) inputs with higher contribution for O. fragilis. The more δ15N-enriched values as well as higher contribution of bacteria, detritus and animal material inputs to the diet of O.nigra supported a broad range of food sources to the diet of O. nigra. The terrestrial and/or green algae did not contribute greatly to the diet of ophiurids despite a significant increase of these food sources at the end of the study period in both inside sites.

PCBs are among the most problematic marine contaminants. Converging towards the oceans via the rivers and the atmosphere, they concentrate in sediments where they become a permanent threat to organisms living at their contact. PCBs are extremely resistant, bioaccumulated and some congeners are considered as highly toxic. The North Sea is considered as a highly contaminated area ;however little information is available regarding the impact of PCBs on key benthic organisms of this region.<p>Ubiquist, abundant and generally recognized as a good bioindicator species, the common NE Atlantic sea star Asterias rubens (L.) is an ecosystem-structuring species in the North Sea and was chosen as an experimental model. The present study focused on the characterization of PCB bioaccumulation in A. rubens exposed through different routes (seawater, food, sediments) and on subsequent biological responses, at immune and sucellular levels. The considered responses were respectively (i) the production of reactive oxyggen species (ROS) by sea stars amoebocytes, which constitutes the main line of defence of echinoderms against pathogenic challenges and (ii) the induction of a cytochrome P450 immunopositive protein (CYP1A IPP) which, in vertebrates, is involved in PCB detoxification.<p>Experimental exposures carried out have shown that A. rubens efficiently accumulates PCBs. Exposure concentrations were always adjusted to match those encountered in the field. PCB concentrations reached in sea stars during the experiments matched the values reported in field studies ;therefore our experimental protocol was found to accurately simulate actual field situations. Uptake kinetics were related to the planar conformation of the considered congeners :non-coplanar PCB uptake was described using saturation models, whereas coplanar PCBs (c-PCBs) were bioaccumulated according to bell-shaped kinetics. Non-coplanar congeners generally reached saturation concentrations whithin a few days or a few weeks, which means that sea stars can be used to pinpoint PCB contamination shortly after occurrence. On the other hand, c-PCB concentrations reached a peak followed by a sudden drop, indicating the probable occurrence of c-PCB-targeted metabolization processes in sea stars. Our experimental studies also demonstrated that seawater was by far the most efficient route for PCB uptake in sea stars and that even if PCB levels in seawater are extremely low compared to sediment-associated concentrations, seawater constitutes a non-negligible route for PCB uptake in marine invertebrates. Among the different body compartments, bodywall displayed the highest bioaccumulative potency and can therefore be considered as particularly interesting for field biomonitoring applications. Rectal caeca, which play a central role in digestion and excretion processes in sea stars, have also rised particular interest as results suggest these organs could be involved in the elimination of PCB 77 degradation products. <p>The field work carried out during the present study showed that PCB concentrations measured in A. rubens tissues reflect environmental levels of certain congeners. As it was the case in experimental conditions, A. rubens differentially accumulated PCB congeners according to their planarity. Strong relationships were found between concentrations measured in sediments and those determined in sea stars body wall for certain non-coplanar congeners (e.g. 118 and 138), thus allowing to consider A. rubens as a suitable bioindicator species for medium-chlorinated PCB congeners. On the other hand, sea stars appeared to be able to regulate -to a certain extent- their content in coplanar PCBs. This implies that (i) A. rubens cannot be strictly considered as an indicator organism for c-PCBs and (ii) c-PCBs probably affect essential aspects of sea star biology, potentially leading to deleterious effects.<p>The present study addressed effects of PCB exposure on A. rubens biology, in both experimental and field conditions. In experimental conditions, PCBs were found to significantly alter ROS production by sea stars amoebocytes. This alteration also occurred in a congener-specific way :c-PCBs were found to significantly affect, and probably impair sea stars immune system, whereas non-coplanar congeners had no effect. In the field, the PCB contribution to immunotoxicity could not be determined because none of our studies considered ROS production along with c-PCB concentration measurements. However, the levels of ROS production by sea stars amoebocytes measured in field and experimental conditions were found to potentially lead to altered immunity, and therefore to impair sea stars defence against pathogenic agents. <p>A specially designed ELISA was used to measure CYP1A IPP in experimental and field conditions. Experimental work has shown that the induction of this protein was related to PCB exposure in a congener-specific fashion :c-PCBs alone were found to strongly induce the production of CYP1A IPP according to a dose-dependent relationship. These results have highlighted many similarities between the dioxin-like responsiveness of CYP1A IPP induction in sea stars and that occurring in vertebrates. This strongly suggests similarities in the toxicity-triggering mechanism of dioxins and c-PCBs. In the field, CYP1A IPP induction was found to be significantly related to PCB levels determined in bottom sediments. It can thus be considered as a valuable biomarker. Further research is however needed to better characterize the influence of physico-chemical and physiological parameters on CYP1A induction to refine the interpretation of the information gathered via this biomarker. <p>Results obtained in our study have lead to questionning international regulations applying to PCB biomonitoring in the marine environment. For instance, we strongly suggest that the selection of congeners to be systematically considered should be revised to include c-PCBs. Indeed, in our experiments PCB toxicity was almost always attributable to the sole c-congeners. Historically, determination of c-PCB concentrations was extremely difficult due to analytical limitations ;however, nowadays, these problems have been overcome and do no more justify their exclusion from monitoring studies. <p>Although A. rubens appeared to be quite resistant to PCB contamination, levels measured in sea stars from the southern North Sea can possibly affect their immune and endocrine systems in a subtle way, but with relatively low risk for this species at the short-term. However, this does not mean that other species in this region undergo similarly low risks, or that sea star-structured ecosystems may not become affected in the long-term<p> / Doctorat en sciences, Spécialisation biologie animale / info:eu-repo/semantics/nonPublished

The Sulaiy Formation, which is the oldest unit in the Lower Cretaceous succession, is conformably overlain by the Yamama Formation and it is a challenge to identify the precise age of the two formations using foraminifera and other microfossil assemblages. In the eastern side of Saudi Arabia, the Sulaiy Formation and the base of Yamama Formation are poorly studied. The main objectives of this study is to enhance the understanding of the Sulaiy Formation sequence stratigraphical correlation, regional lateral variations and palaeoenvironmental investigation. Lithological and semi-quantitative micropalaeontological analysis of 1277 thin sections taken from core samples from nine cored wells providing a geographically representative distribution from the Saudi Arabian Gulf. These cores intersected the base of the Yamama Formation and the Sulaiy Formation in the total thickness of cored wells of 843.23 meters (2766.5 feet). On the evidence provided by the foraminifera, the Sulaiy Formation is considered to represent the Berriasian to the lowermost Valanginian. The investigation of the micropalaeontology has provided considerable insights into the biocomponents of Sulaiy and the base of Yamama formations in order to identify their biofacies. These microfossils include rotalid foraminifera, miliolid foraminifera, agglutinated foraminifera, calcareous algae, calcispheres, stromatoporoids, sponge spicules, problematica (e.g. Lithocodium aggregatum), molluscs, corals, echinoderms and ostracods. Systematics of planktic and benthic foraminifera is accomplished using the foraminiferal classification by Loeblich and Tappan (1988) as the main source. The assemblage contains foraminifera that recorded for the first time in the Sulaiy Formation. Other microfossils were identified and recorded to help in the identification of the sedimentary environments. The investigation of the micropalaeontology and the lithofacies analysis have provided evidence the identification of the various lithofacies. About twenty four microfacies were identified on the basis of their bio−component and non-skeletal grains. The lithofacies and the bio−component results have provided the evidence of the sedimentary palaeoenvironmental model namely the Arabian Rimmed Carbonate Platform. This palaeoenvironmental depositional model is characterised by two different platform regimes. They are the Platform Interior and the Platform Exterior each of which have unique sedimentary lithofacies zones that produce different types of lithofacies. Each lithofacies is characterised by special depositional conditions and palaeobathymetry that interact with sea level changes and the accommodation space. The important palaeoenvironments are intertidal, restricted lagoon (subtidal), open marine, deeper open marine, inner shoal, shoal and platform margin. Generating, and testing, a depositional model as a part of formulating a sequence stratigraphical interpretation of a region is a key to understanding its geological development and – ultimately – reservoir potential. The micropalaeontology and sedimentology of the Sulaiy Formation in the subsurface have indicated a succession of clearly defined shallowing−upwards depositional cycles. These typically commence with a deep marine biofacies with wackestones and packstones, capped with a mudstone-wackestone maximum flooding zone and an upper unit of packstone to grainstones containing shallow marine biofacies. The upper part of the Sulaiy Formation is highstand-dominated with common grainstones that host the Lower Ratawi reservoir which is capped by karst that defines the sequence boundary. This karst is identified by its abundant moldic porosity that enhanced the the reservoir quality by increasing its porosities into greater values. Integration of the sedimentology and micropalaeontology has yielded a succession of shoaling−upwards depositional cycles, considered to be 4th order sequences, that are superimposed on a large scale 3rd order system tract shallowing−upwards, highstand-associated sequence of the Sulaiy Formation. The Lower Ratawi Reservoir is located within the latest high-stand portion of a third-order Sulaiy Formation sequence. The reservoir consists of a succession of several sequences, each of which is sub-divided into a lower transgressive systems tract separated from the upper highstand systems tract by a maximum flooding surface (MFS/Z). The last of these depositional cycles terminates in beds of porous and permeable ooid, or ooidal-peloidal, grainstone. The reservoir is sealed by the finer-grained sediments of the Yamama Formation.