Modelling paralytic shellfish toxins (PST) accumulation in Crassostrea gigas by using Dynamic Energy Budgets (DEB)

As other filter-feeders, Crassostrea gigas can concentrate paralytic shellfish toxins (PST) by consuming dinoflagellate phytoplankton species like Alexandrium minutum. Intake of PST in oyster tissues mainly results from feeding processes, i.e. clearance rate, pre-ingestive sorting and ingestion that are directly influenced by environmental conditions (trophic sources, temperature). This study aimed to develop a mechanistic model coupling the kinetics of PST accumulation and bioenergetics in C. gigas based on Dynamic Energy Budget (DEB) theory. For the first time, the Synthesizing Units (SU) concept was applied to formalize the feeding preference of oysters between non-toxic and toxic microalgae. Toxin intake and accumulation were both dependent on the physiological status of oysters. The accumulation was modelled through the dynamics of two toxin compartments: (1) a compartment of ingested but non-assimilated toxins, with labile toxins within the digestive gland eliminated via faeces production; (2) a compartment of assimilated toxins with a rapid detoxification rate (within a few days). Firstly, the DEB-PST model was calibrated using data from two laboratory experiments where oysters have been exposed to A. minutum. Secondly, it was validated using data from another laboratory experiment and from three field surveys carried out in the Bay of Brest (France) from 2012 to 2014. To account for the variability in PST content of A. minutum cells, the saxitoxin (STX) amount per energy units in a toxic algae (ρPST) was adjusted for each dataset. Additionally, the effects of PST on the oyster bioenergetics were calibrated during the first laboratory experiment. However, these effects were shown to depend on the strain of A. minutum. Results of this study could be of great importance for monitoring agencies and decision makers to identify risky conditions (e.g. production areas, seawater temperature), to properly assess detoxification step (e.g. duration, modalities) before any commercialization or to improve predictions regarding closing of shellfish areas

Ecological distribution and population structure of Acantholobulus schmitti (Rathbun, 1930) (Crustacea, Decapoda, Xanthoidea) on the southeastern Brazilian coast

This investigation analyzed the ecological distribution and population structure of A. schmitti on the southeastern coast of Brazil. Crabs were sampled monthly from January 1998 to December 1999 at the following bays: Ubatumirim (UBM), Ubatuba (UBA) and Mar Virado (MV). Water and sediment samples were also collected from all sampling sites for an analysis of environmental factors. Acantholobus schmitti was most abundant at UBM (224), followed by UBA (154) and MV (23) but its abundance showed no association with the environmental factors analyzed. The low abundance of these crabs in MV may be due to the high wave action that moved biodetritic material accumulated on the bottom and frequently removed small crabs from their sheltered positions among the shell fragments. The individuals captured included 269 males and 132 females, of which only 4 specimens were brooding females. Juvenile recruitment occurred throughout the year, but was less intense in the spring. The major abundance of individuals as well as of ovigerous females occurred during 1999, when the entrance of the South Atlantic Central Waters (SACW) was stronger than in previous year. This environmental influence could be the main factor modulating this population

Why should you manage your research data following FAIR principles: Réutiliser les données des autres et rendre les siennes réutilisables… tout un défiAtelier 6 - DOCTIS-COPE

IntroductionCycle de vie des données de rechercheDonnées de rechercheMétadonnéesJeu de donnéesFAIR is in the airWe should CAREFAIR-Réutilisable- Différence entre réutilisable et réplicable- Documentation détaillée- Normes de qualité- Accessibilité- Entrepôts et catalogues de données- l'importance des formats- Licences et restrictions- Interopérabilité- Normes et vocabulaire contrôléPhase de pratiqueDoctoralLa formation DOCTIS-COPE s’adresse aux doctorants de l’EDSML (école doctorale des Sciences de la Mer et du Littoral). L’enjeu de cette formation est de transmettre aux futurs chercheurs et enseignants-chercheurs les bonnes pratiques et les valeurs de l’intégrité scientifique, en leur donnant les outils, les méthodes et les ressources nécessaires. La formation vise également à stimuler une prise de conscience et un auto-questionnement critique de leur part en faveur de pratiques professionnelles exemplaires, notamment pour publier de manière intègre.https://isblue.fr/actualites/doctis-cope-formation-doctorale-integrite-scientifique-comment-publier-de-maniere-integre/La formation se déroule en 6 ateliers en présentiel de 3 heures, animés par des experts, sur le thème de la publication : #1 Analyse d’un article rétracté #2 Droits d’auteurs, propriété intellectuelle, plagiat #3 Conditions d’autorat #4 Science ouverte et publication #5 Choix d’une revue scientifique #6 Gestion des données et principes FAIRLa présentation partagée ici correspond à l'atelier numéro 6.Le but de cet atelier est de :1- Rappeler les définitions de base: données, métadonnées, jeux de données, cycle de vie... dans le contexte de la recherche pour des doctorants2- Expliciter le concept de réutilisabilité pour les données de rechercheIl se décompose en une partie théorique (diapo 1 à 28) suivit d'une partie pratique (diapo 28 à 39

Shell allometry and length-mass-density relationship for Mytilus edulis in an experimental food-regulated situation

We examined the influence of food availability and population density on the morphometry and shell length body mass relationship of Mytilus edulis. Mussels were reared in the laboratory for 22 mo at 8 different density levels in 11 chambers supplied with natural seston at 2 different concentrations. This allowed us to assess separately the effects of food availability and mussel density. The shell length/width and shell height/width ratios were affected by food, density and time. Mussels tended to be narrower (flatter) at high density and at low food level. Therefore, narrow shells could result from reduced food concentration in high density situations without implying physical interference. Shell mass was also influenced by both food and density levels, but to a lesser extent than tissue dry mass. In contrast with soft tissue mass, shell mass increased significantly for all food and density levels between October 1995 and October 1996, The elevation of the shell length-body mass-population density relationship was lower at low food availability, The slope of the tridimensional relationship, however, increased with decreasing food level, indicating apparent asymmetric competition for all food-density treatments pooled together, This pattern, however, is misleading because mussels obviously cannot interact among chambers. Since the slopes of length mass relationships are used in predicting self-thinning exponents in space-regulated situations, it follows that self-thinning exponents in mussels should be sensitive to background food level, thus limiting the use of self-thinning relationships for resolving factors regulating growth

Why should you manage your research data following FAIR principles: Réutiliser les données des autres et rendre les siennes réutilisables… tout un défiAtelier 6 - DOCTIS-COPE

IntroductionCycle de vie des données de rechercheDonnées de rechercheMétadonnéesJeu de donnéesFAIR is in the airWe should CAREFAIR-Réutilisable- Différence entre réutilisable et réplicable- Documentation détaillée- Normes de qualité- Accessibilité- Entrepôts et catalogues de données- l'importance des formats- Licences et restrictions- Interopérabilité- Normes et vocabulaire contrôléPhase de pratiqueDoctoralLa formation DOCTIS-COPE s’adresse aux doctorants de l’EDSML (école doctorale des Sciences de la Mer et du Littoral). L’enjeu de cette formation est de transmettre aux futurs chercheurs et enseignants-chercheurs les bonnes pratiques et les valeurs de l’intégrité scientifique, en leur donnant les outils, les méthodes et les ressources nécessaires. La formation vise également à stimuler une prise de conscience et un auto-questionnement critique de leur part en faveur de pratiques professionnelles exemplaires, notamment pour publier de manière intègre.https://isblue.fr/actualites/doctis-cope-formation-doctorale-integrite-scientifique-comment-publier-de-maniere-integre/La formation se déroule en 6 ateliers en présentiel de 3 heures, animés par des experts, sur le thème de la publication : #1 Analyse d’un article rétracté #2 Droits d’auteurs, propriété intellectuelle, plagiat #3 Conditions d’autorat #4 Science ouverte et publication #5 Choix d’une revue scientifique #6 Gestion des données et principes FAIRLa présentation partagée ici correspond à l'atelier numéro 6.Le but de cet atelier est de :1- Rappeler les définitions de base: données, métadonnées, jeux de données, cycle de vie... dans le contexte de la recherche pour des doctorants2- Expliciter le concept de réutilisabilité pour les données de rechercheIl se décompose en une partie théorique (diapo 1 à 28) suivit d'une partie pratique (diapo 28 à 39

Why should you manage your research data following FAIR principles: Réutiliser les données des autres et rendre les siennes réutilisables… tout un défiAtelier 6 - DOCTIS-COPE

IntroductionCycle de vie des données de rechercheDonnées de rechercheMétadonnéesJeu de donnéesFAIR is in the airWe should CAREFAIR-Réutilisable- Différence entre réutilisable et réplicable- Documentation détaillée- Normes de qualité- Accessibilité- Entrepôts et catalogues de données- l'importance des formats- Licences et restrictions- Interopérabilité- Normes et vocabulaire contrôléPhase de pratiqueDoctoralLa formation DOCTIS-COPE s’adresse aux doctorants de l’EDSML (école doctorale des Sciences de la Mer et du Littoral). L’enjeu de cette formation est de transmettre aux futurs chercheurs et enseignants-chercheurs les bonnes pratiques et les valeurs de l’intégrité scientifique, en leur donnant les outils, les méthodes et les ressources nécessaires. La formation vise également à stimuler une prise de conscience et un auto-questionnement critique de leur part en faveur de pratiques professionnelles exemplaires, notamment pour publier de manière intègre.https://isblue.fr/actualites/doctis-cope-formation-doctorale-integrite-scientifique-comment-publier-de-maniere-integre/La formation se déroule en 6 ateliers en présentiel de 3 heures, animés par des experts, sur le thème de la publication : #1 Analyse d’un article rétracté #2 Droits d’auteurs, propriété intellectuelle, plagiat #3 Conditions d’autorat #4 Science ouverte et publication #5 Choix d’une revue scientifique #6 Gestion des données et principes FAIRLa présentation partagée ici correspond à l'atelier numéro 6.Le but de cet atelier est de :1- Rappeler les définitions de base: données, métadonnées, jeux de données, cycle de vie... dans le contexte de la recherche pour des doctorants2- Expliciter le concept de réutilisabilité pour les données de rechercheIl se décompose en une partie théorique (diapo 1 à 28) suivit d'une partie pratique (diapo 28 à 39

The AquaDEB project: Physiological flexibility of aquatic animals analysed with a generic dynamic energy budget model (phase II).

This second special issue of the Journal of Sea Research on development and applications of Dynamic Energy Budget (DEB) theory concludes the European Research Project AquaDEB (2007-2011). In this introductory paper we summarise the progress made during the running time of this 5. years' project, present context for the papers in this volume and discuss future directions. The main scientific objectives in AquaDEB were (i) to study and compare the sensitivity of aquatic species (mainly molluscs and fish) to environmental variability within the context of DEB theory for metabolic organisation, and (ii) to evaluate the inter-relationships between different biological levels (individual, population, ecosystem) and temporal scales (life cycle, population dynamics, evolution). AquaDEB phase I focussed on quantifying bio-energetic processes of various aquatic species (e.g. molluscs, fish, crustaceans, algae) and phase II on: (i) comparing of energetic and physiological strategies among species through the DEB parameter values and identifying the factors responsible for any differences in bioenergetics and physiology; (ii) considering different scenarios of environmental disruption (excess of nutrients, diffuse or massive pollution, exploitation by man, climate change) to forecast effects on growth, reproduction and survival of key species; (iii) scaling up the models for a few species from the individual level up to the level of evolutionary processes. Apart from the three special issues in the Journal of Sea Research - including the DEBIB collaboration (see vol. 65 issue 2), a theme issue on DEB theory appeared in the Philosophical Transactions of the Royal Society B (vol 365, 2010); a large number of publications were produced; the third edition of the DEB book appeared (2010); open-source software was substantially expanded (over 1000 functions); a large open-source systematic collection of ecophysiological data and DEB parameters has been set up; and a series of DEB tele-courses and symposia have been further developed and expanded, bringing together people from a wide variety of backgrounds (experimental and theoretical biologists, mathematicians, engineers, physicists, chemists, environmental sciences, computer scientists) and training levels in DEB theory. Some 15 PhD students graduated during the running time of AquaDEB with a strong DEB component in their projects and over 15 will complete their thesis within a few years. Five post-doctoral projects were also part of the training network. Several universities (Brest, Marseille, Lisbon, Bergen) included DEB courses in their standard curriculum for biology students. © 2011 Elsevier B.V

The aquadeb project (phase i): Analysing the physiological flexibility processes by using dynamic energy budgets.

The European Research Project AquaDEB (2007–2011, http://www.ifremer.fr/aquadeb/) is joining skills and expertise of some French and Dutch research institutes and universities to analyse the physiological flexibility of aquatic organisms and to link it to ecological and evolutionary processes within a common theoretical framework for quantitative bioenergetics [Kooijman, S.A.L.M., 2000. Dynamic energy and mass budgets in biological systems. Cambridge University Press, Cambridge]. The main scientific objectives in AquaDEB are i) to study and compare the sensitivity of aquatic species (mainly molluscs and fish) to environmental variability of natural or human origin, and ii) to evaluate the related consequences at different biological levels (individual, population, ecosystem) and temporal scales (life cycle, population dynamics, evolution). At mid-term life, the AquaDEB collaboration has already yielded interesting results by quantifying bio-energetic processes of various aquatic species (e.g. molluscs, fish, crustaceans, algae) with a single mathematical framework. It has also allowed to federate scientists with different backgrounds, e.g. mathematics, microbiology, ecology, chemistry, and working in different fields, e.g. aquaculture, fisheries, ecology, agronomy, ecotoxicology, climate change. For the two coming years, the focus of the AquaDEB collaboration will be in priority: (i) to compare energetic and physiological strategies among species through the DEB parameter values and to identify the factors responsible for any differences in bioenergetics and physiology; and to compare dynamic (DEB) versus static (SEB) energy models to study the physiological performance of aquatic species; (ii) to consider different scenarios of environmental disruption (excess of nutrients, diffuse or massive pollution, exploitation by man, climate change) to forecast effects on growth, reproduction and survival of key species; (iii) to scale up the models for a few species from the individual level up to the level of evolutionary processes

Factors influencing disease-induced mortality of Pacific oysters Crassostrea gigas

Mortalities of oyster Crassostrea gigas seed associated with ostreid herpesvirus OsHV-1 μVar have been observed in many oyster-producing countries since 2008. The present study, comprised of 4 complementary experiments, aimed to identify factors associated with disease-induced oyster mortality in order to propose mitigation strategies. Our first experiment compared survival of oysters from natural spatfall with others sampled from nurseries, after thermal elevation in the laboratory from <14 to 21°C. A total of 60% of the tested wild seed batches (n = 51) were infected by OsHV-1, exhibited mortality and were able to transmit the disease to cohabited naïve oysters. Comparatively, only 1 out of the 32 tested batches sampled from nurseries presented similar characteristics. In a second experiment, we studied the effects that timing and duration of exposure to field conditions had on risk of infection and mortality in the laboratory at 21°C. Naïve oysters deployed in the field during winter and spring, when seawater temperatures were <14.7°C, showed no mortality in the laboratory, and OsHV-1 DNA was not detected by PCR. However, in oysters transferred to the field, OsHV-1 was observed when seawater temperature reached ~15.3°C. Our third experiment showed that the odds of mortality decreased with age of oysters when facing the disease. Further, we observed that odds of disease mortality decreased with water renewal and increased with the biomass of neighbouring infected oysters under controlled conditions. Based on these findings, we propose mitigation strategies in terms of the regulation of oyster movements between sites, timing of seeding and spatial planning, taking into account seawater temperature and seed origin

Effet de la quantité de nourriture sur la dynamique du δ13C et du δ15N dans les tissus mous du bivalves Crassostrea gigas dans le contexte de la théorie des Budgets d'Energie Dynamiques (DEB)

Nous avons utilisé un modèle basé sur la théorie des Budgets d'Energie Dynamiques, paramétré pour l'espèce Crassostrea gigas et calibré sur des données de la littérature, afin de quantifier l'impact de la quantité de nourriture f sur le fractionnement isotopique Δ. Une augmentation d'un facteur 5 de f entraîne une diminution de 35 % et 43 % du Δ13C et Δ15N respectivement. Ces résultats devraient permettre d'améliorer l'outil isotopique et de mieux comprendre les relations proies/prédateurs dans les écosystèmes côtiers