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A methology for the stocks assessments of cultivated oysters among along the French Atlantic coasts ArchiMer
Bacher, Cedric; Baud, Jean-pierre; Bodoy, Alain; Deslous-paoli, Jean-marc; Dreno, Jean-paul; Heral, Maurice; Maurer, Daniele; Prou, Jean.
An assessment of the reared stocks of the Pacific oyster (Crassostrea gigas ) has been recently conducted on the major French areas of molluscs culture. The methodology proposed included both estimates of densities obtained by subsampling in the field, and aerial photographs which covered the cultivated, intertidal area. The size and the number of samples were designed to reach a precision of 10% on the final assessment in each area. The field work consisted in weighing and counting the oyster in unit areas of 0.5 m2 for the bottom culture or in trays or bags, for the off bottom technique. These results give a better knowledge of the technique evolution and of the general structures in the cultivated areas.
Tipo: Text Palavras-chave: Modeling; Estimation; Stocks; Crassostrea gigas; Oysters.
Ano: 1986 URL: http://archimer.ifremer.fr/doc/1986/acte-2864.pdf
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A physical-biogeochemical coupling scheme for modeling marine coastal ecosystems ArchiMer
Filgueira, Ramon; Grant, Jon; Bacher, Cedric; Carreau, Michel.
Ecological modeling of dynamic systems such as marine environments may require detailed spatial resolution when the modeled area is greatly influenced by complex physical circulation. Therefore, the simulation of a marine ecosystem must be underlain by a physical model. However, coupling hydrodynamic and biogeochemical models is not straightforward. This paper presents a modeling technique that can be used to build generic and flexible fully-spatial physical-biogeochemical models to study coastal marine ecosystems using a visual modeling environment (VME). The model core is constructed in Simile, a VME that has the capacity to create multiple instances of submodels that can be interconnected, producing a fully-spatial simulation. The core is designed to...
Tipo: Text Palavras-chave: Physical-biogeochemical coupling; Marine spatial planning; Aquaculture; Simile.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00071/18231/15842.pdf
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A probabilistic approach of flow-balanced network based on Markov chains ArchiMer
Leguerrier, Delphine; Bacher, Cedric; Benoit, Eric; Niquil, Nathalie.
We used Markov chains to assess residence time, first passage time, rare of transfers between compartments, recycling index with a general mathematical formalism. Such a description applies to any flow-balanced system that can be modelled as a series of discrete stages or compartments through which matter flows. We derived a general set of equations from a probabilistic approach and applied them to a food web and a physical system derived from the literature. We therefore analysed preferential pathways of matter and behaviour of these systems and showed how it was possible to build up and exploit indices on the basis of a transition probability matrix describing the network, and to characterize with a generic algorithm: (1) the total indirect relationships...
Tipo: Text Palavras-chave: First passage time; Box model; Food web model; Network; Transfer rate; Residence time; Markov chain.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-2268.pdf
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A spatially explicit ecosystem model of seston depletion in dense mussel culture ArchiMer
Grant, J; Bacher, Cedric; Cranford, P; Guyondet, T; Carreau, M.
A fully-coupled biological-physical-chemical model of a coastal ecosystem was constructed to examine the impact of suspended mussel culture on phytoplankton biomass in Tracadie Bay, Prince Edward Island, Canada. Due to the extent of mussel culture there, we hypothesised that shellfish filtration would control the concentration and distribution of phytoplankton and other suspended particles in the bay. Circulation was delineated with a tidally-driven 2D numerical model and used to drive an ecosystem model with a focus on pelagic components including phytoplankton production, nutrients, detritus, and mussels. The benthos were treated as a sink. Nutrients and seston were forced by tidal exchange and river input, with phytoplankton additionally forced by...
Tipo: Text Palavras-chave: Towed sensors; Nutrient dynamics; Circulation model; Phytoplankton; Carrying capacity; Shellfish aquaculture; Estuaries; Ecosystem model.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-6951.pdf
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Amélioration de l'évaluation des stocks de mollusques cultivés en Charente- Maritime ArchiMer
Bacher, Cedric; Deslous-paoli, Jean-marc; Heral, Maurice; Prou, Jean.
The expansion of shellfish culture businesses (oysters, mussels, clams...) gives way to a competition for the use of limited food resources, especially in the Marennes-Oléron basin where water circulation is slow. Increasing the amount of cultivated molluscs leads, from a biological point of view, to:- a drop in growth performances- a rise in chronic mortalities, higher and higher, due to a weakness in the physiological state with a lack of stocks which would have compensated the habitat seasonal shortages (end of winter, etc...)- a greater weakness to diseases, linked to a deficient physiological state and a density rise which increases the proximity rate and thus, parasite propagation speed.For these primary reasons, and for the future of oyster culture,...
Tipo: Text Palavras-chave: Modélisation; Estimation; Echantillonnage; Mollusques; Marennes Oléron; Evaluation stocks.
Ano: 1986 URL: http://archimer.ifremer.fr/doc/1986/rapport-3841.PDF
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Applying Dynamic Energy Budget (DEB) theory to simulate growth and bio-energetics of blue mussels under low seston conditions ArchiMer
Rosland, R; Strand, O; Alunno-bruscia, Marianne; Bacher, Cedric; Strohmeier, T.
A Dynamic Energy Budget (DEB) model for simulation of growth and bioenergetics of blue mussels (Mytilus edulis) has been tested in three low seston sites in southern Norway. The observations comprise four datasets from laboratory experiments (physiological and biometrical mussel data) and three datasets from in situ growth experiments (biometrical mussel data). Additional in situ data from commercial farms in southern Norway were used for estimation of biometricalrelationships in the mussels. Three DEB parameters (shape coefficient, half saturation coefficient, and somatic maintenance rate coefficient) were estimated from experimental data, and the estimated parameters were complemented with parameter values from literature to establish a basic parameter...
Tipo: Text Palavras-chave: Low seston; Modelling; DEB theory; Mytilus edulis; Mussel culture.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6266.pdf
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Assessing phytoplankton realized niches using a French National Phytoplankton Monitoring Network ArchiMer
Hernandez Farinas, Tania; Bacher, Cedric; Soudant, Dominique; Belin, Catherine; Barille, Laurent.
Relating environmental factors to species occurrence is a fundamental step in a better understanding of the community structure, the spatial and temporal dynamics of populations and how species may respond to environmental changes. In this paper, we used phytoplankton occurrence data, from a French national phytoplankton monitoring network, and environmental variables with the aim of characterizing the realized ecological niches of phytoplankton groups. We selected 35 phytoplankton taxa representing the most important taxa in terms of occurrence frequency and abundance along the French coast of the eastern English Channel, the Southern Bight of the North Sea and the Atlantic Ocean. We show that environmental variables such as nutrient concentration, water...
Tipo: Text Palavras-chave: Phytoplankton; Environment; Niche position; Tolerance; Kernel density; Outlying mean index.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00255/36627/35263.pdf
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Assessing the sensitivity of bivalve populations to global warming using an individual-based modelling approach ArchiMer
Thomas, Yoann; Bacher, Cedric.
Climate change exposes benthic species populations in coastal ecosystems to a combination of different stressors (e.g. warming, acidification and eutrophication), threatening the sustainability of the ecological functions they provide. Thermal stress appears to be one of the strongest drivers impacting marine ecosystems, acting across a wide range of scales, from individual metabolic performances to geographic distribution of populations. Accounting for and integrating the response of species functional traits to thermal stress is therefore a necessary step in predicting how populations will respond to the warming expected in coming decades. Here, we developed an individual‐based population model using a mechanistic formulation of metabolic processes...
Tipo: Text Palavras-chave: Benthic species; Biogeography; Climate scenario; Dynamic energy budget; Global warming; Phenology; Population dynamics; Temperature tolerance.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00450/56163/57710.pdf
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Assessment and interpretation of temporal or spactial differences in shellfish productivity of typical French ecosystems ArchiMer
Mazurie, Joseph; Soletchnik, Patrick; Ropert, Michel; Fleury, Pierre-gildas; Auby, Isabelle; Maurer, Daniele; Bacher, Cedric.
Monitoring of Crassostrea gigas performances, from two year-classes, during 12 years, in various French shellfish farming areas have revealed great inter-annual and inter-sites differences in reproduction, growth, mortality or quality of oysters (meat content, Polydora infestation...). The presentation attempts to highlight how a comparative analysis of existing temporal or spatial data on molluscs, water quality, geography or meteorogoly may help to better understand and manage shellfish ecosystems. The range of hydrobiological conditions (food availability, turbidity, temperature...) recorded at national, pluriannual scale, in relation to shellfish performances, enlarges the base of such relationship. However, undirect causative factors, either natural...
Tipo: Text Palavras-chave: Climatic modulation; Hydro geography; Reproduction; Growth; Spatial differences; Water quality; Mortality; Shellfish productivity.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/acte-3318.pdf
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Bassin de la Charente et Baie associée de Marennes-Oléron ArchiMer
Bacher, Cedric; Fillon, Alain; Prou, Jean; Heral, Maurice.
Les modèles d'apports de nitrates par le fleuve Charente, les modèles de productivité de production primaire et les modèles de croissance des huîtres développés précédemment ont été adaptés pour préciser l'impact de la Charente en période d'étiage sur la productivité des huîtres. L'impact de la construction éventuelle du barrage de la Charente a été évalué en fonction de son dimensionnement et de ses modalités de gestion.
Tipo: Text Palavras-chave: Bassin de Marennes-Oléron; Modélisation; Crassostrea gigas; Charente; Trézence.
Ano: 1997 URL: http://archimer.ifremer.fr/doc/00077/18796/16373.pdf
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Building functional groups of marine benthic macroinvertebrates on the basis of general community assembly mechanisms ArchiMer
Alexandridis, Nikolaos; Bacher, Cedric; Desroy, Nicolas; Jean, Fred.
The accurate reproduction of the spatial and temporal dynamics of marine benthic biodiversity requires the development of mechanistic models, based on the processes that shape macroinvertebrate communities. The modelled entities should, accordingly, be able to adequately represent the many functional roles that are performed by benthic organisms. With this goal in mind, we applied the emergent group hypothesis (EGH), which assumes functional equivalence within and functional divergence between groups of species. The first step of the grouping involved the selection of 14 biological traits that describe the role of benthic macroinvertebrates in 7 important community assembly mechanisms. A matrix of trait values for the 240 species that occurred in the Rance...
Tipo: Text Palavras-chave: Assembly mechanisms; Benthic communities; Biological traits; Emergent groups; Functional diversity; Functional redundancy.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00369/47975/48000.pdf
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Capacité trophique du bassin de Marennes-Oléron : couplage d'un modèle de transport particulaire et d'un modèle de croissance de l'huître Crassostrea gigas ArchiMer
Bacher, Cedric.
The trophic relationship between a population of cultivated oysters and potential food was modeled in Marennes-Oleron Bay. Coupling the transport process of particulate matter with assimilation by a population of oysters was achieved through a box mode!. Transport between boxes was based on a mass conservation equation. Parameters were derived from volumes of the boxes, tidal movements and residual 110ws between boxes, and were computed from a numerical hydrodynamical model. Consumption, assimilation and respiration terms were put into an energetic budget equation which enabled simulation of growth. A result of the model was the variability of growth along an axis from North to South, which was related to the oysters' accumulated consumption of food....
Tipo: Text Palavras-chave: Marennes Oleron Bay; Growth; Energetic budget; Crassostrea gigas; Trophic capacity; Box model; Marennes Oléron; Croissance; Bilan énergétique; Crassostrea gigas; Capacité trophique; Modèle en boîtes.
Ano: 1989 URL: http://archimer.ifremer.fr/doc/1989/publication-2882.pdf
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Caractérisation des facteurs de risques associés au mortalités estivales - Synthèse du thème 3 - Risque associé au stress environnemental - 2002-2005 ArchiMer
Burgeot, Thierry; Gagnaire, Beatrice; Renault, Tristan; Haure, Joel; Moraga, D.; David, E.; Boutet, L.; Sauriau, P.g.; Malet, Nathalie; Bouchet, V.; Lapegue, Sylvie; Bouilly, Karine; Le Moullac, Gilles; Arzul, Genevieve; Knoery, Joel; Quiniou, Francoise; Bacher, Cedric; Soletchnik, Patrick.
Les mortalités d'huîtres observées sur les côtes françaises apparaissent principalement à proximité du sédiment et pendant la gamétogenèse. Les interactions de facteurs environnementaux sur les écosystèmes conchylicoles comme la température, les apports des bassins versants et le compartiment sédimentaire illustrent un risque de mortalité lié à différentes sources de stress (Thème 1). Les variations de la qualité de la ressource trophique pendant l'effort de gamétogenèse favorise une baisse de l'énergie disponible (Thème 2) et contraint l'organisme fragilisé à fournir un effort d'adaptation (Fent 2004). L'apparition d'un stress pendant cette période sensible des huîtres pourrait constituer un facteur aggravant de mortalité. L'objectif de cette étude est...
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Ano: 2006 URL: http://archimer.ifremer.fr/doc/00304/41538/40746.pdf
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Cartographie krigée des mollusques suspensivores compétiteurs trophiques des huîtres du bassin de Marennes-Oléron : l'implications pour la planification de l'échantillonnage ArchiMer
Sauriau, Pierre-guy; Bacher, Cedric.
Stock assessement of wild soft-bottom mol/uses has been part of a general approach to shellfish management in oyster farming in Marennes-Oleron Bay. A sampling survey is described as a stratified random sampling after optimum allocation of the sample sire in each stratum. The aim of this study is ta ilIustrate the use of kriging techniques in the case of suspension-feeders. Regarding suspension-feeding molluscs. trophic competitors of the oyster Crassostrea gigas the whole stratified design produced an estimation with a precision around 25%. Then the geostatistical technique. i.e. kriging was used to depict the spatial and variability patterns of several trophic groups. The biomass data are expressed in ash-free. dry-weight units. In addition, the...
Tipo: Text Palavras-chave: Marennes Oléron; Crassostrea gigas; Krigeage; Suspensivore; Echantillonnage stratifié; Peuplement benthique.
Ano: 1991 URL: http://archimer.ifremer.fr/doc/1991/publication-3055.pdf
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Climate Change Influences Carrying Capacity in a Coastal Embayment Dedicated to Shellfish Aquaculture ArchiMer
Guyondet, T.; Comeau, L. A.; Bacher, Cedric; Grant, J.; Rosland, R.; Sonier, R.; Filgueira, R..
A spatially explicit coupled hydrodynamic-biogeochemical model was developed to study a coastal ecosystem under the combined effects of mussel aquaculture, nutrient loading and climate change. The model was applied to St Peter's Bay (SPB), Prince Edward Island, Eastern Canada. Approximately 40 % of the SPB area is dedicated to mussel (Mytilus edulis) longline culture. Results indicate that the two main food sources for mussels, phytoplankton and organic detritus, are most depleted in the central part of the embayment. Results also suggest that the system is near its ultimate capacity, a state where the energy cycle is restricted to nitrogen-phytoplankton-detritus-mussels with few resources left to be transferred to higher trophic levels. Annually, mussel...
Tipo: Text Palavras-chave: Climate change; Nutrient loading; Mussel culture; Carrying capacity; Coastal ecosystem; Numerical modelling.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00275/38624/37191.pdf
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Comparaison des relations trophiques de Ruditapes philippinarum en milieux estuarien et océanique à partir d'un modèle de croissance ArchiMer
Bacher, Cedric; Goulletquer, Philippe.
A comparison of trophic relationships for Ruditapes philippinarum in estuarine and oceanic areas: the use of a growth mode!. Trophic relationships in Ruditapes philippinarum were studied in estuarine and oceanic areas of Marennes-Oleron during 1985 and 1986. Principal components analysis (P.C.A.) was used to reveal the fluctuations of the descriptors from the principal axes. Changes in dry weight were predicted in each area through an allometric growth model and were related to the principal axes derived from the P.C.A. The results of the model were used to compare the growth in each area and to point out the descriptors responsible for the discrepancies, such as autumnal blooms or silt resuspension. Attention was paid to the sampling strategy related to...
Tipo: Text
Ano: 1989 URL: http://archimer.ifremer.fr/doc/1989/publication-2884.pdf
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Conditions d'apparition de densités accrues de dinoflagellés Dinophysis dans le pertuis d'Antioche et les eaux adjacentes. Campagnes Dinopertuis 89 ArchiMer
Delmas, Daniel; Herbland, Alain; Maestrini, Serge; Mornet, Francoise; Morand, Philippe; Spano, Anna-maria; Burgeot, Thierry; Margat, Sylvie; Charpentier, Gabriel; Fillon, Alain; Leguay, Didier; Thomas, Gerard; Bacher, Cedric; Heral, Maurice; Prou, Jean.
Environmental and species features which lead to increases in cell density of the D.S.P. Dinoflagellate Dinophysis in inshore and offshore waters of the île de Ré - île d'Oléron area, France (cruises "Dinopertuis89"). Four weekly sampling series have been carried out, within 10 May – 31 May 1989, at 24 stations located from inshore to offshore waters of the "île de Ré" - "île d’Oléron" area, with the aim to investigate (i) whether Dinophysis increases in cell density occur first in offshore waters and then, eventually, are pushed to the coast, or develop simultaneously in the whole area, and (ii) whether there are some environmental conditions which are related to Dinophysis blooms. Depths of sampling have been stated on the bas is of STD profiles. All...
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Ano: 1990 URL: http://archimer.ifremer.fr/doc/00174/28532/26916.pdf
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Contribution of benthic microalgae to the temporal variation in phytoplankton assemblages in a macrotidal system ArchiMer
Hernandez Farinas, Tania; Ribeiro, Lourenco; Soudant, Dominique; Belin, Catherine; Bacher, Cedric; Lampert, Luis; Barille, Laurent.
Suspended marine benthic microalgae in the water column reflect the close relationship between the benthic and pelagic components of coastal ecosystems. In this study, a 12-year phytoplankton time-series was used to investigate the contribution of benthic microalgae to the pelagic system at a site along the French-Atlantic coast. Furthermore, all taxa identified were allocated into different growth forms in order to study their seasonal patterns. The highest contribution of benthic microalgae was observed during the winter period, reaching up to 60% of the carbon biomass in the water column. The haptobenthic growth form showed the highest contribution in terms of biomass, dominant in the fall-winter period when the turbidity and the river flow were high....
Tipo: Text Palavras-chave: Co-inertia; Dynamic linear models; Epipelon; Epiphyton; Haptobenthos; Microphytobenthos growth forms; Seasonality; Tychoplankton.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00392/50345/51035.pdf
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Development of shellfish production models ArchiMer
Bacher, Cedric.
Mathematical models for biological processes are presented as a set of tools for research, which ilave been created for specifie tasks impact studies, energy budget, test of hypothesis. Before using it, the mecanisms involved must be analysed, depending upon wether a whole ecosystem or one animal is studied (biological scale), physical conditions are taken into account (physical scale), with a predetermined scale for time. The no general method for analysis can be, as conditions of studies are so different, but sorne typical cases can show the approach of the modelizer and the recent developments of its tools.
Tipo: Text Palavras-chave: Shellfish; Test of hypothesis; Energy budget; Impact studies; Mathematical models; Conchyliculture; Validation hypothèse; Bilan énergétique; Etude d'impact; Modélisation.
Ano: 1985 URL: http://archimer.ifremer.fr/doc/1985/acte-6220.PDF
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Dynamic model of the short-term variability of microphytobenthic biomass on temperate intertidal mudflats ArchiMer
Guarini, Jean-marc; Blanchard, Gf; Gros, Philippe; Gouleau, Dominique; Bacher, Cedric.
In the present paper, we list and document the relevant behavioral and physiological processes controlling primary productivity of epipelic microalgae on intertidal mudflats in order to develop a simplified model. We first propose, in an attempt to characterize the 'photosynthetically active biomass' of the epipelic community, a new approach to describe the photic environment at the sediment surface, by substituting a discrete a-layer model in place of continuous vertical light distribution. This concept thus allows us to build a functional representation of the distribution of the photosynthetically active biomass in the sediment and, by then integrating the light and temperature forcing of the latter biomass, to predict the dynamics of the whole epipelic...
Tipo: Text Palavras-chave: Microphytobenthos; Intertidal mudflat; Primary production; Dynamic model; Migratory rhythm; Ecophysiological response.
Ano: 2000 URL: http://archimer.ifremer.fr/doc/00000/10540/7601.pdf
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