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WOS:000453497600006; Dynamic Energy Budget (DEB) theory constitutes a coherent set of universal biological processes that have been used as building blocks for modeling biological systems over the last 40 years in many applied disciplines. In the context of extracting parameters for DEB models from data, we discuss the methodology of fitting multiple models, which share parameters, to multiple data sets in a single parameter estimation. This problem is not specific to DEB models, and is (or should be) really general in biology. We discovered that a lot of estimation problems that we suffered from in the past originated from the use of a loss function that was not symmetric in the role of data and predictions. We here propose two much better symmetric candidates, that proved to work well in practice. We illustrate estimation problems and their solutions with a Monte-Carlo case study for increasing amount of scatter, which decreased the amount of information in the data about one or more parameter values. We here validate the method using a set of models with known parameters and different scatter structures. We compare the loss functions on the basis of convergence, point and interval estimates. We also discuss the use of pseudo-data, i.e. realistic values for parameters that we treat as data from which predictions can differ. These pseudo-data are used to avoid that a good fit results in parameter values that make no biological sense. We discuss our new method for estimating confidence intervals and present a list of concrete recommendations for parameter estimation. We conclude that the proposed method performs very well in recovering parameter values of a set of models, applied to a set of data. This is consistent with our large-scale applications in practice.

International audience; Low concentrations of oxygen determine marine species distribution and abundance along the Peruvian 1 coast with consequences for human activity such as fishing and aquaculture. In order to assess bioener-2 getic consequences of oxygen limitation on the Peruvian scallop Argopecten purpuratus, we first devel-3 oped a Dynamic Energy Budget (DEB) model of growth and reproduction calibrated on field experimen-4 tal datasets. Then, we included oxygen availability as an additional forcing variable using a simple rule 5 based on the ability of the scallop to regulate oxygen consumption. The resulting model was tested using 6 growth/reproduction monitoring and simultaneous high frequency environmental records in Paracas Bay 7 (Peru) at two different depths: suspended in the water column and on the sea bottom. Simulations indicated 8 that scallops growth and reproduction was not food-limited. The negative observed effects of hypoxia on 9 growth and reproduction could be explained by a decrease in both assimilation and reserve mobilization. 10 However, hypoxic conditions in summer were not sufficient to explain the observed losses in somatic tissue 11 weights and the disruption of reproduction. The latter two patterns were better simulated when assuming in-12 creased somatic maintenance costs due to the presence of H 2 S during milky turquoise water discolouration 13 events observed during summer. 14

International audience; The present study aimed to improve understanding of the environmental conditions influencing the reproductive cycle of the great scallop Pecten maximus in two locations in Brittany (France). We also evaluated potential consequences of future climate change for reproductive success in each site.We simulated reproductive traits (spawning occurrences and synchronicity among individuals) of P. maximus, using an existing Dynamic Energy Budget (DEB) model. To validate and test the model, we used biological and environmental datasets available for the Bay of Brest (West Brittany, France) between 1998 and 2003. We also applied the scallop DEB model in the Bay of Saint-Brieuc (North Brittany, France) for the same period (1998-2003) to compare the reproductive cycle in different environmental conditions. In order to accurately model the P. maximus reproductive cycle we improved the scallop DEB model in two ways: through (1) energy acquisition, by incorporating microphytobenthos as a new food source; and (2) the reproductive process, by adding a new state variable dedicated to the gamete production. Finally, we explored the effects of two contrasting IPCC climate scenarios (RCP2.6 and RCP8.5) on the reproductive cycle of P. maximus in these two areas at the 2100 horizon.In the Bay of Brest, the simulated reproductive cycle was in agreement with field observations. The model reproduced three main spawning events every year (between May and September) and asynchronicity in the timing of spawning between individuals. In the Bay of Saint-Brieuc, only two summer spawning events (in July and August) were simulated, with a higher synchronicity between individuals. Environmental conditions (temperature and food sources) were sufficient to explain this well-known geographic difference in the reproductive strategy of P. maximus. Regarding the forecasting approach, the model showed that, under a warm scenario (RCP8.5), autumnal spawning would be enhanced at the 2100 horizon with an increase of seawater temperature in the Bay of Brest, whatever the food source conditions. In the Bay of Saint-Brieuc, warmer temperatures may impact reproductive phenology through an earlier onset of spawning by 20 to 44 days depending on the year.

WOS:000419410100010; The importance of seagrass habitat for the diversity of benthic fauna has been extensively studied worldwide. Most of the information available is, however, about a diversity while little consideration has been given to 13 diversity. To fill the knowledge gaps regarding the variability of epifaunal and infaunal seagrass assemblages at large spatial and temporal scales, we scrutinized an extensive dataset covering five years of monitoring of eight intertidal Zostera marina meadows around Brittany (France). High species richness arose at the regional scale from the combination of high local diversity of the meadows and substantial among-meadows 13 diversity. Epifauna and infauna appeared as distinct self-communities as they displayed different spatial and temporal patterns and varied in their responses to local hydrological conditions. Infauna had higher total 13 diversity than epifauna due to a tighter link to the great variability of local environmental conditions in the region. Both exhibited substantial variations in species composition and community structure with variations of dominant species that were accompanied by extensive change in numerous rare species. The dominant epifaunal species were all grazers. Changes in species composition were induced mostly by species replacement and rarely by richness differences between meadows. Indeed, species richness remained within a narrow range for all seagrass beds, suggesting a potential carrying capacity for species richness of the meadows. Overall, all meadows contributed equally to the regional turnover of seagrass macrofauna, emphasizing high variability and complementarity among beds at the regional scale. The implications of this substantial within-seagrass variability for the functioning of benthic ecosystems at broad scale and for conservation purposes in habitat mosaics warrant further investigations but our results clearly advocate taking into account within-habitat variation when evaluating the diversity of benthic habitats and the potential effect of habitat loss.

International audience; In macrotidal coastal ecosystems, spatial heterogeneity of the water column properties is induced by both oceanic and continental influences. Hydrodynamic processes generate a land-sea gradient of environmental conditions, affecting the biological performances of sedentary organisms. The aim of the present study is to establish an extensive spatial assessment in the reproductive investment of the wild Pacific oyster Crassostrea gigas in Arcachon Bay. This is done by looking for a relationship between the Lawrence and Scott condition index (LSCI) and two tidal processes: the immersion level (IL) and the local oceanic flushing time (LoFt). The LSCI of C. gigas was assessed, just before gamete release, at 68 sampling stations in Arcachon Bay. Oyster performance was overall low and spatially variable. Significant differences in the LSCI were detected between the outer and inner bay. Oyster reefs located toward the mouth of the bay exhibited high LSCI (between 9 and 11), while oyster reefs located in inner bay, especially in south-eastern part around the Eyre River, had low LSCI (below 6). Linear modelling allowed to highlight significant effects of both tidal processes IL and LoFt on the obtained LSCI gradient. IL, LoFt explained 33% of the spatial variability observed on LSCI (IL = 3%; LoFt = 17%; LoFt + IL: 13%), 6% were attributed to the intra-station variation (ISv). Thus, high IL and rapid LoFt favor a better development of somatic-gonadal volume, probably because of longer feeding time and higher supply of food from the ocean by tide flows. Disentangling the effects of IL and LoFt on LSCI allowed to describe the spatial pattern in 61% of variability not explained by both tidal factors. A residual gradient directed southeast-northwest highlighted that others factors, independent from IL and LoFt seems to hamper inner bay oyster reproductive performance. Consequently, investigating on the ecological functioning (Eyre influences), trophic potential and anthropogenic pressures of this zone seem crucial on the understanding of C. gigas reproductive pattern in Arcachon Bay.

International audience; The oceans and seas receive coarse woody debris since the Devonian, but the kinetics of wood degradation remains one of many unanswered questions about the fate of driftwood in the marine environment. A simple gravimetric experiment was carried out at a monitoring station located at the exit of a steep, forested Mediterranean watershed in the Eastern Pyrenees. The objective was to describe and quantify, with standardized logs (in shape, structure and constitution), natural degradation of wood in the sea. Results show that the mass decrease of wood logs over time can be described by a sigmoidal curve. The primary process of wood decay observed at the monitoring station was due to the arrival and installation of wood-boring species that consumed more than half of the total wood mass in six months. Surprisingly, in a region where there is little remaining wood marine infrastructure, “shipworms”, i.e. xylophagous bivalves, are responsible for an important part of this wood decay. This suggests that these communities are maintained probably by a frequent supply of a large quantity of riparian wood entering the marine environment adjacent to the watershed. By exploring this direct link between terrestrial and marine ecosystems, our long term objective is to determine how these supplies of terrestrial organic carbon can sustain wood-based marine communities as it is observed in the Mediterranean Sea.

International audience; We investigated the rhythm of micro-striae formation in the shell of Argopecten purpuratus and environmental influence on micro-growth increments by monitoring growth over a 98-day period between April and July 2007 under bottom and suspended culture (2m above the bottom) rearing conditions. The transfer of individuals to the study site induced the formation of a notable growth mark that allowed us to count the number of micro-striae formed between transfer and sampling dates. Micro-striae counts showed a deposition rate of one stria per day independent of rearing condition. This result allowed us to analyse the relationships between growth increments and environmental conditions. We therefore examined the deviations between observed growth rates and growth rates predicted from a Von Bertalanffy growth function. Cross-correlation analysis revealed significant correlations, without time-lag, between these deviations and both particulate organic carbon and nitrogen concentrations in the bottom treatment. Additionally, we observed negative correlations with temperature and current speed at this depth with time-lags of 1 and 10 days respectively. In the suspended treatment, we observed a significant negative correlation with temperature, only with a 12-day lag-time. Our results show that growth response to environmental variability is not always instantaneous. This delay can be explained by the time delay over which metabolic processes need to be performed (e.g. digestion, use/movements of reserves, growth, reproduction). Further modeling studies could help to better understand these processes.

Anthropogenic pressures in estuaries may impair not only the fitness of organisms and the evolutionary processes necessary to the survival, but also the management of exploited marine resources. In order to assess these impacts, phenotypic and genotypic data pertaining to young-of-the-year (YOY) sole ( Solea solea ) were screened in differentially contaminated North East Atlantic estuaries ranging from Portugal (Mondego) to the English Channel (Seine). YOY sole inhabiting each estuary was found being phenotypically distinct from each other; each of them being impacted by pollution when comparing observed phenotypic data with published literature. According to the strong pollution in the Seine estuary, the corresponding YOY sole sample showed significantly lower body mass, size and condition factor compared to other samples. Using fifteen genetic markers, the Mondego estuary demonstrated low, but significant levels of genetic differentiation with most of the samples. Using neutrality tests, two loci were found to be putatively under directional selection ( Soso7 and Soso23 ), but only locus Soso7 demonstrated significant positive heterozygosity–fitness correlation (HFC) for body size and body mass, suggesting a possible ongoing adaptive process. The candidate locus MT associated to a detoxifying metallothionein gene did not show significant genetic differentiation, but ( i ) significant deficit in heterozygote in the Seine estuary as already reported in other coastal samples impacted by metallic contaminants, and ( ii ) significant positive HFC with body mass were found. Selective rather than demographic processes better explain an observed genetic structure in YOY sole and are predominantly associated with the heavily contaminated Seine estuary whose nursery function and capacity are degraded.

International audience; Estuaries are important areas highly susceptible to anthropogenic degradations like pollution. Estuarine species have thus to cope with many types of constraints depending on the estuaries' characteristics. The European flounder Platichthys flesus is considered as a sentinel species for the monitoring of estuarine water quality. In this study, juvenile flounders (0+ group) were sampled from three contrasted Channel estuaries, i.e. the Seine, the Canche and the Tamar, and we characterized their liver proteomes by using a two-dimensional electrophoresis based proteomic approach. We showed that 27 protein spots differentially accumulated between the 3 populations. Six of these proteins were identified by MALDI TOF-TOF mass spectrometry. Flounders from the Seine and from the Tamar, two highly polluted estuaries, displayed common differences, i.e. an increase of the energetic- and the glutathione-metabolism. The most accumulated protein in the Seine's samples (6.7-fold) was a Vitelline Membrane Outer layer protein 1 homolog, suggesting oogenesis deregulation in these juvenile (sexually immature) flounders. Future works applying this kind of proteomic approach on flounders experimentally exposed to conditions that mimic environmental constraints will help to better understand the significance of these environmental proteomic signatures.

International audience; When the Pacific oyster (Crassostrea gigas, Thunberg) was introduced into France for aquaculture in the mid-sixties, it was initially confined to the sites where it was farmed. Subsequent global warming most likely facilitated the establishment of wild populations throughout the French coastline. This phenomenon of spread has become so great that oyster reefs have recently appeared in sheltered estuaries, on both soft and hard substrate. The present study examined two such sites in the Bay of Brest, Brittany. It is the first to investigate the impacts of this new substrate on the biocoenosis of uncolonised intertidal habitats in France. Increased species richness and abundance of intertidal macrofauna were observed in the presence of oyster reefs on both, mud (4 and 20 fold respectively) and rock (5 fold for both). The dominance of suspension feeders in mud changed to carnivores in reefs and their underlying sediment. Calculation of biotic coefficients (BC) of the soft-bottom fauna revealed only a slight organic enrichment, and the organic and silt composition in the sediment beneath oyster reefs were not significantly different from that on bare sites. On rock, the dominance of grazers remained unchanged between bare rock and oyster reef, while reef on rock was also characterised by deposit and detritic feeders. C. gigas is suspected to cause a homogenisation of coastal habitats with an impoverishment of overall quality but we detected only 11 common species between reefs on mud (60 species) and those on rock (55 species).

In the SW lagoon of New Caledonia (South Pacific), the pectinid Bractechlamys vexillum (Reeve) is a characteristic species of the 1000-km² grey sand bottoms benthic community, with an average density of 1.65 ind m − 2 and a mean dorso-ventral shell height of 47 mm. To assess the role of B. vexillum populations in the transfer of matter at the water–sediment interface of the lagoon ecosystem, in situ measurements were performed of individual biodeposition of total particulate matter, particulate organic matter, particulate organic carbon and nitrogen, chlorophyll a , and pheopigments. Fluxes of particulate matter in sediment traps, with and without individuals placed in cages, were compared at various seasons (66 experiments) and related to concentrations in seston. Particulate matter biodeposit production was significantly linked to B. vexillum biomass and to suspended chlorophyll a and pheopigment concentrations, but not to temperature or to other particulate material concentrations in seston. Daily average biodeposit production of total particulate matter and particulate organic carbon by unit of biomass were 298 mg g AFDW − 1 d − 1 and 45 mg g AFDW − 1 d − 1 , respectively. At the study site, biodeposition by the B. vexillum population was 570 mg m − 2 d − 1 of total particulate matter and 68 mg m − 2 d − 1 of organic carbon, which represent 4.8% and 6.4% of natural sedimentation, respectively. This relatively low figure at the local scale results, however, in a total contribution of B. vexillum to particulate sedimentation in the whole lagoon of 34 · 10 3 metric tons year − 1 for total particulate matter and 4 · 10 3 metric tons year − 1 for organic carbon.

International audience; Diatoms are a major component of phytoplankton community. They tend to dominate under natural high-nutrient concentrations, as well as during artificial Fe fertilisation experiments. They are main players in the biogeochemical cycle of carbon (C), as they can account for 40% of the total primary production in the Ocean and dominate export production, as well as in the biogeochemical cycles of the other macro-nutrients, nitrogen (N), phosphorus (P), and silicon (Si). Another important nutrient is Fe, which was shown to have a direct or indirect effect on nearly all the biogeochemical parameters of diatoms. In the present paper, an inventory is made of the growth, physiology and fate of many diatom species, including maximum growth rate, photosynthetic parameters (maximum specific rate of photosynthesis, photosynthetic efficiency and light adaptation parameter), nutrient limitation (half-saturation constant for growth/uptake), cellular elemental ratios, and loss terms (sinking rates, autolysis rates and grazing rates). This is a first step for improvement of the parameterisation of physiologically based phytoplankton growth and global 3D carbon models. This review is a synthesis of a large number of published laboratory experiments using monospecific cultures as well as field data. Our compilation confirms that size is an important factor explaining variations of biogeochemical parameters of diatoms (e.g. maximum growth rate, photosynthesis parameters, half-saturation constants, sinking rate, and grazing). Some variations of elemental ratios can be explained by adaptation of intracellular requirements or storage of Fe, and P, for instance. The important loss processes of diatoms pointed out by this synthesis are (i) sinking, as single cells as well as through aggregation which generally greatly increases sinking rate, (ii) cell autolysis, which can significantly reduce net growth rates, especially under nutrient limitation when gross growth rates are low, and (iii) grazing by both meso- and micro-zooplankton. This review also defines gaps concerning our knowledge on some important points. For example, we need to better know which iron species is available for phytoplankton, as well as the impact of Fe on the variation of the elemental ratios, especially in terms of assimilation and regeneration of C and N. A better quantification of prey selection by microzooplankton and mesozooplankton in natural environments is also needed, including preference for the various phytoplankton and zooplankton species as well as for aggregates and faecal pellets.