The Dynamic Energy Budget (DEB) model (Kooijman, S.A.L.M., 1986. Energy budgets can explain body size relations. pp.) has been adapted to describe the dynamics of growth and reproduction of the Pacific oyster (Crassostrea gigas) reared in different areas under conditions ranging from controlled to natural. The values of the model parameters were estimated from available physiological data and from published information. The sets of data used to validate the model came from three long-term growth experiments (> 5 months) performed on Pacific oysters reared under different conditions of food and environment. The forcing variables were temperature and phytoplankton densities, the latter being assessed from in vivo fluorescence and chlorophyll-a concentration measurement. The successful validation of the model on the three data sets demonstrated its ability to capture the dynamics of the energy budget in the Pacific oyster in various environments with the same set of parameters. The only parameter that varied between simulations was the half-saturation coefficient (XK), because of a different diet composition between the three environments under test. The model successfully reproduced quantitatively the growth and reproduction and the timing of spawning. These first simulation data led us to propose several promising perspectives of application for this model in shellfish ecosystems.

Chlorophyll a fluorescence has been increasingly applied to benthic microalgae, especially diatoms, for measurements of electron transport rate (ETR) and construction of rapid light response curves (RLCs) for the determination of photophysiological parameters (mainly the maximum relative ETR (rETR max), the light saturation coefficient (E k) and the maximum light use coefficient). Various problems with the estimation of ETR from the microphytobenthos have been identified, especially in situ. This study further examined the effects of light history of the cells and light dose accumulation during RLCs on the fluorescence measurements of ETR using the benthic diatom Navicula phyllepta. RLCs failed to saturate when using incremental increases in irradiance, however curves with decreasing irradiance did saturate. Patterns indicating photoacclimation in response to light histories were observed, with higher rETR max and E k , and lower , at high light compared to low light. However these differences could be negated by increasing the RLC irradiance duration from 30 to 60 s. It is suggested that problems arose as a result of rapid fluorescence variations due to ubiquinone, Q A , oxidation and non-photochemical chlorophyll fluorescence quenching, NPQ, which depended upon the light history of the cells and the RLCs accumulated light dose. Also, RLCs with irradiance duration of 10 s were shown to have an error possibly specific to the fluorimeter programming. It is suggested that RLCs, using a Diving-PAM fluorimeter on benthic diatoms, should be run using decreasing irradiance steps of 30 s duration.

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Recent theoretical considerations have highlighted the importance of the pelagic-benthic coupling in marine food webs. In continental shelf seas, it was hypothesized that the trophic network structure may change along an inshore-offshore gradient due to weakening of the pelagic-benthic coupling from coastal to offshore areas. We tested this assumption empirically using the eastern English Channel (EEC) as a case study. We sampled organisms from particulate organic matter to predatory fishes and used baseline-corrected carbon and nitrogen stable isotope ratios (δ13C and δ15N) to determine their trophic position. First, hierarchical clustering on δ13C and δ15N coupled to bootstrapping and estimates of the relative contribution of pelagic and benthic carbon sources to consumers' diet showed that, at mesoscale, the EEC food web forms a continuum of four trophic levels with trophic groups spread across a pelagic and a benthic trophic pathway. Second, based on the same methods, a discrete approach examined changes in the local food web structure across three depth strata in order to investigate the inshore-offshore gradient. It showed stronger pelagic-benthic coupling in shallow coastal areas mostly due to a reorganization of the upper consumers relative to the two trophic pathways, benthic carbon sources being available to pelagic consumers and, reciprocally, pelagic sources becoming accessible to benthic species. Third a continuous approach examined changes in the mean and variance of upper consumers' δ13C and δ15N with depth. It detected a significant decrease in δ13C variance and a significant increase in δ15N variance as depth increases. A theoretical two-source mixing model showed that an inshore-offshore decrease in the pelagic-benthic coupling was a sufficient Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site. condition to produce the δ13C variance pattern, thus supporting the conclusions of the discrete approach. These results suggest that environmental gradients such as the inshore-offshore one should be accounted for to better understand marine food webs dynamics. Highlights ► Marine food web is reorganized along a seaward gradient in the English Channel. ►Stronger coupling of the pelagic and benthic pathways from offshore to the coast. ►Shift of pelagic predators to the benthic pathway in shallow areas. ►Adaptive foraging of pelagic predators may explain food web reorganization.

Oyster culture structures support a host of epibionts belonging to the same suspensionfeeding guild, which are considered to be potential competitors for food with cultivated oysters. In an intertidal shellfish ecosystem on the northern French coast, an approach based on stable isotopes ( 13 C and 15 N) was used to investigate intra-and interspecific food resource partitioning among cultivated oysters and the main associated wild sessile epibionts such as polychaetes, barnacles, mussels and ascidians. The main objective of the present study was to determine inter-and intraspecific food partitioning, along with small-scale spatial variability, within the guild of suspension feeders. We demonstrated that interspecific competition was limited among co-occurring suspension-feeders (ascidians, serpulid and terebellid polychaetes, bivalves and barnacles). None of the studied species had similar δ 13 C and δ 15 N signatures, indicating that relative contributions of organic matter sources may differ for each suspension-feeding species. Spatial variability was investigated both from the view of intra-and interspecific variability. Intraspecific variability was examined with regard to species' feeding biology and the trophic plasticity of co-occurring suspension-feeders. Mantel tests indicated that spatial heterogeneity resulted not only from environmental conditions, such as elevation above sea level (a.s.l.) and sediment features, but also from the inherent spatial structure of isotopic signatures. Our results show that isotopic approaches that are limited to sampling in one area and at one time are at risk of mistaking trophic interactions.

The successful application of variable chlorophyll fluorescence methodology to higher plants and other phototrophs inspired workers in the 1990s to apply the methods to microalgal communities inhabiting benthic soft sediments, the microphytobenthos (MPB) of estuarine and other coastal habitats. It was quickly identified that particular aspects of the physiology (cellular vertical migration within the sediment matrix), photophysiology (high capacity for down regulation, e.g. NPQ, and chlororespiration in the dark) and the effects of the physical structure of the sediment/biofilm matrix (light attenuation by the matrix itself) confounded the interpretation of fluorescence information obtained. In this chapter, the authors attempt to explain these and other issues pertinent to MPB biofilms and to summarise how methods have been developed to alleviate the problems encountered. Although much work is still needed to fully understand fluorescence data for the MPB, studies to date have been highly illuminating with regard to rhythms of productivity, photoacclimatory mechanisms and the behavioural ecology and physiology of MPB at an integrated biofilm level and at a cellular level. This chapter therefore introduces benthic biofilms and relevant specific fluorescence methodological issues, expands on subsurface fluorescence signal and migration, discusses down regulatory nonphotochemical quenching (NPQ) resulting from xanthophylls cycle induction, compares measurement of electron transport rate proxies, examines light curve methodology, and concludes by comparing fluorescence productivity measurements with those of other methodologies such as oxygen evolution and carbon uptake. Contents 1. Introduction to benthic biofilms 2. The effects of subsurface signal 2.1 Microphytobenthic biofilms on soft sediments 2.2 Stromatolites -the effect of "layered" biofilms 2.3 Deconvolution of depth integrated signals 3. Down regulation through Non Photochemical Quenching 3.1 NPQ and the Xanthophyll cycle in diatoms 3.2 NPQ in the dark 4. The quantification of the microalgal biomass using fluorescence 5. Calculation of electron transport rate: ETR v rETR 5.1 Multiple and single turnover methods 5.2 The MT-method. 5.3 The ST-method 5.4 Assumptions and uncertainties.

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