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This study presents the fecal contamination dynamic at the two bathing sites of Aytré Bay (Charente Maritime, France). We quantified fecal indicator bacteria (FIB) abundances (Escherichia coli and enterococci) from water and sediment samples over one-year survey. Then we measured biological (bacterial abundance, chlorophyll-a), physico-chemical (dissolved nutrients and oxygen, salinity, pH …) and climatic (temperatures, rainfall and tidal coefficient) parameters. Results showed that FIB abundances were occasionally higher than the European regulatory threshold during winter, summer and fall. The "poor quality" of the bathing water was due to high enterococci abundance. We found negative significant correlations between FIB and water temperature and salinity, and positive significant correlations between FIB and rainfall, PO

electronic publication at this time; International audience; A prey–predator experimental setup was conducted in a shallow coastal ecosystem characterized by a bare intertidal mudflat to test if benthic biofilm resuspension causing microalgae inputs and carbon export toward nanoflagellates would favour the highest planktonic trophic level (i.e. mesozooplankton) when nutrient concentrations are high in the water column. Mesozooplankton predation and somatic production were studied by comparing the evolution of the prey assemblage (diversity and abundances) in the presence and absence of these predators during 24 h experiments. The results were then statistically analysed according to the cross-calculation method. Biofilm resuspension caused (i) a direct input of benthic microorganisms that had changed prey structure in term of diversity and/or size and (ii) a differential growth ability between prey taxa. Both reasons implied a bottom-up control on both micro- and mesozooplankton. The carbon export toward heterotrophic nanoflagellates favoured pelagic ciliate growth while mesozooplankton benefited from largest diatoms with high growth rates, both benthic and R-strategist pelagic species. Even if these microbial and herbivorous pathways are controlled by benthic inputs, they seemed to be totally disconnected since ciliates represented only a small part of mesozooplankton diet. The sensitivity of mesozooplankton production appeared species-dependent with the most tolerant taxa dominating the zooplankton assemblages. This suggests a role of the intensities and the frequencies of biofilm resuspension on the spatio-temporal structuring of mesozooplankton in macrotidal coastal ecosystems.

International audience; Intertidal mudflats are ecosystems submitted to natural hydrodynamical forcings during each tide. When the off-shore water flows at high tide, a proportion of the biofilm produced at low tide can be resuspended in the water column and interact with the pelagic food web. As a consequence, the resuspension creates a link between the benthos and the pelagos, modifying their properties and the stability of the meta-ecosystem they form together. The aim of this study is to describe the consequences of the microbial biofilm resuspension on the pelagic food web, and to investigate the question of the stability of the benthos–pelagos coupling resulting from the biofilm resuspension. Two food webs were considered, corresponding to different hydrodynamical conditions in sum-mer condition: one allowing the biofilm massive resuspension, and one without resuspension, but with particle sedimentation. The Monte-Carlo Markov Chain Linear Modelling was used to estimate the unknown flows of the food web. The comparison of the Ecological Network Analysis indices for the two food webs allowed defining their respective differences of structure and functioning. The results showed that the massive resuspension of the microbial biofilm stimulates pelagic primary production and microbial food web via a higher bacterivory. The higher activity of the whole system coupled with both a drop in the specialisation of the trophic pathways and a low cycling activity demonstrated that when massive resuspension occurs, the system is disturbed. In con-trast, when sedimentation occurs, the food webs show functioning features pointing out to a higher stability of the whole system.

In shallow macrotidal ecosystems with large intertidal mudflats, the sediment-water coupling plays a crucial role in structuring the pelagic microbial food web functioning, since inorganic and organic matter and microbial components (viruses and microbes) of the microphytobenthic biofilm can be suspended toward the water column. Two experimental bioassays were conducted in March and July 2008 to investigate the importance of biofilm input for the pelagic Microbial and Viral Loops. Pelagic inocula (

Resuspension of microphytobenthic biomass that builds up during low tide has been acknowledged as a major driver of the highly productive food web of intertidal mudflats. Yet, little is known about the contribution to pelagic food web of the resuspension of other microorganisms such as viruses, picoeukaryotes, cyanobacteria, bacteria, nanoflagellates, and ciliates, living in biofilms associated with microphytobenthos and surficial sediment. In the present study, a novel approach that involves simultaneous Lagrangian and Eulerian surveys enabled to disentangle the effects of resuspension and mixing with offshore waters on the dynamics of water column microorganisms during a rising tide in the presence of waves. Temporal changes in the concentration of microorganisms present in the water column were recorded along a 3 km cross-shore transect and at a fixed subtidal location. In both surveys, physical and biological processes were separated by comparing the time-evolution of sedimentary particles and microorganism concentrations. During a rising tide, sediment erosion under wave action occurred over the lower and upper parts of the mudflat, where erodibility was highest. Although erosion was expected to enrich the water column with the most abundant benthic microorganisms, such as diatoms, bacteria and viruses, enrichment was only observed for nanoflagellates and ciliates. Grazing probably overwhelmed erosion transfer for diatoms and bacteria, while adsorption on clayed particles may have masked the expected water column enrichment in free viruses due to resuspension. Ciliate enrichment could not be attributed to resuspension as those organisms were absent from the sediment. Wave agitation during the water flow on the mudflat likely dispersed gregarious ciliates over the entire water column. During the rising tide, offshore waters imported more autotrophic, mainly cyanobacteria genus Synechococcus sp. than heterotrophic microorganisms, but this import was also heavily grazed. Finally, the water column became a less heterotrophic structure in the subtidal part of the semi-enclosed bay, where mixing with offshore waters occurs (50% decrease), compared to the intertidal mudflat, when resuspension occurs. The present study suggests that this differential evolution resulted predominantly from dilution with offshore waters less rich in heterotrophic microorganisms. Indeed, any input of microorganisms accompanying physical transfers due to bed erosion or offshore water mixing was immediately buffered, probably to the benefit of grazers.

Population dynamics in the microbial food web are influenced by resource availability and predator/parasitism activities. Climatic changes, such as an increase in temperature and/or UV radiation, can also modify ecological systems in many ways. A series of enclosure experiments was conducted using natural microbial communities from a Mediterranean lagoon to assess the response of microbial communities to top-down control [grazing by heterotrophic nanoflagellates (HNF), viral lysis] and bottom-up control (nutrients) under various simulated climatic conditions (temperature and UV-B radiations). Different biological assemblages were obtained by separating bacteria and viruses from HNF by size fractionation which were then incubated in whirl-Pak bags exposed to an increase of 3°C and 20% UV-B above the control conditions for 96 h. The assemblages were also provided with an inorganic and organic nutrient supply. The data show (i) a clear nutrient limitation of bacterial growth under all simulated climatic conditions in the absence of HNF, (ii) a great impact of HNF grazing on bacteria irrespective of the nutrient conditions and the simulated climatic conditions, (iii) a significant decrease in burst size (BS) (number of intracellular lytic viruses per bacterium) and a significant increase of VBR (virus to bacterium ratio) in the presence of HNF, and (iv) a much larger temperature effect than UV-B radiation effect on the bacterial dynamics. These results show that top-down factors, essentially HNF grazing, control the dynamics of the lagoon bacterioplankton assemblage and that short-term simulated climate changes are only a secondary effect controlling microbial processes.

The Charente River provides nutrient- and virus-rich freshwater input to the Marennes Oleron Basin, the largest oyster-producing region in Europe. To evaluate virioplankton distribution in the Charente Estuary and identify which environmental variables control dynamic of virioplankton abundance, five stations defined by a salinity gradient (0–0.5, 0.6–5, 13–17, 20–24, and higher than 30 PSU) were surveyed over a year. Viral abundance was related to bacterioplankton abundance and activities, photosynthetic pigments, nutrient concentration, and physical parameters (temperature and salinity). On a spatial scale, virus displayed a decreasing pattern seaward with abundance ranging over the sampling period from 1.4 × 107 to 20.8 × 107 viruses mL−1 making virioplankton the most abundant component of planktonic microorganisms in the Charente Estuary. A good correlation was found between viral and bacterial abundance (r s = 0.85). Furthermore, bacterial abundance was the most important predictor of viral abundance explaining alone between 66% (winter) and 76% (summer) of viral variability. However, no relation existed between viral abundance and chlorophyll a. Temporal variations in viral distributions were mainly controlled by temperature through the control of bacterial dynamics. Spatial variations of viral abundance were influenced by hydrodynamic conditions especially during the winter season where virioplankton distribution was entirely driven by mixing processes.

International audience; Resuspension thresholds in terms of friction velocity were experimentally quantified for the prokaryotes, protists and for the first time, viruses of intertidal mudflat biofilms. Differences in resuspension thresholds could be related to the type, behaviour and size of microorganisms and their association with particles. Free microorganisms (viruses, bacteria and some nanoflagellates) were resuspended by weak flow at friction velocities lower than 2 cm s− 1. Chlorophyll a, some nanoflagellates and attached bacteria were resuspended together with the bed's muddy sediment, which required friction velocities larger than 3 cm s− 1. Diatoms smaller than 60 μm were resuspended at velocities between 3 and 5 cm s− 1, while those larger than 60 μm were resuspended at higher friction velocities (5.5 to 6.5 cm s− 1).The thresholds of resuspension also depended on the micro-scale position of microorganisms in the sediment (horizontal and vertical distributions). In the field, the vertical distribution of chlorophyll a (a proxy of microphytobenthos) was skewed, with a maximum in the first 2 mm of sediment. Along the neap–spring tidal cycle, chlorophyll a revealed an increase in MPB biomass in the first 2 mm of the sediment, in relation to light increases with exposure durations. The horizontal distribution of chlorophyll a could be inferred from erosion experiments. During the initial phase of biofilm growth, the distribution of chlorophyll a seemed horizontally homogeneous, and was uniformly eroded at the beginning of the increase in chlorophyll a. From these results, we can make a hypothesis: in the subsequent phase of biofilm growth until the maximum of emersion duration, the eroded quantity of chlorophyll a was larger than expected based from chlorophyll a vertical distribution, suggesting that biofilm horizontal distribution became patchy and enriched chlorophyll a was preferentially eroded. When emersion duration and biofilm growth decreased, the trend was reversed, and eroded quantity of chlorophyll a was lower than expected from chlorophyll a vertical distribution, suggesting that areas with low chlorophyll a were preferentially eroded. Such erosion patterns when biofilm growth decreased probably resulted from the bulldozing activity of a surficial sediment bioturbator, the gastropod Peringia ulvae. Our study did not directly prove this horizontal distribution but it should be further discussed. This distribution needs to be studied to acquire real evidence of patchy distributions.

International audience; The migratory shorebirds of the East Atlantic flyway land in huge numbers during a migratory stopover or wintering on the French Atlantic coast. The Brouage bare mudflat (Marennes-Oléron Bay, NE Atlantic) is one of the major stopover sites in France. The particular structure and function of a food web affects the efficiency of carbon transfer. The structure and functioning of the Brouage food web is crucial for the conservation of species landing within this area because it provides sufficient food, which allows shorebirds to reach the north of Europe where they nest. The aim of this study was to describe and understand which food web characteristics support nutritional needs of birds. Two food-web models were constructed, based on in situ measurements that were made in February 2008 (the presence of birds) and July 2008 (absence of birds). To complete the models, allometric relationships and additional data from the literature were used. The missing flow values of the food web models were estimated by Monte Carlo Markov Chain – Linear Inverse Modelling. The flow solutions obtained were used to calculate the ecological network analysis indices, which estimate the emergent properties of the functioning of a food-web. The total activities of the Brouage ecosystem in February and July are significantly different. The specialisation of the trophic links within the ecosystem does not appear to differ between the two models. In spite of a large export of carbon from the primary producer and detritus in winter, the higher recycling leads to a similar retention of carbon for the two seasons. It can be concluded that in February, the higher activity of the ecosystem coupled with a higher cycling and a mean internal organization, ensure the sufficient feeding of the migratory shorebirds.

Background Small size eukaryotes play a fundamental role in the functioning of coastal ecosystems, however, the way in which these micro-organisms respond to combined effects of water temperature, UVB radiations (UVBR) and nutrient availability is still poorly investigated. Results We coupled molecular tools (18S rRNA gene sequencing and fingerprinting) with microscope-based identification and counting to experimentally investigate the short-term responses of small eukaryotes ( Conclusions This multifactorial experiment highlights the potential impacts, over short time scales, of changing environmental factors on the structure of various functional groups like small primary producers, parasites and saprotrophs which, in response, can modify energy flow in the planktonic food webs.

International audience; The abundance and composition of microbial communities were investigated during 2007 in Marennes Oléron Bay (France) in order to characterize the biological relationships governing the planktonic food web. Compared to the results of previous years, there was lower abundance and lower magnitude of variations in autotrophic and heterotrophic microbial entities in 2007. Using a Spearman rank correlation analysis, a significant link for biological abundance was only noted between bacteria and ciliates. However, an interesting relationship was highlighted between chlorophyll a and bacterial aminopeptidase and β-glucosidase exoenzymatic activities. Two characteristic periods of virus-bacteria uncoupling were observed in spring and autumn 2007. Using multivariate analysis, the clustering of monthly viral community structures (defined by RAPD-fingerprinting) was related to bacterial proteolysis activity and secondarily to flagellates. Spring and autumn were characterized by phytoplanktonic blooms of large cells (> 10µm) and small cells (< 10µm), respectively, during the virus-bacteria uncoupling phases. High predation by flagellates in the autumn, during a period of microbial food web activity, involved the highest viral fingerprint richness, inferring a top-down control in driving the number of virus-host systems. We discuss the proteolysis level as a descriptor in structuring viral assemblages and argue that changes in the quantity and quality of DOM may bridge phytoplankton to bacteria and reflect changes in phytoplankton composition.

Summary As agents of mortality, viruses and nanoflagellates impact on picoplankton populations. We examined the differences in interactions between these compartments in two French Atlantic bays. Microbes, considered here as central actors of the planktonic food web, were first monitored seasonally in Arcachon (2005) and Marennes-Oleron (2006) bays. Their dynamics were evaluated to categorize trophic periods using the models of Legendre and Rassoulzadegan as a reference framework. Microbial interactions were then compared through 48 h batch culture experiments performed during the phytoplankton spring bloom, identified as herbivorous in Marennes and multivorous in Arcachon. Marennes was spatially homogeneous compared with Arcachon. The former was potentially more productive, featuring a large number of heterotrophic pathways, while autotrophic mechanisms dominated in Arcachon. A link was found between viruses and phytoplankton in Marennes, suggesting a role of virus in the regulation of autotroph biomass. Moreover, the virus–bacteria relation was weaker in Marennes, with a bacterial lysis potential of 2.6% compared with 39% in Arcachon. The batch experiments (based on size-fractionation and viral enrichment) revealed different microbial interactions that corresponded to the spring-bloom trophic interactions in each bay. In Arcachon, where there is a multivorous web, flagellate predation and viral lysis acted in an opposite way on picophytoplankton. When together they both reduced viral production. Conversely, in Marennes (herbivorous web), flagellates and viruses together increased viral production. Differences in the composition of the bacterial community composition explained the combined flagellate-virus effects on viral production in the two bays.

As agents of mortality, viruses and nanoflagellates impact on picoplankton populations. We examined the differences in interactions between these compartments in two French Atlantic bays. Microbes, considered here as central actors of the planktonic food web, were first monitored seasonally in Arcachon (2005) and Marennes-Oléron (2006) bays. Their dynamics were evaluated to categorize trophic periods using the models of Legendre and Rassoulzadegan as a reference framework. Microbial interactions were then compared through 48 h batch culture experiments performed during the phytoplankton spring bloom, identified as herbivorous in Marennes and multivorous in Arcachon. Marennes was spatially homogeneous compared with Arcachon. The former was potentially more productive, featuring a large number of heterotrophic pathways, while autotrophic mechanisms dominated in Arcachon. A link was found between viruses and phytoplankton in Marennes, suggesting a role of virus in the regulation of autotroph biomass. Moreover, the virus-bacteria relation was weaker in Marennes, with a bacterial lysis potential of 2.6% compared with 39% in Arcachon. The batch experiments (based on size-fractionation and viral enrichment) revealed different microbial interactions that corresponded to the spring-bloom trophic interactions in each bay. In Arcachon, where there is a multivorous web, flagellate predation and viral lysis acted in an opposite way on picophytoplankton. When together they both reduced viral production. Conversely, in Marennes (herbivorous web), flagellates and viruses together increased viral production. Differences in the composition of the bacterial community composition explained the combined flagellate-virus effects on viral production in the two bays.

12 páginas, 6 figuras, 2 tablas., Batch culture experiments using viral enrichment were conducted to test the response of a coastal bacterial community to autochthonous (i.e., co-existing) or allochthonous riverine viruses. The effects of viral infections on bacterial dynamics and activity were assessed by epifluorescence microscopy and thymidine incorporation, respectively, whereas the effect of viral infection on bacterial community composition was examined by polymerase chain reaction-single strand conformation polymorphism 16S ribosomal RNA fingerprinting. The percentages of high nucleic acid-containing cells, evaluated by flow cytometry, were significantly correlated (r 2 =0.91, n=12, p, This work was supported by grants from the French ‘Programme National en Environnement Côtier’ (PNEC, ART 5), the ‘Contrat de Plan Etat Région’ (CPER 2000–2005) and the ‘Conseil Général de Charente-Maritime’ (PhD grant to J.-C. Auguet). EO Casamayor is a ‘Ramon y Cajal’ Fellow supported by project REN 2003-08333 from the Spanish Ministry of Education and Science (MEC) and the European Community. At the final writing period for this work, J.-C. Auguet benefited from a SEUI-MEC Spanish postdoctoral fellowship.

Changes in the composition of viral communities were investigated along a salinity gradient and at different times by means of transmission electron microscopy (TEM) and pulsed field gel electrophoresis (PFGE). Samples were collected in fresh (Charente River), estuarine (Charente Estuary), and coastal (Pertuis d'Antioche, French Atlantic coast) waters. Both methods revealed similar patterns in viral community structure with a dominance of small viral particles (capsid and genome size). Viruses with a head size below 65 nm made up 71 +/- 5% of total virus-like particles, and virus-like genomes (VLG) below 100 kb accounted for 89 +/- 9% of total VLG. Despite this apparent stability of virioplankton composition over spatial scale (salinity gradient), the occurrence of large viruses (capsid and genome size) in estuarine and seawater samples indicated the presence of viral populations specific to a geographical location. Temporal changes in the structure (capsid and genome size) of viral communities were more pronounced than those reported at the spatial scale. From January to May 2003, seasonal changes in viral abundance and bacterial production occurred concomitantly with an increase in viral genomic diversity (richness), suggesting that virioplankton composition was strongly linked to changes in microbial activity and/or in the structure of the host communities. Although PFGE and TEM yielded complementary results in the description of virioplankton structures, it seems that the use of PFGE alone should be enough for the monitoring of community changes.

International audience; To assess the in situ impact of oysters, Crassostrea gigas, on planktonic protist and bacteria communities and the potential contribution of protozoa to their food resource intake, the abundance and the diversity of protists and bacteria were followed in 2 Atlantic coastal ponds, with and without oysters. The protist biomass in such ponds was high, with a maximum in spring of 982 μg C l-1 and a minimum in winter of 179 μg C l-1. Whatever the season, the presence of oysters (20 m-2 corresponding to on average 23 mg dry weight m-2) induced a significant decrease in > 5 μm protist abundance. On the contrary, planktonic organisms < 5 μm, such as Chlorophyta flagellates and bacteria, developed similarly in both ponds. It can be assumed that such a depletion in micro-sized protists was especially related to the grazing activity of C. gigas, which efficiently retains > 5 μm particles. In spring, oyster grazing triggered dramatic changes in the protist community by lowering the taxonomic diversity. In autumn and winter, the presence of oysters deeply influenced the taxonomic structure of the protist communities: > 5 μm protists could only develop in the control pond, whereas they were removed by filtration into the oyster pond; on the contrary, < 5 μm protists that were not retained, were favoured in the oyster pond. The set of results showed that hetero/mixotrophic protists represent an important potential resource in coastal ponds: flagellates > 5 μm were the main protist resource for C. gigas; ciliates represented the second resource with a substantial contribution in autumn; diatoms and dinoflagellates, though efficiently removed represented a weak carbon resource. Our study supports the hypothesis that oysters may access to the strong bacterioplanktonic production through hetero/mixotrophic protists, which would thus allow the transfer of carbon from the microbial loop towards C. gigas.

International audience

A method was developed to analyse virus-like particles (VLPs) in seston-rich waters and to quantify their dynamics in a coastal marsh of the Bay of Biscay, French Atlantic coast. The method combined clarification and concentration steps with electron microscopy to obtain information on particle abundance, type and size distribution (e.g. presence of tailed phages, Fuselloviridae, etc.). The mean recovery rates of T2-phages using this method were 71 to 79%, higher than other published rates. The transmission electron microscopy (TEM) counts were validated with T2 plaque lysis assay and epifluorescent (DAPI-stained) particle counting: the TEM method was valid for environmental particle concentrations above 1 to 2 × 10 6 VLP ml -1 ; TEM counts were lower than T2- plaque counts (TEM/lysis median = 0.293) but higher than DAPI counts (TEM/DAPI median = 2.39). The method was used to evaluate the coupling between viral and bacterial dynamics in a marsh pond during 2 months. The VLP abundance varied from 1 to 30 × 10 6 ml -1 and the viral population was dominated by small particles (20 to 64 nm). Tailed phages, identified as bacteriophages, were always less abundant than non-tailed VLPs (4 to 23% of total virus), yet their dynamics were better linked with bacterial development than those of total virus. Our results demonstrate that the best way to characterise bacterial lysis from virus in seston-rich coastal environments would be to study the dynamics of tailed phages and virus size-classes rather than the commonly applied total VLPs.