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Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.

International audience; Since its identification in 2003, little has been revealed about the spread of grapevine Pinot gris virus (GPGV), an emerging grapevine virus. According to studies from Italy, GPGV transmission in the vineyard can be fast but progressive over the years. To gain new insights into the spread of GPGV infections, we tested 67 grapevines in a single vineyard parcel in southern France. These vines were sampled over 8 years (2013 to 2020) and tested for GPGV by reverse-transcription PCR using a new primer pair designed from the recently described genetic diversity of GPGV worldwide. While focusing on a portion of the samples (n = 20), we observed a drastic increase in newly GPGV-infected vines from 2014 (5%, 1 of 20) to 2015 (80%, 16 of 20) and 2016 (90%, 18 of 20). Infected vines were scattered throughout the vineyard with no distinct pattern of distribution, and some rare vines remained negative through 2020. Using all available genomic information, we performed Bayesian-based phylogeographic analyses that identified a major intravineyard transmission in 2014 to 2015. To test our model, we analyzed 47 additional grapevines and confirmed the outbreak of GPGV in 2015, validating our in silico projection. Interestingly, some grapevines remained negative throughout the study, in spite of their close proximity to infected plants. These results raise questions about the dynamics of vector populations and environmental conditions that may be required for virus spread to occur in the vineyard.

The recently described member of the genus Trichovirus grapevine Pinot gris virus (GPGV) has now been detected in most grape-growing countries. While it has been associated with severe mottling and deformation symptoms under some circumstances, it has generally been detected in asymptomatic infections. The cause(s) underlying this variable association with symptoms remain(s) subject to speculations. GPGV genetic diversity has been studied using short genomic regions amplified by RT-PCR but not so far at the pan-genomic level. In an attempt to gain insight into GPGV diversity and evolutionary history, a systematic datamining effort was performed on our own high-throughput sequencing (HTS) data as well as on publicly available sequence read archive files. One hundred new complete or near complete GPGV genomic sequences were thus obtained, together with 69 new complete genomes for the other grapevine-infecting Trichovirus, grapevine berry inner necrosis virus (GINV). Phylogenetic and diversity analyses revealed that both viruses likely have their origin in Asia and that China is the most probable country of origin of GPGV. However, despite their common taxonomy, origin, and host, these two trichoviruses display very distinct genetic features and evolutionary traits. GINV shows an important overall genetic diversity, and is likely evolving under a balancing selection in a very restricted region of the world. On the contrary, GPGV shows a worldwide distribution with a modest genetic diversity and presents a strong selective sweep pattern. Taken together, these results show how two closely related trichoviruses differ drastically in their evolutionary history and epidemiological success. Possible causes for these differences are discussed. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

International audience; The 161-49 C is a rootstock widely used in France. In 2010, its surface represented more than 4% of potential of the nurseries (82 ha), ranking in 8th position for rootstock varieties in France (statistics 2011 from FranceAgriMer). Although ten clones are officially registered in the French catalogue, clones 176 and 198 represent 85% of the total potential of production. For 6-8 years, severe declines of young vines grafted with this rootstock have been reported in several vineyards of Languedoc (south of France). While the number of declines increased in Languedoc, similar cases were reported in other French and foreign vineyards. Given the importance of the problem for the viticulture industry, a survey was performed in France to identify affected plots, assess the extent of decline, and to try to identify factors potentially involved in the decline. The first goal of this paper is to report main results of this survey, which was performed on about 230 plots. Another aim of this study is to describe the specific symptoms associated with the syndrome, which can be confused with several other issues (tyloses, black-foot disease, viruses, physiological problems, soil infertility, etc.). Vines sampled in several plots were submitted to a range of observations and anatomical analyses. In this paper, we present and discuss the symptoms and the anatomy alterations associated with the disorder.

(IF 1.70; Q1); International audience; In organic-rich shallow habitats, benthic macrofauna is known to play a major role in the geochemical functioning of surficial sediments through its metabolism, as well as its bioirrigation and/or bioturbation activity. In this paper, the effects of benthic macrofauna on metabolic fluxes at the sediment-water interface were studied at four dates, from winter to late summer, on two major macrobenthic communities of the eastern English Channel (macrotidal system): the fine sand Abra alba community (2 stations) and the sandy gravel Ophiothrix fragilis community (1 station). Oxygen and ammonium fluxes showed temporal changes that could be attributed to the variation of sea water temperature. Once the effect of temperature removed (using Q10 = 2.5), the average fauna mediated fluxes (FFauna) represented respectively 77% and 76% of average total fluxes. Considering the whole dataset, species number and biomass showed a significant correlation with fauna mediated fluxes of O2 and NH4+, while the relationships with abundance were not significant. The species composition of the community might influence ecosystem functioning, but in the present study, functional groups have a very poor relationship with FFauna (O2) and FFauna (NH4+). Despite the presence of engineer species, establishing general and simple rules to link macrofaunal parameters to functional attributes remains very difficult, suggesting that communities rather followed the idiosyncrasy and rivet hypothesis.

Grapevine hammerhead viroid-like RNA (GHVd) is a poorly characterized circular, single-stranded RNA molecule discovered through the bioinformatic analysis of small interfering RNAs of Italian grapevines of the Pinot noir variety (Wu et al., 2012). It is 375 nucleotides long and shares many structural features of viroids or of some small circular satellite RNA molecules. In particular, it has a predicted secondary structure similar to those of members of the Pelamoviroid genus with a branched region stabilized by a kissing-loop pseudoknot, and an extensively base-paired arm that encodes in its plus and minus strands self-cleaving hammerhead ribozymes (Wu et al., 2012; Giguere et al., 2014). Outside of conserved nucleotides in these hammerhead ribozymes, the primary sequence of GHVd has no significant similarities to any entries in Genbank. Besides the original Italian Pinot noir grapes, GHVd has been detected in Pinot noir plants of the 115 clone grown in California (Wu et al., 2012). Given that infectivit...

UMR BFP - Equipe Virologie; First Report of Grapevine asteroid mosaic-associated virus Infecting Grapevine (Vitis vinifera) in France

International audience; Distributions of microphytobenthos are highly heterogeneous at scales as small as a few centimetres. However, the sampling protocols currently used for the absolute determination of microphytobenthos biomass through chlorophyll a concentration measurements in surface sediments are too limited to take this variability into account, typically relying on 3-5 samples taken within a randomly located 1 m2 quadrat in a given environment. We address this issue by objectively and quantitatively inferring the minimum number of samples required to obtain reliable estimates of microphytobenthos biomass on the basis of high-resolution sub-sampling (225 regularly spaced samples) within each of nine 1 m2 quadrats at an unvegetated sheltered intertidal sandbank of the Gold Coast (Queensland, Australia). The results were generalised using data obtained in previous studies on an exposed sandy shore and on sheltered estuarine sandy muds of the Eastern English Channel. Estimates of chlorophyll a concentration exhibited a high degree of heterogeneity, both between and within quadrats. The number of samples needed to estimate the average chlorophyll a concentration, and hence mean microphytobenthos biomass with 95% confidence intervals, ranged from 15 to 115, and mainly depended on the presence of global and local gradients within the quadrats. These results have major implications for intertidal ecology by implying a possible systematic bias in the measurement of both microphytobenthos biomass and production of up to 40%. Finally, we emphasise that this issue can be circumvented using field spectrometry or PAM fluorescence measurements coupled with traditional sediment sampling techniques, and urge for unified protocols to be adopted for the routine use of these combined methods

International audience; This study aimed to explore the spatial and temporal variability of benthic metabolism in a temperate mesotidal lagoon. This was achieved by measuring fluxes of CO2 in static chambers during emersion, both under light and dark conditions. Three sample sites were selected according to their tidal level (upper or mid), their sediment type (sand or mud) and the presence/absence of the seagrass Zostera noltei. The three sites were investigated at three seasons (end of winter, spring and beginning of autumn). At each site and each season, three benthic chambers were used simultaneously in successive incubations over the emersion period. The sediment chlorophyll-a content varied seasonally in the upper sands (reaching 283 mg.m− 2 in spring) but not in the mid muds (averaging 142 mg m− 2 in bare muds and 186 mg m− 2 in muds covered by seagrass). The maximum sediment CO2-uptake under light was 9.89 mmol m− 2 h− 1 in the mid bare muds, in early autumn. The maximum sediment CO2-release under darkness was 6.97 mmol m− 2 h− 1 in the mid muds covered by seagrass, in spring. Both CO2-fluxes measured in the light and in the dark increased over periods of emersion. This increase, not related to light nor temperature variations, could be explained by changes in the amount and chemistry of pore water during the air exposure of sediments. The benthic trophic state index, based on the maximum light CO2-flux versus maximum dark CO2-flux ratio, assigned to each site at each season indicated that the sediments were net autotrophic in spring in upper sands and in mid muds covered by seagrass and highly autotrophic in other cases. The most autotrophic sediments were the mid-level bare muds whatever the season. The relevance of this index is discussed compared to carbon annual budget.

International audience; The photosynthetic activity and productivity of four dominant canopy intertidal macroalgae were measured under emersion and immersion, at saturating light levels (PAR > 300 μmol photons m−2 s−1), and compared at two sites (eastern and western English Channel) in spring and summer. The photosynthetic activity of thalli was measured by the electron transport rate (ETR) using pulse-amplitude modulated (PAM) fluorescence and the productivity of individuals and of communities was measured by carbon fluxes in closed chambers. Under emersion, when thalli were still hydrated, the uppermost species Pelvetia canaliculata had higher photosynthetic activity (mean ETR between 327 and 460 μmol e− m−2 s−1) and individual gross productivity (between 60 and 212 μmol C gDW−1 h−1) than the lowermost species Laminaria digitata (mean ETR between 24 and 53 μmol e− m−2 s−1 and gross productivity between 2 and 38 μmol C gDW−1 h−1), whatever the site and season. P. canaliculata had higher ETR in air than underwater (averaged 146 μmol e− m−2 s−1) and L. digitata had lower ETR in air than underwater (averaged 112 μmol e− m−2 s−1), while they exhibited respectively 3 and 5 times higher gross productivity underwater. At the community scale, the low mid-shore zone of Fucus serratus had the highest mean gross productivity under emersion (47 mmol C m−2 h−1) while rates were higher for the uppermost than lowermost zone at the eastern site (average 20 and 6 mmol C m−2 h−1 respectively) and of the same order of magnitude for both zones at the western site (about 30 mmol C m−2 h−1). Finally, the variability of under emersion primary productivity among sites and seasons was reduced when the measurements were performed on entire communities compared to isolated individuals of the dominant species.

International audience; Shorebird populations are declining worldwide due to the combined effect of climate change and anthropogenic forcing, the ongoing coastal urbanisation amplifying the alteration of their habitat in both rate and magnitude. By focusing on a highly anthropogenically-influenced region in Northern France, we studied the impact of a seawall construction on wintering shorebird populations through potential alterations in the abundance and availability of their food resources. We concurrently investigated changes in the spatial distribution of muddy-sand beach macrobenthic communities between two periods of contrasting anthropogenic impacts and examined year-to-year trends of wintering shorebirds. Our study reveals that the seawall construction led to a major spatial reorganisation of the macrobenthic communities with a drastic reduction of the muddy-sand community. However, no relation between macrobenthic changes and shorebird abundances was detected. Fluctuations in shorebird abundances appeared to be congruent with flyway population trends. This result suggests that the response of shorebirds to human-induced perturbations is much more complex than expected. While an assessment of potential disturbances induced by coastal engineering constructions is needed, the pathways by which alterations could propagate through an ecosystem are not linear and as such difficult to determine. Ecosystems appear as complex adaptive systems in which macroscopic dynamics emerge from non-linear interactions at entangled smaller/larger scales. Our results confirm that an in-depth knowledge of the local, regional and global factors that influence trends of shorebirds and their habitat use is essential for accurate and effective management and conservation strategies.

International audience; Comprehending marine invasions requires a better knowledge of the biological traits of invasive species, and the future spread of invasive species may be predicted through comprehensive overviews of their distribution. This study thus presents the current distribution of a non-indigenous species, the Asian shore crab Hemigrapsus takanoi, as well as the species population characteristics (size distribution and cohorts), based on a five-year survey (2008e2012) along the French coast of the English Channel. Two large populations were found near harbours: one on the Opal Coast (where density reached 61 ! 22 ind.m"2, mean ! s.d., in Dunkirk harbour) and one on the Calvados coast (density up to 26 ! 6 ind.m"2, mean ! s.d, in Honfleur harbour). H. takanoi exhibited a short life cycle, a rapid growth, an early sexual maturity and a high adult mortality. These features, combined with previously described high fecundity and high dispersal ability, endow this species with an 'r-selected strategy'. This strategy, which usually characterises species with a high colonisation ability, would explain the success of H. takanoi for colonising the French coast of the Channel. However, the species was found only in harbours and their vicinity; H. takanoi thus exhibited a discontinuous distribution along the 700 km of coastline. These results are discussed regarding sediment preference and potential introduction vectors. Hemigrapsus takanoi is now considered as established on the French coast and further studies are needed to evaluate the consequences of its introduction on the structure and functioning of the impacted shores

Funding provided by French National Centre for Scientific Research/INSU program EC2CO-MicroBien (Microbiologie Environnementale -BIOPOURPRE Project), European Community (ASSEMBLE grant agreement n° 227799), Region Pays de la Loire (France), Marine Alliance for Science and Technology for Scotland and the Scottish Funding Council and participating institutions. There is a relative absence of studies dealing with mats of purple sulphur bacteria in the intertidal zone. These bacteria display an array of metabolic pathways that allow them to disperse and develop under a wide variety of conditions, making these mats important in terms of ecosystem processes and functions. Mass blooms of purple sulphur bacteria develop during summer on sediments in the intertidal zone especially on macroalgal deposits. The microbial composition of different types of mats differentially affected by the development of purple sulphur bacteria was examined, at low tide, using a set of biochemical markers (fatty acids, pigments) and composition was assessed against their influence on ecosystem functions (sediment cohesiveness, CO2 fixation). We demonstrated that proliferation of purple sulphur bacteria has a major impact on intertidal mats diversity and functions. Indeed, assemblages dominated by purple sulphur bacteria (Chromatiaceae) were efficient exopolymer producers and their biostabilisation potential was significant. In addition, the massive growth of purple sulphur bacteria resulted in a net CO2 degassing whereas diatom dominated biofilms represented a net CO2 sink. Publisher PDF

International audience; A major challenge in ocean and coastal management is to find simple ways to evaluate the health of such complex ecosystems. This task may prove complicated as selection criteria needs to be established for choosing appropriate indicators and evaluation tools which do not mask or leave out inherent ecosystem properties and dynamics. Here, we review some empirical analyses and modelling techniques which can be used to derive environmental health indicators. With a series of case studies ranging from the combined use of structural and functional attributes of the system, to modelling outputs that integrate the biological and physical environments, we illustrate the usefulness and complementarities of these methods to assess ecosystem health. The choice of relevant indicators will depend on the ecological questions raised as well as the biological and habitat components considered which can range from a single level (individual or population) to multiple levels (community or ecosystem-based indicators) in the ecosystem. Each method has its own capabilities and limitations that may render it useful or insufficient in some cases. We suggest, however, that, whenever possible, the combination of ecological attributes and tools should be used to improve our knowledge and assessment of marine ecosystems for better management and conservation in the future.

International audience; The use of benthic indicators has increased dramatically during the last decades. The number of articles published on the subject, as well as the number of citations, has been particularly increasing since the early 90's, notably in relation with the implementation of directives for the management of aquatic/marine ecosystems such as the Water Framework Directive and the Marine Strategy Framework Directive. Current benthic indicators suffer from severe drawbacks and their practical use is still discussed and might have reached a dead end. Indicators based on species composition are not totally satisfactory, mainly because they exhibit a high spatio-temporal variability (e.g. variable at both seasonal and pluri-annual scales) and are user-dependent (e.g. divergent results from US orEuropeexperts.) In turn, modifications of behaviour, metabolism, phenotype or stable isotopes composition in invertebrates usually occur at short time scales, compared to detectable changes in community composition, and makes their use particularly relevant as indicators of perturbation. It is argued in this paper that these functional indicators might be relatively quickly implemented in the intertidal, and represent an effective alternative to current benthic indicators.

International audience; The invasion process can be described as a succession of stages initiated by the transport of organisms from their native range to a new area where they persist, proliferate and spread. It is important to monitor the demographic development of invaders for management purposes. This study focuses on the different stages of population development during the invasion process and underlines the importance of understanding and monitoring the 'persistence phase'. The distribution of Hemigrapsus sanguineus (Asian shore crab) in the English Channel, along the French coast, was first undertaken in 2008. In 2010, 35 sites were surveyed and it appeared that the abundance of this species had already established a 2-5 fold increase since 2008. The present study presents the geographical distribution of H. sanguineus in 2011 and 2012 which includes a further 39 sites (72 sampling stations in 2012). All populations observed during previous years persisted in 2011 and 2012. In 2012, H. sanguineus was detected at 61 sites; 36 intensely colonised (including 3 newly colonised sites compared to 2011); 22 had trace numbers and 3 sites had 'proven presence'. In addition to males with carapaces up to 39 mm width (CW), abundances increased by a factor of 2 since 2010, which testifies for the naturalized status of the species along the French coast of the English Channel. Since 2008, La Hougue proved to be the most abundantly colonised site along the French coast. By 2011 it had an average density of 101±19 ind.m-2, with an abundance of 258±54 individuals (under 30 boulders). Populations were subsequently halved in 2012. Increasing densities and abundances recorded between 2008 and 2011 at la Hougue suggest that H. sanguineus had reached the 'expansion phase', but the dynamics of H. sanguineus populations at the most colonised sites (12 sampling sites with abundance >200 individuals under 30 boulders), suggest that maximum values had already peaked and that the 'persistence phase' was probably reached. The implementation of pluri-annual surveys seems of prime importance to correctly evaluate population dynamics of alien species.

Carbon dioxide (CO2) exchanges between a tidal flat (Wadden Sea, Netherlands) and the atmosphere were measured during a three-year survey. CO2 exchanges were monitored during 1-2 days each month between September 2006 and September 2009 using a flux chamber. The flux of CO2 was separated into two fluxes: the dark flux and the gross light flux, with the dark flux representing the flux during darkness and the gross light flux the difference between the net CO2 flux (measured under light) and the dark flux. It was argued that dark and light fluxes may deviate from respiration and photosynthesis, as the fluxes between wet tidal sediment and the atmosphere are affected by the partial pressure of CO2 in pore water, which is only gradually changed by sources and sinks of CO2 in the sediment. Light and dark fluxes were empirically related to environmental parameters in order to interpolate between succeeding measurements. The dark flux appeared to increase with temperature and the light flux became more intense with increasing irradiance with signs of saturation at high light levels on many but not all measurement days. These relations with environmental parameters showed seasonal and inter-annual variability. Fluxes were negligible just after the site was emersed and it took up to 3 h of emersion until fluxes were adapted to environmental conditions. Dark and light fluxes both showed strong seasonality with high values in summer and low values in winter. The tidal flat appeared as a source of atmospheric CO2 in the first year of measurement (+0.35 mol CO2 m(-2) yr(-1)) and a sink in the following two years (-1.59 and -0.72 mol CO2 m(-2) yr(-1)). Since the source of CO2 was observed during an extremely warm year, we suggest that climate warming might influence the carbon budget of tidal flats. (C) 2011 Elsevier Ltd. All rights reserved.

International audience; The European Marine Strategy Framework Directive (MSFD 2008/56/EC-17/06/2008) will be implemented in regions/subregions determined by their hydrology, oceanographic and biogeographic features. In this framework, Dauvin (2012) claimed that the English Channel (EC) is characterized by hydrologic, oceanographic and biogeographic features that support its division in two main ecosystems: the Western Basin (WBEC) and the Eastern Basin (EBEC). We think that this statement is controversial and that the conclusions drawn by Dauvin (2012) were not supported by the data presented, especially regarding the use of the term 'ecosystem'. We therefore re-evaluated this viewpoint with regard to the data and terminology used....

International audience; Successful grafting in plants requires the development of a functional vascular system between the scion and the rootstock. Understanding the spatial organization of the graft interface is important to the evaluation of new rootstock genotypes and to the development of new grafting technologies. Until now the graft interface has only been studied using 2D classical histology and low resolution 3D magnetic resonance imaging. Here we investigate the ability of X-ray tomography to examine the graft interface of Vitis vinifera in high resolution and in 3D. Data were collected using a Skyscan 1076, scanning parameters, such as. X-ray energy, filter selection, pixel size and rotation angles, were optimized to study the particularities of the graft interface. The X-ray tomography technique was then used to evaluate graft quality. Two young vines were compared; one graft was classified as of 'good' quality, whereas the other was classified as of 'bad' quality. We were able to distinguish the "omega cut", the pith, the phloem and the xylem vessels in the images. The analysis shows several differences between the two vines. In the good graft, tissues appear well-connected in the wood and phloem, and had a regular structure; the wood appears homogenous with a lot of vessels that form a compact mass. By contrast, in the bad graft, the structures appear disorganized and not completely connected. Numerous new vessels, continuous between the scion and the rootstock, are visible in the "good graft" whereas only few ones are visible in the "bad one". It is the first time, to our knowledge, that 3D imaging of the graft interface and the vascular connections across it have been reported, opening new avenues for graft quality assessment in woody plants.

International audience; In situ measurements of both community metabolism (primary production and respiration) and PAM fluorometry were conducted during emersion on intertidal sediments in the Mont Saint-Michel Bay, in areas where oysters and mussels were cultivated. Results highlighted a low benthic metabolism compared to other intertidal areas previously investigated with the same methods. Comparisons between gross community primary production and relative electron transport rates confirmed this statement. More specifically, primary productivity remained very low all over the year, whereas the associated microalgal biomass was estimated to be high. We suggest that the microphytobenthic community studied was characterized by a self-limitation of its primary productivity by its own biomass, as previously shown in Marennes-Oléron Bay for example. The almost permanent high biomass would represent a limiting factor for micromigration processes within the first millimetres of the sediment. This could be explained by very low resuspension processes occurring in the western part of the bay, enhanced by the occurrence of numerous aquaculture structures that could decrease tidal currents in the benthic boundary layer

The eastern English Channel, the narrow channel of water separating northern France and southeast England is an area of intense human use of the array of resources concentrated into its relative small area. The vulnerability of living resources and their habitats brought together French and British maritime experts within a common project (called CHARM): to create an atlas of marine resource habitats in the eastern English Channel so as to provide planners and decision-makers with the necessary information to help managing the use of its living and non-living resources. This multidisciplinary and richly illustrated atlas provides abundant information on the legal framework and physical environment; benthic invertebrates, fish and their habitats; fishing activities; and a first attempt at developing a trophic network model (using ECOPATH software) and a marine conservation planning exercise (using MARXAN software, at a spatial resolution of 25 km(2)). Although most of the data used were collected elsewhere, some were collected especially for the project. Similarly, most of the analyses performed on the data where entirely original for this geographical area. The CHARM atlas has significantly improved the knowledge about the eastern Channel while contributing to the recognition that such holistic or multidisciplinary approaches to exploited marine systems are necessary to efficiently and durably manage their resources use., La Manche orientale, ce bras de mer qui sépare l’Angleterre de la France, est une zone très riche d’un point de vue écologique et soumise à une forte utilisation anthropique d’une gamme de ressources concentrées sur une superficie relativement faible. La fragilité des ressources marines vivantes et leurs habitats a rassemblé des experts maritimes français et britanniques autour d’un projet commun (nommé CHARM) dans le but de réaliser un atlas des habitats des ressources marines de laManche orientale. Cet atlas contient les informations nécessaires aux planificateurs et décideurs pour une meilleure gestion des ressources marines, vivantes ou non. Dans ce document pluridisciplinaire, richement illustré, on peut trouver des informations sur le cadre juridique et l’environnement, les invertébrés benthiques, les poissons et leurs habitats ; les activités de pêche ; et également sur le développement d’un modèle de réseau trophique (utilisant le logiciel ECOPATH) et un premier exercice de planification spatiale de la conservation (utilisant le logiciel MARXAN, à une résolution spatiale de 25 km2). Bien que la plupart des données aient été collectées en dehors du projet, certaines l’ont été spécialement pour le projet. De même, la plupart des analyses faites sur ces données sont entièrement inédites pour cette zone géographique. L’atlas CHARM contribue de façon significative à une meilleure connaissance de la Manche orientale tout en démontrant la nécessité de développer ce genre d’approche intégrée ou pluridisciplinaire sur les milieux marins exploités, afin de fournir les connaissances scientifiques nécessaires pour gérer efficacement et de manière durable l’utilisation de leur ressources.

From 1999 to 2005, studies carried out in the frame of regional and national French programs aimed to determine whether the Phaeocystis globosa bloom affected the intertidal benthic communities of the French coast of the eastern English Channel in terms of composition and/or functioning. Study sites were chosen to cover most of the typical shore types encountered on this coast (a rocky shore, an exposed sandy beach and a small estuary). Both the presence of active Phaeocystis cells and their degradation product (foam) did have a significant impact on the studied shores. The primary production and growth rates of the kelp Saccharina latissima decreased during the bloom because of a shortage of fight and nutrient for the macroalgae. On sandy sediments, the benthic metabolism (community respiration and community primary production), as well as the nitrification rate, were enhanced during foam deposits, in relation with the presence of bacteria and active pelagic cells within the decaying colonies. In estuarine sediments, the most impressive impact was the formation of a crust at the sediment surface due to drying foam. This led to anoxic conditions in the surface sediment and resulted in a high mortality among the benthic community. Some organisms also tended to migrate upward and were then directly accessible to the higher trophic level represented by birds. Phaeocystis then created a shortcut in the estuarine trophic network. Most of these modifications lasted shortly and all the systems considered came back to their regular properties and activities a few weeks after the end of the bloom, except for the most impacted estuarine area. (C) 2008 Elsevier Ltd. All rights reserved.

International audience; In order to provide an accurate annual rate of net benthic community production, community photosynthetic response to incident irradiance and respiration were measured at different times of the year, at mid-tide level on the muddiest part of the Mont Saint-Michel Bay. As the water turbidity prevented any photosynthesis by the microphytobenthos during immersion periods, primary production was measured only during emersion periods. In contrast respiration was expected to vary according to the tidal cycle and was measured during both emersion and immersion periods. Primary production and respiration rates under emersion were assessed using in situ infra-red gas analysis of CO(2) exchange measured in a benthic chamber. Respiration rates under immersion were assessed through total CO(2) concentration variations in incubated cores. When respiration rate was considered constant over a day and equal to the rate measured under emerged conditions, the community respiration was 54.56 gC m(-2) yr(-1). Taking into account the variations of respiration during the emersion/immersion cycle, community respiration increased to 101.76 gC m(-2) yr(-1) (86% increase). Assuming that community primary production varied as a function of irradiance from the time of exposure until flooding, GCP was 53.22 gC m(-2) yr(-1) when calculated with theoretical irradiance and 45.86 gC m(-2) yr(-1) after correction for cloudiness (14% decrease). Then, by integrating the effect of vertical migration of microphytobenthos, the rate was adjusted to 23.49 gC m(-2) yr(-1) (49% decrease). The net community production budget, calculated as the difference between the GCP and the CR budgets taking into account the corrections described above, was -78.27 gC m(-2) yr(-1). This example of annual budget calculation highlights the need to integrate several processes occurring over various time scales to accurately reflect the metabolic balance of a system The results also confirmed the heterotrophic status generally suggested for intertidal muddy sediments. (C) 2009 Elsevier Ltd. All rights reserved.

International audience; Fatty acids (FAs) profiles and stable isotope signatures of the ghost shrimp, Trypaea australiensis and the soldier crab, Mictyris longicarpus were determined at an unvegetated sandbank of Southport (Gold Coast, Queensland, Australia), in November 2005 and February 2006. Additionally, the FAs composition of the faeces and feeding pellets of M. longicarpus and the surface sediment at the study site were also analysed. Trypaea australiensis was found to selectively feed principally on benthic diatoms, as revealed by the high contribution of the marker lipid (20:5 (n-3)) to tissue total FAs and the delta 13C and delta 15N isotopic signatures of shrimp tissues. Although the diet of T. australiensis did not change between the two sampling periods, the shrimps appeared to reduce their feeding activity in summer, presumably in relation to a restricted metabolism, as revealed by a decrease in the contribution of the microalgal markers in their tissues. The FAs composition of the tissues of the soldier crab indicated that bacteria and diatoms constituted the base of its diet (contributions of branched 15:0 and 17:0, 18:1 (n-7) and 20:5 (n-3)). However, the isotopic signatures of the crabs suggested that meiofauna may represent an intermediate link between the crab and these micro-organisms

Short-term variability in benthic community primary production was studied during the course of emersion on a study site located in the Bay of Somme (eastern English Channel, France). Primary production was estimated at the community level through in situ measurements of carbon dioxide fluxes (infra-red analysis) in benthic chambers. Throughout the emersion period, gross com- munity production (GCP) exhibited strong variations that were strongly correlated with natural vari- ations in light. Light response curves explained the variations in GCP during the greater part of the emersion period, and vertical migrations of the microphytobenthos were suggested to explain the remaining variations (i.e. just before or just after immersion of the study site). A time lag was observed between the start of emersion and the maximum GCP, which was positively correlated with the time lag between emersion and local noon. The introduction of this time lag within the annual budget calculation enhanced production variability at a 2 wk time scale (i.e. tidal cycle), but light variability at the small time scale (i.e. cloudiness) remained the major factor inducing production vari- ability. Results highlighted that omitting the time lag between emersion time and the maximum GCP within annual budget calculations led to large overestimations of annual GCP, since the annual bud- get for the study site was recalculated as being 67 g C m -2 yr -1 compared to 110 g C m -2 yr -1 when the short-term variability was not taken into account.

Benthic community metabolism during emersion was measured in a three-year survey by monitoring CO2 fluxes in benthic chambers on an exposed sandy beach of the eastern English Channel (Wimereux, France). The three-year chronology of variations in benthic metabolism was characterised by a high variability around a low value for gross community primary production (GCP: 17.47 ± 40.85 mgC m−2 h−1, mean ± SD) and community respiration (CR: 1.66 ± 1.97 mgC m−2 h−1, mean ± SD). Although benthic metabolism remained low most of the time, some high values of primary production and respiration were occasionally detected. High primary production rates (up to 213.94 mgC m−2 h−1 measured at the end of summer) matched with the development of Euglena sp., together with the occurrence of phytoplanktonic species on the sediment, whereas high community respiration rates were detected at the end of spring on Phaeocystis sp. foam deposits. Community respiration was positively correlated with bacterial abundance, suggesting that CR was mainly supported by microfauna.

We compared 3 simple techniques for estimating the concentration of microphytoben- thos chlorophyll a at the sediment surface using high spectral-resolution field spectra. The tech- niques are based on relationships established between chlorophyll a (chl a) absorption at ~673 nm estimated from field reflectance spectra and chl a concentration in field samples. For ease of applica- tion, the best approach should provide an estimate that is independent of the physical properties of the sediment such as grain size, moisture content, etc. and of sediment type and illumination condi- tions. To achieve as comprehensive a picture as possible, tidal flats from the French shore of the east- ern English Channel that differed in sediment type and dynamics were studied at low tide and at var- ious times of the year in order to cover seasonal blooms and illumination variations. The preliminary results show that all 3 methods are fairly robust (R 2 > 0.8), with very little difference between them, indicating little influence of the measurement conditions on reflectance in the wavelength range used (570 to 720 nm) and great stability of the instrument (a portable field spectrometer) used in the field. Validation of the 3 approaches was made with further, more recently acquired data set, and a very close correlation (R 2 > 0.93, slope ~1) was found between measured and estimated chl a con- centrations for all 3 techniques at the range of chlorophyll concentrations encountered that time at the Baie de Somme site (50 to 200 mg m -2 ). The influence of sampling strategy and sediment optical properties with respect to spectral signatures must, however, be investigated in more detail. More measurements are required to fully validate the relationships found and to ensure that they are generally applicable to most intertidal flat environments.

This paper describes a closed-chamber method for measuring CO2 fluxes in intertidal soft sediments during periods of emersion. The method relies on closed-circuit incubations of undisturbed sediment and measurement of CO2 exchanges using an infrared gas analyser. The method was assessed during field experiments, both in light and dark conditions, on an exposed sandy beach and in an estuary. The rates of gross community production measured under moderate diance (4.2 mg C m(-2) h(-1) on the exposed sandy beach and 35 mg C m(-2) h(-1) in the estuary) are in good agreement with rates reported in the literature. In conjunction with appropriate sampling strategies, this method can be useful for estimating and comparing production of intertidal areas or for assessing factors that influence production.