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The three sympatric angel shark species occurring in the Mediterranean – Squatina squatina (the angelshark), Squatina aculeata (the sawback angelshark), and Squatina oculata (the smoothback angelshark) – are all classed as Critically Endangered on the International Union for Conservation of Nature (IUCN) Red List. There is a clear need to better quantify their current status, using appropriate non-destructive methods, to help inform future conservation measures. This study introduces an environmental DNA (eDNA) assay able to detect and distinguish S. aculeata, S. oculata, and S. squatina in the Mediterranean Sea by combining probe-based quantitative polymerase chain reaction (qPCR) technology and Sanger sequencing. The assay targets a 173-bp barcode in the mitochondrial cytochrome c oxidase I (COI) gene. It was tested in silico, in vitro on tissue-extracted DNA, and on eDNA extracted from filtration samples. This genus-specific assay was applied to detect the presence of S. squatina in eDNA samples collected in Corsica, France. The target barcode was found in seven of 76 eDNA samples, revealing the presence of S. squatina in north-western Corsica, where the shark has never been observed, and confirming its existence on the eastern coast. The study also demonstrates that using eDNA sampling, based on 30 L of seawater filtered close to the substrate with a waterproof peristaltic pump, it was possible to detect the eDNA of this rare benthic species. The results of detection can help identify critical areas for angel shark conservation and facilitate the development of local public awareness initiatives. This novel qPCR assay should be used for future applications in the Mediterranean and eastern Atlantic targeting angel sharks to better identify the remaining populations. In this study the qPCR assay was applied for S. squatina eDNA, but application to S. aculeata and S. oculata still needs to be validated in the field.

Aim Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors. Location Tropical, temperate and polar coastal areas. Time period Present day. Major taxa studied Marine fishes. Methods We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.

To mitigate the ongoing threats to coastal ecosystems, and the biodiversity erosion they are causing, Marine Protected Areas (MPAs) have emerged as powerful and widespread conservation tools. Strictly no-take MPAs, also called marine reserves, undeniably promote fish biomass and density, but it remains unclear how biodiversity responds to protection. Identifying which facets of biodiversity respond to protection is critical for the management of MPAs and the development of relevant conservation strategies towards the achievement of biodiversity targets. We collected 99 environmental DNA (eDNA) samples inside and outside nine marine reserves in the Mediterranean Sea to assess the effect of protection on 11 biodiversity indicators based on fish traits, phylogeny and vulnerability to fishing. We controlled for the effect of environmental heterogeneity (habitat, bathymetry, productivity, temperature, and accessibility) using a Principal Component Analysis, and for spatial autocorrelation due to potential unmeasured factors. We found a positive and significant effect of protection on only 3 out of 11 indicators: functional and phylogenic diversity but also the ratio between demerso-pelagic and benthic species richness. Rather, total fish richness responded significantly and negatively to protection. We did not detect any significant effect of protection on threatened and elasmobranch species richness, probably due to their large home range compared to the size of Mediterranean marine reserves. Synthesis and applications: Our findings highlight the importance of looking beyond the mere number of species to fully depict and understand the effect of marine reserves on biodiversity and evaluate the effectiveness of conservation measures. Rather, we propose a dashboard of three eDNA-based indicators that can provide an early signal of ecosystem deterioration or recovery. eDNA metabarcoding offers a powerful tool to supply site-specific and standardized taxonomic-, phylogenetic- and trait-based biodiversity assessments, in complement to other classical technics, such as visual censuses or video surveys, able to estimate species abundance but also individual life-stage and size.

The Mediterranean seagrass Posidonia oceanica, which provides highly valuable ecosystem services, is subject to increasing anthropogenic pressures, causing habitat loss or fragmentation. Whilst airborne images and acoustic data can be used for monitoring seagrass coverage at a macro-scale and over long time periods, monitoring its health in the short term requires precision mapping in order to assess current regression/progression of individual meadows. However, current fine-scale underwater techniques in the field are imprecise and time-demanding. We propose an automatic classification approach based on underwater photogrammetry for an operational, cost- and time-effective fine-scale monitoring method. The method uses a property of the sparse cloud generated during bundle adjustment—the reconstruction uncertainty—to map seagrass patches. The mean precision, recall and F1 score of the method over 21 study sites with different morphologies were 0.79, 0.91 and 0.84, respectively. However, the fragmentation level of the meadows had a significant negative effect on classification performances. The temporal monitoring of 3 sites using this method proved its operability and showed a positive evolution index of the corresponding meadows over a period of 3 yr. This method is generalizable for most encountered configurations and can be integrated in a large monitoring system, as it enables the production of numerous seagrass maps over a short period of time. Moreover, our methodology could be generalized and applied in the study of other submerged aquatic vegetation by adjusting the method’s parameters.

International audience; Assessing non-material nature contributions to people has become one major challenge in biodiversity sciences. Among them, the aesthetic value of biodiversity is of strong importance as it contributes to human well-being and increases the collective willingness to engage in conservation efforts. Using the endangered coralligenous reefs along the French Mediterranean coastline as a case study, we propose a quantitative approach to estimate the aesthetic and ecological values of a marine ecosystem. We combined human image evaluation and deep learning algorithms to provide a quantitative estimation of the aesthetic value of 7692 photographic quadrats among 160 stations located between 20 and 90 m depth and gathered on 95 sites. To understand how aesthetic value is related to biodiversity metrics, environmental variables and anthropogenic pressures we used a structural equation modelling approach. We found that taxonomic diversity and species composition explained a significant part of the aesthetic value of the coralligenous reefs. Taxonomic diversity showed a net positive effect and species composition analysis highlighted both positive and negative effects of some species on the aesthetic value. Net negative effects of functional and phylogenetic diversities were found, which illustrates an aesthetic bias in human perception of ecological value. The aesthetic and ecological values were mapped along the French Mediterranean coastline in three dimensions (longitude, latitude, depth); this synthetic visualization could be of strong interest for conservation and communication purposes about this endangered benthic key-ecosystem of the Mediterranean Sea. Overall, our approach provides a geographically scalable estimate of the aesthetic value of biodiversity which is still an underestimated facet of nature contributions to people. It could be transposed to other marine ecosystems such as coral reefs but also to terrestrial landscapes for which an increasing number of images evaluated for human preference are becoming available.

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

Many factors are known to influence the invasion of alien species depending on the spatial scales considered. Caulerpa taxifolia and Caulerpa cylindracea are two green macroalgae that are classified as among the most invasive exotic macroalgae in the world. Their spread into the Mediterranean Sea seems to be favored by the concomitant decline of Posidonia oceanica. We studied the effect of four anthropogenic pressures and four environmental factors, and the conservation statuts of P. oceanica seagrass, on the presence/absence and abundance of these caulerpae along 336 km of French Mediterranean coastline (159,691 ha of seabed) using generalized linear model (GLM). Our results showed that the presence of caulerpae increased as the conservation status of the P. oceanica seagrass decreased and as boat anchoring intensity is high. Also, the increase in turbidity values significantly reduced the presence of caulerpae independently of variations in other environmental factors. Urban effluents were the human factor that interacted the most by disturbing all environmental variables. These results contribute to understanding the large-scale factors which have promoted caulerpae invasion and highlight the necessity to improve marine habitat's conservation for prevent biological invasions.

The configuration of a habitat often reflects its conservation status and, to be effective, the conservation actions to be implemented must be adapted to local environmental conditions and human activities. Here, we take advantage of a fine resolution map (1:10000) of marine habitats to study the spatial configuration of Posidonia oceanica seagrass beds, a marine habitat of great ecological and economic importance. Six different composition and landscape descriptors were calculated at different scales (grid cells of 400 m × 400 m, 200 m × 200 m and 100 m × 100 m) between 0 and 40 m deep along 1700 km of French Mediterranean coastline (mainland and Corsica). A Random Forest approach was applied to relate these landscape descriptors to anthropogenic and environmental factors and to assess their relative importance. The best predictive power of the Random Forest models was obtained for 100 m × 100 m grid cells with models explaining 87% of the variance of the decline index and 70% of the variance of the cohesion index. The identification of threshold points for all environmental variables allowed to localize seagrass beds in either good or bad environmental conditions. We also identified sites whose spatial configuration was degraded despite good environmental conditions. These were sites with greater influence from human activities that could benefit from proactive conservation measures.

International audience; Monitoring the ecological status of natural habitats is crucial to the conservation process, as it enables the implementation of efficient conservation policies. Nowadays, it is increasingly possible to automate species identification, given the availability of very large image databases and state-of-the-art computational power which makes the training of automated machine learning-based classification models an increasingly viable tool for monitoring marine habitats. Coralligenous reefs are an underwater habitat of particular importance, found in the Mediterranean. This habitat is of a similar biocomplexity to coral reefs. They have been monitored in French waters since 2010 using manually annotated photo quadrats (RECOR monitoring network). Based on the large database of annotations accumulated therein, we have trained convolutional neural networks to automatically recognise coralligenous species using the data gathered from photo quadrats. Previous studies conducted on similar habitats performed well, but were only able to consider a limited number of classes, resulting in a very coarse description of these often-complex habitats. We therefore designed a custom network based on off-theshelf architectures which is able to discriminate between 61 classes with 72.59% accuracy. Our results showed that confusion errors were for the most part taxonomically coherent, showing accuracy performances of 84.47% when the task was simplified to 15 major categories, thereby outperforming the human accuracy previously recorded in a similar study. In light of this, we built a semi-automated tool to reject unsure results and reduce error risk, for when a higher level of accuracy is required. Finally, we used our model to assess the biodiversity and ecological status of coralligenous reefs with the Coralligenous Assemblage Index (CAI) and the Shannon Index. Our results showed that whilst the prediction of the CAI was only moderately accurate (pearson correlation between observed and predicted CAI = 0.61), the prediction of Shannon Index was more accurate (pearson correlation = 0.74). In conclusion, it will be argued that the approach outlined by this study offers a cost and time-effective tool for the analysis of coralligenous assemblages which is suitable for integration into a large-scale monitoring network of this habitat.

Coral reefs are vulnerable ecosystems where a great number of fish species live. Some fish are beautiful, and some are not. This study compared the human perception of fish beauty with the ecological roles and characteristics of these fishes. It appears that ugly fish have a wider variety of roles in the coral reef ecosystem than beautiful fish do. This means that the ugly fish seem to be more important for ecosystems. The results of this study warn us about the need to preserve not just cute fishes, but the entire ecosystem, which means protecting the ugly fish as well as the beautiful ones.

International audience; During the last fifty years, there has been a dramatic increase in the development of anthropogenic activities, and this is particularly threatening to marine coastal ecosystems. The management of these multiple and simultaneous anthropogenic pressures requires reliable and precise data on their distribution, as well as information (data, modelling) on their potential effects on sensitive ecosystems. Focusing on Posidonia oceanica beds, a threatened habitat-forming seagrass species endemic to the Mediterranean, we developed a statistical approach to study the complex relationship between human multiple activities and ecosystem status. We used Random Forest modelling to explain the degradation status of P. oceanica (defined herein as the shift from seagrass bed to dead matte) as a function of depth and 10 anthropogenic pressures along the French Mediterranean coast (1700 km of coastline including Corsica). Using a 50 x 50 m grid cells dataset, we obtained a particularly accurate model explaining 71.3 % of the variance, with a Pearson correlation of 0.84 between predicted and observed values. Human-made coastline, depth, coastal population, urbanization, and agriculture were the best global predictors of P. oceanica's degradation status. Aquaculture was the least important predictor, although its local individual influence was among the highest. Non-linear relationship between predictors and seagrass beds status was detected with tipping points (i.e. thresholds) for all variables except agriculture and industrial effluents. Using these tipping points, we built a map representing the coastal seagrass beds classified into four categories according to an increasing pressure gradient and its risk of phase shift. Our approach provides important information that can be used to help managers preserve this essential and endangered ecosystem.

Cultural and recreational values of biodiversity are considered as important dimensions of nature's contribution to people. Among these values, the aesthetics can be of major importance as the appreciation of beauty is one of the simplest forms of human emotional response. Using an online survey, we disentangled the effects of different facets of biodiversity on aesthetic preferences of coral reef fish assemblages that are among the most emblematic assemblages on Earth. While we found a positive saturating effect of species' richness on human preference, we found a net negative effect of species abundance, no effect of species functional diversity and contrasting effects of species composition depending on species' attractiveness. Our results suggest that the biodiversity–human interest relationship is more complex than has been previously stated. By integrating several scales of organization, our study is a step forward in better evaluating the aesthetic value of biodiversity.

Global changes affect the entire planet at all scales, terrestrial and marine. The impact of anthropogenic pressures on marine ecosystems has been relatively little studied because of the lack of data and the difficulty to acquire it. Fine resolution cartographic data (1:10 000) of marine habitats on French Mediterranean coasts have recently become available (Andromede Oceanologie, 2014). This allows using landscape ecology approaches to study the spatial configurations of these habitats, their evolution through time and confront that to anthropogenic and environmental pressures. Here we take advantage of this new data to study Posidonia oceania meadows, a marine habitat of great ecological and economic importance. Posidonia oceanica is an endemic species to the Mediterranean Sea. Posidonia oceanica is also an indicator of the ecological quality of coastal waters since changes in its spatial distribution reflect changes in environmental conditions. The spatial cover of Posidonia oceanica meadows has declined sharply in the last 50 years, in particular because of increased human activities along the coast. In this study, we tested the relative influence (and possible interactions) of anthropogenic coastal pressures and environmental variables (Previmer data) on the decline of Posidonia oceanica meadows in the French Mediterranean sea. Different composition and configuration landscape descriptors were calculated for different grid cells (400m x 400m; 200m x 200m, 100m x 100m), between 0 and 40 m depth over 1800 km of French Mediterranean coastline (Mainland + Corsica). An approach using Random Forest was applied to explain these indices with the anthropogenic and environmental factors and to identify the factors that contribute the most to the decline of Posidonia oceanica meadows. With a model that explains 87% of overall variance, our results show a very important effect of environmental factors on the decline and the patchs cohesion of Posidonia oceanica meadows. Anthropogenic pressures also have a destructive effect on the posidonia, because if the intensity of the pressures is high, the decline is strong and the cohesion between the patches is weak.The identification of tipping points for all environmental variables shows that some seagrasses are in areas of good environmental conditions and others in weak environmental conditions. The human impact on the seagrass surface regression and their spatial organization is clearly shown and it is important to define priority areas for conservation actions.

International audience; As a cultural ecosystem service, the aesthetic value of landscapes contributes to human well-being, but studies linking biodiversity and ecosystem services generally do not account for this particular service. Therefore, congruence between the aesthetic perception of landscapes, ecological value and biodiversity remains poorly understood. Here, we describe the conceptual background, current methodologies and future challenges of assessing landscape aesthetics and its relationship with biodiversity. We highlight the methodological gaps between the assessment of landscape aesthetics, ecological diversity and functioning. We discuss the challenges associated with connecting landscape aesthetics with ecological value, and the scaling issues in the assessment of human aesthetics perception. To better integrate aesthetic value and ecological components of biodiversity, we propose to combine the study of aesthetics and the understanding of ecological function at both the species and landscape levels. Given the urgent need to engage society in conservation efforts, this approach, based on the combination of the aesthetic experience and the recognition of ecological functioning by the general public, will help change our culture of nature and promote ecologically oriented conservation policies.

International audience; (150 words) Global shipping is economically important, but has many adverse environmental effects. Anchoring contributes greatly to this adverse impact, as it is responsible for mechanical disturbance of highly sensitive marine habitats. Recovery of these ecosystems is limited by slow regrowth. Anchoring pressure on coastal seabed habitats was estimated using AIS (Automatic Identification System) data along 1800 km of Mediterranean coastline between 2010 and 2015. A comparison with field observations showed that these results were most consistent for large boats (> 50 m). An analysis of AIS data coupled with a seabed map showed that around 30 % of the habitats between 0 and-80 m exhibited anchoring pressure. Posidonia oceanica seagrass beds were the most impacted habitat in terms of duration. This methodology efficiently estimates spatial and temporal anchoring pressure principally due to large boats and should interest managers of marine protected areas as much as coastline managers.

The aesthetic value of landscapes contributes to human well-being. However, studies which have investigated the link between biodiversity and ecosystem services have not taken aesthetic value into account. In this study we evaluated how the aesthetics of coralligenous reefs, a key marine ecosystem in the Mediterranean, is perceived by the general public and how aesthetic preferences are related to biodiversity facets (taxonomic, phylogenetic and functional diversities). We performed both biodiversity measures and online-surveys of aesthetic perception on photographic quadrats sampled along the French Mediterranean coast. Our results show that species richness and functional richness have a significant positive effect on aesthetic value. Most of the ecological literature, exploring the relationship between biodiversity and ecosystem functioning and service has focused so far on ‘economical’ aspects of biodiversity (provision or regulation). Our results illustrate that cultural facets, such as ‘beauty’, should also be central in our motivations to preserve ecological diversity.

International audience; Multi-facet diversity indices have been increasingly widely used in conservation ecology but congruence analyses both on horizontal and vertical axes have not yet been explored. We investigated the vertical and horizontal distributions of alpha and beta taxonomic (TD), functional (FD) and phylogenetic diversity (PD) in a three-dimensional structured ecosystem. We focused on the Mediterranean coralligenous assemblages which form complex structures both vertically and horizontally, and are considered as the most diverse and threatened communities of the Mediterranean Sea. Although comparable to tropical reef assemblages in terms of richness, biomass and production, coralligenous assemblages are less known and more rarely studied, in particular because of their location in deep waters. Our study covers the entire range of distribution of coralligenous habitats along the French Mediterranean coasts, representing the most complete database so far developed for this important ecosystem. To our knowledge, this is the first analysis of spatial diversity patterns of marine biodiversity on both horizontal and vertical scales. Our study revealed that taxonomic diversity differed from functional and phylogenetic diversity patterns at the station level, the latter two being strongly structured by depth, with shallower stations generally richer than deeper ones. Considering all stations, phylogenetic diversity was less congruent to taxonomic diversity (Pearson's correlation of r= 0.48) but more congruent to functional diversity (r=0.69) than randomly expected. Similar congruence patterns were revealed for stations deeper than 50 m.(r= 0.44 and r= 0.84, respectively) but no significantly different congruence level than randomly expected was revealed among diversity facets for more shallow stations. Mean functional alpha- and alpha-diversity were lower than phylogenetic diversity and even lower than taxonomic alpha- and beta-diversity for both vertical and horizontal scales. Low FD and PD values at both alpha- and beta-diversity indicated functional and phylogenetic clustering. Community dissimilarities (beta-diversity) increased over depth especially in central and eastern part of the French Mediterranean littoral and in northern Corsica, indicating coralligenous vertical structure within these regions. Overall horizontal beta-diversity was higher within the 50-70 m depth belts. We conclude that taxonomic diversity alone is inadequate as a basis for setting conservation goals for this ecosystem and additional information, at least on phylogenetic diversity, is needed to preserve the ecosystem functioning and coralligenous evolutionary history. Our results highlight the necessity of considering different depth belts as a basis for regional scale conservation efforts. Current conservation approaches, such as the existing marine protected areas, are insufficient in preserving coralligenous habitats. The use of multi-facet indices should be considered, focusing on preserving local diversity patterns and compositional dissimilarities, both vertically and horizontally. (C) 2015 Elsevier Ltd. All rights reserved.

Coralligenous assemblages represent the unique calcareous formations of biogenic origin in the Mediterranean Sea. Despite their importance in terms of biodiversity and biomass production, community analyses remain scarce. Actual sampling of these assemblages is complicated to carry out because their depth distribution (down to − 120 m) necessitates complex diving logistics. We highlight a rapid, cost-effective, objective and accurate method for the sampling of coralligenous assemblages and tested its efficiency in delineating a depth gradient. We compared seven photographic methods for estimating the percentage cover of sessile organisms: visual estimates (VS) with the aid of a 25, 64 or 100 square-grid and random-point-quadrats (RQ) with 25, 64 or 100 random points or 64 stratified random points. Comparisons were made using two simulated quadrats for which percent cover values were known. RQ with 64 random points was the method that accumulated the highest number of advantages. Using this method, two field sites were sampled by divers at three depths (− 50, − 60 and − 70 m) with increasing replication (10, 20, 30 and 40 photographic quadrats). The communities deduced from the 30 and 40 photos were similar. Community analyses showed an effect of depth nested in site on the assemblages observed. With increasing depth, encrusting algae get replaced by Porifera. Dissimilarity between − 50 m and − 60 m/− 70 m was mainly due to Crambe tailliezi abundance. This methodology will be a useful tool for managers and administrators; it guarantees fast abundance estimation, non-destructive repeated sampling, the possibility of comparison among researchers and the permanent record of deep-sea communities.

Posidonia oceanica is an endemic seagrass from the Mediterranean Sea. It is an indicator of water quality and of the ecological state of coastal ecosystems. The aim of this paper is to test acoustic telemetry for monitoring the position of P. oceanica meadow limits with varied types. After evaluating the accuracy of the system, we present results from a spatiotemporal survey of P. oceanica meadows on nine sites located on the French coast. The method has been demonstrated to be highly efficient for high precision underwater mapping regardless of meadow type, with 1 cm accuracy for a distance of 40 m between the base and the pointer. A temporal survey led at Cerbere–Banyuls shows a weak global progression of 4 m 2 (progression of 26 m 2 - regression of 22 m 2 ) between 2006 and 2010. Finally, we discuss the cost and efficiency of this method, and wether it should be generalized for further studies.

The present study focused on the isolation of culturable bacteria from mussels and sea water to identify Vibrionaceae potentially pathogenic for humans. Three sites located on the French Atlantic coast were monitored monthly (twice each month during summer) for 1 year. Environmental parameters were surveyed (water temperature, salinity, turbidity, chlorophyll a) and bacteria were detected by culture and identified by API 20E(R) systems (BioMerieux) and PCR. A total of seven species were detected (Grimontia hollisae, Photobacterium damselae, Vibrio alginolyticus, V. cholerae, V. fluvialis, V. vulnificus and V. parahaemolyticus) and species diversity was higher at the end of summer. Surprisingly, V. cholerae non-O1/non-O139 was detected in spring. No site effect was detected. Using Sorensen similarity indices and statistical analyses, we showed that chlorophyll a had a significant influence on the bacterial community detected in mussels and assemblages were more similar to one another when chlorophyll a values were above 20 mu g l(-1). No significant effect of any parameter was found on the community detected in water samples. Such surveys are essential for the understanding of sanitary crises and detection of emerging pathogens.

Heterogeneities in immune responsiveness may affect key epidemiological parameters and the dynamics of pathogens. The roles of immunogenetics in these variations remain poorly explored. We analysed the influence of Major histocompatibility complex (Mhc) genes and epigamic traits on the response to phytohaemagglutinin in males from cyclic populations of the montane water vole (Arvicola scherman). Besides, we tested the relevance of lateral scent glands as honest signals of male quality. Our results did not corroborate neither the hypotheses of genome-wide heterozygosity-fitness correlation nor the Mhc heterozygote advantage. We found a negative relationship between Mhc hetetozygosity and response to phytohaemagglutinin, mediated by a specific Mhc homozygous genotype. Our results therefore support the hypothesis of the Arte-Dqa-05 homozygous genotype being a ‘good’ Mhc variant in terms of immunogenetic quality. The development of the scent glands seems to be an honest signal for mate choice as it is negatively correlated with helminth load. The ‘good gene’ hypothesis was not validated as Arte-Dqa-05 homozygous males did not exhibit larger glands. Besides, the negative relationship observed between the size of these glands and the response to phytohaemagglutinin, mainly for Mhc homozygotes, corroborates the immunocompetence handicap hypothesis. The Mhc variants associated with larger glands remain yet to be determined.

International audience; The impact of 85 years of coastal development on shallow seagrass beds (Posidonia oceanica L. (Delile)) in South Eastern France: a slow but steady loss without recovery Abstract: Shallow Posidonia oceanica beds (0 to-15 m), the most common seagrass in the Mediterranean, were mapped from aerial pictures dating from the 1920's and from 2012 along 800 km of coastline in SouthEastern France (Provence-Alpes-Côte-d'Azur region). Changes in P. oceanica beds spatial distribution (limits and areal extents) during these 85 years were analyzed in terms of concordance (remaining areas), positive discordance (expanding areas) or negative discordance (lost areas). Lost areas were linked with direct or indirect impacts of coastal development (artificialized coastlines (namely harbours, ports of refuge, landfills, artificial beaches, groynes and pontoons, submarine pipelines and aquatic farms) visible on the pictures. The comparison showed that 73 % of the shallow limits have declined. Considering areal extents, remaining seagrass meadows areas accounted for the major part (85 %), while lost areas accounted for 13 % and expanding areas for 1.1%. Lost areas were mainly linked with artificialized coastlines but 44 % remained with undetermined causes (invisible pressures and/or mixed effects). The analysis of 96 coastal facilities participating to the artificialized (namely man-made) coastlines showed that the highest impact over the longest distance (5 km) was caused by harbours. Only artificial beaches had such a distant impact. Pontoons were the least surrounded by lost seagrass meadows areas. These quantitative data offer important information for marine conservation.

Dans un contexte en constante évolution, l’élaboration, la mise en œuvre et l’évaluation des politiques publiques de biodiversité nécessitent d’anticiper les changements futurs possibles afin de pouvoir se préparer à temps. Or les informations concernant ces changements sont nombreuses et les enjeux qui pourraient s’avérer importants à l’avenir sont souvent peu visibles. Pour répondre à ce défi, une expertise multiacteurs et multidisciplinaire s’inspirant des démarches d’horizon scanning et intitulée BioPIQuE 2013 a permis d’identifier 25 questions émergentes, dont 10 questions stratégiques, pour les politiques publiques de biodiversité en France métropolitaine d’ici à 2020. Ces questions émergentes sont autant d’opportunités et de risques que l’ensemble des acteurs qui souhaitent avancer vers une plus grande prise en compte des enjeux de biodiversité peuvent saisir., Because drivers and pressures on biodiversity, societal expectations, and ecological knowledge evolve rapidly, biodiversity conservation policies need to adapt continuously. Anticipating such changes can however be difficult given the profusion and complexity of data and when signals indicating future risks and opportunities may be weak. To tackle this challenge, the French Environment ministry asked a research team at AgroParisTech to develop a new method for identifying emerging issues for biodiversity policies by 2020 in France (except for overseas territories). This project, called BioPIQuE 2013, involved both scientists and stakeholders in an interdisciplinary assessment. As a result, 25 emerging issues were identified, among which 10 issues were highlighted for their strategic interest. A majority of these issues are current trends not yet taken into account by biodiversity policies (such as “why do we have to and how can we improve our ability to restore – with ambitious biodiversity objectives – urbanised and highly degraded areas?”), and a few of them are weak signals (such as “how can we deal with trade-offs and conflicts between biodiversity policies and other environmental policies?”). All stakeholders, including researchers, NGOs, public administrations, private companies and politicians, can find in the results some inputs for developing their biodiversity conservation strategies.

International audience; Ecosystem services provided by oceans and seas support most human needs but are threatened by human activities. Despite existing maps illustrating human impacts on marine ecosystems, information remains either large-scale but rough and insufficient for stakeholders (1 km² grid, lack of data along the coast) or fine-scale but fragmentary and heterogeneous in methodology. The objectives of this study are to map and quantify the main pressures exerted on near-coast marine ecosystems, at a large spatial scale though in fine and relevant resolution for managers (one pixel = 20 x 20 m). It focuses on the French Mediterranean coast (1,700 km of coastline including Corsica) at a depth of 0 to 80 m. After completing and homogenizing data presently available under GIS on the bathymetry and anthropogenic pressures but also on the seabed nature and ecosystem vulnerability, we provide a fine modeling of the extent and impacts of 10 anthropogenic pressures on marine habitats. The considered pressures are man-made coastline, boat anchoring, aquaculture, urban effluents, industrial effluents, urbanization, agriculture, coastline erosion, coastal population and fishing. A 1:10 000 continuous habitat map is provided considering 11 habitat classes. The marine bottom is mostly covered by three habitats: infralittoral soft bottom, Posidonia oceanica meadows and circalittoral soft bottom. Around two thirds of the bottoms are found within medium and medium high cumulative impact categories. Seagrass meadows are the most impacted habitats. The most important pressures (in area and intensity) are urbanization, coastal population, coastal erosion and man-made coastline. We also identified areas in need of a special management interest. This work should contribute to prioritize environmental needs, as well as enhance the development of indicators for the assessment of the ecological status of coastal systems. It could also help better apply and coordinate management measures at a relevant scale for biodiversity conservation.

Infection by the cestodeTaenia taeniaeformiswas investigated within numerous cyclic populations of the fossorial water voleArvicola terrestrissampled during 4 years in Franche-Comté (France). The relative influence of different rodent demographic parameters on the presence of this cestode was assessed by considering (1) the demographic phase of the cycle; (2) density at the local geographical scale (2); (3) mean density at a larger scale (>10 km2). The local scale corresponded to the rodent population (intermediate host), while the large scale corresponded to the definitive host population (wild and feral cats). General linear models based on analyses of 1804 voles revealed the importance of local density but also of year, rodent age, season and interactions between year and season and between age and season. Prevalence was significantly higher in low vole densities than during local outbreaks. By contrast, the large geographical scale density and the demographic phase had less influence on infection by the cestode. The potential impacts of the cestode on the fitness of the host were assessed and infection had no effect on the host body mass, litter size or sexual activity of voles.

Posidonia oceanica is a marine angiosperm endemic from the Mediterranean. Despite their protection, its meadows are regressing. The economic valuation of ecosystem services (ES) assesses the contribution of ecosystems to human well-being and may provide local policy makers help in territorial development. To estimate the economic value of P. oceanica seagrass and the meadows that it forms to better account its presence in coastal development, identification and assessment of ES provided are first performed. Then goods and benefits (GB) and their economical values are estimated. In total, 25ES are identified and 7 GB are economically evaluated. The economic value of GB provided by P. oceanica ranges between 25.3 mil- lion and 45.9 million €/year which means 283–513 €/ha/year. Because of the lack of existing available data, only 7 GB linked to 11/25ES have been estimated. Despite this overall undervaluation, this study offers a value for coastal development policies to take into account.

cosson@supagro.inra.fr; International audience; Trichuris arvicolae and T. muris are gastro-intestinal nematodes of respectively arvicoline and murine rodents. We aim to investigate the ecology of these Trichuris species using population genetics. We sampled nematodes from rodents trapped in the East of France. After confirming the species identification of the nematodes using ITS1-5.8S-ITS2 ribosomal DNA sequences, we isolated and characterized twelve dinucleotide microsatellite loci in T. arvicolae. A multiplex panel was developed. Application to a set of 30 individuals allowed clear and easy characterization of allele sizes. The number of alleles ranged from 2 to 6 per locus with observed heterozygosities ranging from 0 to 0.93. A test on eleven T. muris revealed that eight loci among twelve amplified, and five were polymorphic. These sets of microsatellite loci provide high throughput capacity for population genetic studies

International audience; We surveyed 12 Populations of the montane water vole (Arvicola scherman), previously known as the fossorial form of the Water vole A. terrestris, in eastern France for antibodies (immunoglobulin G) to Puumala virus (PUUV), lymphocytic choriomeningitis virus (LCMV), and COWPOX virus (CPXV). Antibodies to PUUV Were found in 9 (5.5%) of 164 voles from 7 populations, antibodies to LCMV were found in 13 (26.0%) of 50 voles from 2 Populations, and antibodies to CPXV were found in 66 (41.8%,) of 158 votes from 7 populations. Antibody status to CPXV Was statistically associated with the phase of the A. scherman population density cycle and the percentage of grassland areas surrounding the sampling sites.

8th International Congress on Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases Bangkok, THAILAND, OCT 30-NOV 02, 2006; International audience; Puumala virus (PUUV) is a hantavirus specifically harboured by the bank vole, Myodes (earlier Clethrionomys) glareolus. It causes a mild form of hemorrhagic fever with renal syndrome (HFRS) in humans, called Nephropathia epidemica (NE). The clinical severity of NE is variable among patients and depends on their major histocompatibility complex (MHC) genetic background. In this study we investigated the potential role of class II MHC gene polymorphism in the susceptibility/resistance to PUUV in the wild reservoir M. glareolus. We performed an association study between the exon 2 of the DQA gene and PUUV antibodies considering a natural population of bank voles. Because immune gene polymorphism is likely to be driven by multiple parasites in the wild, we also screened bank voles for other potential viral and parasitic infections. We used multivariate analyses to explore DQA polymorphism/PUUV associations while considering the potential antagonist and/or synergistic effects of the whole parasite community. Our study suggests links between class II MHC characteristics and viral infections including PUUV and Cowpox virus. Several alleles are likely to be involved in the susceptibility or in the resistance of bank voles to these infections. Alternatively, heterozygosity does not seem to be associated with PUUV or any other parasite infections. This result thus provides no evidence in favour of the hypothesis of selection through overdominance. Finally this multivariate approach reveals a strong antagonism between ectoparasitic mites and PUUV, suggesting direct or indirect immunogenetic links between infections by these parasites. Other datasets are now required to confirm these results and to test whether the associations vary in space and/or time.

Contact: deter@supagro.inra.fr; International audience; Hantaviruses are among the main emerging infectious agents in Europe. Their mode of transmission in natura is still not well known. In particular, social features and behaviours could be crucial for understanding the persistence and the spread of hantaviruses in rodent populations. Here, we investigated the importance of kinclustering and dispersal in hantavirus transmission by combining a fine-scale spatiotemporal survey (4 km2) and a population genetics approach. Two specific host-hantavirus systems were identified and monitored: the bank vole Myodes, earlier Clethrionomys glareolus––Puumala virus and the common vole Microtus arvalis—Tula virus. Sex, age and landscape characteristics significantly influenced the spatial distribution of infections in voles. The absence of temporal stability in the spatial distributions of viruses suggested that dispersal is likely to play a role in virus propagation. Analysing vole kinship from microsatellite markers, we found that infected voles were more closely related to each other than non-infected ones. Winter kin-clustering, shared colonies within matrilineages or delayed dispersal could explain this pattern. These two last results hold, whatever the host-hantavirus system considered. This supports the roles of relatedness and dispersal as general features for hantavirus transmission.

International audience; The stress response is initially adaptive, operating to maintain homeostasis. However, chronic long‐term exposure to stressors may have detrimental effects. We proposed that chronic stress may be a major factor in demographic vole cycles, inducing decline in high‐density populations. We monitored four populations of the fossorial water vole Arvicola scherman, which undergo pluriannual demographic cycles in the Jura Mountains (France). Sampling was conducted during the high densities and the decline. We measured fecal corticosterone metabolites (FCMs) to assess stress levels and injected phytohemagglutinin to estimate the cell‐mediated immune response. We demonstrated that stress levels increase between the high densities and the decline in most of the vole populations. At the individual level, FCM concentrations varied with reproductive status and body condition. During the outbreak, we observed significantly higher levels of FCM concentrations in nulliparous females than in females that had previously reproduced. Moreover, a significant negative correlation was observed between concentrations of FCMs and both immunocompetence and body condition during population decline. These results might reflect an impairment of the female reproductive capability in high densities and accelerated senescence affecting immune function during decline, both arising from chronic stress.

Contact: deter@supagro.inra.fr; International audience; The goal of this study is to determine whether a parasitic nematode may regulate, or destabilise by inducing demographic cycles, its host populations. We explore three host-parasite systems through population dynamic models. The hosts considered are the fossorial water vole, Arvicola terrestris, the common vole Microtus arvalis and the bank vole Myodes (Clethrionomys) glareolus and the parasitic nematode is Trichuris arvicolae. Three differential equation-based mathematical models are developed including host immunity and the existence of trade-off between immunity and host survival. Using parameters estimated from field data and laboratory observations, all these models show that T. arvicolae can induce host population regulation but not demographic cycles. The regulation effect of the nematode is un-ambiguous for the water vole (reduction of 50.2% of the host population size), but less obvious for the common vole (5.9%) and even less for the bank vole (1.4%). Important biological parameters to be taken into account in such models are discussed. Experimental confirmation of the regulatory potential of the nematode and of the costs of mounting an immune response against this nematode are now required.

Correspondance: fax: +33 4 99 62 33 45; e-mail: nathalie.charbonnel@supagro.inra.fr; International audience; We investigated the factors mediating selection acting on two MHC class II genes (DQA and DRB) in water vole (Arvicola scherman) natural populations in the French Jura Mountains. Population genetics showed significant homogeneity in allelic frequencies at the DQA1 locus as opposed to neutral markers (nine microsatellites), indicating balancing selection acting on this gene. Moreover, almost exhaustive screening for parasites, including gastrointestinal helminths, brain coccidia and antibodies against viruses responsible for zoonoses, was carried out. We applied a co-inertia approach to the genetic and parasitological data sets to avoid statistical problems related to multiple testing. Two alleles, Arte-DRB-11 and Arte-DRB-15, displayed antagonistic associations with the nematode Trichuris arvicolae, revealing the potential parasite-mediated selection acting on DRB locus. Selection mechanisms acting on the two MHC class II genes thus appeared different. Moreover, overdominance as balancing selection mechanism was showed highly unlikely in this system

Correspondance: alexander.plyusnin@helsinki.fi; International audience; The first genome sequences of Tula (TULV) and Puumala (PUUV) hantaviruses undoubtedly originated from France were recovered from tissue samples of European common voles and bank voles captured in Jura region. Genetic analysis of S and M segments of French PUUV strain revealed its highest similarity to strains from neighboring Belgium and Germany and also from Slovakia. On phylogenetic trees, French PUUV strain was placed within the central European lineage formed by strains from these three countries. Both of our French TULV strains clustered together and formed a distinct, well-supported genetic lineage.

Correspondance: deter@supagro.inra.fr; International audience; Parasites have detrimental effects on host fitness. Consequently, they play a major role for host population dynamics. In this study, we investigated experimentally the impact of the nematode Trichuris arvicolae on the reproduction of its host, the common vole Microtus arvalis. Wild common voles were trapped in east of France and reared in standardized conditions before being experimentally infected. Infection with Trichuris arvicolae did not affect host consumption of food or water. Parasitized females gave birth to slightly less pups (mean 3.36 ± 0.38) than unparasitized females (mean 3.60 ± 0.40). Controlling for natal litter size using analysis of covariance (ANCOVA), T. arvicolae infection had a significant effect on the individual mass at birth, with pups from parasitized females having significantly lower mass (2.11 g ± 0.01) than pups from unparasitized females (2.20 g ± 0.01). Other measures of host reproductive outputs (time to first reproduction, mass of pups at weaning, litter survival) were not affected by maternal parasite infection. We discuss how these changes in M. arvalis reproductive investments associated with T. arvicolae infection must now be investigated in the context of physiological trade-offs

Human activities are the main cause of global changes with adverse impacts on all biodiversity, both terrestrial and marine. In this context, many countries, including France, wish to stop this problem by improving networks for monitoring and managing ecosystems using new methods and approaches that aim, in particular, to achieve good ecological status of their water masses. This is the main objective of this thesis project, focusing on a Mediterranean sentinel ecosystem, the Posidonia oceanica seagrass. P. oceanica is an underwater plant endemic to the Mediterranean, and an indicator of the quality of its environment. By linking its spatial distribution with biological data and anthropogenic pressures, it is possible to develop new indicators that are easy to measure at the scale of the entire French coastline (1800 km).Through a multidisciplinary approach, combining participatory mapping, analysis of old images and current ecological data, we have been able to identify the location of former P. oceanica seagrass that have now disappeared and quantify the extent of the decline (70% in 66 years for example in Agde and Rochelongue). Our results also show that the indices of landscape composition and configuration reflect well the state of conservation of a P. oceanica seagrass. Using these landscape indices, we have developed a new approach to define key conservation areas for the management of P. oceanica based on the influence of environmental variables and human activities. Finally, we have also shown that by degrading the P. oceanica seagrass, human activities favour the installation of invasive exotic algae, but can also act as a barrier to invasions by modifying local environmental conditions and making them unfavourable to invasive species.These results suggest multiple applications to improve the management and monitoring of the marine environment in the French Mediterranean.; Les activités humaines sont la principale cause des changements globaux avec des conséquences néfastes sur l’ensemble de la biodiversité, aussi bien terrestre que marine. Dans ce contexte, de nombreux pays dont la France souhaite endiguer ce phénomène à travers l’amélioration des réseaux de surveillance et de gestion des écosystèmes à l’aide de nouvelles méthodes et approches qui visent, notamment l’atteinte d’un bon état écologique de leurs masses d’eaux. C’est l’objectif principal que s’est fixé ce projet de thèse, en se concentrant sur un écosystème sentinelle de Méditerranée, les herbiers de Posidonia oceanica. P. oceanica est une plante sous-marine endémique de méditerranée, indicatrice de la qualité de son environnement. En croisant sa distribution spatiale avec des données biologiques et de pressions anthropiques, il est possible de proposer des nouveaux indicateurs faciles à calculer à l’échelle de tout le littoral français (1800 km).Nous avons par une approche multidisciplinaire, mêlant cartographie participative, analyse d’images anciennes et données écologiques actuelles, pu localiser d’anciens herbiers aujourd’hui disparus et quantifier l’importance du déclin (70 % en 66 années par exemple à Agde et Rochelongue). Nos résultats montrent aussi que les indices de composition et de configuration paysagère reflètent bien l’état de conservation d’un herbier de P. oceanica. En utilisant ces indices paysagers, nous avons mis en place une nouvelle approche pour définir des zones de conservation clés pour la gestion de P. oceanica sur la base de l’influence de variables environnementales et d’activités humaines. Enfin nous avons aussi montré qu’en dégradant les herbiers de P. oceanica, les activités humaines favorisent l’installation d’algues exotiques envahissantes, mais peuvent aussi constituer un frein à ces mêmes invasions en modifiant les conditions locales environnementales et en les rendant défavorables aux espèces invasives.Ces résultats laissent présager de multiples applications pour améliorer la gestion et la surveillance du milieu marin en Méditerranée française.

Human activities are the main cause of global changes with adverse impacts on all biodiversity, both terrestrial and marine. In this context, many countries, including France, wish to stop this problem by improving networks for monitoring and managing ecosystems using new methods and approaches that aim, in particular, to achieve good ecological status of their water masses. This is the main objective of this thesis project, focusing on a Mediterranean sentinel ecosystem, the Posidonia oceanica seagrass. P. oceanica is an underwater plant endemic to the Mediterranean, and an indicator of the quality of its environment. By linking its spatial distribution with biological data and anthropogenic pressures, it is possible to develop new indicators that are easy to measure at the scale of the entire French coastline (1800 km).Through a multidisciplinary approach, combining participatory mapping, analysis of old images and current ecological data, we have been able to identify the location of former P. oceanica seagrass that have now disappeared and quantify the extent of the decline (70% in 66 years for example in Agde and Rochelongue). Our results also show that the indices of landscape composition and configuration reflect well the state of conservation of a P. oceanica seagrass. Using these landscape indices, we have developed a new approach to define key conservation areas for the management of P. oceanica based on the influence of environmental variables and human activities. Finally, we have also shown that by degrading the P. oceanica seagrass, human activities favour the installation of invasive exotic algae, but can also act as a barrier to invasions by modifying local environmental conditions and making them unfavourable to invasive species.These results suggest multiple applications to improve the management and monitoring of the marine environment in the French Mediterranean.; Les activités humaines sont la principale cause des changements globaux avec des conséquences néfastes sur l’ensemble de la biodiversité, aussi bien terrestre que marine. Dans ce contexte, de nombreux pays dont la France souhaite endiguer ce phénomène à travers l’amélioration des réseaux de surveillance et de gestion des écosystèmes à l’aide de nouvelles méthodes et approches qui visent, notamment l’atteinte d’un bon état écologique de leurs masses d’eaux. C’est l’objectif principal que s’est fixé ce projet de thèse, en se concentrant sur un écosystème sentinelle de Méditerranée, les herbiers de Posidonia oceanica. P. oceanica est une plante sous-marine endémique de méditerranée, indicatrice de la qualité de son environnement. En croisant sa distribution spatiale avec des données biologiques et de pressions anthropiques, il est possible de proposer des nouveaux indicateurs faciles à calculer à l’échelle de tout le littoral français (1800 km).Nous avons par une approche multidisciplinaire, mêlant cartographie participative, analyse d’images anciennes et données écologiques actuelles, pu localiser d’anciens herbiers aujourd’hui disparus et quantifier l’importance du déclin (70 % en 66 années par exemple à Agde et Rochelongue). Nos résultats montrent aussi que les indices de composition et de configuration paysagère reflètent bien l’état de conservation d’un herbier de P. oceanica. En utilisant ces indices paysagers, nous avons mis en place une nouvelle approche pour définir des zones de conservation clés pour la gestion de P. oceanica sur la base de l’influence de variables environnementales et d’activités humaines. Enfin nous avons aussi montré qu’en dégradant les herbiers de P. oceanica, les activités humaines favorisent l’installation d’algues exotiques envahissantes, mais peuvent aussi constituer un frein à ces mêmes invasions en modifiant les conditions locales environnementales et en les rendant défavorables aux espèces invasives.Ces résultats laissent présager de multiples applications pour améliorer la gestion et la surveillance du milieu marin en Méditerranée française.

In a context of climate change and the erosion of marine biodiversity, ecological monitoring of the most sensitive marine habitats is of paramount importance. In particular, there is a need for operational methods that enable decision-makers and managers to establish relevant conservation measures and to evaluate their effectiveness. TEMPO and RECOR are two monitoring networks focusing on Posidonia meadows and coralligenous reefs, the two richest and most sensitive habitats in the Mediterranean. The objective of this thesis is to meet the needs of effective monitoring of marine habitats by developing methods for assessing their health, based on two key image analysis methods: convolutional neural networks and photogrammetry. The results show that convolutional neural networks are capable of recognizing the main species of coralligenous assemblages in underwater photographs from RECOR, with a precision similar to that of an expert taxonomist. Furthermore, we have shown that photogrammetry can reproduce a marine habitat in three dimensions with a high degree of accuracy, sufficient for monitoring habitat structure and species distribution at a fine scale. Based on these reconstructions, we have developed a method for automatic mapping of Posidonia meadows, enabling temporal monitoring of the ecological quality of this sensitive habitat. Finally, we characterized the three-dimensional structure of coralligenous reefs based on their photogrammetric reconstructions and studied the links with the structuring of the assemblages that make them up. This PhD work has led to the development of operational methods that are now integrated into the TEMPO and RECOR monitoring networks. Results of this work paves the way for future research, in particular concerning characterization of the biological activity of coralligenous reefs thanks to the coupling of photogrammetry, neural networks and underwater acoustics., Dans un contexte de changement climatique et d’érosion de la biodiversité marine, la surveillance écologique des habitats marins les plus sensibles est primordiale et nécessite des méthodes opérationnelles de suivi permettant aux décideurs et gestionnaires d’établir des mesures de conservation pertinentes et d’évaluer leur efficacité. TEMPO et RECOR sont deux réseaux de surveillance centrés sur les herbiers de posidonie et les récifs coralligènes, les deux habitats les plus riches et sensibles de Méditerranée. L’objectif de cette thèse est de répondre aux besoins de la surveillance des habitats marins par le développement de méthodes d’évaluation de leur état de santé, basées sur deux techniques d’analyses d’images clés : les réseaux de neurones convolutifs et la photogrammétrie. Les résultats montrent que les réseaux de neurones convolutifs sont capables de reconnaître les principales espèces des assemblages coralligènes sur des photos sous-marines issues de RECOR, avec une précision semblable à celle d’un expert taxonomiste. Par ailleurs, nous avons montré que la photogrammétrie permettait de reproduire en 3D un habitat marin avec une grande précision, suffisante pour un suivi de la structure de l’habitat et de la distribution d’espèces à fine échelle. À partir de ces reconstructions, nous avons mis au point une méthode de cartographie automatique des herbiers de posidonie, permettant de réaliser un suivi temporel de la qualité écologique de cet habitat sensible. Enfin, nous avons caractérisé la structure 3D des récifs coralligènes à partir de leurs reconstructions photogrammétriques et étudié les liens avec la structuration des assemblages qui les composent. Ce travail de thèse a permis de développer des méthodes opérationnelles, aujourd’hui intégrées aux réseaux de surveillance TEMPO et RECOR, et ouvre la voie à de futures recherches, notamment la caractérisation de l’activité biologique des récifs coralligènes grâce au couplage entre photogrammétrie, réseaux de neurones et acoustique sous-marine.

During the last century, human activities were at the origin of increasing pressures impacting marine coastal ecosystems. Scientific data concerning this phenomena are fragmentary and the grid scale (1 x 1 km pixel) is insufficient to permit relevant local decision making. The management of these multiple and simultaneous threats necessitates reliable and accurate data concerning the distribution of pressures and the localization of the most sensitive ecosystems. This is at the origin of two European directives: the Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). In response to these directives, the objectives of this work were to characterize the vulnerability and sensitivity of two priority ecosystems: Posidonia oceanica seagrass beds and coralligenous reefs. Focusing on the French Mediterranean coastline (depth ranging from 0 to – 100 m), results were: the fine-scale (20 x 20 m pixel size) quantification and localization of the encountered anthropogenic pressures, the quantification and localization of these two priority ecosystems, and the assessment of their ecological state. Seagrass beds decline was modelled in link with depth and pressures; resistance thresholds to pressures, but also management priority areas were defined. This work should contribute to improve the development of indicators for the ecological state of coastal ecosystems. It should also help to better apply and coordinate management actions at a relevant scale for biodiversity conservation.; Au cours du siècle dernier, le développement des activités anthropiques a engendré une augmentation des pressions sur les écosystèmes marins côtiers. Les données scientifiques pour aborder ce phénomène sont fragmentaires et d’une précision insuffisante (de l’ordre du km) pour la prise de décisions locales. La gestion de ces menaces multiples et simultanées exige pourtant des données fiables et précises sur la répartition des pressions et la localisation des écosystèmes les plus sensibles. Ces constations ont été à la base de la rédaction de deux directives européennes (la DCE, directive cadre eau et la DCSSM, directive cadre stratégie sur le milieu marin). Afin de répondre à ces directives, les objectifs de ce projet doctoral ont été de caractériser la vulnérabilité et d’aborder la sensibilité de deux écosystèmes marins prioritaires : les herbiers de posidonie et les communautés coralligènes. Ce projet focalisé sur la méditerranée française a permis la quantification et la localisation de ces écosystèmes et des pressions anthropiques auxquelles ils sont soumis, ainsi que l’estimation de leur état écologique à une résolution fine (de l’ordre de 20 m). Le déclin des herbiers a également pu être modélisé en relation avec les pressions et la profondeur et a permis de définir des seuils de résistance de cet habitat aux différentes pressions et des zones prioritaires de gestion. Ce travail devrait contribuer à améliorer l'élaboration d'indicateurs pour l'évaluation de l'état de santé des systèmes côtiers. Il pourrait également aider à mieux appliquer et coordonner les mesures de gestion à une échelle pertinente pour la conservation de la biodiversité.