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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.

Monitoring the biodiversity of key habitats and understanding the drivers across spatial scales is essential for preserving ecosystem functions and associated services. Coralligenous reefs are threatened marine biodiversity hotspots that are challenging to monitor. As fish sounds reflect biodiversity in other habitats, we unveiled the biogeography of coralligenous reef sounds across the north-western Mediterranean using data from 27 sites covering 2000 km and 3 regions over a 3-year period. We assessed how acoustic biodiversity is related to habitat parameters and environmental status. We identified 28 putative fish sound types, which is up to four times as many as recorded in other Mediterranean habitats. 40% of these sounds are not found in other coastal habitats, thus strongly related to coralligenous reefs. Acoustic diversity differed between geographical regions. Ubiquitous sound types were identified, including sounds from top-predator species and others that were more specifically related to the presence of ecosystem engineers (red coral, gorgonians), which are key players in maintaining habitat function. The main determinants of acoustic community composition were depth and percentage coverage of coralligenous outcrops, suggesting that fish-related acoustic communities exhibit bathymetric stratification and are related to benthic reef assemblages. Multivariate analysis also revealed that acoustic communities can reflect different environmental states. This study presents the first large-scale map of acoustic fish biodiversity providing insights into the ichthyofauna that is otherwise difficult to assess because of reduced diving times. It also highlights the potential of passive acoustics in providing new aspects of the correlates of biogeographical patterns of this emblematic habitat relevant for monitoring and conservation.

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.

[Departement_IRSTEA]Territoires [TR1_IRSTEA]GEUSI [Axe_IRSTEA]TETIS-ATTOS [ADD1_IRSTEA]Dynamique et fonctionnement des écosystèmes; International audience; Underwater photogrammetry has been increasingly used to study and monitor the three-dimensional characteristics of marine habitats, despite a lack of knowledge on the quality and reliability of the reconstructions. More particularly, little attention has been paid to exploring and estimating the relative contribution of multiple acquisition parameters on the model resolution (distance between neighbor vertices), accuracy (closeness to true positions/measures) and precision (variability of positions/measures). On the other hand, some studies used expensive or cumbersome camera systems that can restrict the number of users of this technology for the monitoring of marine habitats. This study aimed at developing a simple and cost-effective protocol able to produce accurate and reproducible high-resolution models. Precisely, the effect of the camera system, flying elevation, camera orientation and number of images on the resolution and accuracy of marine habitat reconstructions was tested through two experiments. A first experiment allowed for testing all combinations of acquisition parameters through the building of 192 models of the same 36 m(2) study site. The flying elevation and camera system strongly affected the model resolution, while the photo density mostly affected bundle adjustment accuracy and total processing time. The camera orientation, in turn, mostly affected the reprojection error. The best combination of parameters was used in a second experiment to assess the accuracy and precision of the resulting reconstructions. The average model resolution was 3.4 mm, and despite a decreasing precision in the positioning of markers with distance to the model center (0.33, 0.27, and 1.2 mm/m Standard Deviation (SD) in X, Y, Z, respectively), the measures were very accurate and precise: 0.08% error +/- 0.06 SD for bar lengths, 0.36% +/- 0.51 SD for a rock model area and 0.92% +/- 0.54 SD for its volume. The 3D geometry of the rock only differed by 1.2 mm +/- 0.8 SD from the ultra-high resolution in-air reference. These results suggest that this simple and cost-effective protocol produces accurate and reproducible models that are suitable for the study and monitoring of marine habitats at a small reef scale.

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.

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.

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.

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.

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.