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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.

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.

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.

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.

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.

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.

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.

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.