The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well.This abstract has been translated to other languages (File S1).

Coastal areas play a crucial role in the economical, social and political development of most countries; they support diverse and productive coastal ecosystems that provide valuable goods and services.Globally flooding and coastal erosion represent serious threats along many coastlines, and will become more serious as a consequence of human-induced changes and accelerated sea-level rise. Over the past indicate that the construction of coastal defence structures will affect coastal ecosystems. The consequences can be seen on a local scale, as disruption of surrounding soft-bottom environments and introduction of new artificial hard-bottom habitats, with consequent changes to the native assemblages of the areas. Proliferation of coastal defence structures can also have critical impacts on regional species diversity, removing isolating barriers, favouring the spread of non-native species and increasing habitat heterogeneity. Knowledge of the environmental context in which coastal defence structures are placed is fundamental to an effective management of these structures as, whilst there are some general consequences of such construction, many effects are site specific. Advice is provided to meet specific management goals, which include mitigating specific impacts on the environment, such as minimising changes to surrounding sediments, spread of exotic species or growth of nuisance species, and/or enhancing specific natural resources, for example enhancing fish recruitment or promoting diverse assemblages for ecoturism. The DELOS project points out that the downstream effects of defence structures on coastal processes and regional-scale impacts on biodiversity necessitate planning and management at a regional (large coastline) scale. To effectively understand and manage coastal defences, environmental management goals must be clearly stated and incorporated into the planning, construction, and monitoring stages.

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Seagrass meadows form ecologically and economically valuable coastal habitat on every continental margin except the Antarctic, but their areal extent is declining by approximately 2-5 % per year. Seagrass wasting disease is a contributing factor in these declines, with the protist Labyrinthula identified as the etiologic agent. To help elucidate the role of Labyrinthula spp. in global seagrass declines, we surveyed roughly one fourth of all seagrass species to identify Labyrinthula diversity at the strain and/or species level, combining results from culturing methods and two common nuclear DNA markers: the ITS and 18S regions of the ribosomal RNA gene complex. After assaying a subset of the resulting isolates (of which 170 were newly sequenced), we produced a cladogenic context for putative seagrasspathogenic versus non-pathogenic Labyrinthula while also defining host and geographic ranges. Assays also suggest that pathogenicity is consistently high (when present; and, even when comparing susceptibility of US East-versus West Coast Zostera marina hosts) while virulence is variable, that some isolate-host combinations have the potential for host cross-infection, and that several modes of transmission can be effective. Taken together, these data provide additional means for delimiting putative species of Labyrinthula, suggesting at least five seagrass-pathogenic and perhaps ten or more non-pathogenic marine Bspecies^, yielding a working definition for ecologists and epidemiologists attempting to reconcile the sundry data related to seagrass wasting disease.