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We investigated the use of eDNA metabarcoding for supplementing traditional diver-based monitoring of biodiversity of marine boulder reefs within the photic zone. The applied sampling design made it possible to evaluate the usefulness of eDNA monitoring as a supplement for traditional monitoring. Specifically, this study aimed to (1) assess the local influence of boulder reefs on biodiversity across the North Sea to Baltic Sea transition zone and (2) investigate the importance of environmental gradients for patterns in community structure. On samples collected during August 2020, we compared the composition and abundance of species associated with nine reefs, representing an environmental gradient of salinity (16–33 psu), water temperature (16–21°C) and water depth (6–29 m). At each reef site, water was sampled near the bottom just above the reef and on average 2.6 km upstream and downstream (location) and sequenced with metabarcoding using COI, 18S and 12S rDNA primers. eDNA identified 400 species, diver-based observations identified 184 with an overlap of 70 species (12%) and 81 genera (18%). While eDNA identified many infaunal species, it did not detect several macroalgal species which dominated in the diver-based observations. Multivariate analysis of eDNA and diver-based community structure both distinguished between reef communities, with a significant match between patterns observed by the two methods (r = 0.37, p = 0.02). Furthermore, the eDNA approach made it possible to identify significant differences in species composition between upstream, above-reef and downstream locations, suggesting that eDNA leaves a local footprint in benthic habitats. Patterns in both eDNA and diver-based species composition and richness were significantly related to geographical distance, salinity, water temperature and water depth. Despite of low detection of macroalgae, the eDNA sampling provided a substantial supplement to traditional diver-based monitoring of biodiversity around benthic hotspots in the Danish marine waters and therefore we recommend to add eDNA methods to conventional monitoring programs in the future.

During the last century, eutrophication significantly reduced the depth distribution and density of the habitat forming eelgrass meadows (Zostera marina) in Danish coastal waters. Despite large reductions in nutrient loadings and improved water quality, Danish eelgrass meadows are currently not as widely distributed as expected from improvements in water clarity alone. This point to the importance of other environmental conditions such as sediment quality, wave exposure, oxygen conditions and water temperature that may limit eelgrass growth and contribute to constraining current distributions. Recently, detailed local models have been set up to evaluate the importance of such regulating factors in selected Danish coastal areas, but nationwide maps of eelgrass distribution and large-scale evaluations of regulating factors are still lacking. To provide such nationwide information, we applied a spatial habitat GIS modeling approach, which combines information on six key eelgrass habitat requirements (light availability, water temperature, salinity, frequency of low oxygen concentration, wave exposure, and sediment type) for which we were able to obtain national coverage. The modeled potential current distribution area of Danish eelgrass meadows was 2204 km2 compared to historical estimates of around 7000 km2, indicating a great potential for further distribution. While validating the modeled eelgrass distribution area in three areas (83–111 km2) that hold large eelgrass meadows, we found an agreement of 67% with in situ monitoring data and 77% for eelgrass areas as identified from summer orthophotos. The GIS model predicted higher coverage especially in shallow waters and near the depth limits. Areas of disagreement between GIS-modeled and observed coverage generally exhibited higher exposure level, mean summer temperature and salinity compared to areas of agreement. A sensitivity analysis showed that the modeled area distribution of eelgrass was highly sensitive to light conditions, with 18–38% increase in coverage following an increase in light availability of 20%. Modeled coverage of eelgrass was also sensitive to wave exposure and temperature conditions while less sensitive to changes in oxygen and salinity conditions. Large regional differences in habitat conditions suggest spatial variation in the factors currently limiting the recovery of eelgrass and, hence, variations in actions required for sustainable management.

As a response to increasing human pressures on marine ecosystems, the legislation aimed at improving the conservation and management of marine coastal areas in European and Contiguous Seas (ECS) underwent crucial advances. ECS, however, still remain largely affected by increasing threats leading to biodiversity loss. Here, by using emblematic case studies and expert knowledge, we review current conservation tools, comparing their application in different areas to assess their effectiveness, potential for synergies, and contradictions. Despite regional differences in their application, the existing legislative frameworks have the potential to regulate human activities and to protect marine biodiversity. However, four challenges remain to be addressed to fully achieve environmental policy goals: (1) Lack of shared vision representing a limitation in transboundary collaboration. Although all EU countries are committed to fulfil EU Directives and other binding international legislative acts, a remarkable heterogeneity exists among countries in the compliance with the common legislation on conservation and in their degree of implementation. (2) Lack of systematic procedures for the selection of protected marine sites. Regional and national approaches in designating Natura 2000 sites and nationally designated marine protected areas (MPAs) reflect varying conservation targets and importance of conservation issues in political agendas. (3) Lack of coherent ecological networks. Natura 2000 sites and other MPAs are still far from reaching the status of effective networks in all considered case studies. (4) Hotspot of conflicts with private economic interests prevailing over conservation aims. Recommendations are given to overcome the fragmented approach still characterizing the conservation and management of coastal marine environments. Holistic, integrated, ecosystem-based, cross-cutting approaches can avoid conflicts among institutions so as to provide effective and timely solutions to current and future challenges concerning the conservation and management of marine ecosystems and associated goods and services.