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59 Research products, page 1 of 6

  • European Marine Science
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  • Other research product . Other ORP type . 2022
    Open Access Dutch; Flemish
    Authors: 
    Katharina Biely;
    Publisher: Zenodo
    Project: EC | SUFISA (635577)

    The documents in these folders represent part of the qualitative data collection documentation. Research has been performed in Flanders (Belgium) in 2016 and 2017. Involved stakehodlers were flemish sugar beet farmers, processors as well as other value chain members. Though, the main stakeholders involved were farmers. The raw data cannot be published. Anonymized interview transcripts and focus group transcripts exist. However, as indicated in the informed consent, farmers did not agree to the raw data being published. The codes that resulted from data analysis are in this folder. Interview questions differed slightly from farmer to farmer as follow up questions may have been posed if needed. First interviews were performed, then focus groups were conducted and finally a workshop was organized. The qualitative reserach followed the research strategy and plan determined by the SUFISA project. On the project webpage (https://www.sufisa.eu/) more information can be found.

  • Other research product . Other ORP type . 2022
    Open Access English
    Authors: 
    Katharina Biely;
    Publisher: Zenodo
    Project: EC | SUFISA (635577)

    This is the English version of the informed consent that has been used for staekholder interactions. Similar forms have been used for focus groups and workshops.

  • Open Access English
    Authors: 
    Tanhua, Toste; Kazanidis, Georgios; Sá, Sandra; Neves, Caique; Obaton, Dominique; Sylaios, Georgios;
    Publisher: Zenodo
    Project: EC | EurofleetsPlus (824077), EC | NAUTILOS (101000825), EC | iAtlantic (818123), EC | Blue Cloud (862409), EC | JERICO-S3 (871153), EC | AtlantECO (862923), EC | ODYSSEA (727277), EC | EuroSea (862626), EC | ATLAS (678760), EC | MISSION ATLANTIC (862428)

    Ten innovative EU projects to build ocean observation systems that provide input for evidence-based management of the ocean and the Blue Economy, have joined forces in the strong cluster ‘Nourishing Blue Economy and Sharing Ocean Knowledge’. Under the lead of the EuroSea project, the group published a joint policy brief listing recommendations for sustainable ocean observation and management. The cooperation is supported by the EU Horizon Results Booster and enables the group to achieve a higher societal impact. The policy brief will be presented to the European Commission on 15 October 2021. The ocean covers 70% of the Earth’s surface and provides us with a diverse set of ecosystem services that we cannot live without or that significantly improve our quality of life. It is the primary controller of our climate, plays a critical role in providing the air we breathe and the fresh water we drink, supplies us with a large range of exploitable resources (from inorganic resources such as sand and minerals to biotic resources such as seafood), allows us to generate renewable energy, is an important pathway for world transport, an important source of income for tourism, etc. The Organisation for Economic Cooperation and Development (OECD) evaluates the Blue Economy to currently represent 2.5% of the world economic value of goods and services produced, with the potential to further double in size by 2030 (seabed mining, shipping, fishing, tourism, renewable energy systems and aquaculture will intensify). However, the overall consequences of the intensification of human activities on marine ecosystems and their services (such as ocean warming, acidification, deoxygenation, sea level rise, changing distribution and abundance of fish etc.) are still poorly quantified. In addition, on larger geographic and temporal scales, marine data currently appear fragmented, are inhomogeneous, contain data gaps and are difficult to access. This limits our capacity to understand the ocean variability and sustainably manage the ocean and its resources. Consequently, there is a need to develop a framework for more in-depth understanding of marine ecosystems, that links reliable, timely and fit-for-purpose ocean observations to the design and implementation of evidence-based decisions on the management of the ocean. To adequately serve governments, societies, the sustainable Blue Economy and citizens, ocean data need to be collected and delivered in line with the Value Chain of Ocean Information: 1) identification of required data; 2) deployment and maintenance of instruments that collect the data; 3) delivery of data and derived information products; and 4) impact assessment of services to end users. To provide input to the possible future establishment of such a framework, ten innovative EU projects to build user-focused, interdisciplinary, responsive and sustained ocean information systems and increase the sustainability of the Blue Economy, joined forces in a strong cluster to better address key global marine challenges. Under the lead of the EuroSea project, the group translated its common concerns to recommendations and listed these in the joint policy brief ‘Nourishing Blue Economy and Sharing Ocean Knowledge. Ocean Information for Sustainable Management.’. Following up on these recommendations will strengthen the entire Value Chain of Ocean Information and ensure sound sustainable ocean management. In this way, the 10 projects jointly strive to achieve goals set out in the EU Green Deal, the Paris Agreement (United Nations Framework Convention on Climate Change) and the United Nations 2021-2030 Decade of Ocean Science for Sustainable Ocean Development. Toste Tanhua (GEOMAR), EuroSea coordinator: “It was great to collaborate with these other innovative projects and make joint recommendations based on different perspectives and expertise.”

  • Open Access
    Authors: 
    Grehan, A; Hynes, S; Callery, O; Norton, D; Gafeira, J; Burnett, K; Foley, N; Stirling, D; González-Irusta, J-M; Morato, T; +1 more
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    The Convention on Biological Diversity in 2004 set out 12 principles to underpin implementation of the ecosystem approach that can be broadly grouped into four categories: People - The care of nature is a shared responsibility for all of society; we most value all knowledge and perspectives; we most involve more of society in decisions. Scale and Dynamics - Work at the right geographic scale and timescale; look well ahead into the future; work with inevitable environmental change. Functions and services - Maintain the flow of ecosystem services; work within the capacity of natural systems; balance the demand for use and conservation of the environment. Management - Allow decisions to be led locally, as far as practicable; assess the effects of decisions on others; consider economic factors. Fifteen years later the integration of ecosystem services and natural capital into environmental assessment is still very much in its infancy. Despite their seemingly remote nature, deep sea benthic habitats generate ecosystem services which provide benefits to society. Examples of these ecosystem services include provisioning ecosystem services such as fisheries, regulating ecosystem services such as nutrient cycling and maintenance of biodiversity and cultural ecosystems such as existence value. This report examines the assessment, mapping and valuation of ecosystem services in the marine and specifically for deep sea benthic habitats in the ATLAS case studies. For the provisioning ecosystem service of fisheries, a comparison is made between qualitative and quantitative approaches in methods of measuring and mapping ecosystem services generated from benthic habitats. In addition, this report has collated maps assessing the risk of fisheries impact - the most widespread and impacting human activity in the North Atlantic – in areas where vulnerable marine ecosystems and fish habitat are likely to occur in each ATLAS case study. This work presented as an atlas will provide a foundation to underpin subsequent testing of blue growth scenarios in each of the case studies.

  • Open Access
    Authors: 
    van Oevelen, D; de Froe, E; Mohn, C; Soetaert, K;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    [1] An important goal of WP2 was to develop mechanistic and predictive models for the distribution and metabolic activity of cold-water corals (CWCs) and deep-water sponges (DWS) and use these models to understand how their distribution is affected by the Atlantic Meridional Overturning Circulation (AMOC). [2] Output from hydrodynamic models (VIKING20 or ROMS-Agrif) was used to simulate transport of reactive organic matter in the water column around CWC reefs of DWS grounds. The approach is inspired by Soetaert et al. (2016), in which suspended organic matter dynamics above coral mounds was simulated. Here, we extend this methodology by having CWCs and DWS feeding on the suspended organic matter in the bottom layer using simple formulations for passive (CWC) and active (DWS) suspension feeding and metabolic activity. Physiological model formulation was based on data collected within ATLAS (Deliverables 2.1 and 2.2). [3] We focus on three ATLAS Study regions: 1) large CWC mounds, dominated and formed by the scleractinians Lophelia pertusa and Madrepora oculata, in the Logachev mound province in the south-eastern section of Rockall Bank, 2) coral gardens, dominated by the soft-coral Viminella flagellum, on Condor seamount, and 3) extensive sponge grounds, dominated by Geodia barretti along the east Canadian shelf break in Davis Strait. [4] We faced considerable computational challenges when developing the coupled models. CWC and DWS growth is slow, which implies that long simulation periods are needed to reach a (dynamic) steady state. Long simulation periods are not feasible given the high spatial and temporal (i.e. with tidal dynamics) resolution of the models. A 3-step solution procedure is proposed to tackle this issue, in which in step 1 initial suspended organic matter (OM) concentrations in the water column are calculated. In step 2, the bottom layer concentrations from step 1 are used to calculate initial concentrations for CWCs or DWS. In step 3, the coupled model is run with suspended organic matter (step 1) and CWC or DWS (step 2) as starting conditions. This approach sufficed for most of the model applications, but we acknowledge that some regions in the different model domains have not yet reached a (dynamic) steady state. [5] The coupled models, based on hydrodynamics, organic matter biogeochemistry and physiology of reef-forming organisms, successfully predicted the coral and sponge distribution and biomass in the three case study areas and thereby provide a new mechanistic tool to understand the distribution (see figure below) and metabolic (not shown) activity of hotspot ecosystems. [6] A striking result for Rockall Bank and Condor Seamount was that the suspended organic matter concentration in the bottom layer of the model domain was heavily modified by the passive suspension feeding CWCs. The initial PSF biomass (step 2) immediately depleted the organic matter concentration in the bottom layer to near zero across the whole model domain (see figure of Condor seamount below). As a result, the remaining organic matter concentration was insufficient to meet demands, which invoked a slow but steady reduction in PSF biomass over time. We conclude that the impact of PSF on bottom layer suspended OM concentration extends over large areas of the seafloor, including regions where the natural biomass is low. [7] The distribution of CWC at Rockall Bank and Condor seamount could be accurately modelled with suspended organic matter being parameterized as labile, fast-sinking organic matter, e.g. labile marine snow and zooplankton faecal pellets. The relatively fast sinking rate of this organic matter, gives a relatively low concentration in the water column, but the high current velocities around coral mounds ensure sufficient interception by the passive suspension feeding CWCs. [8] In contrast, the concentration of labile, fast-sinking organic matter OM proved grossly insufficient to meet the carbon demands of the active suspension feeding DWS. Only when we parameterized the suspended organic matter as slow sinking, relatively refractory organic matter the ambient concentration was sufficient to allow growth of DWS. This organic matter is likely characterised by smaller particles (microbial and [colloidal] DOM). The modelled DWS distribution matched field observations substantially better with slow-sinking organic matter as opposed to predictions based on fast-sinking organic matter. Experimental work (Deliverable 2.2) already hinted at these different feeding preferences between active and passive suspension feeders. We hypothesize that CWC (i.e. passive suspension feeders) and DWS (i.e. active suspension feeders) distribution on shelf breaks and slopes can be explained by a niche separation based on organic-matter type. [9] Model simulations for different AMOC states were run for each of the three case study areas. We cannot conclude from the results to what extent AMOC influences the biomass of CWC and DWS. As mentioned in [4], it proved challenging to reach a (dynamic) steady state for the models. As a result, it remained unclear whether the small differences in hydrodynamics between AMOC states truly governed differences in biomass development. In addition, tidal dynamics proved important for the transport of organic matter to the CWCs and the tidal forcing is not influenced by AMOC. We do however believe that the models are well suited for the exploration of mechanistic relations between distributions of CWCs and DWS and for example reductions in export of organic matter or changes in the type of exported organic matter.

  • Other research product . Other ORP type . 2021
    Open Access
    Authors: 
    Collart, T; Larkin, K; Pesant, S; Gafeira, J;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    Marine data are needed for many purposes: for acquiring a better scientific understanding of the marine environment, but also, increasingly, to provide information and knowledge to support ocean and coastal economic developments and underpin evidence‐based ocean and wider environmental management decision making. Data must be of sufficient quality and at the right resolution to meet the specific users’ needs. They must also be accessible in a timely manner and in appropriate formats – not only in raw data but as integrated datasets, data products, etc. – for use by marine and maritime professionals. Such expert users span scientific research, policy and industry. In addition, providing engaging and user‐friendly interfaces and tools for wider society to explore marine data and information e.g. through visualisations, is vital to promote a knowledge‐driven, ocean literate society. In addition, the blue economy, policy makers, researchers and wider society increasingly require data that are Findable, Accessible, Interoperable and Reusable (FAIR) across multiple parameters, spatial scales and resolutions. Many data services and initiatives already exist in Europe and there is a drive towards collaboration and interoperability of these to ensure data can be discovered through web services by human queries and through machine‐to‐machine communication. This ATLAS deliverable (D8.4) is driven by the philosophy of Open Data and Open Science, adding value to the diverse datasets produced by ATLAS, making them more FAIR and so, ultimately, increasing their long‐term use and impact. To this end, project partner Seascape Belgium (SBE) provided and customised a web‐GIS Platform for the ATLAS project. Using an open source geospatial content management system – GeoNode – the ATLAS GeoNode was developed as a tool to share, visualise and download geospatial data with the ATLAS consortium and wider stakeholders. In addition, ATLAS data and data products are being ingested into the European Marine Observation Data Network (EMODnet) as a long‐term solution to data availability, discovery and use. This report summarises the work conducted by SBE, in collaboration with University of Bremen (UniHB) and the PANGAEA2 information and data publisher for earth and environmental data, British Geological Survey (BGS) and others partners, to valorise the marine data being produced by ATLAS, namely building on existing methods and tools to add value, use and impact of marine data along the pipeline from data production to end‐user. This contributes in particular to the 3rd key objective of ATLAS, to transform new data, tools and understanding and make it accessible to wider stakeholders for effective ocean governance. To achieve this, SBE has worked together with UniHB (as data management and WP8 lead) and BGS to assess, optimise and – where possible – innovate the data flows in place. A key focus has been at the mid‐point of the “data pipeline”, where curated data can be ‘valorised’ through methods including data visualisation and data integration, to make them more accessible to multiand inter‐disciplinary research communities and to wider stakeholders including policy and industry. SBE administers the EMODnet Secretariat, and so has been able to facilitate direct dialogues between EMODnet Data Ingestion and the seven thematic areas of EMODnet (Bathymetry, Biology, Chemistry, Geology, Human Activities, Physics and Seabed Habitats) with ATLAS data providers to ensure a longer‐term ingestion of data into EMODnet. As a North Atlantic basin scale project with strong industry partnerships ATLAS has offered an opportunity to assess data flows and pipelines from major research activities and projects via existing data publishers and assembly centres to EMODnet, and to recommend further ways to optimise these in the future. This report also looks at the relevance of ATLAS data and outputs to policy and industry, including recommendations from meetings and consultations conducted by ATLAS WP6 and WP7. These include recommendations from ATLAS D6.4 that a desire from offshore maritime industry to see greater connectivity and interoperability between marine data to increase their impact and use and to streamline the process of marine data discovery, uptake and exploitation. Particular focus has also been dedicated to investigate the flow of data from PANGAEA data publisher to EMODnet. This has resulted in stronger collaborations between the two initiatives, leading to more systemic and operational exchanges in data flows, including a move towards automated data harvesting. The project has also offered an opportunity to develop an innovative online GIS platform as a community tool for sharing and integrating geospatial data. This was developed as a pilot and the positive user feedback shows its potential for making data ‘come alive’, connecting it to wider stakeholders and offering useful maps and products which marine and maritime professionals can use for their professional needs e.g. marine spatial planning. Recommendations from this report in terms of data stewardship and data flows can be taken forward by marine data initiatives and by the marine research community in the future. The advances that have been taken in ATLAS towards FAIR data are important steps towards streamlining the ingestion of data into EMODnet. In EMODnet, data are discoverable through data and web services, contributing to the European Union’s policy on marine knowledge, the “Marine Knowledge 2020” initiative. Here, EMODnet has a key mandate to transform Europe’s fragmented data landscape into an interoperable sharing framework, in addition to supporting coordinated European observation activities. This will increases the information available, and therefore the efficiency, for marine and maritime professionals from industry, public authorities and academia to discover and use marine data, information and knowledge. This encourages innovation that reduces our present uncertainty as to what is happening beneath the sea surface. Beyond 2020, EMODnet is working with key data initiatives to federate existing infrastructure and contribute to a Blue‐Cloud cyber platform3 that will offer enhanced capabilities for marine research including a virtual research laboratories, computational power and storage and the latest data discovery and interoperability to access data from a large diversity of data initiatives and data providers.

  • Open Access
    Authors: 
    Carreiro-Silva, M; Fox, A; Carlsson, J; Carlsson, JEL; Orejas, C; Roterman, CNR; Rakka, M; Boavida, J; González- Irusta, J; Morato, T; +4 more
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    In the marine realm, the management of fishery resources, the control and prevention of invasive species and the conservation plans for threatened species or vulnerable ecosystems (some already suffering well characterized declines such as coral reefs –Aichi target 10-, seagrass, and mangroves) requires the knowledge of interconnection and interdependency of stocks, populations and communities constituting these ecosystems. A particular challenge in marine systems is that most marine organisms exhibit a complex life cycle with two phases, including an adult stage with limited or no movements and a larval dispersive stage. In addition, many fish species can have dispersive phases during the larval, juvenile and adult phases. The direct observation and study of migratory movements is almost impossible in the oceans due to i) the reduced potential to fully access the marine environment, ii) the often minute size of the dispersing stages, iii) the often extremely large population sizes sensu stricto, and iv) the generally substantial migration distances, at adult or larval stages, with no strict a priori relationship with life history traits suspected to influence dispersal potential (Riginos et al., 2011). All those technical challenges to direct observation are of course exacerbated in the deep-sea, making models of predictive connectivity and indirect inferences a strong need. Molecular data interpreted in the theoretical framework of population genetics (Hellberg et al., 2002), ideally integrated with modelling approaches, have thus a central role to play in the study of marine connectivity. Both predictive modelling and indirect inferences based on population genomics (and in some cases on biochemical analysis of calcified structures such as otoliths or shells) need to be fed by a good knowledge of the biology and ecology of species being studied. More precisely, Lagrangian modelling of particles requires input from a diversity of fields to deliver the most accurate predictions. Mostly three fields of research are at stake that are all represented in ATLAS consortium. First, oceanographic data are needed to establish the way currents can act as conveying belt for the dispersal of particles or in some cases adult stages. Second, habitat mapping and modelling to feed the model with knowledge of the geographic locations where dispersing life stages can be emitted from and those they can viably settle because many marine, and in particular deep-sea species have a spatially fragmented distribution. Third, reproductive biology information including the nature, duration and behaviour of the dispersing life stage because most deep-sea species’ dispersal relies on the pelagic larval stages (Cowen and Sponaugle 2009, Hilário et al. 2015), is required to accurately choose the oceanographic data in terms of season when dispersal can take place and define a confidence interval for its duration, chose the depth of currents to be considered at different time steps, and account for the ability to mitigate or enhance their influence through active dispersal. Genomic data need to be interpreted with a good knowledge of historical habitat modifications (at evolutionary time scales) to understand the signature left on the genomic composition of species by past patterns of past connectivity and indirectly reconstruct their modification, as well as that of species distribution range under the effect of past environmental changes. These can be done through the analysis of sequence divergence, allelic frequency and modelling. Multi-locus genotype based analysis can then be used to infer more contemporary patterns of connectivity that would correspond to a similar time scale as the predictions issued from Lagrangian modelling. In all cases, a good knowledge of the reproductive biology of species (particularly their ability to reproduce and persist through sexual reproduction, but also to self-fertilize) is also required to accurately transform observations of the geographic distribution of genetic polymorphism into inferences as to the present or past patterns of connectivity. However, deep-sea species are harder to manipulate than their coastal counterparts, making it extremely difficult to observe or keep them in aquaria facilities in order to obtain the relevant information required for sound modelling predictions. During the ATLAS project, we successfully induced spawning and reared larvae of the octocoral Viminella flagellum under aquaria conditions. This was the first time that the larvae biology of a deep-sea octocoral has been studied. In addition, we have characterized the reproductive biology and gametogenic cycle of four CWC species that form important Vulnerable Marine Ecosystems (VMEs) in the Mediterranean and the Azores. Studies on coral reproduction revealed that all species studied were gonochoric (separate sexes), broadcast spawners (release of gametes into the water column) with continuous gametogenic cycles. The dendrophyllids Dendrophyllia cornigera and Dendrophyllia ramea from the Mediterranean come from relatively shallow depth ca. 50-100 m depth and their spawning seems to be coupled with seawater temperature. In contrast, spawning in the octocorals Dentomuricea meteor and V. flagellum collected from 200-500m deep the Azores seem to follow seasons with high primary productivity, in spring and autumn. Assexual reproduction was also studied for the octocorals Acanthogorgia armata and Acanella arbuscula based on aquaria observations. These octocorals displayed the ability of polyp bailout, with polyp dissociation from the mother colony resulting in free negatively buoyant polyps without any calcareous material. Polyp bailout is described as a stress response and an expression of reverse development, i.e. the ability of adult forms to develop into earlier developmental stages, which have higher probabilities of dispersal. It therefore may represent an important mechanism of dispersal under unfavourable conditions caused by increasing anthropogenic activities and climate change. Larvae biology of the octocoral V. flagellum was studied under aquaria conditions, and the data produced used for the connectivity modelling studies in section 4. This is the first study on the larvae biology of a deep-sea octocoral, with results indicating a lower pelagic larvae duration (PDL) than the reef-bulding species Lophelia pertusa (12 days in V. flagellum compare with 3-5 weeks in L. pertusa).This influences the dispersal ability of this species, which seems to be much shorter that L. pertusa. On the basis of this knowledge, and the one produced in WP3 for habitat mapping and modelling (for species for which enough data were available) and WP1 for water masses movements, the Lagrangian modelling could be adapted to fit several species studied in ATLAS, for which a benthic adult stage rendered coherent the hypothesis of a mainly larval driven dispersal. This included 2 invertebrates (the reef-building coral L. pertusa and the octocoral V. flagellum) and one fish species (Helicolenus dactylopterus) (section 5). Modelling of dispersal of the echinoid Cidaris cidaris was attempted but proved impossible due to the limited presence records of this species on public databases that could be used in habitat distribution models; likely erroneous records of presence derived from video and photographic data owing to morphological similarity with other taxa, and poor constraint in the population genetics of C. cidaris populations in the North Atlantic and Mediterranean. In order to account for uncertainties for many other species for which the reproductive biology could not be studied and information is lacking, nine ‘generic’ models were produced at the scale of the North Atlantic. Those include lower, average and higher bounds for larval duration and movement in the water column. The aim of this exercise was to produce connectivity matrices that could be i) compared to inferences based on population genetics data in order to select the prediction that would best match the inference of connectivity and ii) be available for future studies as knowledge of the reproductive biology of species will inform the choice of one of the nine available scenarios that would best fit the species being studied (available at Zenodo). These generic connectivity matrices clearly show the increased dispersal potential of increasing PLDs and drifting closer to the surface. They also highlight the regions of stronger currents as important sources of larvae, particularly currents along the continental slopes. Individual species models for the corals L. pertusa, V. flagellum and the fish H. dactylopterus demonstrate how hydrodynamically-based modelled connectivity can be combined with species-specific habitat suitability models to suggest connectivity by species. Model outputs show how this predicted connectivity varies considerably with the assumptions made about larval behaviour. One common feature was that populations along the eastern boundary of the North Atlantic may be generally more strongly connected. However, as currents are generally weak here (compared to those on the western and northern boundaries of the basin) this conclusion is probably dependent on the existence of a near-continuous band of suitable habitat from the mouth of the Mediterranean northwards. Connectivity models for L. pertusa under future climate scenarios suggest present day regions of high connectivity - important sources and sinks of larvae – will have much reduced connectivity, with the best connectivity future sites found northwards along the coast of Greenland and Canada. In addition, in the south areas, the reduced population in the Azores, previously supplying larvae to the US and European coasts via intermediate seamounts, becomes connected only along the mid-Atlantic ridge, with some larvae still coming in from the US coast. Predictions of future distribution and connectivity for H. dactylopterus show expansion in the suitable habitat range to the north and west particularly into the Labrador Sea. However, predictions show that with the exception of the Azores and seamounts in the Mid-Atlantic Ridge, H. dactylopterus may become a single strongly connected component under future conditions, suggesting that H. dactylopterus population may become more robust and resilient under changed future conditions. Finally, both sampling and genomic resources could be gathered to deliver inferences of connectivity at different time scales for two invertebrate VME indicator species (L. pertusa and Madrepora oculata), and their commensal polychaete Eunice norvegica, the associated invertebrate species to VMEs (Cidaris cidaris) and three species exploited by fisheries, i.e. two fish species (Capros aper and Trachurus trachurus) and one crustacean (Nephrops norvegicus) (section 6). Results from genetic analyses and modelling simulations are mostly concordant for , indicating that L. pertusa forms a large panmictic genetic cluster (ie, a group with random mating) along most of the NE Atlantic European margins (excluding the Mediterranean Sea). The large individual aggregations associated to a long larval dispersal time mediated by ocean currents may lead to high gene flow among the distant NE Atlantic cold-water coral reefs. Cases of inconsistent findings between observed genetic data and dispersal simulations, such as the location of hypothetical past climatic refugia that may have acted as post-glacial colonization sources, highlighted that other processes not yet captured may be operating (eg, the degree to which larval dispersal is driving genetic patterns across the seascape, habitat quality, variation in reproduction, population density and local selection), as well as differences between the location of genetic samples and modelled spatial extent. Despite local discrepancies, biophysical models have helped understand the complex process of gene flow and can inform future work. With the echinoid Cidaris cidaris, the population genetics results are tentative as the high-resolution genomic single nucleotide polymorphism (SNP) dataset is still undergoing quality control and analysis. The preliminary examination of COI mitochondrial gene fragments indicates no clear barriers to connectivity between North Atlantic and Western Mediterranean specimens, or between specimens collected between 200 m and 1200 m depth; consistent with a theorised highly dispersive planktotrophic larval phase in the Cidaris genus, whereby larvae feed near the surface and are transported by faster surface currents. The higher resolution genomic SNP dataset may yet reveal subtle patterns of geographic constraints on long-distance gene flow, or regionally determined variability in selective pressures, however. The genetic studies of Caprus aper clearly demonstrated that the species does not constitute a single panmictic population across the sampled range. Samples from the Mediterranean Sea showed the largest genetic differentiation. Similarly, studies on Nephrops norvegicus indicated that the Mediterranean samples from the Adriatic Sea are significantly differentiated from the Atlantic samples analysed. Furthermore, both species showed further diferentiation, although weaker, among the Atlantic samples. The studies of Trachururs trachurus are ongoing (samples from the Mediterranenan Sea are yet to be analysed) but the preliminary results indicate that the species is represented by multiple populations. In summary, there is clear population structure within all three species exploited by fisheries and this information could be used by managers to improve the management of these marine resources. Among all ten species for which advances could be made either in terms of knowledge of the reproductive biology, dispersal modelling or population genomics, a full set of information could be gathered for the emblematic reef-building L. pertusa, and the consortium is also trying to finalize the genomic data production for the exploited fish H. dactylopterus. Perpectives beyond this report include the finalization of data production and analysis, and the test of a new method to go beyond the usual “side by side” comparison of predicted (lagrangian modelling) versus realized (inferences from population genomics) dispersal by integrating the Lagrangian matrices of connectivity as priors of a Bayesian analysis (Gaggiotti, 2017) of the genetic dataset characterizing the metapopulation system being studied. Such integrative framework has long been expected by the scientific community addressing connectivity through the use of a diversity of tools and theoretical framework as the ones detailed in this report. The recent development of this new analytical tool will allow testing this approach on the scleractinian coral L. pertusa. All results obtained here will be used to deliver information useful for the conservation and management of VMEs and fisheries resources (WP 6 and 7), an advance that will be formalized in the next report of WP4, DL4.5 “Integrated management considering connectivity patterns”.

  • Open Access
    Authors: 
    Carlsson, J;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    Environmental (e)DNA methods (quantitative PCR and metabarcoding) are non-invasive, rapid and cost-efficient tools for detecting single species and monitoring biodiversity with considerable potential for informing aquatic conservation and management. Methods for implementing eDNA are constantly developing and these tools have received significant interest from industry. There have been substantial efforts to develop best practice approaches, standardisation and workflows (c.f. COST-action DNAqua-Net CA15219) that might ultimately complement or replace existing methods and develop new metrics for the implementation of the European Water Framework Directive. These eDNA based methods also have the potential to contribute to the implementation of the Marine Strategy Framework Directive. While the use of eDNA in freshwater has received by far the most attention, there is great potential for using eDNA in the marine environment to address a wide range of questions using non-invasive sampling; ranging from spatial and temporal biodiversity assessments, to assessing distribution patterns and range expansions/contractions of single species. In the ATLAS project, WP3 focused on evaluating the accuracy and sensitivity of meta-barcoding and qPCR methods with the objective of selecting a set of primers amplifying distinct DNA fragments to optimise metabarcoding across the Tree of Life, covering a maximum number of lineages, and developing species-specific probes for PCR detection of VME indicator species, fishery targets and bycatch species. The emergence of eDNA tools to assess marine biodiversity and detect specific target marine species has generated great hopes to describe biodiversity of ecosystems that have been difficult to access (e.g. deep-sea habitats); as sampling of water and sediments is relatively simple as compared to traditional methods requiring specialised equipment (ROV, camera sledges, fishery gear, etc.). Nevertheless, few examples of such applications existed and even fewer, if any, in the deep sea. The great challenges for using eDNA techniques to assess deep-sea biodiversity are to obtain DNA from more or less blindly collected, low biomass taxa and subsequently low DNA concentration seawater or sediment samples. University College Dublin and IFREMER were tasked with evaluating the performance of next-generation genomic tools (metabarcoding of eDNA) for assessing biodiversity and quantitative qPCR (plankton samples) as a sensitive tool to detect and quantify biomass of target species. The accuracy and sensitivity of metabarcoding and qPCR will be validated on samples assessed using classical taxonomy in selected Case Studies. In respect of the development of qPCR assays, six target species were selected for assay development. Quantitative (q)PCR assays successfully detected and semi-quantified five target species showing that despite extremely low DNA concentration and the large volumes of water in which these species are found, eDNA is a very sensitive tool offering a promising method for detection of target species in the marine environment, including the deep sea. However, it was not possible to develop an assay for Lophelia pertusa due to low polymorphism usually encountered at mitochondrial DNA for scleractinian corals, and the lack of existing sequence data from closely related species. The metabarcoding efforts by IFREMER resulted in the development of six complementary sets of primers capable of assessing biodiversity from deep-sea sediments across the entire Tree of Life. In general, metabarcoding protocols were capable of characterising biodiversity of low biomass deep-sea sediments; even for understudied deep-sea metazoan taxa. These protocols were applied to 350 samples collected during the ATLAS-MEDWAVES cruise, demonstrating the sensitivity of metabarcoding in deep-sea habitats. The development of eDNA species-specific assays and metabarcoding methods demonstrate the utility of eDNA-based methods for assessing and managing deep-sea biodiversity. Further, in line with the successful deployment of these tools in freshwater and in marine waters as demonstrated in this WP, these approaches could also be used to supplement or replace traditional methods such as morphology-based biodiversity used in the marine environment, including in the deep sea where specimens can be extremely small and difficult to identify (c.f. Danovaro et al. 2016). Similarly, future and current applications of eDNA include biodiversity assessments and baselines for Environmental Impact Studies of deep-sea industry operations such as mineral extraction (Boschen et al. 2016). We have demonstrated the usefulness of eDNA methods in the deep sea despite the great challenges they represent in terms of accessing samples and often low concentration of biomass.

  • Open Access
    Authors: 
    Ankamah-Yeboah, I; Xuan, BB; Hynes, S; Needham, K; Armstrong, CW;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    This report presents an assessment of how the public perceives, and values deep-sea ecosystem services in the North Atlantic, and provides a foundation for evaluating and balancing Blue Growth with conservation management in the deep sea. Nonmarket valuation is used to evaluate public perceptions of the deep sea environment and the socio-economic values of new marine management plans. This report presents the results of two discrete choice experiment surveys that were employed to assess the values held by the Scottish and Norwegian public for the Mingulay reef complex and Hola off Lofoten-Vesterålen (LoVe), respectively. Regarding public perception, the results show that public knowledge and awareness of deep-sea ecosystems is relatively higher among Norwegians than among the Scottish public. Specifically, awareness of cold-water corals is high for the LoVe case study amongst the Norwegian public and low for the Mingulay reef complex in the Scottish case. Despite this limited knowledge, many respondents thought changes in the deep sea would have at least some effect on them personally. On average, the public perceives deep-sea conditions to be at most ‘fairly good’ but are pessimistic about its management: a significantly higher share, 76% of Norwegians perceive the deep sea to be poorly-managed compared to 12% of those surveyed in Scotland. Results from both countries highlight eco-centric attitudes towards the marine environment, implying that the general public recognise the value of ecosystem services, the current ecological crisis and the need for sustainable management. Demographic profiles of respondents and their experiences play influential roles, with exposure to media-art like the Blue-Planet II series showing prominence in most perception dimensions. To determine whether the perceived public support translates into monetary support for new management scenarios, a discrete choice experiment was conducted to assess trade-offs for improvement in a number of deep-sea environment attributes; environmental health and quality, an increase in the size of marine protected areas (MPAs) and new marine related job creation. Latent class logit results revealed two distinct groups of public preferences: a minority of respondents who derive minimal value from the marine environment and a second group who exhibit significant positive preferences for all the management attributes and exhibit strong preferences for new policy options. The most valued of the new policy attributes were those related to the key pressures of the marine environment: commercial fish stocks and marine litter designated as Descriptors 3 and 10 respectively in the GES of the MSF Directive. This was followed by the size of the marine protected area, whilst the creation of jobs is the least valued. Overall, however, weighted average willingness to pay estimates, indicate that the public in both countries is willing to pay to support conservation of the unfamiliar deep-sea ecosystem irrespective of the individual attributes delivered in a new marine management plan. The results highlight the importance of the deep-sea ecosystems to the public and provide support for further collective action required by the EU in moving beyond the 2020 Marine Strategy Framework Directive (MSFD) objective of achieving good environmental status for Europe’s seas.

  • Other research product . Other ORP type . 2021
    Open Access
    Authors: 
    Johnson, C; Inall, M; Gary, S; Cunningham, S;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    An overarching goal of ATLAS is to investigate the sensitivity of North Atlantic Ocean ecosystems to basin-scale physical processes. This report examines relationships between four pertinent climate indices and key physical variables using both output from a high-resolution ocean model and an observational dataset. After describing long-term mean conditions and determining seasonal cycles, we use a composite approach to create mean conditions for high and low states of each climate index. The Atlantic Meridional Overturning Circulation (AMOC) shows cooler bottom conditions around the boundaries of the western subpolar gyre during a high state, which may be linked to more energetic conditions in this area. The North Atlantic Oscillation (NAO) shows clear anti-correlation between European and North American Shelves: during a high NAO, bottom conditions on the eastern boundary are warmer and more saline, whilst western areas are cooler and fresher. Bottom kinetic energy also shows an east-west disconnect, with less energetic conditions in the eastern overflow currents during a high NAO and a corresponding increase in western overflows. The most striking feature in the Subpolar Gyre (SPG) composites, is a strong area of cooler bottom conditions around the northern and western boundaries of the subpolar North Atlantic during a high SPG. In contrast, during a high Atlantic Multi-decadal Oscillation (AMO), bottom conditions in the same areas are warmer and more saline although areas deeper than around 2000 m in the North Atlantic are cooler and fresher. This is the first study to show that climate indices are associated with spatially-coherent changes in bottom conditions across the North Atlantic region. Although changes are relatively small, due to the multi-annual nature of the climate indices any changes may persist for several years. As such, vulnerable sessile ecosystems may be exposed to sustained changes in mean conditions, with this deviation in the baseline also altering the likelihood of extreme events such as mean heatwaves. Thus, a thorough knowledge of natural variability is essential for the understanding of deep-sea ecosystems, predicting their response to future changes, and evaluation of management frameworks.

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  • Other research product . Other ORP type . 2022
    Open Access Dutch; Flemish
    Authors: 
    Katharina Biely;
    Publisher: Zenodo
    Project: EC | SUFISA (635577)

    The documents in these folders represent part of the qualitative data collection documentation. Research has been performed in Flanders (Belgium) in 2016 and 2017. Involved stakehodlers were flemish sugar beet farmers, processors as well as other value chain members. Though, the main stakeholders involved were farmers. The raw data cannot be published. Anonymized interview transcripts and focus group transcripts exist. However, as indicated in the informed consent, farmers did not agree to the raw data being published. The codes that resulted from data analysis are in this folder. Interview questions differed slightly from farmer to farmer as follow up questions may have been posed if needed. First interviews were performed, then focus groups were conducted and finally a workshop was organized. The qualitative reserach followed the research strategy and plan determined by the SUFISA project. On the project webpage (https://www.sufisa.eu/) more information can be found.

  • Other research product . Other ORP type . 2022
    Open Access English
    Authors: 
    Katharina Biely;
    Publisher: Zenodo
    Project: EC | SUFISA (635577)

    This is the English version of the informed consent that has been used for staekholder interactions. Similar forms have been used for focus groups and workshops.

  • Open Access English
    Authors: 
    Tanhua, Toste; Kazanidis, Georgios; Sá, Sandra; Neves, Caique; Obaton, Dominique; Sylaios, Georgios;
    Publisher: Zenodo
    Project: EC | EurofleetsPlus (824077), EC | NAUTILOS (101000825), EC | iAtlantic (818123), EC | Blue Cloud (862409), EC | JERICO-S3 (871153), EC | AtlantECO (862923), EC | ODYSSEA (727277), EC | EuroSea (862626), EC | ATLAS (678760), EC | MISSION ATLANTIC (862428)

    Ten innovative EU projects to build ocean observation systems that provide input for evidence-based management of the ocean and the Blue Economy, have joined forces in the strong cluster ‘Nourishing Blue Economy and Sharing Ocean Knowledge’. Under the lead of the EuroSea project, the group published a joint policy brief listing recommendations for sustainable ocean observation and management. The cooperation is supported by the EU Horizon Results Booster and enables the group to achieve a higher societal impact. The policy brief will be presented to the European Commission on 15 October 2021. The ocean covers 70% of the Earth’s surface and provides us with a diverse set of ecosystem services that we cannot live without or that significantly improve our quality of life. It is the primary controller of our climate, plays a critical role in providing the air we breathe and the fresh water we drink, supplies us with a large range of exploitable resources (from inorganic resources such as sand and minerals to biotic resources such as seafood), allows us to generate renewable energy, is an important pathway for world transport, an important source of income for tourism, etc. The Organisation for Economic Cooperation and Development (OECD) evaluates the Blue Economy to currently represent 2.5% of the world economic value of goods and services produced, with the potential to further double in size by 2030 (seabed mining, shipping, fishing, tourism, renewable energy systems and aquaculture will intensify). However, the overall consequences of the intensification of human activities on marine ecosystems and their services (such as ocean warming, acidification, deoxygenation, sea level rise, changing distribution and abundance of fish etc.) are still poorly quantified. In addition, on larger geographic and temporal scales, marine data currently appear fragmented, are inhomogeneous, contain data gaps and are difficult to access. This limits our capacity to understand the ocean variability and sustainably manage the ocean and its resources. Consequently, there is a need to develop a framework for more in-depth understanding of marine ecosystems, that links reliable, timely and fit-for-purpose ocean observations to the design and implementation of evidence-based decisions on the management of the ocean. To adequately serve governments, societies, the sustainable Blue Economy and citizens, ocean data need to be collected and delivered in line with the Value Chain of Ocean Information: 1) identification of required data; 2) deployment and maintenance of instruments that collect the data; 3) delivery of data and derived information products; and 4) impact assessment of services to end users. To provide input to the possible future establishment of such a framework, ten innovative EU projects to build user-focused, interdisciplinary, responsive and sustained ocean information systems and increase the sustainability of the Blue Economy, joined forces in a strong cluster to better address key global marine challenges. Under the lead of the EuroSea project, the group translated its common concerns to recommendations and listed these in the joint policy brief ‘Nourishing Blue Economy and Sharing Ocean Knowledge. Ocean Information for Sustainable Management.’. Following up on these recommendations will strengthen the entire Value Chain of Ocean Information and ensure sound sustainable ocean management. In this way, the 10 projects jointly strive to achieve goals set out in the EU Green Deal, the Paris Agreement (United Nations Framework Convention on Climate Change) and the United Nations 2021-2030 Decade of Ocean Science for Sustainable Ocean Development. Toste Tanhua (GEOMAR), EuroSea coordinator: “It was great to collaborate with these other innovative projects and make joint recommendations based on different perspectives and expertise.”

  • Open Access
    Authors: 
    Grehan, A; Hynes, S; Callery, O; Norton, D; Gafeira, J; Burnett, K; Foley, N; Stirling, D; González-Irusta, J-M; Morato, T; +1 more
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    The Convention on Biological Diversity in 2004 set out 12 principles to underpin implementation of the ecosystem approach that can be broadly grouped into four categories: People - The care of nature is a shared responsibility for all of society; we most value all knowledge and perspectives; we most involve more of society in decisions. Scale and Dynamics - Work at the right geographic scale and timescale; look well ahead into the future; work with inevitable environmental change. Functions and services - Maintain the flow of ecosystem services; work within the capacity of natural systems; balance the demand for use and conservation of the environment. Management - Allow decisions to be led locally, as far as practicable; assess the effects of decisions on others; consider economic factors. Fifteen years later the integration of ecosystem services and natural capital into environmental assessment is still very much in its infancy. Despite their seemingly remote nature, deep sea benthic habitats generate ecosystem services which provide benefits to society. Examples of these ecosystem services include provisioning ecosystem services such as fisheries, regulating ecosystem services such as nutrient cycling and maintenance of biodiversity and cultural ecosystems such as existence value. This report examines the assessment, mapping and valuation of ecosystem services in the marine and specifically for deep sea benthic habitats in the ATLAS case studies. For the provisioning ecosystem service of fisheries, a comparison is made between qualitative and quantitative approaches in methods of measuring and mapping ecosystem services generated from benthic habitats. In addition, this report has collated maps assessing the risk of fisheries impact - the most widespread and impacting human activity in the North Atlantic – in areas where vulnerable marine ecosystems and fish habitat are likely to occur in each ATLAS case study. This work presented as an atlas will provide a foundation to underpin subsequent testing of blue growth scenarios in each of the case studies.

  • Open Access
    Authors: 
    van Oevelen, D; de Froe, E; Mohn, C; Soetaert, K;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    [1] An important goal of WP2 was to develop mechanistic and predictive models for the distribution and metabolic activity of cold-water corals (CWCs) and deep-water sponges (DWS) and use these models to understand how their distribution is affected by the Atlantic Meridional Overturning Circulation (AMOC). [2] Output from hydrodynamic models (VIKING20 or ROMS-Agrif) was used to simulate transport of reactive organic matter in the water column around CWC reefs of DWS grounds. The approach is inspired by Soetaert et al. (2016), in which suspended organic matter dynamics above coral mounds was simulated. Here, we extend this methodology by having CWCs and DWS feeding on the suspended organic matter in the bottom layer using simple formulations for passive (CWC) and active (DWS) suspension feeding and metabolic activity. Physiological model formulation was based on data collected within ATLAS (Deliverables 2.1 and 2.2). [3] We focus on three ATLAS Study regions: 1) large CWC mounds, dominated and formed by the scleractinians Lophelia pertusa and Madrepora oculata, in the Logachev mound province in the south-eastern section of Rockall Bank, 2) coral gardens, dominated by the soft-coral Viminella flagellum, on Condor seamount, and 3) extensive sponge grounds, dominated by Geodia barretti along the east Canadian shelf break in Davis Strait. [4] We faced considerable computational challenges when developing the coupled models. CWC and DWS growth is slow, which implies that long simulation periods are needed to reach a (dynamic) steady state. Long simulation periods are not feasible given the high spatial and temporal (i.e. with tidal dynamics) resolution of the models. A 3-step solution procedure is proposed to tackle this issue, in which in step 1 initial suspended organic matter (OM) concentrations in the water column are calculated. In step 2, the bottom layer concentrations from step 1 are used to calculate initial concentrations for CWCs or DWS. In step 3, the coupled model is run with suspended organic matter (step 1) and CWC or DWS (step 2) as starting conditions. This approach sufficed for most of the model applications, but we acknowledge that some regions in the different model domains have not yet reached a (dynamic) steady state. [5] The coupled models, based on hydrodynamics, organic matter biogeochemistry and physiology of reef-forming organisms, successfully predicted the coral and sponge distribution and biomass in the three case study areas and thereby provide a new mechanistic tool to understand the distribution (see figure below) and metabolic (not shown) activity of hotspot ecosystems. [6] A striking result for Rockall Bank and Condor Seamount was that the suspended organic matter concentration in the bottom layer of the model domain was heavily modified by the passive suspension feeding CWCs. The initial PSF biomass (step 2) immediately depleted the organic matter concentration in the bottom layer to near zero across the whole model domain (see figure of Condor seamount below). As a result, the remaining organic matter concentration was insufficient to meet demands, which invoked a slow but steady reduction in PSF biomass over time. We conclude that the impact of PSF on bottom layer suspended OM concentration extends over large areas of the seafloor, including regions where the natural biomass is low. [7] The distribution of CWC at Rockall Bank and Condor seamount could be accurately modelled with suspended organic matter being parameterized as labile, fast-sinking organic matter, e.g. labile marine snow and zooplankton faecal pellets. The relatively fast sinking rate of this organic matter, gives a relatively low concentration in the water column, but the high current velocities around coral mounds ensure sufficient interception by the passive suspension feeding CWCs. [8] In contrast, the concentration of labile, fast-sinking organic matter OM proved grossly insufficient to meet the carbon demands of the active suspension feeding DWS. Only when we parameterized the suspended organic matter as slow sinking, relatively refractory organic matter the ambient concentration was sufficient to allow growth of DWS. This organic matter is likely characterised by smaller particles (microbial and [colloidal] DOM). The modelled DWS distribution matched field observations substantially better with slow-sinking organic matter as opposed to predictions based on fast-sinking organic matter. Experimental work (Deliverable 2.2) already hinted at these different feeding preferences between active and passive suspension feeders. We hypothesize that CWC (i.e. passive suspension feeders) and DWS (i.e. active suspension feeders) distribution on shelf breaks and slopes can be explained by a niche separation based on organic-matter type. [9] Model simulations for different AMOC states were run for each of the three case study areas. We cannot conclude from the results to what extent AMOC influences the biomass of CWC and DWS. As mentioned in [4], it proved challenging to reach a (dynamic) steady state for the models. As a result, it remained unclear whether the small differences in hydrodynamics between AMOC states truly governed differences in biomass development. In addition, tidal dynamics proved important for the transport of organic matter to the CWCs and the tidal forcing is not influenced by AMOC. We do however believe that the models are well suited for the exploration of mechanistic relations between distributions of CWCs and DWS and for example reductions in export of organic matter or changes in the type of exported organic matter.

  • Other research product . Other ORP type . 2021
    Open Access
    Authors: 
    Collart, T; Larkin, K; Pesant, S; Gafeira, J;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    Marine data are needed for many purposes: for acquiring a better scientific understanding of the marine environment, but also, increasingly, to provide information and knowledge to support ocean and coastal economic developments and underpin evidence‐based ocean and wider environmental management decision making. Data must be of sufficient quality and at the right resolution to meet the specific users’ needs. They must also be accessible in a timely manner and in appropriate formats – not only in raw data but as integrated datasets, data products, etc. – for use by marine and maritime professionals. Such expert users span scientific research, policy and industry. In addition, providing engaging and user‐friendly interfaces and tools for wider society to explore marine data and information e.g. through visualisations, is vital to promote a knowledge‐driven, ocean literate society. In addition, the blue economy, policy makers, researchers and wider society increasingly require data that are Findable, Accessible, Interoperable and Reusable (FAIR) across multiple parameters, spatial scales and resolutions. Many data services and initiatives already exist in Europe and there is a drive towards collaboration and interoperability of these to ensure data can be discovered through web services by human queries and through machine‐to‐machine communication. This ATLAS deliverable (D8.4) is driven by the philosophy of Open Data and Open Science, adding value to the diverse datasets produced by ATLAS, making them more FAIR and so, ultimately, increasing their long‐term use and impact. To this end, project partner Seascape Belgium (SBE) provided and customised a web‐GIS Platform for the ATLAS project. Using an open source geospatial content management system – GeoNode – the ATLAS GeoNode was developed as a tool to share, visualise and download geospatial data with the ATLAS consortium and wider stakeholders. In addition, ATLAS data and data products are being ingested into the European Marine Observation Data Network (EMODnet) as a long‐term solution to data availability, discovery and use. This report summarises the work conducted by SBE, in collaboration with University of Bremen (UniHB) and the PANGAEA2 information and data publisher for earth and environmental data, British Geological Survey (BGS) and others partners, to valorise the marine data being produced by ATLAS, namely building on existing methods and tools to add value, use and impact of marine data along the pipeline from data production to end‐user. This contributes in particular to the 3rd key objective of ATLAS, to transform new data, tools and understanding and make it accessible to wider stakeholders for effective ocean governance. To achieve this, SBE has worked together with UniHB (as data management and WP8 lead) and BGS to assess, optimise and – where possible – innovate the data flows in place. A key focus has been at the mid‐point of the “data pipeline”, where curated data can be ‘valorised’ through methods including data visualisation and data integration, to make them more accessible to multiand inter‐disciplinary research communities and to wider stakeholders including policy and industry. SBE administers the EMODnet Secretariat, and so has been able to facilitate direct dialogues between EMODnet Data Ingestion and the seven thematic areas of EMODnet (Bathymetry, Biology, Chemistry, Geology, Human Activities, Physics and Seabed Habitats) with ATLAS data providers to ensure a longer‐term ingestion of data into EMODnet. As a North Atlantic basin scale project with strong industry partnerships ATLAS has offered an opportunity to assess data flows and pipelines from major research activities and projects via existing data publishers and assembly centres to EMODnet, and to recommend further ways to optimise these in the future. This report also looks at the relevance of ATLAS data and outputs to policy and industry, including recommendations from meetings and consultations conducted by ATLAS WP6 and WP7. These include recommendations from ATLAS D6.4 that a desire from offshore maritime industry to see greater connectivity and interoperability between marine data to increase their impact and use and to streamline the process of marine data discovery, uptake and exploitation. Particular focus has also been dedicated to investigate the flow of data from PANGAEA data publisher to EMODnet. This has resulted in stronger collaborations between the two initiatives, leading to more systemic and operational exchanges in data flows, including a move towards automated data harvesting. The project has also offered an opportunity to develop an innovative online GIS platform as a community tool for sharing and integrating geospatial data. This was developed as a pilot and the positive user feedback shows its potential for making data ‘come alive’, connecting it to wider stakeholders and offering useful maps and products which marine and maritime professionals can use for their professional needs e.g. marine spatial planning. Recommendations from this report in terms of data stewardship and data flows can be taken forward by marine data initiatives and by the marine research community in the future. The advances that have been taken in ATLAS towards FAIR data are important steps towards streamlining the ingestion of data into EMODnet. In EMODnet, data are discoverable through data and web services, contributing to the European Union’s policy on marine knowledge, the “Marine Knowledge 2020” initiative. Here, EMODnet has a key mandate to transform Europe’s fragmented data landscape into an interoperable sharing framework, in addition to supporting coordinated European observation activities. This will increases the information available, and therefore the efficiency, for marine and maritime professionals from industry, public authorities and academia to discover and use marine data, information and knowledge. This encourages innovation that reduces our present uncertainty as to what is happening beneath the sea surface. Beyond 2020, EMODnet is working with key data initiatives to federate existing infrastructure and contribute to a Blue‐Cloud cyber platform3 that will offer enhanced capabilities for marine research including a virtual research laboratories, computational power and storage and the latest data discovery and interoperability to access data from a large diversity of data initiatives and data providers.

  • Open Access
    Authors: 
    Carreiro-Silva, M; Fox, A; Carlsson, J; Carlsson, JEL; Orejas, C; Roterman, CNR; Rakka, M; Boavida, J; González- Irusta, J; Morato, T; +4 more
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    In the marine realm, the management of fishery resources, the control and prevention of invasive species and the conservation plans for threatened species or vulnerable ecosystems (some already suffering well characterized declines such as coral reefs –Aichi target 10-, seagrass, and mangroves) requires the knowledge of interconnection and interdependency of stocks, populations and communities constituting these ecosystems. A particular challenge in marine systems is that most marine organisms exhibit a complex life cycle with two phases, including an adult stage with limited or no movements and a larval dispersive stage. In addition, many fish species can have dispersive phases during the larval, juvenile and adult phases. The direct observation and study of migratory movements is almost impossible in the oceans due to i) the reduced potential to fully access the marine environment, ii) the often minute size of the dispersing stages, iii) the often extremely large population sizes sensu stricto, and iv) the generally substantial migration distances, at adult or larval stages, with no strict a priori relationship with life history traits suspected to influence dispersal potential (Riginos et al., 2011). All those technical challenges to direct observation are of course exacerbated in the deep-sea, making models of predictive connectivity and indirect inferences a strong need. Molecular data interpreted in the theoretical framework of population genetics (Hellberg et al., 2002), ideally integrated with modelling approaches, have thus a central role to play in the study of marine connectivity. Both predictive modelling and indirect inferences based on population genomics (and in some cases on biochemical analysis of calcified structures such as otoliths or shells) need to be fed by a good knowledge of the biology and ecology of species being studied. More precisely, Lagrangian modelling of particles requires input from a diversity of fields to deliver the most accurate predictions. Mostly three fields of research are at stake that are all represented in ATLAS consortium. First, oceanographic data are needed to establish the way currents can act as conveying belt for the dispersal of particles or in some cases adult stages. Second, habitat mapping and modelling to feed the model with knowledge of the geographic locations where dispersing life stages can be emitted from and those they can viably settle because many marine, and in particular deep-sea species have a spatially fragmented distribution. Third, reproductive biology information including the nature, duration and behaviour of the dispersing life stage because most deep-sea species’ dispersal relies on the pelagic larval stages (Cowen and Sponaugle 2009, Hilário et al. 2015), is required to accurately choose the oceanographic data in terms of season when dispersal can take place and define a confidence interval for its duration, chose the depth of currents to be considered at different time steps, and account for the ability to mitigate or enhance their influence through active dispersal. Genomic data need to be interpreted with a good knowledge of historical habitat modifications (at evolutionary time scales) to understand the signature left on the genomic composition of species by past patterns of past connectivity and indirectly reconstruct their modification, as well as that of species distribution range under the effect of past environmental changes. These can be done through the analysis of sequence divergence, allelic frequency and modelling. Multi-locus genotype based analysis can then be used to infer more contemporary patterns of connectivity that would correspond to a similar time scale as the predictions issued from Lagrangian modelling. In all cases, a good knowledge of the reproductive biology of species (particularly their ability to reproduce and persist through sexual reproduction, but also to self-fertilize) is also required to accurately transform observations of the geographic distribution of genetic polymorphism into inferences as to the present or past patterns of connectivity. However, deep-sea species are harder to manipulate than their coastal counterparts, making it extremely difficult to observe or keep them in aquaria facilities in order to obtain the relevant information required for sound modelling predictions. During the ATLAS project, we successfully induced spawning and reared larvae of the octocoral Viminella flagellum under aquaria conditions. This was the first time that the larvae biology of a deep-sea octocoral has been studied. In addition, we have characterized the reproductive biology and gametogenic cycle of four CWC species that form important Vulnerable Marine Ecosystems (VMEs) in the Mediterranean and the Azores. Studies on coral reproduction revealed that all species studied were gonochoric (separate sexes), broadcast spawners (release of gametes into the water column) with continuous gametogenic cycles. The dendrophyllids Dendrophyllia cornigera and Dendrophyllia ramea from the Mediterranean come from relatively shallow depth ca. 50-100 m depth and their spawning seems to be coupled with seawater temperature. In contrast, spawning in the octocorals Dentomuricea meteor and V. flagellum collected from 200-500m deep the Azores seem to follow seasons with high primary productivity, in spring and autumn. Assexual reproduction was also studied for the octocorals Acanthogorgia armata and Acanella arbuscula based on aquaria observations. These octocorals displayed the ability of polyp bailout, with polyp dissociation from the mother colony resulting in free negatively buoyant polyps without any calcareous material. Polyp bailout is described as a stress response and an expression of reverse development, i.e. the ability of adult forms to develop into earlier developmental stages, which have higher probabilities of dispersal. It therefore may represent an important mechanism of dispersal under unfavourable conditions caused by increasing anthropogenic activities and climate change. Larvae biology of the octocoral V. flagellum was studied under aquaria conditions, and the data produced used for the connectivity modelling studies in section 4. This is the first study on the larvae biology of a deep-sea octocoral, with results indicating a lower pelagic larvae duration (PDL) than the reef-bulding species Lophelia pertusa (12 days in V. flagellum compare with 3-5 weeks in L. pertusa).This influences the dispersal ability of this species, which seems to be much shorter that L. pertusa. On the basis of this knowledge, and the one produced in WP3 for habitat mapping and modelling (for species for which enough data were available) and WP1 for water masses movements, the Lagrangian modelling could be adapted to fit several species studied in ATLAS, for which a benthic adult stage rendered coherent the hypothesis of a mainly larval driven dispersal. This included 2 invertebrates (the reef-building coral L. pertusa and the octocoral V. flagellum) and one fish species (Helicolenus dactylopterus) (section 5). Modelling of dispersal of the echinoid Cidaris cidaris was attempted but proved impossible due to the limited presence records of this species on public databases that could be used in habitat distribution models; likely erroneous records of presence derived from video and photographic data owing to morphological similarity with other taxa, and poor constraint in the population genetics of C. cidaris populations in the North Atlantic and Mediterranean. In order to account for uncertainties for many other species for which the reproductive biology could not be studied and information is lacking, nine ‘generic’ models were produced at the scale of the North Atlantic. Those include lower, average and higher bounds for larval duration and movement in the water column. The aim of this exercise was to produce connectivity matrices that could be i) compared to inferences based on population genetics data in order to select the prediction that would best match the inference of connectivity and ii) be available for future studies as knowledge of the reproductive biology of species will inform the choice of one of the nine available scenarios that would best fit the species being studied (available at Zenodo). These generic connectivity matrices clearly show the increased dispersal potential of increasing PLDs and drifting closer to the surface. They also highlight the regions of stronger currents as important sources of larvae, particularly currents along the continental slopes. Individual species models for the corals L. pertusa, V. flagellum and the fish H. dactylopterus demonstrate how hydrodynamically-based modelled connectivity can be combined with species-specific habitat suitability models to suggest connectivity by species. Model outputs show how this predicted connectivity varies considerably with the assumptions made about larval behaviour. One common feature was that populations along the eastern boundary of the North Atlantic may be generally more strongly connected. However, as currents are generally weak here (compared to those on the western and northern boundaries of the basin) this conclusion is probably dependent on the existence of a near-continuous band of suitable habitat from the mouth of the Mediterranean northwards. Connectivity models for L. pertusa under future climate scenarios suggest present day regions of high connectivity - important sources and sinks of larvae – will have much reduced connectivity, with the best connectivity future sites found northwards along the coast of Greenland and Canada. In addition, in the south areas, the reduced population in the Azores, previously supplying larvae to the US and European coasts via intermediate seamounts, becomes connected only along the mid-Atlantic ridge, with some larvae still coming in from the US coast. Predictions of future distribution and connectivity for H. dactylopterus show expansion in the suitable habitat range to the north and west particularly into the Labrador Sea. However, predictions show that with the exception of the Azores and seamounts in the Mid-Atlantic Ridge, H. dactylopterus may become a single strongly connected component under future conditions, suggesting that H. dactylopterus population may become more robust and resilient under changed future conditions. Finally, both sampling and genomic resources could be gathered to deliver inferences of connectivity at different time scales for two invertebrate VME indicator species (L. pertusa and Madrepora oculata), and their commensal polychaete Eunice norvegica, the associated invertebrate species to VMEs (Cidaris cidaris) and three species exploited by fisheries, i.e. two fish species (Capros aper and Trachurus trachurus) and one crustacean (Nephrops norvegicus) (section 6). Results from genetic analyses and modelling simulations are mostly concordant for , indicating that L. pertusa forms a large panmictic genetic cluster (ie, a group with random mating) along most of the NE Atlantic European margins (excluding the Mediterranean Sea). The large individual aggregations associated to a long larval dispersal time mediated by ocean currents may lead to high gene flow among the distant NE Atlantic cold-water coral reefs. Cases of inconsistent findings between observed genetic data and dispersal simulations, such as the location of hypothetical past climatic refugia that may have acted as post-glacial colonization sources, highlighted that other processes not yet captured may be operating (eg, the degree to which larval dispersal is driving genetic patterns across the seascape, habitat quality, variation in reproduction, population density and local selection), as well as differences between the location of genetic samples and modelled spatial extent. Despite local discrepancies, biophysical models have helped understand the complex process of gene flow and can inform future work. With the echinoid Cidaris cidaris, the population genetics results are tentative as the high-resolution genomic single nucleotide polymorphism (SNP) dataset is still undergoing quality control and analysis. The preliminary examination of COI mitochondrial gene fragments indicates no clear barriers to connectivity between North Atlantic and Western Mediterranean specimens, or between specimens collected between 200 m and 1200 m depth; consistent with a theorised highly dispersive planktotrophic larval phase in the Cidaris genus, whereby larvae feed near the surface and are transported by faster surface currents. The higher resolution genomic SNP dataset may yet reveal subtle patterns of geographic constraints on long-distance gene flow, or regionally determined variability in selective pressures, however. The genetic studies of Caprus aper clearly demonstrated that the species does not constitute a single panmictic population across the sampled range. Samples from the Mediterranean Sea showed the largest genetic differentiation. Similarly, studies on Nephrops norvegicus indicated that the Mediterranean samples from the Adriatic Sea are significantly differentiated from the Atlantic samples analysed. Furthermore, both species showed further diferentiation, although weaker, among the Atlantic samples. The studies of Trachururs trachurus are ongoing (samples from the Mediterranenan Sea are yet to be analysed) but the preliminary results indicate that the species is represented by multiple populations. In summary, there is clear population structure within all three species exploited by fisheries and this information could be used by managers to improve the management of these marine resources. Among all ten species for which advances could be made either in terms of knowledge of the reproductive biology, dispersal modelling or population genomics, a full set of information could be gathered for the emblematic reef-building L. pertusa, and the consortium is also trying to finalize the genomic data production for the exploited fish H. dactylopterus. Perpectives beyond this report include the finalization of data production and analysis, and the test of a new method to go beyond the usual “side by side” comparison of predicted (lagrangian modelling) versus realized (inferences from population genomics) dispersal by integrating the Lagrangian matrices of connectivity as priors of a Bayesian analysis (Gaggiotti, 2017) of the genetic dataset characterizing the metapopulation system being studied. Such integrative framework has long been expected by the scientific community addressing connectivity through the use of a diversity of tools and theoretical framework as the ones detailed in this report. The recent development of this new analytical tool will allow testing this approach on the scleractinian coral L. pertusa. All results obtained here will be used to deliver information useful for the conservation and management of VMEs and fisheries resources (WP 6 and 7), an advance that will be formalized in the next report of WP4, DL4.5 “Integrated management considering connectivity patterns”.

  • Open Access
    Authors: 
    Carlsson, J;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    Environmental (e)DNA methods (quantitative PCR and metabarcoding) are non-invasive, rapid and cost-efficient tools for detecting single species and monitoring biodiversity with considerable potential for informing aquatic conservation and management. Methods for implementing eDNA are constantly developing and these tools have received significant interest from industry. There have been substantial efforts to develop best practice approaches, standardisation and workflows (c.f. COST-action DNAqua-Net CA15219) that might ultimately complement or replace existing methods and develop new metrics for the implementation of the European Water Framework Directive. These eDNA based methods also have the potential to contribute to the implementation of the Marine Strategy Framework Directive. While the use of eDNA in freshwater has received by far the most attention, there is great potential for using eDNA in the marine environment to address a wide range of questions using non-invasive sampling; ranging from spatial and temporal biodiversity assessments, to assessing distribution patterns and range expansions/contractions of single species. In the ATLAS project, WP3 focused on evaluating the accuracy and sensitivity of meta-barcoding and qPCR methods with the objective of selecting a set of primers amplifying distinct DNA fragments to optimise metabarcoding across the Tree of Life, covering a maximum number of lineages, and developing species-specific probes for PCR detection of VME indicator species, fishery targets and bycatch species. The emergence of eDNA tools to assess marine biodiversity and detect specific target marine species has generated great hopes to describe biodiversity of ecosystems that have been difficult to access (e.g. deep-sea habitats); as sampling of water and sediments is relatively simple as compared to traditional methods requiring specialised equipment (ROV, camera sledges, fishery gear, etc.). Nevertheless, few examples of such applications existed and even fewer, if any, in the deep sea. The great challenges for using eDNA techniques to assess deep-sea biodiversity are to obtain DNA from more or less blindly collected, low biomass taxa and subsequently low DNA concentration seawater or sediment samples. University College Dublin and IFREMER were tasked with evaluating the performance of next-generation genomic tools (metabarcoding of eDNA) for assessing biodiversity and quantitative qPCR (plankton samples) as a sensitive tool to detect and quantify biomass of target species. The accuracy and sensitivity of metabarcoding and qPCR will be validated on samples assessed using classical taxonomy in selected Case Studies. In respect of the development of qPCR assays, six target species were selected for assay development. Quantitative (q)PCR assays successfully detected and semi-quantified five target species showing that despite extremely low DNA concentration and the large volumes of water in which these species are found, eDNA is a very sensitive tool offering a promising method for detection of target species in the marine environment, including the deep sea. However, it was not possible to develop an assay for Lophelia pertusa due to low polymorphism usually encountered at mitochondrial DNA for scleractinian corals, and the lack of existing sequence data from closely related species. The metabarcoding efforts by IFREMER resulted in the development of six complementary sets of primers capable of assessing biodiversity from deep-sea sediments across the entire Tree of Life. In general, metabarcoding protocols were capable of characterising biodiversity of low biomass deep-sea sediments; even for understudied deep-sea metazoan taxa. These protocols were applied to 350 samples collected during the ATLAS-MEDWAVES cruise, demonstrating the sensitivity of metabarcoding in deep-sea habitats. The development of eDNA species-specific assays and metabarcoding methods demonstrate the utility of eDNA-based methods for assessing and managing deep-sea biodiversity. Further, in line with the successful deployment of these tools in freshwater and in marine waters as demonstrated in this WP, these approaches could also be used to supplement or replace traditional methods such as morphology-based biodiversity used in the marine environment, including in the deep sea where specimens can be extremely small and difficult to identify (c.f. Danovaro et al. 2016). Similarly, future and current applications of eDNA include biodiversity assessments and baselines for Environmental Impact Studies of deep-sea industry operations such as mineral extraction (Boschen et al. 2016). We have demonstrated the usefulness of eDNA methods in the deep sea despite the great challenges they represent in terms of accessing samples and often low concentration of biomass.

  • Open Access
    Authors: 
    Ankamah-Yeboah, I; Xuan, BB; Hynes, S; Needham, K; Armstrong, CW;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    This report presents an assessment of how the public perceives, and values deep-sea ecosystem services in the North Atlantic, and provides a foundation for evaluating and balancing Blue Growth with conservation management in the deep sea. Nonmarket valuation is used to evaluate public perceptions of the deep sea environment and the socio-economic values of new marine management plans. This report presents the results of two discrete choice experiment surveys that were employed to assess the values held by the Scottish and Norwegian public for the Mingulay reef complex and Hola off Lofoten-Vesterålen (LoVe), respectively. Regarding public perception, the results show that public knowledge and awareness of deep-sea ecosystems is relatively higher among Norwegians than among the Scottish public. Specifically, awareness of cold-water corals is high for the LoVe case study amongst the Norwegian public and low for the Mingulay reef complex in the Scottish case. Despite this limited knowledge, many respondents thought changes in the deep sea would have at least some effect on them personally. On average, the public perceives deep-sea conditions to be at most ‘fairly good’ but are pessimistic about its management: a significantly higher share, 76% of Norwegians perceive the deep sea to be poorly-managed compared to 12% of those surveyed in Scotland. Results from both countries highlight eco-centric attitudes towards the marine environment, implying that the general public recognise the value of ecosystem services, the current ecological crisis and the need for sustainable management. Demographic profiles of respondents and their experiences play influential roles, with exposure to media-art like the Blue-Planet II series showing prominence in most perception dimensions. To determine whether the perceived public support translates into monetary support for new management scenarios, a discrete choice experiment was conducted to assess trade-offs for improvement in a number of deep-sea environment attributes; environmental health and quality, an increase in the size of marine protected areas (MPAs) and new marine related job creation. Latent class logit results revealed two distinct groups of public preferences: a minority of respondents who derive minimal value from the marine environment and a second group who exhibit significant positive preferences for all the management attributes and exhibit strong preferences for new policy options. The most valued of the new policy attributes were those related to the key pressures of the marine environment: commercial fish stocks and marine litter designated as Descriptors 3 and 10 respectively in the GES of the MSF Directive. This was followed by the size of the marine protected area, whilst the creation of jobs is the least valued. Overall, however, weighted average willingness to pay estimates, indicate that the public in both countries is willing to pay to support conservation of the unfamiliar deep-sea ecosystem irrespective of the individual attributes delivered in a new marine management plan. The results highlight the importance of the deep-sea ecosystems to the public and provide support for further collective action required by the EU in moving beyond the 2020 Marine Strategy Framework Directive (MSFD) objective of achieving good environmental status for Europe’s seas.

  • Other research product . Other ORP type . 2021
    Open Access
    Authors: 
    Johnson, C; Inall, M; Gary, S; Cunningham, S;
    Publisher: Zenodo
    Project: EC | ATLAS (678760)

    An overarching goal of ATLAS is to investigate the sensitivity of North Atlantic Ocean ecosystems to basin-scale physical processes. This report examines relationships between four pertinent climate indices and key physical variables using both output from a high-resolution ocean model and an observational dataset. After describing long-term mean conditions and determining seasonal cycles, we use a composite approach to create mean conditions for high and low states of each climate index. The Atlantic Meridional Overturning Circulation (AMOC) shows cooler bottom conditions around the boundaries of the western subpolar gyre during a high state, which may be linked to more energetic conditions in this area. The North Atlantic Oscillation (NAO) shows clear anti-correlation between European and North American Shelves: during a high NAO, bottom conditions on the eastern boundary are warmer and more saline, whilst western areas are cooler and fresher. Bottom kinetic energy also shows an east-west disconnect, with less energetic conditions in the eastern overflow currents during a high NAO and a corresponding increase in western overflows. The most striking feature in the Subpolar Gyre (SPG) composites, is a strong area of cooler bottom conditions around the northern and western boundaries of the subpolar North Atlantic during a high SPG. In contrast, during a high Atlantic Multi-decadal Oscillation (AMO), bottom conditions in the same areas are warmer and more saline although areas deeper than around 2000 m in the North Atlantic are cooler and fresher. This is the first study to show that climate indices are associated with spatially-coherent changes in bottom conditions across the North Atlantic region. Although changes are relatively small, due to the multi-annual nature of the climate indices any changes may persist for several years. As such, vulnerable sessile ecosystems may be exposed to sustained changes in mean conditions, with this deviation in the baseline also altering the likelihood of extreme events such as mean heatwaves. Thus, a thorough knowledge of natural variability is essential for the understanding of deep-sea ecosystems, predicting their response to future changes, and evaluation of management frameworks.