Assessing the environmental status of selected North Atlantic deep-sea ecosystems

The deep sea is the largest biome on Earth but the least explored. Our knowledge of it comes from scattered sources spanning different spatial and temporal scales. Implementation of marine policies like the European Union’s Marine Strategy Framework Directive (MSFD) and support for Blue Growth in the deep sea are therefore hindered by lack of data. Integrated assessments of environmental status require tools to work with different and disaggregated datasets (e.g. density of deep-sea habitat-forming species, body-size distribution of commercial fishes, intensity of bottom trawling) across spatial and temporal scales. A feasibility study was conducted as part of the four-year ATLAS project to assess the effectiveness of the open-access Nested Environmental status Assessment Tool (NEAT) to assess deep-sea environmental status. We worked at nine selected study areas in the North Atlantic focusing on five MSFD descriptors (D1-Biodiversity, D3-Commercial fish and shellfish, D4-Food webs, D6-Seafloor integrity, D10-Marine litter). The objectives of the present study were to i) explore and propose indicators that could be used in the assessment of deep-sea environmental status, ii) evaluate the performance of NEAT in the deep sea, and iii) identify challenges and opportunities for the assessment of deep-sea status. Based on data availability, data quality and expert judgement, in total 24 indicators (one for D1, one for D3, seven for D4, 13 for D6, two for D10) were used in the assessment of the nine study areas, their habitats and ecosystem components. NEAT analyses revealed differences among the study areas for their environmental status ranging from “poor” to “high”. Overall, the NEAT results were in moderate to complete agreement with expert judgement, previous assessments, scientific literature on human-pressure gradients and expected management outcomes. We suggest that the assessment of deep-sea environmental status should take place at habitat and ecosystem level (rather than at species level) and at relatively large spatial scales, in comparison to shallow-water areas. Limited knowledge across space (e.g. distribution of habitat-forming species) and the scarcity of long-term data sets limit our knowledge about natural variability and human impacts in the deep sea preventing a more systematic assessment of habitat and ecosystem components in the deep sea. However, stronger cross-sectoral collaborations, the use of novel technologies and open data-sharing platforms will be critical for establishing environmental baseline indicator values in the deep sea that will contribute to the science base supporting the implementation of marine policies and stimulating Blue Growth

Current marine pressures and mechanisms driving changes in marine habitats

Human activities and the resultant pressures they place on the marine environment have been widely demonstrated to contribute to habitat degradation, therefore, their identification and quantification is an essential step towards any meaningful restoration effort. The overall scope of MERCES Deliverable 1.2 is to review current knowledge regarding the major marine pressures placed upon marine ecosystems in EU waters and the mechanisms by which they impact habitats in order to determine potential restoration pathways. An understanding of their geographical distribution is critical for any local assessment of degradation, as well as for planning conservation and restoration actions. This information would ideally be in the form of maps, which: (a) compile single or multiple activities and pressures over broad scales, integrating and visualizing available data and allowing direct identification of aggregations as well as gaps and (b) may be overlaid with habitat maps (or any other map layer containing additional information), thus combining different data levels and producing new information to be used for example when implementing EU policies. The deliverable also documents typical example habitat case studies, the prominent impacts and consequences of activities and pressures towards the identification of possible restoration or mitigation actions. Finally the deliverable discusses pressures, assessments, marine spatial planning and blue growth potential. Activities and pressures are used in a strict sense, where marine activities are undertaken to satisfy the needs of societal drivers (e.g. aquaculture or tourism) and pressures are considered to be the mechanism through which an activity has an actual or potential effect on any part of the ecosystem (e.g. for demersal trawling activity, one pressure would be abrasion of the seabed). Habitats are addressed using a nested approach from large-scale geological features (e.g. shallow soft bottoms) to species-characterised habitats (e.g. Posidonia meadows) because of the way they are referred to in current policy documents which lack standard and precise definitions

The impact of deep-sea fisheries and implementation of the UNGA Resolutions 61/105 and 64/72. Report of an international scientific workshop, National Oceanography Centre, Southampton

The scientific workshop to review fisheries management, held in Lisbon in May 2011, brought together 22 scientists and fisheries experts from around the world to consider the United Nations General Assembly (UNGA) resolutions on high seas bottom fisheries: what progress has been made and what the outstanding issues are. This report summarises the workshop conclusions, identifying examples of good practice and making recommendations in areas where it was agreed that the current management measures fall short of their target.Peer reviewe

Human activities and resultant pressures on key European marine habitats: An analysis of mapped resources

Human activities exert a wide range of pressures on marine ecosystems, often resulting in the loss of species and degradation of habitats. If effective policies and management practices to restore past damage and reduce future impacts to the marine environment are to be developed, knowledge of the extent, duration and severity of activities and pressures is essential, yet often lacking. As part of the EU H2020 project “Marine Ecosystem Restoration in Changing European Seas”, this study uses an exhaustive review of published records, web resources, and grey literature to comprehensively assess the degree to which human activities and pressures are mapped within European seas. The results highlight a number of limitations and gaps, including: (a) limited geographic coverage at both the regional and sub-regional level; (b) insufficient spatial resolution and accuracy in recorded data for the planning of conservation and restoration actions; (c) a lack of access to the background data and metadata upon which maps are based, thus limiting the potential for synthesis of multiple data sources. Based on the findings, several recommendations for future marine research initiatives arise, most importantly the need for coordinated, geographically extended baseline assessments of the distribution and intensity of human activities and pressures, complying with high-level standardization regarding methodological approaches and the treatment of produced data

Climate-induced changes in the suitable habitat of cold-water corals and commercially important deep-sea fishes in the North Atlantic

The deep sea plays a critical role in global climate regulation through uptake and storage of heat and carbon dioxide. However, this regulating service causes warming, acidification and deoxygenation of deep waters, leading to decreased food availability at the seafloor. These changes and their projections are likely to affect productivity, biodiversity and distributions of deep-sea fauna, thereby compromising key ecosystem services. Understanding how climate change can lead to shifts in deep-sea species distributions is critically important in developing management measures. We used environmental niche modelling along with the best available species occurrence data and environmental parameters to model habitat suitability for key cold-water coral and commercially important deep-sea fish species under present-day (1951–2000) environmental conditions and to project changes under severe, high emissions future (2081–2100) climate projections (RCP8.5 scenario) for the North Atlantic Ocean. Our models projected a decrease of 28%–100% in suitable habitat for cold-water corals and a shift in suitable habitat for deep-sea fishes of 2.0°–9.9° towards higher latitudes. The largest reductions in suitable habitat were projected for the scleractinian coral Lophelia pertusa and the octocoral Paragorgia arborea, with declines of at least 79% and 99% respectively. We projected the expansion of suitable habitat by 2100 only for the fishes Helicolenus dactylopterus and Sebastes mentella (20%–30%), mostly through northern latitudinal range expansion. Our results projected limited climate refugia locations in the North Atlantic by 2100 for scleractinian corals (30%–42% of present-day suitable habitat), even smaller refugia locations for the octocorals Acanella arbuscula and Acanthogorgia armata (6%–14%), and almost no refugia for P. arborea. Our results emphasize the need to understand how anticipated climate change will affect the distribution of deep-sea species including commercially important fishes and foundation species, and highlight the importance of identifying and preserving climate refugia for a range of area-based planning and management tools.S

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts