IQuOD 4th workshop in Tokyo: Copernicus Marine in situ TAC, a service for operational oceanography

Copernicus is a European system for monitoring the Earth. COPERNICUS-CMEMS products and services are meant to serve all marine applications: Marine resources, Maritime safety, Coastal and Marine Environment, Seasonal Forecast & Climate. The service is ambitious as the ocean is complex and many processes are involved, from physical oceanography, biology, geology, ocean-atmosphere fluxes, solar radiations, moon induced tides, anthropic activity. A multi-platform approach is essential, taking into account sea-level stations, coastal buoys, HF radars, river flows, drifting buoys, sea-mammal or fishes fitted with sensors, vessels, gliders, floats.

Integrated indicator framework and methodology for monitoring and assessment of hazardous substances and their effects in the marine environment

Many maritime countries in Europe have implemented marine environmental monitoring programmes which include the measurement of chemical contaminants and related biological effects. How best to integrate data obtained in these two types of monitoring into meaningful assessments has been the subject of recent efforts by the International Council for Exploration of the Sea (ICES) Expert Groups. Work within these groups has concentrated on defining a core set of chemical and biological endpoints that can be used across maritime areas, defining confounding factors, supporting parameters and protocols for measurement. The framework comprised markers for concentrations of, exposure to and effects from, contaminants. Most importantly, assessment criteria for biological effect measurements have been set and the framework suggests how these measurements can be used in an integrated manner alongside contaminant measurements in biota, sediments and potentially water. Output from this process resulted in OSPAR Commission (www.ospar.org) guidelines that were adopted in 2012 on a trial basis for a period of 3 years. The developed assessment framework can furthermore provide a suitable approach for the assessment of Good Environmental Status (GES) for Descriptor 8 of the European Union (EU) Marine Strategy Framework Directive (MSFD).

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.

Performance assessment of a vertical axis turbine in a marine current flume tank and CFD modelling

As advances in numerical modelling techniques support the increased confidence in predictions from computer simulations, the need remains to have experimental verification built into the design process. This paper outlines the experimental investigation carried out on a shielded vertical axis turbine in a marine environment. The experiments consist of performance measurements and the use of particle image velocimetry on a small scale device in a marine current flume. The results demonstrate that the performance of the device can be modelled numerically; in particular, the results show that the numerical model used can correctly predict the increase in performance with Reynolds number.

The Kinome of Pacific Oyster Crassostrea gigas, Its Expression during Development and in Response to Environmental Factors

Oysters play an important role in estuarine and coastal marine habitats, where the majority of humans live. In these ecosystems, environmental degradation is substantial, and oysters must cope with highly dynamic and stressful environmental constraints during their lives in the intertidal zone. The availability of the genome sequence of the Pacific oyster Crassostrea gigas represents a unique opportunity for a comprehensive assessment of the signal transduction pathways that the species has developed to deal with this unique habitat. We performed an in silico analysis to identify, annotate and classify protein kinases in C. gigas, according to their kinase domain taxonomy classification, and compared with kinome already described in other animal species. The C. gigas kinome consists of 371 protein kinases, making it closely related to the sea urchin kinome, which has 353 protein kinases. The absence of gene redundancy in some groups of the C. gigas kinome may simplify functional studies of protein kinases. Through data mining of transcriptomes in C. gigas, we identified part of the kinome which may be central during development and may play a role in response to various environmental factors. Overall, this work contributes to a better understanding of key sensing pathways that may be central for adaptation to a highly dynamic marine environment.

Developing European operational oceanography for Blue Growth, climate change adaptation and mitigation, and ecosystem-based management

Operational approaches have been more and more widely developed and used for providing marine data and information services for different socio-economic sectors of the Blue Growth and to advance knowledge about the marine environment. The objective of operational oceanographic research is to develop and improve the efficiency, timeliness, robustness and product quality of this approach. This white paper aims to address key scientific challenges and research priorities for the development of operational oceanography in Europe for the next 5-10 years. Knowledge gaps and deficiencies are identified in relation to common scientific challenges in four EuroGOOS knowledge areas: European Ocean Observations, Modelling and Forecasting Technology, Coastal Operational Oceanography and Operational Ecology. The areas "European Ocean Observations" and "Modelling and Forecasting Technology" focus on the further advancement of the basic instruments and capacities for European operational oceanography, while "Coastal Operational Oceanography" and "Operational Ecology" aim at developing new operational approaches for the corresponding knowledge areas.