150 years of Marine Infrastructures, Networks and Resource Centres: From Time Series to Genomes and back again.

Transcription

1 150 years of Marine Infrastructures, Networks and Resource Centres: From Time Series to Genomes and back again. Michael Thorndyke Royal Swedish Academy of Sciences Sven Lovén Centre for Marine Science Kristineberg Gothenburg University Swedish Institute for the Marine Environment President of the MARS Network

2 The world's first marine station at Ostend : the 'Dune laboratory' in the oyster farm of Valcke-Deknuyt Founded by Professor Pierre-Joseph van Beneden ( ) For his marine research, Pierre-Joseph found a source of inspiration in Sweden and England. At that time in Kristineberg, Sven Lovén and other Swedish marine scientists joined a colony of naturalists to carry out marine research in what would later (1877) become a research station.

3 Since the 1800 s...

4

5

6 Monitoring plankton with the CPR Survey

7 Northwards shifts in plankton Beaugrand et 2003 Science 296: 1692

8 Western Channel Observatory Incorporates long-term stations E1 and L4 Some data going back many decades Weekly sampling at L4 for ~20 years Suite of regular measurements including: Physico-chemical variables Nutrients Pigments Cell-counts (flow cytometry) Phytoplankton Microzooplankton Zooplankton Recent JPR special issue celebrating 20 years sampling at L4. 10 papers describing WCO, biological control of pco2, effects of high CO2 on fixed N, phytoplankton, zooplankton and meroplankton community dynamics, sardine eggs, fish phenology, zooplankton grazing and predation Expanding remit - WCO now includes: In-situ data buoys at E1 and L4, collecting data in real-time; Multi-scale benthic surveys and meroplankton investigations to link pelagic and benthic dynamics; Detailed in-house links to satellite observations and ecosystem models; Links to operational forecasting

9 Log S Genomic studies at L4 Comprehensive time-series data Ongoing genetic studies at L4 on viruses, archaea, bacteria and plankton Weekly sampling and preservation of environmental DNA samples the most sequenced body of water on the planet >80 Million reads:metagenomic and metatranscriptomic >20 billion base pairs of data!! Example Analysis of ~monthly samples over 7 years >20 million 16S rdna V6 tags 454 pyrosequencing, Illumina runs EhV ,339 bp Robust seasonal cycle in bacterioplankton diversity and community structure Diversity peaks in mid-winter Cycle correlates with day-length Evidence of longer-term change D Stress: 0.14 Season Winter Spring Summer Autumn Serial Day Fitted relationship: Log S = Day Day DX1+0.02DX2 Where DX1 and DX2 are cos and sin descriptors of annual cycle Relationship describes ~70% of total variation in log S CONTACTS: Paul Somerfield, Tim Smyth, Claudia Halsband-Lenk

10 De très grandes lignées évolutives n ont pas de représentants terrestres Les organismes marins reviennent au centre de la biologie évolutive Archaeplastida land plants green algae red algae Rhizaria Alveolates apicomplexans dinoflagellates Chromalveolates oomycetes diatoms Stramenopiles glaucophytes haptophytes cryptophytes brown algae Excavata Amoebozoa animals fungi Ophistokonts Unikonts

11 Marine laboratories are unique and essential for marine research (in partnership with vessels, satellites, remote systems etc.) Providing access to marine ecosystems including valuable (historical) time-series data Providing access to marine models for Biomedicine, ecotoxicology, biodiversity, gene discovery Providing logistics for ex situ experiments, including modern equipment for biology Providing logistics for hosting and catering

12 Marine Laboratories are: ideal places to study organisms in their habitat and in the lab great places for the public to see research happening, and to increase ocean literacy. Marine labs are windows on the ocean able to host large numbers of students at all stages during the year, often in all seasons (classes, field trips, tours, internships) accessible to researchers on a regular basis, short to long term places for graduate students to begin independent research home to experts in taxonomy, ecology, local natural history places to teach small intensive undergraduate/graduate classes

13 Marine Laboratories Are: - getting undergraduates excited, and interested in STEM careers -excellent for research at molecular to ecosystem levels (genomics, biomedical, fisheries, development, ecology, neurobiology, physiology, biomaterials) - ideal for long-term ecological research, real time data collection Dissemination, land/ocean margin research, climate/ocean change effects - places to do research and teach ocean geology, chemistry, physics, engineering etc. - inexpensive test-beds for new ocean instrumentation - land base stations for OOS, buoys and cabled arrays, submersibles -support bases for research vessels, boats, diving research support - places to integrate social science and natural science research and education

14 WAMS activities and mission Exchange programmes, (e.g. Global ERASMUS programme) Training and education, Capacity building In kind sharing of data and access to facilities, Joint development and harmonization of techniques and methods, Integrated research strategies. WAMS fellowships, (WAMS trust fund in cooperation with the IOC). Particularly important activities for WAMS in its initial phase should be: Inventory of the WAMS membership marine sites Portal site for each marine station

15 MARS members and European marine biodiversity research sites MARS members (50 blue dots) BIOMARE Reference and Focal sites (100 red dots) BIOMARE sites are now marine sites for Life-Watch in the ESFRI programme

16

17 Sir John Carew Eccles; Alan Lloyd Hodgkin & Andrew Fielding Huxley 1963

18 Leland H. Hartwell, Tim Hunt & Paul Nurse 2001

19 Roger Tsien, Martin Chalfie & Osamu Shimomura 2008

20

21 The Sea Urchin as a Model System for Analysis of Development Large numbers of gametes > 10 7 eggs per female External fertilization In vitro fertilization yield 100% Egg can be oriented through a subequatorial pigmented band (Mediterranean P. lividus only) Rapid, synchronous development Embryo optically clear simple structure Physically manipulable(cell transplantation/isolation) Gene regulation/functioncan be tested by injection of DNA, mrna, or morpholinos Resources for genomics S. purpuratus : Genome (800 Mb, gene models) EST databases, arrayed libraries P. lividus : on its way..

22 Ocean acidification and calcifying organisms (Gao & Davidson, 2008)

23 ...and back again... Integration to address the challenges Climate change, Global warming, OA... Real threat...time series tells us that Expts and Genomics tell us it is complex More data needed, life histories, diel data Regional approach vital

24 Research Infrastructures and Horizon 2020 EMBRC, Paris, 14 November 2012 Jean-Emmanuel Faure DG Research & Innovation Unit for Research Infrastructures Research and Innovation

25 1 Facilities, resources, organisational systems and services that are used by the research communities to conduct research and innovation in their fields This includes: major scientific equipments (or sets of instruments); knowledge-based resources such as collections, archives or scientific data; e-infrastructures, such as data, computing and software systems; any other infrastructure of a unique nature essential to achieve excellence in research and innovation Policy Research and Innovation

26 2 Why a European approach for research infrastructures? Opening access to the best research infrastructures existing in the individual Member States to all European researchers Avoiding duplication of effort by coordinating and rationalising the use of these research infrastructures Triggering the exchange of best practice, developing interoperability of facilities and resources, developing the training of the next generation of researchers Connecting national research communities and increasing the overall quality of the research and innovation Helping the pooling resources so that the Union can also acquire and operate research infrastructures at world level Policy Research and Innovation

27 3 ESFRI European Strategy Forum on Research Infrastructures Set up by the EU Council of Research Ministers in 2002: Representatives of Ministers of the 27 Member States, 10 Associated States, and of the European Commission To support the development of a European policy for Research Infrastructure and discuss a long term vision at European level Mandated by the EU Council of Research Ministers of November 2004 to develop a strategic roadmap identifying new pan-european Research Infrastructures or major up-grades to existing ones First Roadmap published in 2006, followed by two updates in 2008 and 2010 Policy Research and Innovation

28 4 Implementation of the research infrastructures identified by ESFRI EU Council of Research Ministers, March 2009: «A combination of resources from national budgets, Community programmes, EIB instruments and structural funds should lead to the development of excellent research infrastructures throughout Europe» The European Research Infrastructure Consortium (ERIC): A new legal framework, at EU level, to facilitate the joint establishment and operation of Research Infrastructures of European interest among several countries First ERIC status awarded to SHARE on 17 March 2011, hosted by NL Second ERIC status awarded to CLARIN on 29 February 2012, hosted by NL Applications submitted: ECRIN, Euro-Argo, ESSurvey, EATRIS, C- ERIC, BBMRI, DARIAH Policy Research and Innovation

29 National Roadmaps for Research Infrastructures Roadmap in place Roadmap under preparation National funding reserved for new/updated RIs 5 Research and Innovation

30 6 Structural Funds : 347 billion of EU investments in Europe's regions, of which 25% ( 86 billion) for Research/Innovation : The Commission proposed a budget of 376 billion (including 40 billion funding for the new Connecting Europe Facility) Policy Research and Innovation

31 7 Structural Funds: some novelties Strengthening thematic concentration of resources European Regional Development Fund (ERDF): energy efficiency & renewable energy, research & innovation, competitiveness of SMEs Developing synergies between the Structural funds and Horizon 2020 Common objective of contributing to Europe 2020 Strategy s priorities of smart, sustainable and inclusive growth National and regional authorities to draw up research and innovation strategies for smart specialisation Possible support from more than one Union instrument (Common provisions, Art. 55.8) Specific reference to research infrastructures "of European interest" in the ERDF proposal (ERDF, Art. 5.1.a) Promoting internationalisation Possible allocation to operations located outside the programme area, but within the Union (Common provisions, Art. 60.2) Policy Research and Innovation

32 8 ESFRI Health and Food FP7 support Roadmap 2006 BBMRI - Biobanks and Biomolecular Resources EATRIS Infrastructure for Translational Medicine facilities ECRIN - Clinical trial plateform ELIXIR Data repositories INFRAFRONTIER - Mouse archives and clinics INSTRUCT - Structural biology facilities Roadmap 2008 EMBRC - Marine biology resources ERINHA - High-security labs EU-OPENSCREEN - Chemical libraries EUROBIOIMAGING Imaging facilities Roadmap 2010 ANAEE Experimentation on ecosystems ISBE Infrastructure for systems biology MIRRI Microbial resources 160 M Policy Research and Innovation

33 9 Horizon 2020 Excellent science ( M, constant 2011 prices) European Research Council ( M ) Future and Emerging Technologies (3 100 M ) Marie Curie actions (5 752 M ) European Research infrastructures (including e-infrastructures) (2 478 M ) Societal challenges ( M ) Health, demographic change and wellbeing (8 028 M ) Food security, sustainable agriculture, marine - maritime research, bio-economy (4 152 M ) Secure, clean and efficient energy (5 782 M ) Smart, green, integrated transport (6 802 M ) Climate action, resource efficiency, raw materials (3 160 M ) Inclusive, innovative and secure societies (3 819 M ) Industrial leadership ( M ) Leadership in enabling and industrial technologies (ICT, space, nanotechnologies, advanced materials and advanced manufacturing and processing, biotechnology) ( M ) Access to risk finance (3 538 M ) Innovation in SMEs (619 M ) EIT (1 364 B B ) Policy Research and Innovation JRC (non-nuclear: M )

34 10 Research Infrastructures under H Developing the European RIs for 2020 and beyond Developing new world-class RIs Integrating and opening national RIs of pan-european interest Development, deployment and operation of ICT based e-infrastructures 4.2. Fostering the innovation potential of RIs & their human capital 4.3. Reinforcing European RI policy and international cooperation Policy Research and Innovation

35 Developing new world-class RIs Objective: To ensure the implementation, long-term sustainability and operation and operation of the ESFRI and other world-class RIs EU funding will support: the preparatory phase of future RIs (e.g. detailed construction plans, legal arrangements, multiannual planning, etc.) the implementation phase (e.g. R&D and engineering work, development of regional partner facilities, etc.) the operation phase (e.g. access, data handling, outreach, training and international cooperation activities) design studies for new RIs through a bottom-up approach Policy Research and Innovation

36 Integrating and opening existing national RIs of pan-european interest Objective: To open up key national RIs to all European researchers and to ensure their optimal use and joint development EU funding will support European Research Infrastructures Networks bringing together RIs in a given field covering: Transnational and virtual access activities Networking activities to foster a culture of cooperation Joint research activities to improve the services provided by the infrastructures Policy Research and Innovation

37 13 From FP7 to Horizon 2020 An increased budget, from around 1.7 billion (FP7) to 2.5 billion (Horizon constant prices) New activities to support the implementation and operation of world-class infrastructures such as ESFRI infrastructures Continuation of the successful FP7 Integrating Activities Reinforcement of the support to e-infrastructures New objective of better exploiting the innovation potential and human capital of infrastructures Policy Research and Innovation

38 14 A Reinforced European Research Area ERA Communication (COM(2012)392) Actions for Member States Financial commitments for the construction and operation of ESFRI, global, national and regional RIs of pan-european interest Remove legal and other barriers to cross-border access to RIs Actions for the European Commission Support access to RIs and integration (through Horizon 2020) Encourage Member States to link RI roadmaps to the ESFRI roadmap and smart specialisation strategies in Structural Funds Support training programmes for the management of such RIs A Charter of Access: common standards and harmonized access rules Work with ESFRI to set priorities for implementing the Roadmap Define common evaluation principles, monitoring tools, etc. Promote the alignment of EU and national approaches to e- infrastructures Policy Research and Innovation

39 15 Host country selection: EATRIS example Call for candidate countries and bidding books Assessment by the Advisory Board of EATRIS preparatory phase Location of EATRIS HQ Quality of science and technical support Integration into the scientific and industrial environment Political integration European added value Working conditions Country commitment Assessment report Presentations to the Governmental Partners and voting (anonymous) Policy Research and Innovation

40 16 For further information Europe Innovation Union Horizon FP7 EC Research Infrastructures and ESFRI EC Regional Policy Policy Research and Innovation

41 What for the future?

42 Europe SZN, Italy SLC, Sweden SAMS, UK MBA, UK SOI, UK SARS, Norway CCMAR, Portugal AWI, Germany SBR, France OOVS, France OOBS, France HMRC, Greece

43 Australia Tropical Marine Network Affiliation of Six Research Stations belonging to three universities and the Australian Museum Based largely on the Great Barrier Reef Delivers co-operative education programs and Joint infrastructure developments

44 USA

45 Japan

46

47 WAMS The World Association of Marine Stations A Network of Marine Stations and Institutes for the 21st Century Africa

48 Infrastructure Needs for Ocean Research, for the Next Two Decades, Include: SATELLITES Funding Priorities? RESEARCH VESSELS Submersibles MARINE LABS Experimental facilities, state of the art technology for chemistry, physics & biology BUOYS AND CABLED SYSTEMS

49 The Time is right for WAMS... Knowledge about marine biodiversity is extensive owing to.centuries of its study in many places and by a variety of enterprises..the innumerable academic institutions with shore facilities for study of the marine environment...have provided foci of research and knowledge.. Fautin et al. (2010) PLoS ONE 5(8) Another point of consensus.is the inventory of threats to marine biodiversity. Indeed, most threats identified..are true for the entire world. Birmingham Science News Examiner August 5 th 2010

50 WAMS Founding Steering Group: MARS, The European Marine Network of Marine Institutes and Stations NAML, The National Association of Marine Laboratories USA, AMLC and CARICOMP The Association of Marine Laboratories of the Caribbean, JAMBIO, The Japanese Association for Marine Biology, Japan, PIMS, The Pacific Institutes of Marine Science, POGO Tropical Marine Network (Australia) GOOS Africa (representing African Marine Laboratories) UNESCO IOC UNESCO MAB The scope of the activities within the WAMS stations will follow the theme: From genes to ecosystems

51 MARINE AND COASTAL BIOSPHERE RESERVES

52 Distribution of Coastal and Marine Biosphere Reserves The World Network of Biosphere Reserves : 551 sites in 107 countries (2009) More than 30% of those sites encompass a marine and/or coastal component Countries with different socioeconomic backgrounds and cultures Asia 17% Oceania 7% Europe 27% Africa 12% North America 22% South and Central America 15% Different marine ecosystems such as: mangrove, river deltas, marshland, island and deep ocean systems Distribution of Marine and Coastal Biosphere Reserves per Region