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Supporting research potential for MARine BIodiversity and GENomics in the Eastern Mediterranean

Final Report Summary - MARBIGEN (Supporting research potential for MARine BIodiversity and GENomics in the Eastern Mediterranean)

Executive Summary:
The main objective of MARBIGEN was to fully exploit and further develop the research potential of the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC, HCMR) in the area of biodiversity. MARBIGEN allowed IMBBC to strengthen its already demonstrated research and technological development and to get established in a first-line position in biodiversity science. IMBBC was established as a high- level centre for genomics & biodiversity research by upgrading existing and acquiring new equipment, developing biodiversity research topics through hiring incoming scientific personnel, exploit existing knowledge and experience in excellent EU research entities, and organising workshops, seminars, a conference & other dissemination activities. IMBBC’s capacities were enhanced by: a) assessing biodiversity through up-to-date high throughput genomic technologies, supported by bioinformatics and biodiversity informatics and by introducing 3D phenotyping at meio- and macro- organismal level and b) studying biodiversity changes by developing an in-house facility for in vivo experiments enabling manipulation of environmental conditions, and establishing an innovative experimental site for long-term studies of anthropogenic stressors and climate change impacts on coastal ecosystems. The external evaluation report, an essential part of the project will help IMBBC to remain an attractive partner for future EU proposals and to attract researchers from other EU countries to work in a distant corner of Europe. MARBIGEN has significantly supported the potential of the institute to collect and analyze biodiversity data attracting the attention of the national and international scientific community, allowing new ways of designing and running research projects, facilitating invitations to new consortia and vigorous submissions of proposals in new calls. MARBIGEN not only gave the opportunity to students and post-docs to interact with researchers of international recognition, but has also provided the basis to build long-term collaborations allowing crosstalk and planning of joint projects, heading towards a better integrated critical mass with promising interdisciplinary interactions. Overall, MARBIGEN has undoubtedly made a great contribution in strengthening the research potential and considerably increased the visibility of the institute enabling further enhancement of its research capacity and promotion of local development. The progress made within MARBIGEN has already had significant impact on IMBBC & HCMR, the local and the international scientific community. IMBBC has the role of a scientific input-output and storage hub to address, develop and diffuse knowledge, expertise, and infrastructure and build potential on marine biodiversity and has been established as a well-known and favored place for educational and training events related to the multifacet analysis of biodiversity data.

Project Context and Objectives:
The main objective of MARBIGEN project was to fully exploit and further develop the research potential of the former Institute of Marine Biology and Genetics (IMBG), now Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC hereafter) of the HCMR in the area of biodiversity. The project allowed IMBBC to strengthen its already demonstrated research and technological development and to get established in a first-line position in biodiversity science. The location of IMBBC in the heart of Eastern Mediterranean Sea, which is a biodiversity hot spot and one of the most vulnerable to climatic change sea basins, argues for the significance of establishing it as a high- level centre for genomics and biodiversity research. This was accomplished by upgrading existing and acquiring new equipment, developing biodiversity research topics through hiring incoming scientific personnel, taking advantage of the knowledge and experience existing in excellent research entities of the EU through exchanges of researchers, and the organisation of workshops and seminars, as well as other dissemination and promotion activities, such as the hosting of an international conference, and satellite meetings (e.g. seminars and invited talks). Activities in this context were carried out by: a) enhancing its capacities to assess biodiversity through enforcing current up-to-date high throughput genomics technologies, supported by bioinformatics and biodiversity informatics and by introducing automated and precision 3D phenotyping at meio- and macro- organismal level and b) strengthening its capacity to study changes in biodiversity by the developed in-house experimental facility for in vivo experiments with the potential for manipulation of environmental conditions, as well as an innovative experimental site for long-term studies concerning the impacts on biodiversity of anthropogenic stressors and climate change on coastal ecosystems. Furthermore, essential part of the project comprised the external evaluation report, anticipated to help IMBBC to remain an attractive partner for future EU proposals, as well as to attract researchers from other European countries to work in a distant corner of Europe.
The new infrastructure acquired within the MARBIGEN project has significantly supported the potential of the institute to collect and analyze biodiversity data and at the same time has attracted the attention of the scientific community in Crete, as well as the rest of Greece Europe, and other continents (e.g. America). This, in combination with the incoming researchers hired through MARBIGEN, has allowed new ways of designing and running research projects, and thinking about the value of bioarchived material. They have made the role of IMBBC in running projects much more dynamic, by building a profile that facilitated invitations to new consortia and allowed the vigorous submissions of proposals in new calls. The design and ambition of most projects has changed, which now always consider genomics approaches as an integral part of any biological and ecological project and putting an emphasis on next-generation sequencing (NGS) and bioinformatics. A very important achievement has been the organization of formal bioinformatics training courses focusing on PhD students and researchers not only of HCMR but also from other research entities of Greece and in some circumstances international ones. Under this new functioning scheme, the IMBBC research team has the advantage of using the computer cluster obtained through MARBIGEN for computationally intensive data analysis methods (e.g. microbial diversity, or transcriptome analysis and comparative genomics), that was not possible to conduct in the past. The importance of such an accomplishment is better evaluated when considering the current developments in genomics and bioinformatics that have opened huge possibilities demonstrating at the same time their necessity in expertise, computing power and information storage capacity.
Locally and within an overall very active Cretan research community, MARBIGEN has allowed crosstalk and planning of joint projects, heading towards a better integrated critical mass with promising interdisciplinary interactions. This was achieved by means of interactions strengthened by the incoming researchers and accelerated by the workshops and other dissemination activities supported by MARBIGEN. The research institutions of Crete [i.e. the Biology Department and the Department of Computer Science of the University of Crete, the Institute of Molecular Biology and Biotechnology (IMBB) and the Institute of Computer Science (ICS) of the Foundation for Research and Technology - Hellas (FORTH)] have interacted in such a way as to join forces in terms of expertise and infrastructure as a goal for the close future, to address the scarcity of experts in the domain and to stop the drain of researchers from the periphery to the centre.
Within HCMR and through MARBIGEN dissemination and communication activities, expert groups in marine ecology and oceanography have been helped to realize the importance of genomics in their field. Plans have already been formulated on working jointly to address marine biodiversity in a holistic way, both in coastal, as well as in oceanic ecosystems, a trend that the international community is striving very hard to achieve.

Project Results:
MARBIGEN has directly or indirectly played an important role in gaining new projects and/or a more dynamic role in running projects:
(a) EMBRC is a key an ESFRI infrastructure project for marine research comprised by a network of the best European marine research institutes. It has been making its first paths in the preparatory phase at the time when MARBIGEN was approved, a fact that weighted very decisively for the EMBRC board to consider HCMR as an important partner, despite the already apparent crisis in the Greek economy. Now, with some EMBRC Institutes being excellence centers for MARBIGEN (OOB, Banyuls, France; PML, Plymouth, UK; CCMAR, Faro, Portugal) all forces are put together to offer very sound infrastructure for marine research in Europe. IMBBC expertise in bioinformatics and computational infrastructure established through MARBIGEN activities, as well as other international workshops (i.e. workshop organized by EBI-EMBL within EMBRC, workshops organized at EBI and at the University of Oxford by other HCMR projects as COST and MICRO B3, and workshops organized under the MARBIGEN project), and collaborations on different themes related to biodiversity (e.g. training courses on bioinformatics tools, data storage, genomic standards for data archiving and analysis, etc). Several of these activities have been realized during the execution of MARBIGEN. EMBRC has successfully concluded the preparatory phase (January 2014) and has entered its implementation phase with great achievements anticipated to be accomplished in the future.
(b) LifeWatch is an e-Infrastructure ESFRI project which serves the needs of the biodiversity data and data observatories. During the last two years the construction and operation phase has been prepared and currently 6 EU countries participate in this infrastructure. The Greek Secretariat of Research and Technology (GSRT) has signed a contract with HCMR as a coordinator of a consortium of 51 Greek research institutes and academic establishments. The Greek LifeWatch node will be composed by a network of servers which will host a variety of biodiversity data from the molecular to ecosystem level from both marine and terrestrial ecosytems and a rich collection of tools and services for both the providers and the users of the national node. The main concept is to develop the national cadastre of natural capital and to link it with the EU LifeWatch infrastructure.
(c) SeaBioTech is an FP7 large collaborative project that started on August 1st, 2012, involving mainly biotechnology companies, one of the few EU projects that have the ambition of setting up a biodiscovery pipeline that could go from microbial diversity to biotechnological products. The expertise to be gained by IMBBC / HCMR is expected to be unique for downstream analysis of metagenomics, which is from metabolomics to bioremediation, antibiotic, antibacterial and anticancer drug developments. Two research cruises have already been conducted and microbial samples were collected from extreme environments of the Aegean Sea and their analysis and further manipulation is currently in progress.
(d) COST Action ES1103: “Microbial ecology and the earth system: collaborating for insight and success with the new generation sequencing tools” is a project that brings together the best groups of bioinformatics and mathematical researchers on high-throughput analysis of large-scale biodiversity, genomics and metagenomics data in the marine environment. The participation of IMBBC in this consortium can be considered as a direct effect of MARBIGEN. IMBBC has been invited by Dr. Chris Quince (lecturer in the University of Glasgow), with whom an initial acquaintance and a subsequent close collaboration was first achieved through MARBIGEN workshops and seminars, where he had been invited to Crete. Through the COST project collaboration between IMBBC with the team of Prof. Dr. Alice McHardy of the University of Düsseldorf has also been achieved. Furthermore, a workshop on linking environmental data to genomic and taxonomic data by methods of text mining has also been organized by IMBBC.
(e) IMBBC is a member of the international network of “Genomics Observatories” (GOs) for long term monitoring, integrating environmental, biodiversity and genomics data acquisition and analysis, in order to address globally issues of impact of climate change. The mission of the GOs Network is to work towards Biocoding the Earth; integrating DNA data into Earth observing systems and eventually building a global Genomic Observatory within the Global Earth Observation System of Systems (GEOSS). Under this framework a community of scientists work together to launch the GOs Network defined as "an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms" (more information can be found at http://genomicobservatories.blogspot.gr/).
(f) MICRO B3 is a large scale collaborative project that is meant to change the possibility to integrate and analyse data comprising all components of marine ecosystem functioning and biotechnological developments in pro-karyotic and eukaryotic microbes (i.e. environmental / geographical data, biodiversity data and genomics data). Thanks to the MARBIGEN incoming personnel, IMBBC has now been involved in several activities and has participated in workshops and training courses. HCMR organized MICRO B3’s 1st summer school in 2014, in respect to the global sampling event i.e. Ocean Sampling Day (OSD) that took place on the 21st June 2014 also in Crete organized by IMBBC (more information can be found at http://www.microb3.eu/myosd).
(g) "EVAGORAS: “High-performance computing using reconfigurable hardware for biological, ecological and medical applications", a 2-years project in the context of INTERREG, which was a cross-border cooperation programme between Greece and Cyprus. The objective of the project was to develop FPGA technology (Field-Programmable Gate Array) for the creation of cheap hypercomputer stations for ecological data and bioinformatics analysis. The role of IMBBC / HCMR was to assist the identification of bottlenecks in bioinformatics in terms of CPU time and to compare the performance of algorithms adapted for FPGA systems vs. the computer cluster obtained within MARBIGEN. The project allowed creative interactions with engineer and computer science departments of the Universities of Crete and Cyprus and inscribes in the strengthening of interactions with local (Technical University of Crete in Chania) and neighboring communities in Eastern Mediterranean (University of Cyprus - Electrical and Computer Engineering Department).
(h) EUBON: Building the European Biodiversity Observation Network. This is an FP7 project (Cooperation), which engages 30 partners from 18 countries. Key feature of EU BON is the delivery of relevant data to the various stakeholders and end users ranging from governments at local, national and global scales, businesses and civil society. The integrative EUBON network will facilitate political decisions in different sectors in order to conserve biodiversity. EUBON will work on two interrelated networking levels: (a) a science-based social network, comprising and efficiently linking the relevant communities engaged in all levels of collecting, managing, analyzing, and utilizing biodiversity data; (b) a technological network of inter-operating IT infrastructures and systems that stores and distributes information of all kinds, and provides a platform for data analysis and interpretation. EUBON presents an innovative approach towards integration of biodiversity information systems from on-ground to remote sensing data, for addressing policy and information needs in a timely and customized manner. The establishment of the biodiversity information network will build on existing infrastructures, which were significantly upgraded through the MARBIGEN project, with efforts focusing on integrating existing monitoring schemes and their data. IMBBC is leading the activities in one of the selected study sites in the NW Greece (lagoons of Amvrakikos Gulf). Recently (22-27 June, 2014), a memorandum of understanding (MoU) has been signed between EUBON and BioVeL (Biodiversity Virtual e-Laboratory Project, that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources, offering the possibility to use computerized "workflows" (series of data analysis steps) to process data, be that from one's own research and/or from existing sources). The document was signed by the BioVeL coordinator Alex Hardisty (Cardiff University, UK) and handed over to Alexander Kroupa (Museum für Naturkunde Berlin, Germany), who was there on behalf of the EU BON consortium, during the SPNHC Conference in Cardiff, 22-27 June 2014. Furthermore, the list of MoU signed by EUBON has grown with further institutions/projects joining.
(i) SYNTHESYS3: Synthesis of systematic resources. It is an initiative funded under the FP7 (Infrastructures), which is aiming at creating an accessible, integrated European resource for researchers worldwide. SYNTHESYS3 is implemented by a consortium of 18 European partner institutions, which focuses on improving collections management of new physical and virtual collections. IMBBC has a leading role in developing virtual collections for tomography scans. This was made possible thanks to the acquisition of the micro-CT tomographer through MARBIGEN.
(j) KRIPIS: national programme to support the development of Greek research entities. The IMBBC proposal included projects ranging from global biodiversity assessment in the Gulf of Heraklion and long term monitoring, to a large-scale genomics project on the fast grower species Seriola dumerili (greater amberjack) and the population genomics of significant to the ecosystem and fisheries species of small and large pelagic (anchovy and swordfish, respectively), as well as coastal species (gilthead sea bream).
(k) A recent important achievement of IMBBC was the fact that the proposal entitled “Centre for the sustainable exploitation of Marine Biological Resources in the Eastern Mediterranean” (CMBR) was recently positively evaluated by GSRT and selected to be included in the Greek roadmap for research infrastructures. CMBR is an ambitious developmental and research proposal based mainly on the participation of the institute in the ESFRI RI “European Marine Biological Resource Centre” (EMBRC) for the success of which the role MARBIGEN has been decisive.
Finally, MARBIGEN has enhanced the scientific potential of IMBBC by strengthening its expertise and infrastructure. As such in the near future new proposal submissions are anticipated through these ongoing interactions.

Overall, MARBIGEN project has undoubtedly made a great contribution in strengthening the research potential of the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC). Admittedly the visibility of the institute has been considerably increased at the national, European and international level. And this happened despite some unforeseen circumstances, which kept the execution of the project behind schedule in some aspects during the first year of the project. This increase in visibility will be used as a tool to further enhance the research capacity of the institute and to promote local development.
Conclusively, the progress made within MARBIGEN has had significant impact on the institute and HCMR, the local and the international scientific community. IMBBC has had the role of a scientific input-output and storage hub to address, develop and diffuse knowledge, expertise, and infrastructure and build potential on marine biodiversity. In the institute, MARBIGEN not only gave the opportunity to students and post-docs to interact with researchers of international recognition, but has also provided the basis to build long-term collaborations, also supported through exchanges with the excellence centers involved in it. Last but not least, research activities undertaken during MARBIGEN project have established IMBBC as a well-known and favored place for educational and training events, through the organization of workshops, seminars, conferences, spring and summer schools etc.

Potential Impact:
The mission of the IMBBC is, by building on the capacities created by the research activities and achievements, to facilitate a multidisciplinary approach, to enable clustering and cost-effective combination of services, and to become a training and innovation hub. IMBBC, which comprises a large part of “Thalassocosmos” complex in Gournes (Heraklion, Crete), with the existing infrastructure and activities can represent the core of an educational centre, with emphasis on the eastern Mediterranean world. The IMBBC, linked with numerous universities, research centres and institutes worldwide, has facilities to host students and researchers for training courses, summer schools, seminars and conferences. IMBBC can further contribute to educational opportunities and support actions aiming at public awareness regarding the effects of human activities and the protection of the marine environment in cooperation with the “Cretaquarium”, the other large part of “Thalassocosmos” complex. Especially the IMBBC research infrastructure, when considered in the context of other relevant European initiatives such as the ESFRI projects EMBRC and LIFEWATCH, will provide advanced training and education to professionals in the life sciences, thereby generating a pan-European expertise base in marine science for policy makers and industry. At the same time, it will enable efficient knowledge transfer to match biotechnology companies with advanced and state-of-the-art infrastructure. As a result, the creation of spin-off companies in marine biotechnology will be facilitated, thus promoting not only scientific excellence, but also contributing creating to regional employment and economic growth. The development of hosting facilities for visitors, summer schools, workshops, congresses will accompany the scientific infrastructures, so that a large number of users both from Greece and abroad can be attracted and be able to work under optimal conditions. The former American base (where “Thalassocosmos” is situated) offers great opportunities for such a development. Access to the infrastructure and services to external users will be provided based on the scientific merit of academic users (at full economic cost) and feasibility for industrial users (at full economic cost plus additions). The target users will originate both from the public and private sector, international research programs and networks, academia and government. This hosting facility is currently missing despite the nice setting at Thalassocosmos complex and the availability of space, as well as of buildings that can be easily transformed to accommodate visitors and students. Especially the Department of Aquaculture, already playing a crucial role in the relevant private sector by providing innovative methods, apart from products and services, contributes further to the promotion of educational and training activities in aquaculture, a primary sector which contributes significantly to the country’s national economy. The “underwater biotechnological park” (25,000 m2 at depths of 18-23 m) with a wide spectrum of activities for marine research and technology (e.g. artificial reefs technology, protection of the coastal environment, sustainable development of biological resources, such as commercial sponges, long-term monitoring of local climatic, hydrographic and environmental parameters) includes the development and promotion of innovative aspects of marine tourism (e.g. sport diving in connection with artificial reef technology). IMBBC has already proposed, within the framework of the national road map for infrastructures and smart specialization, to expand its activities for research, technology, education and recreation and to further develop: (1) a research centre of excellence for the study of Mediterranean marine biodiversity and genomics (new research laboratories, outreach activities for the public), and (2) an educational centre in collaboration with other universities/research centres/institutes (laboratories, seminar and conference rooms). This proposal has successfully passed through the second round of evaluation and has been recently selected by GSRT for inclusion into the Greek roadmap for research infrastructures. EU and national projects can be coordinated by IMBBC in cooperation with the local Municipality and the Region of Crete in order to support this concept, too. The educational center and relevant activities can be supplemented and supported by the hospitality industry including activities strongly related to Cretan tradition and culture, which could be considered as good investments, counteracting the unemployment in the area. The establishment of a management board consisting of representatives from a wide range of stakeholders, mainly from the Region of Crete, armoured with well-defined targets could promote adaptive management for strengthening further the interactions of IMBBC with the wider societal area.

List of Websites:
Website address: www.marbigen.org
Contact details: Dr. Antonios Magoulas, Director of the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) (former Institute of Marine Biology and Genetics, IMBG), Hellenic Centre for Marine Research (HCMR)
Tel: +30 2810 337801
Fax: +30 2810 337870