Marine Microbial Biodiversity, Bioinformatics and Biotechnology
With technological advances in the fields of 'Omics' analyses, oceanography and lab automation, marine scientists conduct projects they only dreamed of 10 years ago. The deluge of data produced is beyond the skill-set of many marine scientists and very little data management infrastructure exists. Micro B3 (Biodiversity, Bioinformatics and Biotechnology) will facilitate the whole process from sampling and data acquisition to analysis and interpretation. This will lead to better understanding of marine ecosystems and pave the way for novel biotechnological applications.
Nine interdisciplinary teams of experts in bioinformatics, computer science, biology, ecology, oceanography, bioprospecting, biotechnology, ethics and law are working together in the Micro B3 project. The consortium includes 25 European research groups with 32 participants from universities, research institutes and companies. The primary objective is to integrate biodiversity, genomic, and oceanographic databases into one Information System (IS), the Micro B3-IS, which is based on global standards for sampling and data processing.
Biodiversity research in Micro B3 has already led to novel results concerning the role of marine
viruses as well as providing interactive guidance and tools for ecological analysis. Case studies were chosen to explore the marine microbial ecosystem, including spatial monitoring done through expeditions and temporal monitoring programmes for long-term ecological research sites.
Bioinformatics work has led to interoperable structures for submission, storage and exchange of data between the established archives SeaDataNet, EurOBIS, the European Nucleotide Archive (ENA at EBI) and the Micro B3-IS. For the Ocean Sampling Day (OSD) planned on 21st June 2014, best practice guidelines for microbial
biodiversity assessments in rich environmental context were agreed, tested and gathered in an OSD Handbook. (http://www.microb3.eu/sites/ default/files/deliverables/MB3_D4_3_PU.pdf).
A citizen science and crowd funding campaign (www.my-osd.org) was started to raise awareness for the marine ecosystem. Training is done in bioinformatics, ecological statistics and modelling with an interdisciplinary summer school, metagenomic and annotation courses planned.
To further biotechnological applications, bioinformatics tools were developed for determining functions of still unknown genes found in marine microbes. One is using co-occurrence networks for determining hypothetical functions of unknown genes from marine microbes. Results from genome mining for anti-tumour compounds, enzyme databases, libraries and new expression systems for experimental screening are becoming available. Industry leaders are targeted through expert workshops and Think Tanks to promote understanding of the value of integrating environmental and 'Omics' data.
Intellectual Property Rights issues are addressed through the development of model agreements and organisation of a stakeholder workshop facilitating access to and benefit sharing of marine genetic resources.
The innovative Micro B3-IS allows for seamless processing, integration, visualisation and accessibility of the huge amounts of marine data collected in on-going biodiversity sampling campaigns and long-term observations. Interoperability is a key feature for data transfer of sequence and contextual data to public repositories. Therefore all entries will adhere to the Minimum Information checklists Standard (MIxS) for describing molecular samples as outlined by the international Genomic Standards Consortium (GSC, www.gensc.org). Micro B3 also offers analytical and feedback tools on its platform which are unique in terms of integrating genetic and ecological information and generating collective knowledge. This provides new perspectives for the modelling and exploration of marine microbial communities.