Technological advances in the fields of 'Omics have enabled marine scientists to realise projects they only dreamt of 10 years ago. Large amounts of next generation sequencing data stand in contrast to the small amount of data management infrastructure with integrated analysis software currently available. The Micro B3 Project improved Europe’s capacity for bioinformatics and marine microbial data integration for the benefit of a variety of disciplines in biosciences, technology, computing and law.
Work has focused on mobilizing the larger marine research community for sampling of the world’s ocean, which was accomplished by two global Ocean Sampling Days (OSD) on 21 June 2014 and 2015 (www.oceansamplingday.org). OSD included the citizen science campaign MyOSD (www.my-osd.org). MyOSD is the first citizen science campaign which enabled citizens to perform microbial sampling of the ocean across the globe. This direct participation raised awareness for marine microbes and their important ecological roles.
A data-flow was implemented between four European infrastructures, which allows for direct sharing of metadata and provides access to a wealth of contextual data. The published Micro B3 Standard Operating Procedures and Reporting Standards together with the Micro B3-inspired MIBiG specification (Minimum Information about a Biosynthetic Gene cluster) support marine microbial ecological research, as well as biotechnology for industrial applications.
The Micro B3 Information System is operational for integrated data queries, especially of the OSD data sets, and enables seamless processing, integration, visualisation of and accessibility to huge amounts of marine data. Biodiversity research in Micro B3 has led to many novel results, based on new tools like annotation pipelines, network and statistical analysis in microbial ecology, including interactive guidance for a community-led and -curated service.
For biotechnological applications several bioinformatics tools were developed and tested: the 3DM database system, developed by an SME-academia collaboration, uses dedicated workflows for computational predictions of substrate selectivity of enzymes. A novel tool uses co-occurrence networks for determining hypothetical functions of unknown genes found in marine microbes. Lately, this was extended to create the ultra-fast Biosynthetic Gene Cluster recruiter, which is generating biotechnological relevant enzyme targets for wet-lab testing from metagenomes. Diverse results from genome mining for anti-tumour compounds, enzyme toolboxes, libraries and new expression systems for experimental screening were tested, applied and are now available.
On the legal side, an Access and Benefit Sharing model agreement (ABS-MA) and a data policy were developed, tested during training courses and utilised during the two OSDs. This directly implements the Nagoya Protocol, entered into force on 12 October 2014, on access to genetic resources and the fair and equitable sharing of benefits arising from their utilization to the Convention on Biological Diversity (CBD).
Further cross-cutting activities included a training pipeline enhancing interdisciplinary oceanographic, biodiversity, bioinformatics and biotechnological knowledge. The courses, stakeholder and industry expert workshops integrated many partners and related projects in knowledge exchange and technology transfer with academic and industrial stakeholders.
Overall, Micro B3 particularly fostered (1) Research on ‘environmental intelligence’ of European open ocean and coastal marine ecosystems for better understanding of their diversity and functions they contain. (2) Community interaction, technology transfer and data sharing between science and the bio-economy to overcome fragmentation in European marine research as well as to promote product and service developments. (3) Public awareness of the importance of marine research and the fundamental role of marine microbes in ecosystem functioning.