This grant will support a workshop focused on developing ideas for a training course in marine microbial genomics, consistent with recommendations of the US-European Commission Taskforce on Biotechnology Research. Leading scientists from the US and Europe will meet in October, 2010 in Washington, DC. These experts will discuss recent scientific progress in marine microbiology that has accrued from modern genomic approaches, as well as opportunities and challenges for continued progress given the fast pace of genome technology advances. Analyses of the state of the science and technology will then frame consideration of the most effective ways to train next-generation scientists who will capitalize on these advances and tackle the technological challenges, a prerequisite for continued progress in this important scientific area.
Workshop sessions will examine the computational methods used to process large amounts of DNA sequence information, current and future DNA sequencing methodologies and tools being used to connect gene and genome sequence information with functional properties of the relevant microbes. The outcome of the presentations and discussions will be a workshop report that provides an overview of critical issues and provides recommendations from each session. It will also include a basic description of an advanced training course on the topic of genomic analyses of marine microbes.
Broader impacts: this entire grant is focused on the needs of the United States and the European Commission to continue to work together in the field of marine microbial genomics in order to expedite advances in basic sciences and in biotechnology.
This grant supported a workshop in which scientists from the United States and the European UNion discussed advances in the field of marine metagenomics and the ways to train the next generation of scientists in this rapidly evolving new technology. Marine metagenomics addresses the DNA blueprints of marine microbial life in order to discover new life forms, new genetic and biochemical characteristics of microbial life, new biogeochemical processes and new biotechnological and biomedical applications of these organisms and their genes. A key objective was to develop a specific set of recommendations for the development of an advanced graduate level training course in marine (meta)genomics. But, before finalizing these pedagogical considerations, the participants first addressed the latest science and technology being applied in the field. This included investigations ranging from one or a few species to studies of highly complex and dynamic ecosystems. The meeting was divided into four sessions: 1) bioinformatics tools to process large data sets, 2) current and future sequencing technologies, 3) the challenges to connect the growing amount of sequences with functional properties, and finally 4) advanced training considerations that integrate physiology, biochemistry and genetics with in silico approaches needed to optimize and prioritize experiments. This workshop also served to facilitate further US/EU collaborations in marine (meta)genomics and biotechnology. Some of the more applied considerations included the integration of genomics technologies into early warning systems (i.e., for the detection of toxic red tides) and the use of genome-based approaches to discover biosynthetic processes of possible biomedical significance. The participants of the workshop included leading US and EC researchers from academia, research centers and private companies. This included ten academics from both the US and the EC, two program directors, and four company representatives. Some of the key recommendations arising from this meeting and the discussions that preceded and followed from it are as follows: 1. Continued advances are needed in the utilization of sequence data, including unknown gene characterization, metagenome binning, and the integration of environmental data and metadata. 2. A greater emphasis is needed on the application of high throughput sequencing to uncover positive and negative interactions within and across all domains of life. 3. Incorporation of (meta)genomics into studies addressing more of the biological diversity (i.e., picoeukaryotes and viruses) needs to continue to be a priority. 4. Connecting relatively unknown marine microbes with their functional attributes is a major challenge that needs ongoing support. 5. There is a great need for more reference genomes made available from creative culturing, microcosms and single-cell manipulations. 6. Computational analyses of metabolic fluxes and physiological properties should be extended to a larger collection of organisms and even to metagenomes. 7. More environmental perturbation experiments in microcosms and mesocosms are needed to facilitate the discovery of new functions. 8. It should be recognized that opportunities for major scientific breakthroughs will continue for both large-scale studies across great distances involving complex and dynamic ecosystems and for highly focused small-scale endeavors involving one or a few key species. 9. A continuing bottleneck in marine (meta)genomics is the training of biologists in bioinformatics. An intensive training course lasting at least five days is needed.* *Since the end of this workshop a proposal for a marine genomics training course has been prepared and will be submitted to various US and EC funding agencies for consideration in the near future. A 55 page workshop report was published.
