Metagenomics 2008 -- Discussions The third annual conference, hosted by Calit2 at UC San Diego, drew more than 250 participants from around the world to discuss the stunning potential of metagenomics, which could revolutionize approaches to energy, medicine, agriculture and even national security. Recent, rapid advances in sequencing technologies and in culture-independent genomic analysis and other microbiology techniques have established a solid foundation upon which to build a unique interdisciplinary community for the emerging scientific subfield of metagenomics. At the intersection of many diverse disciplines, metagenomics is already beginning to engage an ever growing and exceptionally wide intellectual community. The UCSD-based Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) project is committed to an annual congress to facilitate the growth of the community. This is the third meeting organized by us in San Diego and the fourth international conference since Metagenomics 2003 in Germany. Metagenomics 2008 will provide invaluable opportunities to discuss and accelerate the implementation of metagenomic research. The conference will include research in microbial ecology, genomics and evolution, bioinformatics, and biogeochemistry, as well as research on multiple organisms interacting with each other and their environment, that is, on ecological genomics, population/community genomics and environmental genomics. Discussions will include important issues in standards and interoperability of data sets, as well as policy considerations for advancing the community. Demos and/or tutorials on advances in next generation sequencing and on knowledgebase resources will also be provided.