While the sequencing and assembly strategies for the Microbial Genomics and Metagenomics Programs are quite different, the scientific goals of the two programs are very much aligned with an underlying common objective to understand the structure and function of microorganisms and microbial communities with mission relevance to the Department of Energy. To achieve this, scientists in the program are pursuing the sequencing of nucleic acids from both individual microbes and entire communities of organisms. This combined approach offers unique opportunities to the scientific community, but also requires coordinated activities between metagenomic and individual microbial genome sequence generation and data analysis.
To capitalize on these emerging opportunities, JGI connected the two separate programs, through a joined Prokaryotic Super-Program, which is founded on four pillars for understanding of microbial life on Earth. The first is that Earth is a microbial planet: more than 60% of earth’s biomass and biodiversity is microbial. Yet, our knowledge and understanding of microbial life is still very limited and we have just begun scratching the surface. The second is that microbes control most of the major biogeochemical cycles on earth and can therefore have significant impact on weather, climate and the environment. The third is that the vast majority of microbes cannot, or have not yet been cultured and thus cannot be studied in isolation. And the fourth is that all life forms exist in a continuum that forms interdependent communities of organisms in which microbial life is an integral part. For example, microbes support the life of all plants and animals, in a way that life without microbes cannot be sustained. Understanding the symbiotic interactions between the host organisms and their microbial communities has far reaching applications in bioenergy, agriculture and global warming.
These pillars have helped us to define and develop the joined Prokaryotic Super-Program and have provided a new vision for its future. Fueled by a new era in sequencing technologies, and new capabilities at the JGI, we can now ask new questions and address challenges that only a few years ago seemed intractable. These are expected to generate the new knowledge required to lead us to a new era of holistic understanding of microbial life.
The first pillar provides a strong scientific need for a phylogenetic-based selection of genome sequencing targets. This reasoning led to the development of the GEBA, Genomic Encyclopedia of Bacteria and Archaea, initiative at the JGI, aiming at the systematic filling of the gaps in sequencing along the bacterial and archaeal branches of the tree of life. The success of the GEBA pilot project has helped in launching several more related projects such as GEBA-Cyano (for the cyanobacterial tree of life), GEBA-RNB (for the root-nodulating bacteria), and others currently underway.
The second pillar directs us to strive for an understanding of the microbial contribution to carbon and nutrient cycles essential for understanding climate, plant growth and health and the movement of environmental toxins. The third and fourth pillars of our understanding of microbial life suggest that the key to this understanding requires advances in metagenomics, a field pioneered at the JGI. Understanding the structure and function of microbial communities requires knowing the organisms that comprise them, as well as their specific roles. To achieve that, we need to dissect each community and identify its individual components, an approach that directly depends on the availability of sequenced reference microbial genomes. Accordingly, it has become evident that the road to success in metagenomics is through microbial genomics. However, studies of such communities have revealed a diversity of microbes far beyond those found in culture collections. It is suspected that these uncultivated organisms harbor considerable as-yet undiscovered genomic, functional, and metabolic features and capabilities. Given that the vast majority of microorganisms are not or cannot be cultured to date, the only way to get those reference genomes with current technologies is to get genome sequences from single cells. This need has led to the development of another major field in microbial genomics, that of single cell genomics, which is directly addressing pillar three, with projects such the microbial dark matter (GEBA-MDM).
Super Program Research Groups