The US Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, is managed by DOE’s Office of Biological and Environmental Research (BER). JGI provides high-throughput DNA sequencing, synthesis and analysis services to the user community in support of BER’s bioenergy and environmental missions. These missions mirror DOE’s and national priorities to develop renewable and sustainable sources of biofuels and bioproducts from plant biomass, to understand the biological processes controlling greenhouse gas accumulation in the atmosphere (especially carbon dioxide and methane, key factors in global climate change), and to gain insights into biogeochemical processes controlling the cycling of key nutrients in environments for sustainable bioenergy production or the mobility of heavy metals and radionuclides at contaminated sites for which DOE has stewardship responsibilities. Projects with direct relevance in these areas will have the best chance for selection. Projects focused on organisms for comparative purposes, on model systems for microbe-microbe or plant-microbe interactions, or on development of improved sequencing-based technologies are also welcomed but the applicant should clearly outline how the proposed work will advance BER-mission relevant science. Projects primarily focused on human health, food/animal agriculture, wastewater treatment, or bioremediation of organics will not be considered. Projects targeting marine systems must clearly demonstrate relevance and translatability to freshwater, coastal or terrestrial systems.
Additional information about DOE’s Biological and Environmental Research program mission can be found at http://science.energy.gov/ber/.
Bioenergy
The United States is one of the world’s largest consumers of petroleum, most of which is used for transportation and industry. Petroleum is also the starting material for the production of almost all plastics. This drives the DOE’s focus on developing lignocellulosic biomass as a clean, renewable and sustainable alternative source for biofuels and bioproduct. Such biofuels would ideally offer energy content on par with gasoline while being compatible with our existing fuel distribution infrastructure. Sequencing projects at the DOE JGI that contribute to meeting this goal focus on one of three categories: terrestrial plants that can be used as feedstocks for biofuel and bioproduct production and their associated microbiomes; fungi, microbes and microbial communities that can break down the lignin and cellulose in plant walls; and organisms that can convert lignocellulosic-derived sugars or lignols into biofuels or other bioproducts currently produced from petroleum (excluding pharmaceutical, cosmetic, and food products).
Environmental Microbiome Processes
Microbes constitute the largest reservoir of biodiversity on Earth. Their activities and interactions are at the core of many environmental processes, and the genetic makeup of microbial species and communities forms the basis of their behavior in the environment. The DOE JGI sequences the genomes of microbes and microbial communities that significantly contribute to element and nutrient cycling, particularly those found in less well-understood terrestrial, subsurface, and terrestrial-aquatic interface ecosystems. JGI also focuses on projects that aim to understand biogenic contributions to the global carbon cycle as well as atmospheric particle formation and evolution. Data from such studies is expected to contribute to better predictive models of global climate. They may also provide a basic understanding of the roles microbiomes play in determining the behavior of the physical environment and provide opportunities for biologically-based mitigation strategies.
The JGI seeks to support projects that will foster a genome-enabled understanding of microbial behavior with an impact on the physical, chemical, and geochemical processes that control the environmental fate of key elements with an impact on BER’s energy and environmental mission objectives. Microbes and microbial communities of interest to the DOE JGI as sequencing targets include: those involved in elemental and nutrient cycles, those that impact sustainable bioenergy crop growth or global carbon cycling, and those involved in the cycling of elements that mediate the transformation or are energetically coupled to contaminants such as heavy metals or radionuclides in soils, freshwater, coastal sediments, and the subsurface.