Enabling Infrastructure for Advancing Energy & Environmental Research

Bioenergy Projects focus on developing plants that can be used as feedstocks for biofuel production, identifying organisms (e.g., fungi and microbes) with enzymes and pathways that can break down the lignin and cellulose in plant cell walls, and characterizing enzymes and pathways that can ferment sugars into biofuels. Carbon Cycle As microbes make up the largest component of the Earth’s biodiversity, understanding how they metabolize carbon, and how environmental changes affect these processes, is crucial for the development of better predictive models for reducing the effects of increasing carbon dioxide emissions. Biogeochemistry The U.S. Department of Energy (DOE) Joint Genome Institute The field of biogeochemistry explores the full spectrum (JGI) is the only federally-funded high-throughput genome of biological, physical, geological and chemical processes sequencing and analysis facility dedicated to genomes of and reactions involved in sustaining life on Earth. One area non-medical microbes, microbial communities, plants, fungi and of emphasis targets microbes and microbial communities (or other targets relevant to DOE missions in energy and environ- metagenomes) that can degrade or otherwise transform environ- ment. The JGI provides collaborators around the world with mental contaminants such as toxic chemicals or heavy metals. access to massive-scale DNA sequencing to underpin modern systems biology research and provide fundamental data on key genes that may link to biological functions, including microbial metabolic pathways and enzymes that are used to generate fuel JGI FACTS molecules, affect plant biomass formation, degrade contami- nants, or capture CO2. The information can then be used to 1,598 FY2017 Users Worldwide—Individual Principal optimize organisms for biofuels production and other DOE missions. Investigators, Collaborators and Annotators (who conduct genome Located in Walnut Creek, California, and supported by the analysis) on active projects DOE Office of Science, the JGI is managed by the University of California through Lawrence Berkeley National Laboratory, 1,113 FY2017 Users in the US (68%) drawing additional staff from its partner laboratories—Lawrence 147 JGI-authored peer-reviewed scientific publications Livermore National Laboratory and the HudsonAlpha Institute for Biotechnology. 1,702 scientific publications since FY2008 Among the JGI’s largest users are the DOE Bioenergy Research Centers, which were established to accelerate basic 8,429 FY2017 projects completed research in the development of next-generation cellulosic and other biofuels through focused efforts on biomass improvement, 280 staff at Walnut Creek, California headquarters biomass degradation, and strategies for fuels production.

18-JG-4864 http://www.jgi.doe.gov/ Selected Recent JGI Publication Highlights

named a Fast-Breaking Paper for Biology A team led by the University of Washing- and Biochemistry by Clarivate Analytics ton’s David Baker reported that structural (Nature, January 16, 2017). models have been generated for 614 (12%) of the protein families that had Aspergillus Diversity for Industrial previously had no structural information Applications available. This accomplishment was made An international team including JGI possible through a collaboration in which researchers reported sequencing the the Baker lab’s protein structure predic- genomes of 10 novel Aspergillus species, tion server, Rosetta, analyzed the publicly more than doubling the number of available metagenomic sequences on the Aspergillus species sequenced to date. JGI’s Integrated Microbial Genomes and Comparing the newly sequenced genomes Microbiomes (IMG/M) system (Science, with the eight other sequenced Aspergillus January 20, 2017). species provided the first ever genus-wide view. The consortium found that Aspergillus 1,003 Microbial Genomes Released has a greater genomic and functional Culminating nearly a decade’s worth of diversity than previously understood, work, JGI’s Prokaryotic Super Program broadening the range of potential applica- head Nikos Kyrpides and his team tions for the fungi considered among the reported the release of 1,003 phyloge- Toward More Effective Carbon most important workhorses in biotechnol- netically diverse bacterial and archaeal Fixation ogy (Genome Biology, February 14, 2017). reference genomes — the single largest By tapping the DNA synthesis expertise release to date. With the release of this of the JGI, a team from the Max Planck Fungal Enzyme Complexes to high-quality genomic information, the JGI Institute (MPI) for Terrestrial Microbiology Break Down Cellulose provides a wealth of new sequences that has reverse engineered a biosynthetic A team led by researchers at the will be invaluable to scientists interested pathway for more effective carbon fixation. University of California (UC), Santa in experiments such as characterizing This novel pathway is based on a new Barbara, has found for the first time that biotechnologically relevant secondary CO2-fixing enzyme that is nearly 20 times early lineages of fungi can form complexes metabolites or studying enzymes that faster than the most prevalent enzyme in of enzymes called “cellulosomes” capable work under specific conditions Nature( nature responsible for capturing CO2 in of degrading plant biomass. Consolidating Biotechnology, June 12, 2017). plants by using sunlight as energy. these enzymes, in effect into protein Successfully reconstituting a synthetic assembly lines, makes them team up to Novel Group of Giant Viruses enzymatic network in a test tube for the work more efficiently than they would as Discovered conversion of CO2 into organic products individuals. Through the “Facilities Giant viruses were first discovered in could lead to potential future applications, Integrating Collaborations for User Science” 2003, and a handful of other giant virus such as artificial photosynthesis Science,( (FICUS) call between JGI and the Environ- groups have been found since. JGI November 18, 2016). mental Molecular Science Laboratory scientists’ report of a novel group of giant (EMSL), the team found cellulosomes in viruses — dubbed “Klosneuviruses” — Antarctic Adaptations in Diatoms anaerobic gut fungi that attack plant with a more complete set of translation To learn more about how the Antarctic biomass as a cluster of enzymes (Nature machinery genes than any other virus alga Fragilariopsis cylindrus adapted to its Microbiology, May 26, 2017). known to date resolved the debate over extremely cold environment, a team led viruses as a possible fourth domain of life by University of East Anglia (UEA) IMG/M Helps Fill Previously by demonstrating that eukaryote translation- scientists conducted a comparative Unknown Protein Structures encoding genes had been taken up by and genomic analysis involving three diatoms The Pfam database contains close to incorporated into the viral genomes by tapping the JGI’s sequencing and 15,000 protein families: groups of (Science, April 7, 2017). annotation expertise. The paper was proteins that share an evolutionary origin.