the PRIMER Fall 2008 Volume 5 Issue 2 also in this issue Guts ’R Us?: CSP 2009 JGI News . 2 Genome of Simplest Animal Reveals Ancient User Community Faces: Lineage . 10 Selections Announced Alexandra Worden . 3 Using Metagenomics Super Bacteria for on Lake Washington Q: What do boat-boring the information that we gener- Super Alfalfa . 4 Microbes. 12 bivalves and stinkbirds have ate from these selections CSP2009 Project at in common? JGI Announcements . 16 promise to take us faster and Contaminated A: Their guts are just two of 44 further down the path toward Hanford Site . 6 new CSP 2009 targets. clean, renewable transporta- In the continuing effort to tion fuels while affording us a tap the vast, unexplored reaches more comprehensive under- Director Rubin of the Earth’s microbial and standing of the global carbon plant domains for bioenergy cycle,” says Eddy Rubin, DOE Reviews and environmental applications, JGI Director. “The range of the DOE JGI has announced its projects spans important ter- Genomics of latest portfolio of DNA sequenc- restrial contributors to bio- ing projects for the coming year. mass production in the Loblolly Biofuels in The 44 projects, culled from pine—the cornerstone of the Nature nearly 150 proposals received U.S. forest products industry— through the Community to phytoplankton, barely visible Genomics is accelerating Sequencing Program (CSP), will to the naked eye, but no less improvements for converting collectively generate more than important to the massive gen- plant biomass into biofuel, thus 60 billion nucleotides of data. eration of fixed carbon in our bringing closer to reality wide- “The scientific and techno- marine ecosystems.” spread use of an alternative to logical advances enabled by With new cont. on page 7 fossil fuel for the world’s trans- portation needs, reports Eddy Rubin, DOE JGI Director, in the August 14 edition of the jour- nal Nature. In “Genomics of cellulosic biofuels,” Rubin lays out a path for how emerging “Similarly, today’s barriers to genomic technologies will con- improving biofuels are signifi- tribute to a biofuels future that cant, but genetics and genomics is substantially different from can catalyze progress towards the present corn-based ethanol delivering, in the not-too-distant industry—and in part mitigate future, economically viable and the food-versus-fuel debate. more socially acceptable biofu- “The Apollo moonshot and els based on lignocellulose.” the Human Genome Project While Rubin acknowledges rallied support for massive that this strategy is in its R&D efforts that created the infancy, rapid progress is capabilities to overcome being made. Among the CSP 2009 targets is the contents of the enlarged crop obstacles that were not con- “Over the past 10,000 of the Hoatzin, Opisthocomus hoazin, or Amazonian stinkbird, which templated at the outset of years, wild plant species were is unique among known avian species by virtue of its fermentative foregut. these initiatives,” says Rubin. selected cont. on page 13 2 / the PRIMER Fall 2008 Vol. 5, Issue 2 JGI-Stanford Moves to HudsonAlpha Institute for Biotechnology In Summer 2008, the DOE JGI’s partner augment the use of DOE JGI genomes in science and technology education, includ- at the Stanford Human Genome Center scientific discovery, bioenergy, and other ing hands-on, research-based programs for (JGI-SHGC) moved to a new home, the directed breeding applications. students and educators, are critical to recently opened HudsonAlpha Institute for HudsonAlpha, a non-profit research insti- enabling discoveries that will improve Biotechnology (www.hudsonalpha.org) in tute, will continue to work as a DOE JGI health and keep America competitive in Huntsville, Alabama. The newly formed partner with a focus on plant and eukaryotic biotechnology. To push the boundaries of research group, the HudsonAlpha Genome genomics. It will also continue to assist scientific and technological capabilities, Sequencing Center, will expand its opera- with genome analysis for collaborators as education specialists at HudsonAlpha are tions into next-generation genome sequenc- well as form the cornerstone collaborative supporting, creating and implementing ing and add capabilities to collect data to group for sequencing and genomic proj- programs toward making Alabama’s stu- ects at HudsonAlpha. Director Rick Myers, dents among the nation‘s best and bright- Jeremy Schmutz, and Jane Grimwood are est while augmenting the enterprising some of the Stanford Human Genome environment that will keep them home. Center researchers who made the move to The HudsonAlpha Institute is the corner- HudsonAlpha. stone of the 150-acre Cummings Research HudsonAlpha’s mission is to use bio- Park Biotech Campus. The campus embodies technology to improve human health and a synergistic cluster of talented scientists quality of life, stimulate economic develop- and business professionals that promises ment, and inspire Alabama’s youth to collaborative innovation to turn knowledge seek careers in science. HudsonAlpha and ideas into commercial products and The Stanford Human Genome Center has believes that education supports innovation, services for improving human health and found a new home at the HudsonAlpha giving rise to increased professional and strengthening Alabama’s progressively Institute in Huntsville, Alabama. economic opportunities. Investments in diverse economy. Photo: Cooper Carry IMG, IMG/M Systems Upgraded, Education Site Launched The DOE JGI has extended the capabili- sequenced at DOE JGI, consisting of 237 ties of the Integrated Microbial Genomes finished and 71 draft genomes. news (IMG) data management system, updated IMG 2.6 includes the first version of the content of the IMG/M metagenome chromosomal gene cassettes (positional data management and analysis system, gene clusters) together with estimates of and launched its educational companion their conservation across IMG genomes. site, IMG/EDU. The User Interface has been improved with Version 2.6 of IMG includes new micro- tools for exploring gene cassettes conser- bial genomes from the Version 29 release vation and includes additional graphical of the National Center for Biotechnology viewers for examining the functional anno- Information’s (NCBI) Reference Sequence tation of genomes. More details on IMG (RefSeq) collection. IMG 2.6 contains a 2.6 are available at: img.jgi.doe.gov/w/ total of 4,207 genomes consisting of doc/releaseNotes.pdf. During the week of September 15, more 1,078 bacteria, 56 archaea, 40 eukary- The content of IMG/M, which provides than 40 participants ventured to JGI’s otes, 2,230 bacteriophages, and 803 tools for analyzing the functional capability Production Genomics Facility from as far plasmids that did not come from a specific of microbial communities based on their away as Australia, Greece, Hong Kong, microbial genome sequencing project. metagenome sequence, has been updated Israel, and Russia for the Microbial Genomics & Metagenomics (MGM) Among these genomes, 3,737 are fin- to include three additional metagenome Workshop. The full agenda can be found ished and 470 are draft genomes. IMG datasets generated from microbial com- online at www.jgi.doe.gov/meetings/ 2.6 contains 308 microbial genomes munity samples that cont. on page 9 mgm/agenda.html. the PRIMER / 3 Fall 2008 Vol. 5, Issue 2 A Conversation with Alexandra Z. Worden BY MADOLYN BOWMAN ROGERS protists, single-celled marine organ- Alexandra Z. Worden, microbial ecolo- isms that feed on picoeukaryotes gist at Monterey Bay Aquarium Research and other small plankton. Institute, studies picoeukaryotes, tiny Worden has a doctoral degree in marine algae less than 2 microns in diam- ecology from the University of eter (about 1/50 the width of a human Georgia and completed an NSF hair). These organisms are part of the Postdoctoral fellowship at Scripps photosynthetic community that forms the Institution of Oceanography in San foundation of marine food webs. Because Diego over a three-year period. After these photosynthetic organisms remove accepting a professorship at the Predatory carbon dioxide from the atmosphere and University of Miami, she spent six protists feed “fix” it into organic molecules, they may months as a visiting scientist at the on picoeukary- play a significant role in global carbon Station Biologique du Roscoff in France otes and other phy- cycling. Worden wants to know what regu- then built her group in the Marine Biology toplankton, tiny organ- lates the growth of these microbes, what and Fisheries Department at UM, where isms which remove carbon dioxide from the atmosphere. Sequencing happens to the carbon they fix, and how she worked until Fall 2007. To view a the predatory protists will improve our this might play a role in climate change. video podcast about Worden and her understanding of photosynthesis, as well as To answer these questions, Worden has research visit: www.youtube.com/user/ its links with carbon cycling and climate turned to the power of genomic analysis. JointGenomeInstitute change. She has been a frequent collaborator with Q. What led you to look at the predatory DOE JGI, serving as champion on marine protists? is essentially released back to the envi- microbiological sequencing projects in 2005 A. It’s critical that we know how preda- ronment. Larger organisms like these and 2007. In one of the 2009 Community tors select their prey, because that dic- predators are better able to move through Sequencing Program (CSP) projects, Worden tates the fate of the prey’s photosyntheti- the water column—some sink—and heads an international collaboration that cally fixed carbon. If one group of they’re also part of the food chain. includes researchers from Austria, Wales, picoeukaryotes is actually eaten, while Q. What led you to start using the University of Southern California, and other groups of phytoplankton are not, it’s genomics? the J. Craig Venter Institute in San Diego. a dramatically different role in carbon A. If you observe picoeukaryotes under The goal is to produce genome sequences cycling and potential sinking of that mate- a microscope, they show up as just a dot.