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 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 , 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 , 40 eukary- The content of IMG/M, which provides than 40 participants ventured to JGI’s otes, 2,230 , 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 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 . 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. of a ubiquitous rial to the deep ocean. So it’s hard to get any handle on their user community faces group of Q. How does being eaten change the physiology—what’s controlling their growth. predatory fate of the carbon? For me, genomics was a way to get at that. A. When you’re a micron [in size], and It’s a window into the capabilities they you’re in seawater, it’s like being in syrup. might have. But it’s really just a first step; You’re not able to move yourself through then you need to find out what genes the water column. If you’re one micron, and they’re using, when and why. If we know you die in the surface ocean, your carbon what factors shift cont. on page 14

I went into this wanting to help the environment, and I am daunted at this stage. Things are changing so fast, people are proposing scientifi- cally unfounded quick fixes, and we’re still at such a basic level of understanding. It is a true call to action.

—Alexandra Z. Worden 4 / the PRIMER

Fall 2008 Vol. 5, Issue 2

Nitrogen-Fixing Bacteria Hold the Key to Alfalfa as a Bioenergy Crop

BY MADOLYN BOWMAN ROGERS The two new strains of S. By harnessing an ancient association meliloti that the DOE JGI between plants and bacteria, researchers will sequence each may one day be able to engineer super- contain desirable efficient crops for bioenergy production. traits. Strain AK83 To advance this goal, the DOE JGI is part- allows alfalfa to nering with scientists at the University of thrive in the desert- Florence in Italy to sequence two new like North Aral Sea strains of nitrogen-fixing bacteria in one of region of Kazakhstan, where the 2009 Community Sequencing Program extremely salty soils prevent many (CSP) projects. plants from growing. Strain Sinorhizobium meliloti is the most well- BL225C comes from an agricul- studied and abundant species of rhizobia, tural region in the north of Italy a group of bacteria that infect the roots of and is highly efficient, producing legumes and form nodules in which they plants with three to four times as fix atmospheric nitrogen into plant matter. much dry weight as strain AK83. Rhizobia enable legumes such as peas, By comparing the genomes of these beans, clover, and alfalfa to grow in nitro- two strains with the previously sequenced gen-poor soils with no need for costly fer- reference strain, researchers may discover tilizers. One strain of S. meliloti has been the genetic basis for traits such as salt sequenced, but because different strains resistance and nodulation efficiency, Biondi have adapted to diverse environments says. This would open the possibility of worldwide, S. meliloti strains exhibit engineering a new strain by combining tremendous genetic variability. desirable traits already present in the Alfalfa (Medicago sativa) serves as the “We think we will find that 10 percent species but not normally found together, a host plant for the of the genome is completely new and dif- process Biondi refers to as “environmen- nitrogen-fixing bac- ferent,” says the project’s lead investigator, tally friendly genetic engineering” because terium, S. meliloti. CSP 2009 Emanuele Biondi, a bacterial geneticist at it doesn’t introduce foreign genes into the the University of Florence. This could species. mean 500 to 800 novel genes per strain. “Our goal is to make a super-strain S. meliloti forms a symbiotic associa- that can survive in extreme environ- tion with alfalfa, a crop traditionally used ments and also can nodulate as animal feed but now under study by very efficiently,” Biondi says. the USDA and the University of Minnesota Such a strain could produce as a promising feedstock for biofuel pro- high-yield alfalfa plants that can duction. Alfalfa’s helper bacteria give it a grow on land unsuitable for agri- competitive advantage over current bioen- culture—an ideal bioenergy crop. ergy crops such as corn, which require fertilizers. Because commercial fertilizer Madolyn Bowman Rogers, PhD, recently production is expensive and produces completed the Science Communication greenhouse gases, alfalfa would be a Program certificate at the University of more environmentally sustainable biofuel California, Santa Cruz and spent the sum- crop than corn and other cereals. In addi- mer of 2008 as a public affairs intern at tion, alfalfa can grow on marginal lands, the U.S. Department of Energy Joint so it would not use up prime cropland. Genome Institute. Researcher Emanuele Biondi the PRIMER / 5

Fall 2008 Vol. 5, Issue 2

Life at the Extreme: Microbes May Provide New Tools For Carbon Sequestration

BY MADOLYN BOWMAN ROGERS would be toxic to most organisms. Genomes with Samples Microbes that eke out their existence in “These are organisms really living at (IMG/M) data management system. a lightless, frigid, buried lake in Antarctica the extreme,” says Phil Hugenholtz, head “This will be the first metagenomic may be the most energy-efficient organisms of the Microbial Ecology Program at the analysis of this system,” Hugenholtz says. on earth. To try to unlock the secrets of DOE JGI and lead investigator for the “Metagenomics gives you insights into their remarkable abilities, the DOE JGI will sequencing project. The collaboration also the functional capabilities of the organ- partner with researchers at the University includes Brian Lanoil of the University of isms present—not just who’s there, but of Alberta and the University of Delaware Alberta (formerly at UC Riverside), Craig what they’re potentially capable of doing. in a 2009 Community Sequencing Cary of the University of Delaware, and And of course that’s the really interesting Program (CSP) project to sequence the Victor Kunin of DOE JGI. thing, working out how they’re adapted to genomes of this microbial community. Although Lake Vostok itself has never that environment.” The microbes survive in the hostile been penetrated, the Vostok microbes The microbes probably get their food environment of Lake Vostok, a freshwater were discovered in ice cores taken from by removing carbon dioxide from the lake about the size of Lake Ontario which just above the lake in 1998. Lanoil is atmosphere and fixing it into organic mol- has lain entombed under more than three leading the project to extract the microbes ecules, Hugenholtz says, a process that kilometers of ice in the middle of from the Vostok ice cores, which remain normally requires tremendous energy. Antarctica for perhaps 15 million years. preserved at the National Ice Core Green plants also produce food this way, The lake’s near-freezing waters contain no Laboratory in Denver, Colorado. but they can power this process using the light, no organic matter for food, and no Lanoil’s team has developed stringent abundant energy of sunlight. geothermal activity or other energy sources. methods to insure the samples are not “Whatever the Lake Vostok microbes In addition, the lake’s crushing pressure contaminated by even a single bacterium do, they must do it very efficiently, of nearly 400 atmospheres causes oxy- from our environment. The microbes will because they don’t have much to eat and gen to become trapped in the waters. be handed off to the DOE JGI for sequenc- they don’t have much to survive on,” co-PI Lake Vostok is saturated with 50 times ing, assembly, and analysis using DOE Kunin says, adding that high oxygen con- normal oxygen concentrations, which JGI’s unique Integrated Microbial centrations also interfere with carbon fixa- tion. Therefore, the microbes have “proba- bly the most efficient carbon sequestra-

Vostok Station CSP 2009 & borehole tion you can get.” Since excess carbon dioxide in the atmosphere contributes to global warming, efficient carbon sequestration methods are of great interest to the DOE. Analysis Glacier Microbes of the bugs’ genomes is expected to reveal novel enzymes and pathways for carbon sequestration, as well as other unusual adaptations to extreme cold, high pressure, and high oxygen. Because Ice from lake these conditions resemble those found on Lake Vostok some outer planets and moons—for example, Jupiter’s moon Europa—the microbes’ genomes could even provide clues to the nature of extraterrestrial life. Microbes were discovered in Lake Vostok ice cores taken in 1998 and are now being extracted and sequenced in hopes of discovering the secret to their survival in extreme A video podcast about the Lake Vostok conditions. CSP project can be viewed at: www.youtube. com/user/JointGenomeInstitute 6 / the PRIMER

Fall 2008 Vol. 5, Issue 2

Uranium Plume Microbes May Inform Stewardship Efforts

BY MADOLYN BOWMAN ROGERS and technetium in subsurface soils. you’re looking at something new, you don’t Microorganisms in the soil may repre- The Hanford Site occupies 560 square want to be second-guessing yourself about sent an untapped resource for cleaning up miles along the Columbia River in southern the quality of the data,” Konopka says. radioactive waste. In a 2009 Community Washington and was a major plutonium By combining sequencing data with Sequencing Project spearheaded by scien- production facility for the Manhattan Project analysis of the physical properties, geo- tists at Pacific Northwest National Laboratory, and during the Cold War, until it ceased chemistry, and mineralogy of the core the DOE JGI will sequence microbes in operations in 1990. During cleanup opera- samples, and using sophisticated data subsurface soil samples from a contami- tions, DOE removed ponds of uranium waste- mining techniques, researchers hope to nated DOE site to glean clues about the water and contaminated sediment from discover how environmental conditions microbes’ biogeochemical abilities. “This study might reveal organisms with novel properties and capabilities that What is 16S rRNA? are relevant to the fate and transport of 16S rRNA is a type of ribosomal RNA found in bacteria and subsurface contaminants,” says the pro- ject’s lead investigator, Allan Konopka, archaea—but not in higher life forms. Because it is highly microbiologist at PNNL. “This fundamental conserved (resistant to mutations), all members of a species scientific information would inform man- have the same 16S rRNA sequence. agement decisions regarding what strate- 16S rRNA sequences act as species ID tags. gies would be best for long term steward- ship at Hanford.” 16S rRNA sequencing can: The sequencing is part of a research program funded by the DOE Environmental • Identify bacterial species Remediation Sciences Program and car- ried out by scientists at PNNL and at sev- • Determine relatedness eral universities and other national labs. • Construct evolutionary trees In the spirit of DOE team science, the project brings together microbiologists, ecologists, geologists, geochemists, Area 300, but a plume of low levels of and microbial communities influence each hydrologists, and mathematical modelers radionuclides have persisted below the other, and how this in turn affects the CSP 2009 to study how subsurface conditions and surface, contaminating groundwater above transport and fate of radionuclides in the microbes in Area 300 of the Hanford Site the drinking water standard. subsurface. interact to affect what happens to uranium During Summer 2008, project scientists Research at other sites suggests that will drill a borehole about 180 feet subsurface microbes can reduce the mobil- deep in Area 300 and extract ity of contaminants, preventing their trans- genetic material from 20 sediment port off site. About one-third of the world’s samples in five key regions, accord- microorganisms have been estimated to ing to Konopka. The DOE JGI will exist in the subsurface, but little is known sequence 16S rRNA [see box] to about their ecology. The project should provide a rough picture of the enable researchers to build better models microbes’ species diversity and phy- of subsurface biogeochemistry, Konopka logenetic relationships. says, and provide valuable information for PNNL scientists chose the DOE JGI decision makers regarding when and based on its reputation for providing where to apply remediation techniques. high-quality sequence data. “When “What we learn here about the subsur- face microbial ecology,” he says, “will be A cross-section of the study plot at the applicable to a broad array of DOE sites Hanford site describes the strategy for sampling the microbial communities resident in the subsurface. in the arid western United States.” the PRIMER / 7

Fall 2008 Vol. 5, Issue 2

CSP 2009 Selections cont. from page 1

sequencing strategies com- fastest-growing, and simplest of flowering ducing hundreds of enzymes with poten- Loblolly pine ing on-line at DOE JGI’s plants. Greater Duckweed, Spirodela tially useful industrial applications. (Pinus taeda) Production Genomics polyrhiza, is still relatively small, at less One such metagenome lurks inside of Facility, Rubin says that the than 10 millimeters tall. Nevertheless, its Bankia setacea, the giant Pacific shipworm. once daunting genome size utility is manifold: as a biotech protein fac- Shipworms, wood-boring marine bivalves, of the Loblolly pine (Pinus tory, toxicity-testing organism, wastewater have been nicknamed “termites of the sea.” taeda)—more than 21 bil- remediator, high-protein animal feed, car- These animals are capable of feeding solely lion bases—is now becom- bon cycling player, as well as basic on wood, utilizing a highly efficient system ing tractable. Loblolly pine research and evolutionary model system. of symbiotic lignocellulose degradation is the most commonly “These plants produce biomass faster that is biologically, functionally, and evolu- planted tree species in than any other flowering plant, and their tionarily distinct from those found in ter- America, accounting for carbohydrate content is readily converted mites, ruminants, and all other cellulose- about 75 percent of all to fermentable sugars by using commer- consuming animals. Like termites, the seedlings planted each year. cially available enzymes developed for corn- ability of shipworms to consume wood

“Its ability to efficiently convert CO2 based ethanol production,” says Rubin. depends on symbiotic bacteria that pro- into biomass and its widespread use as a “Moreover, duckweed relates to all three vide enzymes, including cellulases and plantation tree have also made Loblolly a of DOE JGI’s mission areas: bioenergy, other hydrolases critical for digestion of cost-effective feedstock for cellulosic bio- bioremediation, and global carbon cycling.” wood by the host. The enzymes are also fuel production and a promising tool in Spirodela species, which thrives on potentially valuable for commercial biocon- efforts to curb greenhouse gas levels agricultural and municipal wastewater, effi- version of lignocellulose to ethanol. through carbon sequestration,” says ciently extract excess nitrogen and phos- Analysis of the shipworm symbiont Rubin. Because of the pine’s enormous phate pollutants. Duckweed growth on community metagenome will provide genome, the project will begin with a tar- ponds effectively reduces algal growth (by important insights into the composition geted effort to understand the genome shading), coliform bacteria counts, sus- and function of this unique lignocellulose- structure. Led by Daniel Peterson of pended solids, evaporation, biological oxy- degrading bacterial community and will Mississippi State University, the project is gen demand, and mosquito larvae while allow valuable comparisons to the recently intended to zero in on genes that can be maintaining pH, concentrating heavy met- sequenced termite symbiont metagenome. used for molecular breeding programs to als, sequestering or degrading halogenat- Unlike termites, shipworms accomplish improve Loblolly’s use as a biomass feed- ed organic and phenolic compounds, and the complete degradation of lignocellulose stock, a carbon sequestration tool, and a encouraging the growth of aquatic animals with a simple intracellular consortium of CSP 2009 source of renewable, high-quality raw such as frogs and fowl. This project, sub- just a few related types of microbes. The materials for lumber and pulp fiber. mitted by Todd Michael of the Waksman project was proposed by Daniel Distel of Institute of at Rutgers, The the Ocean Genome Legacy Foundation. The Small Yet Mighty Duckweed State University of New Jersey, unites the Another marine organism, Botryococcus The CSP selections range from these efforts of six institutions. braunii, is a colony-forming green microalga, towering pines to not-so-sizable aquatic less than 10 micrometers in size, which plants such as duckweed—the smallest, Termites of the Sea and other synthesizes long-chain liquid hydrocarbon Aquatic Wonders compounds and sequesters them in the Greater Duckweed The DOE JGI has selected several extracellular matrix of the colony to afford (Spirodela polyrhiza) metagenomes to sequence—complex buoyancy. A type of B. braunii produces a microbial communities that are isolated family of compounds termed botryococ- directly from the environment or reside cenes, which hold promise as an alterna- inside of a larger organism. These lever- tive energy source. Botryococcenes have age DOE JGI’s pioneering expertise honed already been converted to fuel suitable for from previous studies of acid mine drainage internal combustion engines. Geochemical and the termite hindgut, where samples analysis has shown that botryococcenes, yielded scores of different microbes, pro- presumably from cont. on page 13 8 / the PRIMER

Fall 2008 Vol. 5, Issue 2

After the First Decade of Metagenomics, Adolescent Growth Spurt Anticipated

Mostly hidden from the scrutiny of the California in 2004. In the dank recesses need to manage and interpret the terabas- naked eye, microbes have been said to of the mine, protected by moon suits from es and terabytes of metagenomic data run the world. The challenge is how best the highly acidic effluent, the researchers now bubbling up into the public domain, to characterize them given that less than scooped up pink biofilm growing on the DOE JGI launched the Integrated Microbial one percent of the estimated hundreds of surface of acid mine drainage streams. Genomes with Microbiome Samples data millions of microbial species can be cul- Extracting the nucleic acid from the sam- management and analysis system (see tured in the laboratory. The answer is ple and directing DOE JGI’s powerful DNA page 2). IMG/M provides tools for analyz- metagenomics—an increasingly popular sequencing resource on them, the Banfield ing the functional capability of microbial approach for extracting the genomes of team was able to reconstruct the metabolic communities based on the DNA sequence uncultured microorganisms and discerning profiles of the organisms living under such of the metagenome in question. their specific metabolic capabilities directly inhospitable conditions—like putting many “Metagenomic tools are becoming from environmental samples. Humpty-Dumpties back together again. Their more widely available and improving at a Now, some ten years after the term findings, published in Nature (428:37-43 steady pace,” says Hugenholtz. “But, was coined, metagenomics is going main- February 1, 2004), showed that recon- there are still computational and other stream and already paying provocative div- structing the genomes of dominant popu- bottlenecks to be addressed, such as the idends according to a Q&A by the DOE JGI lations from the environment was feasible high percentage of uncharacterized genes Microbial Ecology Program head Philip and that the imprints of evolutionary selec- emerging from metagenomic studies.” Hugenholtz and MIT researcher Gene tion could be discerned in these genomes. In the Nature piece, Hugenholtz and Tyson, published in the September 25 Since this pioneering work, DOE JGI has Tyson go on to cite the emergence of edition of the journal Nature. gone on to characterize many other next-generation sequencing technologies “By employing the techniques of metagenomes with other newly selected which are already creating a deluge of metagenomics we can go beyond the targets in the sequencing queue at the data that has outstripped the computa- identification of specific players to creat- Walnut Creek, California Production tional power available to cope with it. ing an inventory of the genes in that envi- Genomics Facility. These range from the “Nevertheless, it’s not necessary to ronment,” says Hugenholtz. “We find that hindguts of termites, to plumb for microbes compare all the data to glean useful bio- genes occurring more frequently in a par- producing cellulose-degrading enzymes, logical insights,” Hugenholtz says. “What ticular community seem to confer attributes likewise to microbial communities in the we can capture will help steer the direction notable publications beneficial for maintenance of the function cow rumen, foregut of the Tammar toward a relevant data subset to investi- of that particular ecological niche.” Wallaby, and the crop of the Hoatzin, the gate. At least with metagenomics, we have Hugenholtz and Tyson were part of the Amazon stinkbird. An audio podcast, which the environmental genetic blueprints await- team assembled by University of includes an interview with Hugenholtz, can ing our interpretation. We are still far from California, Berkeley geochemist Jillian be found at: nature.edgeboss.net/down- capturing and characterizing the dazzling Banfield to investigate microbial communi- load/nature/nature/podcast/v455/n7212 diversity of the microbial life on earth— ties associated with the acid mine /nature-2008-09-25.mp3?ewk13=1. but at least we have hit upon the gold drainage of Iron Mountain in far Northern Responding to the steadily increasing standard for scratching the surface.”

JGI Bras del Port saltern Acid mine Phosphorus-removing Mediterranean drainage biofilm bioreactors Sea Nine biomes JGI Human gut Sargasso Sea JGI JGI Whale fall; viriome Soils Gutless worm JGI Guerrero Marine viral Drinking Eel river sediments Minnesota Soudan microbiome Termite gut Negro community water (anaerobic methane farm soil Mine Mouse gut microbiome hypersaline oxidizers) Human gut microbiome mat viriome Jan 03 Aug 03 Mar 04 Oct 04 Apr 05 Nov 05 May 06 Dec 06 Jun 06 Jan 08 Aug 08

Marine RNA JGI JGI Coral Coral viriome Neanderthal Human faeces Pleistocene cave holobiont reef viral community bear fossils microbiome Hawaii Ocean Mammoth Oceanic Global Ocean Human gut Time Series fossil viriomes Sampling microbiome the PRIMER / 9

Fall 2008 Vol. 5, Issue 2

Lancelet Genome Shows How Genes Quadrupled During Vertebrate Evolution

BY ROBERT SANDERS, UC BERKELEY MEDIA Instead, the Human Genome Project University of RELATIONS found that humans today have only 20,000 California, Berkeley’s The newly sequenced genome of a dainty, to 25,000 genes, which means that, if our Center for Integrative quill-like sea creature called a lancelet ancestors’ primitive genome doubled and Genomics and pro- provides the best evidence yet that verte- redoubled, most of the duplicate copies of gram head for com- brates evolved over the past 550 million genes must have been lost. An analysis putational genomics years through a four-fold duplication of the of the lancelet—or amphioxus—genome, at the DOE JGI. genes of more primitive ancestors. being published in the June 19 issue of Rokhsar and post- The late geneticist Susumu Ohno Nature, shows this to be the case. doctoral fellow Nicholas H. Putnam per- argued in 1970 that gene duplication was “Amphioxus and humans had a com- formed the genome-wide analyses of the the most important force in the evolution mon ancestor 550 million years ago, which amphioxus genome sequenced by JGI and of higher organisms, and Ohno’s theory allows us to use amphioxus as a surrogate are lead authors of the Nature paper. was the basis for original estimates that for that ancestor in terms of understanding For more information, visit: berkeley. the human genome must contain up to how vertebrate genomes evolved,” says edu/news/media/releases/2008/06/ 100,000 distinct genes. Daniel S. Rokhsar, a faculty member in the 18_lancelet.shtml

IMG Upgraded cont. from page 2 were the subject of recently published analysis and annotation using specific Laboratory (LBNL) Biological Data Manage- studies. These include the metagenomic microbial genomes in the comparative con- ment and Technology Center (BDMTC). and functional analysis of a microbial com- text of all the genomes available in IMG An additional resource, IMG/ACT, munity from Lake Washington in Seattle (www.jgi.doe.gov/education/genomeanno- provides support for managing student (Nature Biotechnology, August 2008), a tation.html). classes and assignments, as well as for hypersaline microbial mat (Molecular “IMG/EDU will serve as the core of a sharing teaching materials and guiding Systems Biology, June 3, 2008), and the web-based portal that enables undergradu- students in their study of gene calls and airborne metagenome in an indoor urban ates to participate in microbial genome functional annotations (jgi.doe.gov/ environment (PLoS One, April 2, 2008). annotation,” says Cheryl Kerfeld, head of education/annotation_tools.html). “The IMG/M system is the most com- DOE JGI’s Education Program. “Currently, IMG/ACT was developed and imple- notable publications prehensive and constantly evolving resource students at 12 schools nationally are mented by the JGI Scientific and Institutional for analyzing metagenomic data, offering using the portal in their molecular biology, Application Group’s Anthony Kosky, Rene an array of valuable analysis tools in con- genetics, microbiology, and biochemistry Perrier, David Hays, Joni Fazo, Leila junction with links to major public data- courses in which they examine gene calls Hornick, Kristen Taylor, Mike Brodhead, bases,” says Nature Biotechnology paper and annotate genes and biochemical path- as well as the JGI Education Program’s author Ludmila Chistoserdova, a microbi- ways. By helping to build curated genomes Kerfeld and Edwin Kim, with input from ologist at the University of Washington. with researchers across the globe, under- the 12 faculty members nationwide who “While very powerful, the system is user- graduates will discover the concepts and are participating in the pilot. friendly and intuitive, a true ‘one-stop- applications of bioinformatics using IMG (img.jgi.doe.gov), IMG/M shop’ for metagenomics researchers.” IMG/EDU.” (img.jgi.doe.gov/m), and IMG/EDU More details on IMG/M are available at: IMG/EDU was developed and imple- (img.jgi.doe.gov/edu) are the result of a img.jgi.doe.gov/img_mw_v241/doc/ mented by Nikos Kyrpides, Natalia Ivanova, collaboration between the DOE JGI and releaseNotes.pdf. Kostas Mavrommatis of the JGI Genome BDMTC. A special version of IMG, IMG/EDU, has Biology Group and Victor Markowitz, Amy For more information on the Microbial been established to support DOE JGI’s Chen, Ken Chu, Krishna Palaniappan, Genomics & Metagenomics (MGM) Education Program in Microbial Genome Ernest Szeto, Yuri Grechkin, and Anna Workshop, go to: www.jgi.doe.gov/ Annotation for teaching microbial genome Ratner of the Lawrence Berkeley National meetings/mgm/index.html 10 / the PRIMER

Fall 2008 Vol. 5, Issue 2

Genome of Simplest Animal Reveals Ancient Lineage, Confounding Array of Complex Capabilities

As Aesop said, appearances are genome of Trichoplax (literally “hairy-plate”) itively place the organism’s evolutionary deceiving—even in life’s tiniest critters. illuminates its ancestral relationship to position. “The latest and most complex From its discovery in the 1880s, clinging other animals. However, despite the find- analysis again suggests that placozoans to the sides of an aquarium, to its recent ing, Trichoplax is the sole member of the populated the oceans long before sponges characterization by the DOE JGI, placozoan (“tablet,” or “flat” animal) phy- evolved,” says Bernd Schierwater, director Trichoplax adhaerens, a simple and primi- lum whose relationship to other animals, of the Institute of Animal Ecology & Cell tive animal, appears to harbor a far more such as bilaterians (such as humans, Biology and head of the Center for complex suite of capabilities than meets flies, worms, and snails) and cnidarians Biodiversity at TiHo Hannover, Germany. the eye. In a paper in the August 21 (such as jellyfish, sea anemones, and Schierwater, a study co-author, joined online edition of the journal Nature, a corals), and sponges is contentious. Stephen Dellaporta and Leo Buss of Yale team of scientists establishes this organ- Earlier mitochondrial DNA studies sug- University in proposing the Trichoplax ism as a branching point of animal evolu- gested that this “mother of all metazoans,” sequencing project in 2004 to DOE JGI’s tion and identifies a set of its genes, or a Trichoplax, was the earliest branch, before Community Sequencing Program. “parts list,” that has evolved along partic- sponges diverged, but this remains debat- “The outcome of the Trichoplax ular branches of the tree of life. able—even among collaborators. adhaerens genome sequencing is so “Our whole genome analysis supports exciting that we are now culturing another placing the placozoans after the sponge A Simple Yet Complex Organism 13 placozoan species in order to identify lineage branched from other animals,” says Originally collected from the Red Sea, the most basal placozoan lineage and Daniel Rokhsar, the paper’s senior author. and cultured over the last 40 years in the genome,” says Schierwater. Rokhsar is head of DOE JGI’s Computational laboratory, Trichoplax is a two-millimeter Trichoplax has no neurons, but has Genomics Program and Professor of flat disk containing fluid sandwiched many genes that are associated with neu- Genetics, Genomics, and Development at between two cell layers. It lacks organs ral function in more complex animals. “It the University of California, Berkeley. and has only four or five cell types. Yet, lacks a nervous system, but it still is able The analysis of the 98 million base-pair despite its apparent simplicity, its genome to respond to environmental stimuli,” encodes a panoply of signaling genes and explains Rokhsar. “It has genes, such as Dan Rokhsar and transcription factors usually associated ion channels and receptors, that we asso- Mansi Srivastava co- notable publicati authored a paper in with more complex animals. ciate with neuronal functions, but no neu- Nature on Trichoplax, “Trichoplax has had just as much time rons have ever been reported.” an organism identi- to evolve as humans, but because of its fied as a branching morphological simplicity, it is tempting to Not So Distant From the Human point on the think of it as a surrogate for an early ani- Genome tree of life. mal,” says Mansi Srivastava, the study’s Of the 11,514 genes identified in the first author and a graduate student under six chromosomes of Trichoplax, 80 percent the direction of Rokhsar at the Center for are shared with cnidarians and bilaterians. Integrative Genomics, U.C. Berkeley. Trichoplax also shares more than 80 per- “Trichoplax is an ancient lineage—a cent of its introns—the regions within genes good representation of the ancestral that are not translated into proteins—with genome that is shedding light on the humans. Even the arrangement of genes kinds of genes, the structures of genes, is conserved between the Trichoplax and and even how these genes were arranged human genomes. This stands in contrast on the genome in the common ancestor to other model systems such as fruit flies 600 million years ago,” says Srivastava. and soil nematodes that have experi- “It has retained a lot of primitive fea- enced a paring down of non-coding regions tures relative to other living animals.” and a loss of the ancestral genome Further research is underway to defin- organizations. cont. on page 14 the PRIMER / 11

Fall 2008 Vol. 5, Issue 2

Other Notable Recent JGI Publications

Genome sequencing and analysis of the Trichoderma reesei is the main industri- Human-specific gain of function in a biomass-degrading fungus Trichoderma al source of cellulases and hemicellulases developmental enhancer reesei (syn. Hypocrea jecorina) used to depolymerize biomass to simple Science September 5, 2008, Vol. 321 Nature Biotechnology May 2008, Vol. 26 sugars that are converted to chemical No. 5894, pp. 1346-50 No. 5, pp. 553-60 intermediates and biofuels, such as Prabhakar S, Visel A, Akiyama JA, Martinez D, Berka RM, Henrissat B, ethanol. Unexpectedly, considering the Shoukry M, Lewis KD, Holt A, Plajzer- Saloheimo M, Arvas M, industrial utility and effective- Frick I, Morrison H, Fitzpatrick DR, Afzal Baker SE, Chapman J, ness of the carbohydrate- V, Pennacchio LA, Rubin EM, Noonan JP. Chertkov O, Coutinho PM, active enzymes of T. reesei, Changes in gene regulation are thought Cullen D, Danchin EG, its genome encodes fewer to have contributed to the evolution of Grigoriev IV, Harris P, cellulases and hemicellu- human development. However, in vivo Jackson M, Kubicek CP, lases than any other evidence for uniquely human develop- Han CS, Ho I, Larrondo LF, sequenced fungus able to mental regulatory function has remained de Leon AL, Magnuson JK, hydrolyze plant cell wall poly- elusive. In transgenic mice, a conserved Merino S, Misra M, Nelson saccharides. Our analysis, noncoding sequence (HACNS1) that B, Putnam N, Robbertse B, Salamov AA, coupled with the genome sequence data, evolved extremely rapidly in humans Schmoll M, Terry A, Thayer N, provides a roadmap for constructing acted as an enhancer of gene expres- Westerholm-Parvinen A, Schoch CL, Yao enhanced T. reesei strains for industrial sion that has gained a strong limb J, Barbote R, Nelson MA, Detter C, applications such as biofuel production. expression domain relative to the orthol- Bruce D, Kuske CR, Xie G, Richardson www.nature.com/nbt/journal/v26/n5/ ogous elements from chimpanzee and P, Rokhsar DS, Lucas SM, Rubin EM, abs/nbt1403.html rhesus macaque. www.sciencemag.org/ Dunn-Coleman N, Ward M, Brettin TS. cgi/content/abstract/321/5894/1346

JGI in the News

Termite Bellies and Biofuels. Scientist Falk Warnecke's research into termite digestion may hold solutions to our energy crisis. (Published in Smithsonian, August 1, 2008, notable publications www.smithsonianmag.com/science-nature/termites-bellies- biofuels.html) Gut Reactions. The termite’s stomach, of all things, has become the focus of large-scale scientific investigations. Could the same proper- ties that make the ter- mite such a costly pest Finishing in the Future help us solve global Keynote speaker and Nobel Prize Winner Sydney Brenner warming? (Published in (right) regales JGI Deputy Director Jim Bristow (left) and JGI The Atlantic, August 20, Microbial Interactions Program head Patrick Chain with tales of 2008, www.theatlantic. genomes he has known at the Third Annual Finishing in the com/doc/200809/ter- Future meeting, which was held May 28-30, 2008 in Santa Fe, mites) New Mexico. The 2009 meeting dates are now are set for May 27-29. For more information, see www.lanl.gov/finishinginthefuture or con- Electron-micrograph image of the termite's third gut, where food is turned into fuel. tact Chris Detter, [email protected]. 12 / the PRIMER

Fall 2008 Vol. 5, Issue 2

Analysis of Lake Washington Microbes Shows the Power of Metagenomic Approaches

BY MADOLYN BOWMAN ROGERS A Microbial First: Isotope Probing Today’s powerful sequencing machines To enrich the samples for the microbes can rapidly read the genomes of entire of interest, the researchers adapted a communities of microbes, but the chal- technique called stable isotope probing. lenge is to extract meaningful information This is the first time the technique has from the jumbled reams of data. In a been used on a microbial community, paper published in Nature Biotechnology Chistoserdova says. The researchers used August 17, a collaboration headed by five different single-carbon compounds researchers at the University of Washington labeled with a heavy isotope of carbon, and the DOE JGI describes a novel approach and fed each compound to a separate for extracting single genomes and discern- sediment sample. The microbes that could ing specific microbial capabilities from mixed consume the compound incorporated the community (“metagenomic”) sequence data. labeled carbon into their DNA, Chistoserdova For the first time, using an enrichment says, while organisms that couldn’t use technique applied to microbial community The Methylamine-enriched microbe commu- the compound did not incorporate the label. nity of Lake Washington sediment features samples, the research team explored the The labeled DNA was then separated out Methylotenera cells. Photo: D. Kunkel; color, sediments in Lake Washington, located E. Latypova. and sequenced. In this way, microbial on Seattle’s eastern edge, and character- “subsamples” were produced that were ized biochemical pathways associated highly enriched for organisms that could with nitrogen cycling and methane utiliza- possibly completely novel pathways.” metabolize methane, methanol, methylat- tion, important for understanding methane Most of the microbes that oxidize sin- ed amines, formaldehyde, and formate. generation and consumption by microbes. gle-carbon compounds are unculturable The functionally enriched samples con- Methane is both a greenhouse gas and a and therefore unknown, as are the vast tained far fewer microbes than the total potential energy source. majority of microbes on Earth. To find sample, Chistoserdova says. The sample “Even if you have lots of sequences, species of interest, the researchers that was fed methylated amines was sim- for complex communities it still doesn’t sequenced microbial communities from ple enough that the research group was tell you which organism is responsible for Lake Washington sediment samples, able to extract the entire genome of a notable publications which function,” says the paper’s senior Chistoserdova says, because lake sedi- novel microbe, Methylotenera mobilis, author, Ludmila Chistoserdova, a microbi- ologist at the University of Washington. “This publication presents an approach, via simplification and targeted metage- “Even if you have lots of sequences, for complex communities it still nomic sequencing, of how you can go doesn’t tell you which organism is responsible for which function. This after the function in the environment.” publication presents an approach, via simplification and targeted Chistoserdova and colleagues study microbes that oxidize single-carbon com- metagenomic sequencing, of how you can go after the function in the pounds such as methane, methanol, and environment,” says the paper’s senior author, Ludmila Chistoserdova. methylated amines, which are compounds contributing to the greenhouse effect and are part of the global . “To utilize these single-carbon com- ment is known to be a site of high methane which normally comprises less than half a pounds, organisms employ very specialized consumption. However, these sediment percent of the community but appears to metabolism,” says Chistoserdova. “We samples contained over 5,000 species of be a first responder to methylated amines suspect that in the environment, there are microbes performing a complex, intercon- in the environment. The researchers were novel versions of this metabolism, and nected array of biochemical tasks. able to construct cont. on page 15 the PRIMER / 13

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CSP 2009 Selections cont. from page 7 ancient B. braunii communities, also com- that of cows and other ruminants. But little cellulose degradation. The annotated prise a portion of the hydrocarbon mass- instead of a rumen, stinkbirds possess a gene set of C. subvermispora and compar- es in several modern-day petroleum and crop, an enlargement of the esophagus ative analyses with the lignin degraders P. coal deposits. where the fermentation takes place—and chrysosporium and Pleurotus ostreatus While algae have been recognized for is the source of the stink. The characteri- (both sequenced by DOE JGI) will advance their role in carbon sequestration and for zation of its contents will likely lead to the the understanding of these complex oxida- biofuels production, little information, identification of novel microbial enzymes tive mechanisms involved in lignocellulose either genetic or metabolic, has been that degrade plant cell walls. conversions. This project was proposed by reported for this particular alga. This proj- The most abundant source of carbon is Dan Cullen from the University of ect, led by Andrew Koppisch and colleagues plant biomass, composed primarily of cel- Wisconsin–Madison. from Los Alamos National Laboratory and lulose, hemicellulose, and lignin. Many Other CSP projects featured in this issue five other institutions, will target the iden- microorganisms are capable of utilizing of The Primer are: predatory protists, led tification of specific metabolic pathways cellulose and hemicellulose as carbon and by Monterey Bay Aquarium Research responsible for hydrocarbon synthesis to energy sources, but a much smaller group Institute’s Alexandra Worden (page 3), the alleviate bottlenecks in biofuels production. of filamentous fungi has evolved with the Hanford Site’s subsurface microbial com- ability to depolymerize lignin, the most munities, led by Pacific Northwest National Other CSP 2009 Projects recalcitrant component of plant cell walls. Laboratory’s Allan Konopka (page 6), One metagenome project entails a Collectively known as white rot fungi, they nitrogen-fixing bacteria, with the University sampling of the foregut of Opisthocomus possess the unique ability to efficiently of Florence (page 4), and microbes frozen hoazin, or hoatzin, a leaf-eating Amazonian depolymerize lignin in order to gain access in Lake Vostok of Antarctica (page 5). pheasant-like stinkbird. The unique fermen- to cell wall carbohydrates for carbon and For the complete list of CSP 2009 tative organ of this prehistoric relic harbors energy sources. Ceriporiopsis subvermispora sequencing projects, see: www.jgi.doe.gov/ an impressive array of novel microbes, like rapidly depolymerizes lignin with relatively sequencing/cspseqplans2009.html.

Genomics of Biofuels cont. from page 1 for their desirable traits, resulting in today’s for genomics to play a significant role. genes associated with the decomposition highly productive food crops. But now, “With the data that we are generating of the most recalcitrant features of the plant given the energy and climate challenges, from plant genomes, we can home in on cell wall, lignin, the phenolic “glue” that we simply don’t have thousands of years. relevant agronomic traits such as rapid imbues the plant with structural integrity So by applying the power of genomics to growth, drought resistance, and pest tol- and pest resistance. The white rot fungus these problems, we are seeking to speed erance, as well as those that define the Phanerochaete chrysosporium produces up both the domestication of energy crops basic building blocks of the plants cell unique extracellular oxidative enzymes that and the technologies for converting them wall—cellulose, hemicellulose, and lignin. effectively degrade lignin by gaining access to suitable biofuels. The result will be a Biofuels researchers are able to take this through the protective matrix surrounding more carbon-neutral approach to meeting information and design strategies to opti- the cellulose microfibrils of plant cell walls. part of our transportation needs.” mize the plants themselves as biofuels Another fungus, the yeast Pichia stipi- In the Nature review, Rubin describes feedstocks—altering, for example, branch- tis, ferments the five-carbon “wood sugar” the processes entailed in biofuel produc- ing habit, stem thickness, and cell wall xylose abundant in hardwoods and agricul- tion from lignocellulose: the harvesting of chemistry, resulting in plants that are less tural harvest residue. Rubin says that biomass, pretreatment and saccharifica- rigid and more easily broken down.” Pichia’s recently sequenced genome has tion, which results in the deconstruction For microbial biomass breakdown, revealed insights into the metabolic path- of cell wall polymers into component sug- Rubin says that many candidates have ways responsible for this process, guiding ars, and then the conversion of those already been identified. These include efforts to optimize it in commercial pro- sugars into biofuels through fermentation. Clostridia species, for their ability to duction strains. Pathway engineering Each step, he says, offers an opportunity degrade cellulose, and fungi that express promises to produce cont. on page 15 14 / the PRIMER

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A Conversation with Alexandra Z. Worden cont. from page 3 their growth or lead to one group being some of them, we also don’t know what are some indications that in the north more abundant than another, we might be they do. But they have the power to give Pacific there have been major shifts in the able to develop models that could predict us insights into mechanisms of control, photosynthetic community in the last 50 a range of possible future scenarios, with, and understanding the mechanisms is years. That’s of huge concern, given that we say, a 1° C temperature change in the really the only way we can develop more don’t know the drivers or consequences system. This would help in appropriate predictive capabilities. for marine life or climate regulation. Given decision making, which, given the current We’re in a high level of urgency for fig- that the oceans are 75 percent of the globe,

CO2 situation, is really needed. uring out fundamental aspects of commu- and given that they drive what we breathe Q. What are some of the challenges of nity and carbon dynamics. I went into this (both in a geological sense and in their this project? wanting to help the environment, and I am role regulating the modern atmosphere), A. After sequencing the genome, we daunted at this stage. Things are changing it’s a pretty big hole in our knowledge. have this unassembled, fragmented blue- so fast, people are proposing scientifically Nevertheless I do feel hopeful. Look at print, a list of parts. We don’t know which unfounded quick fixes, and we’re still at where medicine was 100 years ago and of those parts are important, and for such a basic level of understanding. There where it is now. They did that without the tremendous computational power we have today. In the marine world, we start with Trichoplax, a Simple and Ancient Animal cont. from page 10 that tremendous power. There’s a lot we can figure out if we get enough minds sion (pulling itself into pieces), it may in thinking about the issues at hand. fact have a secret sex life. Q. How has the collaboration with JGI “Some of our new placozoan species helped advance your research? show frequent sexual reproduction while A. It’s an amazing resource. JGI is fab- others never show any signs of sex,” says ulous at sequencing and assembling Schierwater. “The genome data allow us genomes. They’re also now tackling some to search for the genes responsible for of these much larger plant genomes and sex and life cycle complexity.” the untapped diversity of unicellular Adds Rokhsar: “It’s remarkable eukaryotic life. The challenge ahead lies that we have the whole genome in the data analysis—for example, model- sequence, but we still know so lit- ing the genes accurately and annotation. tle about this animal in the wild. Q. What are the personal rewards of Hopefully the genome sequence will your work, and what is its value to stimulate more studies of this society? enigmatic creature.” A. Genomes serve as tools for doing Other authors include DOE JGI’s ecological studies, so getting these tools Jarrod Chapman, Nicholas Putnam, Uffe out to a broader community, in a high- Hellsten, Alan Kuo, Asaf Salamov, Harris quality, annotated format that enables the Shapiro, and Igor Grigoriev; Jane Grimwood scientific community to go from there, is A bright-field high magnification image of and Jeremy Schmutz of the Stanford one reward. Bigger-picture reward, I would Trichoplax adhaerens captured by Nature paper author Ana Signorovitch, Yale Human Genome Center and DOE JGI; Emina love to participate in developing predictive University. Begovic, Therese Mitros, and Meredith carbon cycling models. Carpenter of U.C. Berkeley; Takeshi More broadly, for society, I think we With its pancake shape, gutless feed- Kawashima of the Okinawa Institute of could do preventative medicine in the ing, and genomic primitiveness, the rich Science and Technology; Ana Signorovitch, oceans if we understood the system a little array of metabolic capabilities begs addi- and Maria Moreno, Leo Buss, and Stephen better. So this work has tremendous value tional consideration. While it has been Dellaporta of Yale University; and Kai for advancing a preventative approach for observed to motor around via cilia, eat by Kamm the University of Veterinary the ways humans interact with the envi- mounting its prey, and reproduce by fis- Medicine Hannover, Germany. ronment both on land and in the sea. the PRIMER / 15

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Lake Washington Microbes cont. from page 12 much of M. mobilis’ biochemistry and pre- oped a new quality-control approach that Health, who was not involved in the study, dict that it is also involved in nitrogen involves using a computer tool called LUCY said in an email that the paper describes cycling, demonstrating the utility of to trim out low-quality sequences in combi- “an interesting novel approach” and the metagenomic analysis. nation with the Paracel Genome Assembler, results “constitute a significant advance in which appeared to be more appropriate for the emerging discipline of metagenomics.” A Pioneering New Technique for metagenomic assemblies. This approach “I think other people can use the same Metagenomic Assemblies was pioneered on the Lake Washington approach in different environments, as The DOE JGI performed the sequencing project, Lapidus says, and due to its supe- long as they have an enrichment tech- and assembly of these complex metage- rior results it is now the standard metage- nique,” Chistoserdova says. “For us this nomic data sets. The complexity of the nomic assembly method at the DOE JGI. work is just the beginning because now community’s sequence samples created “The DOE JGI’s unique Integrated we will be using this metagenomic new challenges for genome assembly. “It Microbial Genomics with Microbiome sequence as a scaffold for downstream is very important for metagenomic assem- Samples (IMG/M) [img.jgi.doe.gov/m] experiments in our lake.” blies to rely on high-quality reads,” says data-management system was used for Other authors include DOE JGI’s Natalia Alla Lapidus, microbial geneticist at the detailed annotation, and was instrumental Ivanova, Alex Copeland, Asaf Salamov, DOE JGI and co-author of the paper. If for efficient comparative analysis and Igor Grigoriev, Susannah Tringe, David some of the sequence is of low quality, metabolic reconstruction of the samples,” Bruce (Los Alamos National Laboratory), she says, it can lead to errors in assem- Lapidus says. and Paul Richardson; and Ernest Szeto bly and gene annotation. Michael Galperin, a microbial geneticist and Victor Markowitz of the Data Because of the need for higher quality at the National Center for Biotechnology Management and Technology Center at control, Lapidus says, the DOE JGI devel- Information at the National Institutes of Lawrence Berkeley National Laboratory.

Genomics of Biofuels cont. from page 13 a wider variety of organisms able to ferment ture, the metabolic profile of organisms degraders,” and “fuel producers” complet- the full repertoire of sugars derived from residing in an environmental sample—for ed or in progress. These include the first cellulose and hemicellulose and tolerate the identification of enzymes suitable for tree genome completed—that of the poplar higher ethanol concentrations to optimize industrial-scale biofuel production. Populus trichocarpa—and other plants in fuel yields. “Using this prospecting technique, we the sequencing queue, such as soybean, Rubin also touches on the emerging can survey the vast microbial biodiversity switchgrass, sorghum, eucalyptus, cassava, technology of metagenomics—characteriz- to gain a better picture of the metabolic and foxtail millet. In addition, Rubin points ing, without the need for laboratory cul- potential of genes and how they can be to oil-producing algae as an alternative enlisted for the enzymatic deconstruction source for biodiesel production; the alga of biomass and subsequent conversion to Chlamydomonas reinhardtii is just one of high-energy-value fuels,” he says. several algal species that has been char- As an example, Rubin cites an analysis acterized for their ability to efficiently cap- of the hindgut contents of nature’s own ture and convert sunlight into energy. bioreactor, the termite, which has yielded “Given the daunting magnitude of fossil more than 500 genes related to the enzy- fuel used for transportation, we will likely matic deconstruction of cellulose and have to draw from several different sources hemicellulose (published in Nature to make an appreciable impact with cellu- 450:560-565, November 22, 2007). losic biofuels, all of which will, in some The Nature review goes on to list the significant way, be informed by genomics,” feedstock genomes, microbial “biomass says Rubin.

JGI Director Eddy Rubin is leading an effort, supported by the Energy Biosciences Institute, to identify enzymes produced by the abundant microbes in the rumen of forage-feeding ani- mals that can potentially be adapted for cellulosic biomass conversion to biofuel. 16 / the PRIMER

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Genomics Garden JGI Planning Retreat JGI Operations Manager Ray Turner inspects the bountiful first harvest from the Production Genomics Facility’s bioenergy feedstock garden. The bulk of the Zea mays (corn, shown here) crop was enjoyed by the indigenous ground squirrel population, while the nearby Miscanthus and switchgrass stands were left untouched. The DOE Joint Genome Institute convened a planning retreat on August 27-29, 2008 in Pacifica, California, to jumpstart a strategic plan that will guide JGI’s path forward over the next five years. Evening presentations included those from Steven Beckwith, University of California Vice President for Research and Graduate Studies, and James Siegrist, Lawrence Berkeley National Laboratory Associate Laboratory Director for General Sciences (not pictured). Other participants (pictured) were from LANL, LLNL, NIH, ORNL, PNNL, HudsonAlpha, and DOE, and several other organizations.

Poplar Watch In September, this poplar, or black cot- tonwood, measured here by JGI Instrumentation Engineer Steven Wilson, reached 20’ 8” (630 cm), or nearly five times its height at planting. The tree was planted two years ago in commemo- ration of the publication in the journal Science of JGI-led research on the JGI User Meeting genome of the Populus trichocarpa, the first complete DNA sequence of a tree. SAVE THE DATE march 25-27, 2009

CSO 15510 Contact The Primer David Gilbert, Editor / [email protected] / (925) 296-5643