Organisms in the Program

Sequencing Microbial Genomes to Uncover Potential Applications Relevant to DOE Missions

Draft sequence by the DOE Joint Genome Institute.
New microbes being sequenced by JGI.
§Sequenced by The Institute for Genomic Research.
*Completed and published (see
**Completed, not published (as of February 25, 2005).

Carbon Sequestration

Aureococcus anophagefferens (algae, ~32 Mb): Brown tide-forming pelagophyte, forms coastal blooms, reduces trace metals; can sequester substantial amounts of carbon.

Azotobacter vinelandii AvOP (bacteria, 4.5 Mb): Aerobic, fixes nitrogen; found in soils worldwide; has nitrogenases incorporating molybdenum and vanadium (in addition to iron); relevant to energy use and carbon sequestration.

Bradyrhizobium sp. strain BTAi (bacteria, 9.2 Mb): Versatile photosynthetic; carbon dioxide- and nitrogen-fixing symbiont of legumes; nodule-forming on roots and stems; aids plant in carbon processing.

Calyptogena magnifica (clam) proteobacterial symbiont (bacteria, est. ~ 4 Mb): Isolated from deep sea vents, sulfur oxidizing, nitrogen fixing; fixes carbon dioxide via possibly novel pathway; carbon sequestration.

Chlamydomonas reinhardtii (eukaryotes, ~100 Mb): Green alga, photosynthetic, widespread in environment, 17 chromosomes, widely used model system.

Photosynthetic Green Sulfur Bacteria
Sequester carbon via photosynthesis; produce hydrogen when cocultured with sulfate-reducing bacteria.

Chlorobium limicola DSMZ 245(T) (2.4 Mb): Nonmotile, rod shaped; type strain for all green sulfur bacteria.

Chlorobium phaeobacteroides DSMZ 266T (~2.2 Mb): Rod shaped; does not use nitrogen or sulfide.

Chlorobium phaeobacteroides MN1 Black Sea (2.2 Mb): Photosynthetic in very low light, with chlorophylls that absorb 1 photon every 5 hours.

*Chlorobium tepidum (bacteria, 2.1 Mb): Photosynthetic; may play important role in earth’s overall carbon cycle.

 Chlorobium vibrioforme f. thiosulfatophilum DSMZ 265(T) (2.5 Mb): Curved rod shape.

Chloroflexus aurantiacus J-10-fl (3 Mb): Modern version of organism; needs no oxygen for photosynthesis; uses unique pathway to fix carbon dioxide.

Chloroherpeton thalassium (~3 to 3.5 Mb): Most taxonomically divergent of green sulfur bacteria.

Chloroflexi Bacteria, 7 Strains, est. ~5 Mb each
Gram-negative, filamentous anoxygenic phototrophs; useful in carbon sequestration, biofuels.

Candidatus Chlorothrix halophila: Marine and hypersaline biofilms; produces bacterial chlorophylls (BChl) a and c and chlorosomes.

Chloroflexus aggregans DSMZ 9485: Motile, grows at 55°C in both light and dark.

Chloronema sp. strain UdG9001: Motile, photoautotrophic; isolated from Little Long Lake, Wis.; grows in iron-rich environments.

Heliothrix oregonensis: Bright orange colored, motile; grows optimally at 45° to 55°C; forms monolayers on top of microbial biofilms.

Herpetosiphon aurantiacus DSM 785: Orange colored, isolated from Birch Lake, Minn.; hydrolyzes starch, does not produce BChls.

Roseiflexus castenholzii DSM 13941: Motile, red to reddish-brown colored; has BChl-a but not BChl-c or chlorosomes.

Roseiflexus sp. strain RS-1: Isolated from high-temperature biofilms in Octopus Spring, Yellowstone.

§ Colwellia 34H (bacteria, 5.3 Mb): Psychrophile, important in carbon and nutrient cycling in polar marine environments.

Crocosphaera watsonii WH8501 (cyanobacteria, 3.6 to 5 Mb): Marine, unicellular; confined to waters from 26 to 32ºC; temporally segregates carbon-dioxide fixation from nitrogen fixation.

Emiliania huxleyi 1516 (marine algae, ~5 Mb): Marine coccolithophorids; plays role in global carbon cycling and sulfur transformation.

Frankia Cc13 (bacteria, ~8 to 10 Mb): Actinomycetes, Group II, fixes nitrogen; forms major nitrogen-fixing symbiosis in temperate soils; promotes formation of woody-biomass energy source.

Frankia sp. EAN1pec (bacteria, ~10 Mb): Group III, ubiquitous, fixes nitrogen, forming major nitrogen-fixing symbiosis in temperate soils; promotes formation of woody-biomass energy source; grows well, shows metal resistance.

Jannaschina sp. CCS1 (bacteria, 4.5 to 5 Mb): Member of Roseobacter clade; contributes to oceanic anoxygenic phototrophy, a mode of light-driven energy acquisition.

Micromonas pusilla ssp. Eukarya: 2 strains, ~15Mb each
Abundant in oceans, very small (1 to 3 microns in length); significant planktonic primary producers (carbon-dioxide fixers) in size class; carbon sequestration.

M. pusilla NOUM17(RCC 299): Equatorial Pacific isolate.

M. pusilla CCMP490(RCC 114): U.S.A. East Coast isolate.

Moorella thermoacetica ATCC39073 (bacteria): Fixes carbon dioxide in absence of oxygen; can grow on hydrogen, carbon dioxide, or carbon monoxide as sole carbon source; acetogenic.

Bacteria Involved in Nitrification Affecting Climate Change
Oxidize ammonia; can degrade chlorinated aliphatic hydrocarbons; give insight into basis of biogeochemical nitrogen cycle.

Nitrobacter hamburgensis (~3 Mb): Found in soil; model organism for biochemical, structural, and molecular investigations; has carboxysomes.

Nitrobacter winogradskyi Nb-255 (~3 Mb): Widely distributed, also nitrite oxidizing; can grow with several metabolic modes and anoxically by denitrification; can fix carbon dioxide.

Nitrosococcus oceani (~3 Mb): Gamma proteobacterium that oxidizes ammonia (others are beta proteobacteria).

*Nitrosomonas europaea ATCC19718 (2.2 Mb): Aids incorporation of carbon dioxide into biomass.

Nitrosomonas eutropha (~3 Mb): Physiologically diverse; can oxidize nitrous oxide while reducing either ammonia or hydrogen; important in wastewater treatment systems; potential for remediation of high ammonia concentrations in waters.

Nitrosospira multiformis Surinam (~3Mb): Well-studied, typical of those seen in soil environments.

**Nostoc punctiforme ATCC29133 (bacteria, 10 Mb): Fixes carbon dioxide and nitrogen; produces hydrogen; survives acidic, anaerobic, and low-temperature conditions.

Ostreococcus (eukaryotes, est. 8 to 10 Mb): Fast-growing, ubiquitous; important in marine carbon fixation.

Pelodictyon luteolum DSMZ 273(T) (bacteria, 3.0 Mb): Rod-shaped photosynthetic GSB cells that can form yellow-green hollow microcolonies.

Pelodictyon phaeoclathratiforme BU-1, DSMZ 5477 (bacteria, 3 Mb): Gas vesicle containing green sulfur bacterium cells that can form 3D net-like microcolonies.

**Prochlorococcus isolate NATL2 (prokaryotes, 1.7 to 2.4 Mb): Ocean carbon sequestration.

*Prochlorococcus marinus MED4 (bacteria, 1.7 Mb), *Prochlorococcus marinus MIT9313 (bacteria, 2.4 Mb), and **Prochlorococcus marinus MIT9312 (bacteria, ~2.4 Mb): All ecotypes abundant in temperate and tropical oceans; important in ocean carbon cycling; absorb blue light efficiently; MIT9313 is adapted to lower-light conditions (lower ocean depths) and MIT9312 to higher-light conditions nearer the surface.

Prosthecochloris aestuarii SK413, DSMZ 271(t) (bacteria, 2.5 Mb): Nonmotile, spherical to ovoid green sulfur bacteria; nitrogen-fixing marine strain; high salt requirement.

Rhodopseudomonas palustris Bacteria: 5 strains, ~5.5 Mb each
Metabolically versatile, can produce hydrogen, fix carbon dioxide, biodegrade organic pollutants and plant biomass; biofuels.

R. palustris BisA53: Isolated from Dutch site; grows well on benzoate, tends to aggregate.

R. palustris BisB5: Isolated from Dutch contaminated site; smaller, more motile form; fewer rosettes than sequenced CGA009.

R. palustris BisB18: Isolated from Dutch site; slower growing than CGA009.

**R. palustris CGA0009: Biodegrades under both aerobic and anaerobic conditions.

R. palustris HaA2: Unable to grow on benzoate; isolated from Haren site.

**Rhodospirillum rubrum ATCC11170 (bacteria, 3.4 Mb): Phototrophic; grows in various conditions, including aerobic and anaerobic; fixes nitrogen, grows on hydrogen; model for photosynthesis.

Roseobacter strain TM1040 (bacteria, ~4.5 Mb each): Isolated from dinoflagellate; fixes carbon in marine surroundings.

Sphingopyxis alaskensis RB2256 (bacteria, 3.2 Mb): Makes up large proportion of oceanic biomass; major contributor to global carbon flux; can bioconcentrate trace metals.

**Synechococcus elongates PCC7 942 (cyanobacteria, 2.4 to 2.7 Mb): Carbon fixation; photosynthesis in fresh waters.

Synechococcus sp. C9902 (coastal) and Cc9605 (oligotrophic) (bacteria, ~2.4 Mb each): Fixes carbon dioxide; globally distributed; important in carbon fluxes in marine environment.

*Synechococcus WH8102 (bacteria, 2.4 Mb): Photosynthetic; important to ocean carbon fixation; genetically tractable.

Thalassiosira pseudonana (eukarya, ~25 Mb): Ocean diatom, major participant in biological “pumping” of carbon to ocean depths.

**Thiobacillus denitrificans ATCC23644 (bacteria, ~2 Mb): Fixes carbon; oxidizes sulfur and iron; involved in bioremediation.

Thiomicrospira crunogena (bacteria, 2 Mb): Marine gamma proteobacterium isolated from East Pacific; found in deep sea vents; grows rapidly (doubling time, ~ 1 hour); carbon-concentrating mechanism similar to cyanobacteria; sulfur oxidizing; fixes carbon dioxide; can grow in low to absent oxygen conditions; desulfurylates coal; strips sour gas (hydrogen sulfide) from petroleum.

Thiomicrospira denitrificans (~1.6 Mb): Marine epsilon proteo-bacterium found in hydrothermal vents but also in oxygen-containing, anoxic ocean-transition regions; uses reverse TCA cycle for carbon fixation; sulfur oxidizing; fixes CO2; can grow in low to absent oxygen conditions; desulfurylates coal; strips sour gas (HS) from petroleum.

Trichodesmium erythraeum IMS101 (bacteria, 6.5 Mb): Key nitrogen- fixing microbe; plays major role in tropical and subtropical oceans.

Energy Production

**Anabaena variabilis ATCC29413 (cyanobacteria, 7 to 10 Mb): Filamentous heterocyst-forming; fixes nitrogen and carbon dioxide; produces hydrogen.

Caldicellulosiruptor saccharolyticus (bacteria, 4.3 Mb): Versatile biomass-degrading, hydrogen-producing thermophile; biofuels.

§ Carboxydothermus hydrogenoformans (bacteria, 2.10 Mb): Gram positive; converts carbon monoxide and water to carbon dioxide and hydrogen.

Clostridium phytofermentans (bacteria, ~5 Mb): Degrades plant polymer cellulose, pectin, starch, and xylan to produce ethanol and hydrogen.

Clostridium beijerinckii NCIMB 8052 (bacteria, 6.7 Mb): Produces solvent; converts biomass to fuels and chemicals; potential for alternate energy production.

*Methanobacterium thermoautotrophicum Delta H (archaea, 1.7 Mb): Produces methane; plays role in earth’s overall carbon cycle.

Methanococcoides burtonii DSM6242 (archaea, 3 Mb): Extremophile adapted to cold (less than 5°C); produces methane.

*Methanococcus jannaschii DSM2661 (archaea extremophile, 1.7 Mb): May identify high-temperature, high-pressure enzymes; produces methane.

Methanosaeta thermophila PT(DSM6194) (archaea, ~ 3Mb): Widely distributed in environment; metabolizes acetates into methane; potential producer of biofuel.

Methanosarcina barkeri Fusaro (archaea, 2.8 Mb): Lives in cattle rumen; digests cellulose and other polysaccharides to produce methane; very oxygen sensitive; grows in variety of substrates.

Methanospirillum hungateii JF1 (bacteria, 2.8 Mb): Methanogen; system for studying multispecies microbial assemblage composed of metabolically diverse microorganisms functioning as a single catalytic unit.

Methylobacillus flagellatus KT (proteobacteria, 3.1 Mb): Bioremediation; cycling of one-C compounds; environmentally benign bioprocessing into feedstocks.

Pichia stipitis CBS 6054 (fungi, 12 Mb): Ferments xylose to ethanol; potential to oxidize products of lignin degradation and play a role in cellulose degradation as endosymbiont of beetles; converts biomass to ethanol.

Syntrophomonas wolfei Göttingen DSM 2245B (bacteria, 4.5 Mb): Methanogenic and syntrophic; potential hydrogen producers; useful in bioremediation; system for studying multispecies microbial assemblage of metabolically diverse microorganisms functioning as single catalytic unit.

Syntrophobacter fumaroxidans MPOB (bacteria, 3.3 Mb): Methanogenic proprionate oxidizer; uses fumarate as electron acceptor; can produce hydrogen and formate; syntrophic (i.e., part of bacteria community).

§ Thermotoga neopolitana ATCC49045 (bacteria, ~1.8 Mb): Combines with oxygen to produce hydrogen.


Acidiphilium cryptum JF 5 (bacteria, 2.46 Mb): Reduces iron and iron oxides in very acid conditions (pH 2.2 to 5); possible bioremediation of metals in acid environments.

Acidithiobacillus ferrooxidans (bacteria, 2.9 Mb): Used in mining industry to sequester iron and sulfide.

Acidobacterium sp. (bacteria, two Group 1 strains, one Group 3 strain, est. ~4 Mb each): Ubiquitous in soil, including those contaminated with chromium, zinc, other metals, and PCBs.

Alkaliphillus metalliredigenes (bacteria, ~4 Mb): Reduces iron, other metals, uranium under alkaline conditions (optimal growth, pH 9.6).

Anaeromyxobacter delahogenans 2CP-C (bacteria, 3.38 Mb): Reduces metal (iron, uranium, others); degrades aromatic and halogenated hydrocarbons.

Arthrobacter sp. strain FB24 (bacteria, ~2.4 Mb): Resists metal (reduces chromium, lead); degrades hydrocarbon; resists radiation; widely distributed in soils.

Burkholderia ambifaria (bacteria, 4.7 Mb): Genomovar VII; smallest Burkholderia genome, biocontrol agent.

Burkholderia ambifaria AMMD (bacteria, ~ 7.2 Mb): Ubiquitous rhizosphere colonizer and member of the Burkholderia cepacia complex; nitrogen fixer, organic-pollutant degrader; bioremediation.

Burkholderia xenovorans (formerly Burkholderia fungorum) LB400 (bacteria, 8 Mb): Outstanding degrader of polychlorinated biphenyls (PCBs).

Burkholderia vietnamiensis G4 (bacteria, ~8 to 10 Mb): Genomovar V; degrades trichloroethylene; colonizes rhizosphere.

*Caulobacter crescentus (bacteria, 4.01 Mb): Potential for heavy-metal remediation in waste-treatment plant wastewater.

Chromohalobacter salexigens DSM 3043 (formerly Halomonas elongatee) (bacteria, 4 Mb): Most-halotolerant eubacteria known; displays metal resistance; degrades aromatic hydrocarbons and toxic organics; high halotolerance, suggesting applications in extreme environments.

Dechloromonas RCB (bacteria, 2 Mb): Oxidizes iron. Converts perchlorate to chloride; anaerobically oxidizes benzene to carbon dioxide.

*Dehalococcoides ethenogenes (bacteria, 1.5 Mb): Degrades dangerous solvent trichloroethene to benign products.

Dehalococcoides sp. strain BAV1 (bacteria, 2 Mb): Detoxifies many dichloroethene isomers; potential for bioremediating organic-compound contamination; isolated from Michigan site.

Dehalococcoides sp. strain VS (bacteria, 1.5 Mb): Detoxifies many dichloroethene isomers; potential for bioremediation of organic-compound-contaminated sites, isolated from site in Texas.

Deinococcus geothermalis DSM11300 (bacteria, ~3 Mb): Resists radiation; can bioremediate radioactive mixed waste at temperatures up to 55° C.

*Deinococcus radiodurans R1 (bacteria, 3 Mb): Survives extremely high levels of radiation; possesses DNA-repair capabilities for radioactive waste cleanup.

Desulfitobacterium hafniense DCB-2 (bacteria, 4.6 Mb): Degrades pollutants such as chlorinated organic compounds that include some pesticides.

Desulfotomaculum reducens MI-1 (bacteria, 4 Mb): Gram-positive, spore-forming, metabolically versatile sulfate and metal (iron, manganese, uranium, chromium) reducer. Can reduce uranium and nitrate simultaneously; bioremediation.

**Desulfovibrio desulfuricans G20 (bacteria, 3.1 Mb): Anaerobic; reduces sulfate, uranium, and toxic metals; corrodes iron piping; “sours” petroleum with hydrogen sulfide.

*Desulfovibrio vulgaris Hildenborough (bacteria, 3.2 Mb): High potential for bioremediation through metal and sulfate reduction and sulfate utilization.

Desulfuromonas acetoxidans (bacteria, 4.1 Mb): Marine microbe; reduces iron; oxidizes acetate to carbon dioxide under anoxic conditions via process coupled to sulfur reduction or iron (III).

Ferroplasma acidarmanus fer1 (archaea, 2 Mb): Lives in most acidic conditions on earth; oxidizes iron; transforms sulfide in metal ores to sulfuric acid, leading to contamination of mining sites.

Geobacter metallireducens (bacteria, 6.8 Mb): Widespread in freshwater sediments; gains energy by reducing iron, manganese, uranium, and other metals; oxidizes toluene and phenol.

Geobacter sp. strain FRC-32 (bacteria, ~5 Mb): Iron and uranium reducer, isolated from uranium-contaminated subsurface at U.S. DOE-NABIR Field Research Center; bioremediation.

§ Geobacter sulfurreducens (bacteria, 2.5 Mb): Reduces a variety of metals, including iron and uranium.

Glomus intraradices (fungi, ~11 to 12 Mb): Forms spores to establish a functional symbiotic (and pathogenic) relationship with plant roots.

Kineococcus radiotolerans nov (bacteria, 4.3 to 4.6 Mb): Highly radioresistant; degrades organic pollutants.

Laccaria bicolor (fungi, ~40 Mb): Commonly found mushroom; stimulates root formation, differentiation in various plants.

Mesorhizobium BNC1 (bacteria, 5 Mb): Fixes nitrogen with leguminous plants; agriculturally important.

**Methylobium petroleophilum PM1 (bacteria, 4.6 Mb): Degrades diverse hydrocarbons, including MTBE (methyl tertiary butyl ether, a common fuel additive), benzene, toluene, xylene, and phenol; biodegradation.

§ Methylococcus capsulatus (bacteria, 4.6 Mb): Uses methane as single carbon and energy source; generates pollutant-oxidizing enzymes; used commercially to produce biomass and other proteins.

Mycobacteria: 5 isolates, est. ~5 Mb each
Fast growing, nonpathogenic; degraders of polycyclic aromatic hydrocarbons (PAH); found in soils.

Mycobacterium flavescens: Isolated from PAH-contaminated site in Indiana.

Mycobacterium vanbaalenii: Isolated from PAH-contaminated site in Texas.

Mycobacterium sp. KMS: Isolated from remediated superfund site, Libby, Montana.

Mycobacterium sp. JLS: Isolated from remediated superfund site, Libby, Montana.

Mycobacterium sp. MCS: Isolated from remediated superfund site, Libby, Montana.

Nectria haematococca MPVI (fungi, ~40 Mb): Member of Fusarium solani species complex; ubiquitous; degrades lignins, hydrocarbons, plastics, some pesticides; useful in biorediation.

Nocardioides strain JS614 (bacteria, ~4.5 Mb): Grows aerobically and efficiently on vinyl chloride (VC) and ethene. If starved of VC for more than 1 day, will not recover for more than 40 days; 300-Kb plasmid containing VC- and ethene-degradation pathways.

Novosphingobium aromaticivorans F199 (bacteria, 3.8 Mb): Degrades aromatic compounds in soil, including toluene, xylene, naphthalene, and fluorine.

Bacteria Involved in Microbial Arsenic Transformation: ~2 to 4 Mb each

Bacillus selenitireducens MLS-10: Haloalkaliphile, respires toxic selenium, argon, sulfur, nitrates.

Bacillus selenitireducens MLMS-1: Respires argon, fixes carbon dioxide in apparent absence of RuBisCo.

Clostridium sp. OhILAs: Strict anaerobe, spore forming; respires argon, nitrates, sulfur, and selenium.

Clostridium sp. MLHE-1: Oxidizes arsenite, potentially can fix carbon dioxide via Form 1 RuBisCo.

Paracoccus denitrificans (bacteria, 3.66 Mb): Bioremediates various pollutants; involved in carbon sequestration and denitrification; may be closely related to evolutionary precursor of mitochondria.

Polaromonas naphthalenivorans sp. strain nov CJ2 (bacteria, ~6 Mb): Degrades PAHs, naphthalene in situ in contaminated environment; bioremediation.

Beta proteobacterium sp. JS666 (bacteria, ~4.5 Mb): Only aerobic bacterium reported to grow on cis-dichloroethene (cDCE, a common contaminant at DOE sites); yellow, nonmotile; devoid of vacuoles; prefers 20°C but will not grow at 30°C or on vinyl chloride or ethene.

Pseudoalteromonas atlantica (bacteria, 3.5 Mb): Marine, gram-negative, motile, biofilm forming, secretes degradative enzymes, polysaccharides that bind metals; bioremediation.

Pseudomonas fluorescens PFO-1 (bacteria, 5.5 Mb): Metabolically diverse; degrades pollutants such as styrene, TNT, and polycyclic aromatic hydrocarbons; useful in applications requiring bacteria release and survival in soil.

*Pseudomonas putida (bacteria, 6.1 Mb): High potential for bioremediation by reducing metal and pollutants.

Pseudomonas putida F1 (bacteria, 6.2 Mb): Grows well on a variety of aromatic hydrocarbons including benzene, toluene, ethylbenzene; bioremediation of organics.

Ralstonia eutropha JMP-134 (bacteria, 7.24 Mb): Gram negative; degrades chloroaromatic compounds and chemically related pollutants; potential for bioremediation.

Ralstonia metallidurans CH34 (bacteria, 5 Mb): Contains two “mega” plasmids; resistant to wide variety of heavy metals, which accumulate on the cell surface; strong potential for bioremediation of metals.

**Rhodobacter sphaeroides 2.4.1 (bacteria, 4.4 Mb): Metabolically diverse, grows in wide variety of conditions; photosynthetic, providing fundamental insights into light-driven, renewable-energy production; can detoxify metal oxides, useful in bioremediation.

Metal-Reducing Shewanella Bacteria
Affect metals including uranium, technetium, and chromium; important in carbon cycling in anaerobic environments; thrive in redox gradient environments; produce energy by generating weak electrical current; display metabolic diversity, potential for bioremediation.

Shewanella amazonensis(4.3 Mb): Isolated from sediments in Amazon River delta; active in reduction of iron, manganese, and sulfur compounds; optimal growth at 35° C, with 1% to 3% salt.

Shewanella baltica OS195 (est. ~5 Mb): Second S. baltica strain, ~69% DNA homology with OS155.

 Shewanella baltica OS1155 (3.6 Mb): Isolated from Gotland Deep in central Baltic Sea, predominantly low- and zero-oxygen regions; can use glycogen, cellobiose, and sucrose as sole sources of carbon and energy.

 Shewanella denitrificans OS220 (3.1 Mb): Denitrifies vigorously; isolated from Gotland Deep in central Baltic Sea; uses nitrate, nitrite, and sulfite as electron acceptors.

 Shewanella frigidimarina NCMB400 (2.1 Mb): Isolated from North Sea off coast of Aberdeen; rich in c-type cytochromes, with increased cytochrome synthesis during growth in low- to zero- oxygen conditions when iron is present.

*Shewanella oneidensis MR-1 (bacteria, 4.5 Mb): May degrade organic wastes and reduce or sequester a range of toxic metals.

 Shewanella putrefaciens CN-32 (3.22 Mb): Isolated from uranium-bearing subsurface formation in northwestern New Mexico; reduces array of metals and radionuclides, including solid phase iron and manganese oxides, uranium (VI), technetium (VII), and chromium (VI) with hydrogen, formate, or lactate; has unusual membrane sugars.

Shewanella putrefaciens ML-S2 (est. ~5 Mb): Hypersaline, pH ~10 environment; isolated from Mono Lake, Calif.

 Shewanella putrefaciens p200 (3.2 Mb): Isolated from corroding oil pipeline in Canada; among most genetically characterized metal-reducing Shewanellae; degrades carbon tetrachloride under low- to zero-oxygen conditions.

Shewanella putrefaciens W3-6-1 (est. ~5 Mb): Marine; forms magnetite at 0°C.

Shewanella sp. ANA-3 (est. ~5 Mb): Fast-growing, unique As(V) respiratory mechanism.

Shewanella sp. MR-4 (est. ~5 Mb): Isolated from 5-M depth (oxic) of Black Sea.

Shewanella sp. MR-7 (est. ~5 Mb): Isolated from 60-M depth (anoxic) of Black Sea.

Shewanella sp. PV-4 (4 to 4.5 Mb): Most diverse from other Shewanellae; prefers cold temperatures; produces magnetite at 0°C; reduces cobalt at -4 °C.

Xanthobacter autotrophicus Py2 (bacteria, 5 Mb): Ubiquitous, nutritionally versatile; degrades chlorinated hydrocarbons, fixes nitrogen, synthesizes biodegradable plastics; bioremediation.

Cellulose Degradation

Clostridium thermocellum ATCC27405 (bacteria, ~5 Mb): Degrades cellulose; potentially useful for conversion of biomass (cellulose) to energy.

**Cytophaga hutchinsonii ATCC33406 (bacteria, 4 Mb): Very abundant in nature; decomposes cellulose, lacks cellulosomes.

Flavobacterium johnsoniae (bacteria, 4.8 Mb): Common in soils and freshwaters; degrades chitin and numerous other macro- molecules via direct contact; possible use in biomass conversion.

**Microbulbifer degradans 2-40 (bacteria, 6 Mb): Marine microbe; degrades and recycles insoluble complex polysaccharides via protruding membrane structures called hydrolosomes; potential for conversion of complex biomass to energy.

*Phanerochaete chrysosporium (eukarya, ~30 Mb): “White rot” fungus; aerobic and degrades both celluloses and lignins; can also degrade polyaromatic hydrocarbons.

Postia placenta MAS 698 (eukaryote, ~40 Mb): “Brown-rot fungus” degrades cellulose and hemicellulose, secretes oxalic acid, detoxifies certain metals.

Rubrobacter xylanophilus (actinobacteria, ~2.6 Mb): Thermophile, highly radioresistant; degrades hemicellulose, xylan.

Thermobifida fusca YX (bacteria, 3.6 Mb): Major degrader of organic materials.

Trichoderma reesei RUT-C30, ATCC56765 (fungi, 33 Mb): Efficiently degrades cellulose.

Biotechnology and Applied Microbiology

Acidothermus cellulolyticus ATCC 43068 (bacteria, ~6 Mb): Thermophile isolated from acid hot spring in Yellowstone; degrades cellulose, source of high-temperature enzymes; biotechnology.

Actinobacillus succinogenes 130Z (ATCC 55618) (bacteria, ~2 Mb): From biomass, produces large amounts of succinate; intermediate for production of various chemicals; biotechnology.

*Aquifex aeolicus VF5 (bacteria extremophile, 1.5 Mb): Potential for identifying high-temperature enzymes.

*Archaeoglobus fulgidus DSM4304 (archaea extremophile, 2.1 Mb): Potential for identifying high-temperature and high-pressure enzymes; useful in oil industry.

Aspergillus niger (fungi, ~32 Mb): Common in soils; model for microbial fermentation and bioproduction of organic acids, enzymes, processing and secretion of proteins; biotechnology.

Bifidobacterium longum DJO10A (bacteria, 2.1 Mb): Anaerobic, gram-positive prokaryote; key component in promoting healthy human gastrointestinal tract.

Brevibacterium linens BL2 (bacteria, 3 Mb): Applications in industrial production of vitamins, amino acids for fine chemicals, and cheese; survives high salt, carbohydrate starvation, and extended drying conditions.

*Clostridium acetobutylicum (bacteria, 4.1 Mb): Produces acetone, butanol, and ethanol; useful for industrial enzymology.

Ehrlichia chaffeensis Sapulpa (bacteria, 1 Mb): Intracellular, tick-transmitted rickettsia endemic in wild deer populations; causes human monocytic ehrlichiosis.

**Ehrlichia canis Jake (bacteria, 1 Mb): Closely related to E. chaffeensis; causes tick-borne disease in dogs (canine monocytic ehrlichiosis).

§ Gemmata obscuriglobus UQM 2246 (bacteria, 9 Mb): Planctomycete; widely distributed in freshwater environments; displays a membrane-bound, DNA-containing nucleoid (possibly presaging the nucleus).

*Halobacterium halobium plasmid (archaea, 2.3 Mb): Potential for identifying high-salinity enzymes.

Halorhodospira halophila (bacteria, ~ 4 Mb): Photosynthetic (fixes carbon dioxide), tolerant of high salt concentrations and high pH; biotechnology.

Lactobacillus brevis ATCC367 (bacteria, 2 Mb): Vital in fermentation of food, feed, and wine.

Lactobacillus casei ATCC334 (bacteria, 2.5 Mb): Used as starter culture in dairy fermentations and for bulk lactic acid production; found in the plant, milk, and sourdough environments as well as the human intestinal tract, mouth, and vagina.

Lactobacillus delbrueckii bulgaricus ATCCBAA365 (bacteria, 2.3 Mb): Classic example of the obligate homofermentative pathway for bulk production of lactic acid.

Lactobacillus gasseri ATCC33323 (bacteria, 1.8 Mb): Naturally inhabits gastrointestinal tract of man and animals. Important for healthy intestinal microflora.

Lactococcus lactis cremoris SK11 (bacteria, 2.3 Mb): Used extensively in food fermentation, especially cheese.

Leuconostoc mesenteroides (bacteria, 2 Mb): Important role in several industrial and food fermentations.

Magnetococcus MC-1 (bacteria, 4.5 Mb): Requires limited oxygen; reduces iron; produces magnetite, which has many practical commercial uses.

Magnetospirillum magnetotactic MS-1 ATCC31632 (bacteria, 4.5 Mb): Requires limited oxygen; reduces iron, produces magnetite; possible model for biomineralization and evolutionary responses; may serve as a geomagnetic tracer.

Oenococcus oeni PSU1 (bacteria, 8 Mb): Lactic acid microbe occurring naturally in fruit mashes; used in wineries for fermentation; acid and alcohol tolerant.

Pediococcus pentosaceus ATCC25745 (bacteria, 2 Mb): Gram-positive; facultatively anaerobic lactic acid microbe; acid-tolerant; used as starter culture in sausage, cucumber, green bean, and soya milk fermentations; a ripening agent of cheeses.

Phytophthera ramorum UCD Pr4 (fungi, 24 to 40 Mb): Pathogen of California oak.

Phytophthora sojae P6497 (fungi, 62 to 90 Mb):  Soybean pathogen.

Psychromonas ingrahamii (bacteria, ~ Mb): Grows in Arctic sea ice at –12°C; large, rod-shaped; doubles every 10 days; will promote studies of low-temperature enzymes.

**Pseudomonas syringae B728a (bacteria, 5.6 Mb): Pathogenic to a variety of plant species, severely impacting both food and biomass production.

*Pyrobaculum aerophilum (archaea extremophile, 2.2 Mb): May identify high-temperature enzymes.

*Pyrococcus furiosus (archaea extremophile, 2.1 Mb): May identify high-temperature enzymes.

Streptococcus thermophilus LMD-9 (bacteria, 1.8 Mb): Used as starter in cheese and yogurt fermentations; thermotolerant; noted for exopolysaccharide production.

*Thermotoga maritima M5B8 (bacteria extremophile, 1.8 Mb): Potential for identifying high-temperature, high-pressure enzymes; metabolizes many simple and complex carbohydrates; possible source of renewable carbon and energy.

Microbial Consortia

Acid mine drainage communities (Iron Mountain, Calif.): Main site is very acidic (pH <<0.5) but geochemically well characterized, with six major species (including F. acidarmanus); this site, as well as other nearby sites being sampled, are heavily contaminated with metals; insights into “simple” communities and metal bioremediation.

Active methylotroph community: Dominant members of Lake Washington, Seattle, one-carbon compound metabolizing bacterial population; carbon cycling, bioremediation.

Anaerobic bioreactor granule samples (some 200 BACs from Hanford PNNL site): Potential for methane and hydrogen production; exhibit archetypical systems for metabolic-interaction studies among microbes; relatively simple complex microcosm of organic matter’s methanogenic degradation in the environment.

Boiling thermal pool (Yellowstone National Park): Characterization of complete communities making up extreme environments; relevance for bioremediation, carbon management.

**Chlorochromatium aggregatum (green sulfur bacteria, plus epibiont, 2 to 10 Mb): Two-component culturable consortium; utilizes hydrogen, sulfur, as electron donors for carbon fixation.

Environmental Geobacteraceae: Samples from former uranium mining sites and marine and freshwater sediments.

Microbial population from The Cedars (Calif.): Site with pH ~12, low-salt, high-metal concentrations; limited population diversity, high-carbonate deposition; carbon processing.

Obsidian hot spring (Yellowstone): Community genomic sampling of microbes from 74°C pool; carbon management, bioremediation.

PAH-degrading mycobacteria: Mycobacteria from three sites where pollutants (polycyclic aromatic hydrocarbons) are degraded; bioremediation.

Picoplankton BACs [Hawaii Ocean Time Series (HOTS) site]: Oceanic picoplankton affecting global carbon cycle, energy production, and geochemical and elemental cycling.

Sargasso Sea community: Catalogue of marine microbial diversity in a low-nutrient environment.

Uncultured microbes in soil environments: Being sequenced by JGI-Diversa collaboration.

Viruses infecting globally distributed microalgae: Pathogens of phytoplankton; may regulate phytoplankton populations and therefore carbon-dioxide fixation in oceans.

Technology Development, Pilot Projects

*Borrelia burgdorferi B31 (bacteria, 1.4 Mb): Human pathogen that causes Lyme disease; one linear chromosome (915 kb) supported by DOE; entire genome published by TIGR.

*Brucella melitensis 16M (bacteria, 3.3 Mb): Pathogenic to animals and humans; biothreat agent.

Enterococcus faecium (bacteria, 2.8 Mb): Pathogenic to many organisms, including humans; tolerates relatively high salt and acid concentrations.

Exiguobacterium 255-15 (bacteria, 3 to 4 Mb) (NASA): Isolated from 2- to 3-million-year-old Siberian permafrost sediment; grows well at –2.5°C; associated with infections in humans.

**Haemophilus Somnus 129PT (bacteria, ~2.5 Mb): Vaccine strain of H. somnus, which causes systemic diseases in cattle; lacks surface-binding protein for immunoglobulins.

*Mycoplasma genitalium G-37 (bacteria, 580 kb): Human pathogen; serves as model for minimal set of genes sufficient for free living.

**Psychrobacter 273-4 (bacteria, 2.5 Mb) (NASA): Isolated from 20,000- to 40,000-year-old Siberian permafrost sediment; grows well at –2.5°C; radiation-resistant.

Streptococcus suis 1591 (bacteria, 2.2 Mb): Pathogenic to pigs and humans; causes meningitis, especially in tropical regions.

Xylella fastidiosa Dixon (almond) (bacteria, 2.6 Mb): Pathogenic to economically important plants such as orange and almond trees.

Xylella fastidiosa Ann1 (oleander) (bacteria, 2.6 Mb): Pathogenic to plants, particularly oleanders.

The Microbial Genome Program brochure lists current and completed DOE projects (Acrobat pdf file, 427kb, designed for 17×11″ paper, will fit to 14×8.5″). Visit Adobe for free Acrobat Reader software.