Microbes by Potential Application
*Completed and published (see www.genomesonline.org)
**Completed, not published (as of February 25, 2005)
†Draft sequence
‡New microbes being sequenced
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.
‡Proteobacterial symbiont of Calyptogena magnifica (clam) (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.
‡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.
‡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).
Bioremediation
‡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.
‡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.
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, arsenic, sulfur, nitrates.
‡Bacillus selenitireducens MLMS-1: Respires arsenic, fixes carbon dioxide in apparent absence of RuBisCo.
‡Clostridium sp. OhILAs: Strict anaerobe, spore forming; respires arsenic, 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).
*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 plant, milk, and sourdough environments as well as human intestinal tract, mouth, and vagina.
†Lactobacillus delbrueckii bulgaricus ATCCBAA365 (bacteria, 2.3 Mb): Classic example of 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 magnetotacticum 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; 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 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.
