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Supplementary Material Comprehensive data on the lifestyle, metabolism and physiology of 118 bacterial species which form the basis for the classification shown in Figure 2 INDEX Page 1) Strict pathogens and commensals 2 2) Free-living bacteria with specialized ecological niches 7 3) Bacteria with wide metabolic versatility 12 4) Bacteria that inhabit multiple and/or variable environments 22 5) Bacteria with complex behavior, life cycles or able to actively establish complex symbiotic interactions. 29 1) STRICT PATHOGENS OR COMMENSALS: BACTERIAL STRAIN GENOME SIZE (bps) MCPs/ GENOME GRAM TAXONOMY LIFESTYLE Dichelobacter nodosus VCS1703A 1389350 1 NEGATIVE GAMMAPROTEOBACTERIA; Cardiobacteriales PATHOGEN Xylella fastidiosa 9a5c 2679306 1 NEGATIVE GAMMAPROTEOBACTERIA; Xanthomonadales PLANT PATHOGEN Bacillus anthracis str. Sterne 5228663 1 POSITIVE FIRMICUTES; Bacillales STRICT PATHOGEN Yersinia pestis Nepal516 4534590 1 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales STRICT PATHOGEN Lactobacillus casei ATCC 334 2895264 2 POSITIVE FIRMICUTES; Lactobacillales SIMBIONT EUKARYOTIC HOST Listeria monocytogenes str. 4b F2365 2905187 2 POSITIVE FIRMICUTES; Bacillales SOIL, WATER, FOOD, PATHOGEN Photorhabdus luminescens subsp. laumondii TTO1 5688987 2 NEGATIVE GAMMAPROTEOBACTERIA; NEMATODE SIMBIONT Enterobacteriales Shigella dysenteriae Sd197 4369232 2 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales EUKARYOTE SIMBIONT, ESCHERICHIA-LIKE Lawsonia intracellularis PHE/MN1-00 1457619 3 NEGATIVE DELTAPROTEOBACTERIA, Desulfovibrionales STRICT PATHOGEN Shigella sonnei Ss046 4825265 3 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales EUKARYOTE SIMBIONT, ESCHERICHIA-LIKE PHYSIOLOGY ANAEROBIC OBLIGATE, FERMENTER AEROBIC FACULTATIVE CHEMORGAN OTROPHIC Verminephrobacter eiseniae EF01-2 5566749 3 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales EARTHWORM ENDOSYMBIONT Escherichia coli E24377A 5082025 4 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales SIMBIONT EUKARYOTIC HOST Borrelia burgdorferi B31 910724 4 NEGATIVE SPIROCHAETES; Spirochaetaceae CAUSATIVE AGENT OF LYME DISEASE Helicobacter pylori 26695 1667867 4 NEGATIVE EPSILONPROTEOBACTERIA ; Campylobacterales SIMBIONT GASTRIC MUCOSA Bordetella pertussis strain Tohama I 4086189 5 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales STRICT PATHOGEN Salmonella enterica subsp. enterica serovar Paratyphi A 4585229 5 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales PATHOGEN Bordetella parapertussis 12822 4773551 6 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales STRICT PATHOGEN Leptospira interrogans serovar Copenhageni 4277185 7 NEGATIVE SPIROCHAETES; Leptospiraceae Leptospira borgpetersenii serovar Hardjo-bovis 3576473 8 NEGATIVE SPIROCHAETES; Leptospiraceae Helicobacter hepaticus ATCC 51449 1799146 9 NEGATIVE Xanthomonas oryzae pv. Oryzae 4940217 10 NEGATIVE PATHOGEN, MULTIPLE ANIMAL CAUSATIVE AGENT OF SPECIES AS RESERVOIRS LEPTOSPIROSIS EPSILONPROTEOBACTERIA; Campylobacterales GAMMAPROTEOBACTERIA; Xanthomonadales ANAEROBE FACULTATIVE PATHOGEN ENDOSIMBIOTIC, PATHOGEN PHYTOPATHOGEN, NOT FREE IN SOIL INFORMATION: Dichelobacter nodosus VCS1703A : Formerly Bacteroides nodosus, obligate anaerobe, aerotolerant; causative agent of ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. It has the smallest genome among anaerobic microbes (1.4 Mpbs). The disease is caused by a mixed microbial infection of Fusobacterium necrophorum, which causes skin lesions, and Dichelobacter nodosus, which can then invade and gain access to the deeper tissue. Once aerotolerant Dichelobacter nodosus infects, which it does through the production of a number of fimbrial adhesins, it secretes both extracellular proteases and toxins which result in damage to the soft tissue underneath the horn of the hoof. Xylella fastidiosa 9a5c : Xylem-inhabiting bacterium. It causes serious diseases in grapevines (Pierce’s disease), almonds (Almond leaf scorch), alfalfas (Alfalfa dwarf), and oleanders (Oleander leaf scorch) in California and numerous other diseases in North and South America Bacillus anthracis str. Sterne: Strict pathogen, aerobic facultative; This organism was the first to be shown to cause disease by Dr. Robert Koch, and a vaccine was created from an attenuate strain Yersinia pestis Nepal516: Extremely pathogenic organism, This strain, isolated from a soil sample from Nepal, is being sequenced for comparative genome analysis of Yersinia pestis strains isolated from different parts of the world. Lactobacillus casei ATCC 334: They are commonly found in the oral, vaginal, and intestinal regions of many animals. Aerobic facultative, they are important industrial microbes that contribute to the production of cheese, yogurt, fermented milks, and other products, all stemming from the production of lactic acid, which inhibits the growth of other organisms as well as lowering the pH of the food product. This organism is used as a starter culture during milk fermentation and for the flavor development of certain bacterial-ripened cheeses. This strain was isolated from Emmental cheese and will be used for comparative analysis. Listeria monocytogenes str. 4b F2365: This organism, which causes listeriosis, is one of the leading causes of death from food-borne pathogens especially in pregnant women, newborns, the elderly, and immunocompromised individuals. It is found in environments such as decaying vegetable matter, sewage, water, and soil, and it can survive extremes of both temperatures (1-45C) and salt concentration marking it as an extremely dangerous food-born pathogen, especially on food that is not reheated. The bacterium can spread from the site of infection in the intestines to the central nervous system and the fetal-placental unit. Meningitis (inflammation of the membrane surrounding spinal cord and brain), gastroenteritis (inflammation of mucous membranes of stomach and intestine), and septicemia (systemic spread of bacteria and toxins in the blood) can result from infection. This organism is enteroinvasive, and utilizes an actin-based motility system by using a surface protein, ActA, that promotes actin polymerization, to spread intercellularly using the polymerized cytoskeletal protein as a "motor". There are 13 serovars associated with Listeria monocytogenes, and the serovar 4b strains are more commonly associated with invasive disease. Photorhabdus luminescens subsp. laumondii TTO1: This organism is unusual in that it is symbiotic within one insect, and pathogenic in another, the only organism that is known to exhibit this dual phenotype. This bacterium lives within the gut of an entomopathogenic nematode that attacks the insect larvae of another species. Once the nematode enters the target insect bloodstream bacteria are released, rapidly killing (24-48 hrs) the target via secreted toxins. Enzymes are then released by the bacteria that result in rapid degradation of the insect body, allowing both bacteria and nematode to feed and reproduce. During this period Photorhabdus luminescens releases bacteriocidal products, including antibiotics and bacteriocins, that prevent infection of the larva by competitive microbes. The result is promotion of Photorhabdus luminescens-nematode interactions that result in continuation of the symbiotic relationship. Photorhabdus luminescens is capable of giving off light, a complex process that requires the products of the lux operon. The lux system has been used extensively as a molecular marker in many experiments. The exact biological function of bioluminescence is not known, although it may have a role in protection against reactive oxygen species (ROS). Shigella dysenteriae Sd197: This genus is named for the Japanese scientist (Shiga) who first discovered these organisms in the 1890s. They are closely related to the Escherichia group, and may be considered the same species. These organisms are human-specific pathogens that are transmitted via contaminated food and water and are the leading causes of endemic bacillary dysentery, causing over 160 million cases of infection and 1 million deaths yearly worldwide. The bacteria infect the epithelial lining of the colon, causing acute inflammation by entering the host cell cytoplasm and spreading intercellularly. Shigella spp. are extremely virulent organisms that can cause an active infection after a very low exposure. One important aspect of Shigella pathogenesis is the intercellular spreading phenotype. The bacterium produces a surface protein that localizes to one pole of the cell (IcsA) which binds to and promotes actin polymerization, resulting in movement of the bacterium through the cell cytoplasm, and eventually to neighboring cells, which results in inflammatory destruction of the mucosal lining. Lawsonia intracellularis PHE/MN1-00: This obligate intracellular pathogen infects the mucosa of the lower intestinal tract by initially infecting crypt cells, which are precursors that normally grow and divide in order to replace the epithelial cells. Once infection occurs, the crypt cells are stimulated to grow and divide abnormally, resulting in the proliferative phenotype. In severe cases of the disease the entire bowel can become affected and persist for up to 40 days, greatly affecting the host animal. Shigella sonnei Ss046: This organism is the leading cause of dysentery in industrialized countries. The disease is usually less severe than other types of Shigella, causing mild diarrhea and dehydration. Verminephrobacter eiseniae EF01-2: This species was isolated from the kidney of the earthworm Eisenia foetida. Evidence based on curing experiments, Acidovorax-specific probes, and 16S phylogeny, indicate that earthworm egg capsules contain high numbers of the bacterial endosymbiont. Juvenile earthworms are colonized during embryonic development within the egg capsule, and failing this are not likely to acquire the symbiont by association with colonized adults or their bedding. Escherichia coli E24377A: Typically present in the lower intestine of humans, where it is the dominant facultative anaerobe present, but it is only one minor constituent of the complete intestinal microflora. E. coli is capable of causing various diseases in its host, especially when they acquire virulence traits. Borrelia burgdorferi B31: This organism is the causative agent of Lyme disease, a multisystemic disease that is considered to be the most prevalent tick-born disease in North America and Europe. This organism was isolated from Ixodes scapularis in 1982. The bacterium is a microaerophilic spirochete that contains seven periplasmic flagella per cell end. Motility is by rapid rotation around the long axis, flexation of the cell and locomotion along a helical path. The most distinctive property is the presence of periplasmic flagella wound around the helical protoplasmic cylinder and encased in an outer sheath. B. burgdorferi has an unusual genome, which includes a linear chromosome and numerous circular plasmids, in some cases containing up to 20 different plasmids. Helicobacter pylori 26695: Micro-aerophilic, Gram-negative, slow-growing, spiral-shaped and flagellated organism. H. pylori is probably the most common cause of chronic bacterial infection of humans, present in almost half of the world population. The presence of the bacterium in the gastric mucosa is associated with chronic active gastritis and is implicated in more severe gastric diseases, including chronic atrophic gastritis, peptic ulceration and mucosa-associated lymphoid tissue lymphomas. It is an extracellular pathogen that persists in the gastric environment, which has a very low pH, by production of the urease enzyme, which converts urea to ammonia and carbon dioxide, a process which can counteract the acidic environment by production of a base. Bordetella pertussis strain Tohama I: This organism, which is unable to persist in the environment, is a strict human pathogen that causes whooping cough. Once a common cause of death in children the development of a vaccine has greatly decreased the number of deaths due to Bordetella pertussis. However, this organism infects and estimated 39 million people and kills hundreds of thousands of people each year. Salmonella enterica subsp. enterica serovar Paratyphi A: This group of Enterobactericiae has pathogenic characteristics and is one of the most common causes of enteric infections (food poisoning) worldwide. They were named after the scientist Dr. Daniel Salmon who isolated the first organism, Salmonella choleraesuis, from the intestine of a pig. There are now two Salmonella species, Salmonella bongori and Salmonella enterica. Certain serovars of Salmonella enterica are responsible for more serious diseases such as Typhoid fever. This serovar has a narrow host range and causes a typhoid-like (paratyphoid fever) illness in humans. It is especially prevalent in southern and eastern Asia, and has been associated with some particularly virulent outbreaks. A number of isolates are increasingly antibiotic resistant. This strain is considered wild-type. Bordetella parapertussis 12822: This organism can infect humans and sheep and it is unable to persist in the environment. This organism causes a respiratory disease similar to, but less severe than, Bordetella pertussis in humans and a chronic pneumonia in sheep. Leptospira interrogans serovar Copenhageni: This organism is the causative agent of leptospirosis, a tropical zoonosis transmitted by direct contact with the urine of infected animals. This potentially life-threatening infection has been linked to increased morbidity and mortality in highly populated tropical urban areas. This motile and obligately aerobic organism grows optimally at 28-30 C. Leptospiral serovar diversity results from structural heterogeneity in the carbohydrate component of lipopolysaccharides. Many serovars are adapted for specific mammalian reservoir hosts, which harbor the organisms in their renal tubules and shed them in their urine. Because of the large spectrum of animal species that serve as reservoirs, leptospirosis is considered to be the world's most widespread zoonotic disease. Leptospira borgpetersenii serovar Hardjo-bovis: Leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. Most infections are caused by either Leptospira borgpetersenii or Leptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. L. borgpetersenii uses a host-to-host mode of transmission, whereas L. interrogans is usually acquired from contaminated surface water. Two different strains of L. borgpetersenii serovar Hardjo have been sequenced that have distinct phenotypes and virulence. Strain JB197 was isolated from a beef steer at slaughter in the U.S.A., whereas strain L550 was isolated from a human in Australia who had contracted leptospirosis from infected cattle. These two strains have nearly identical genetic content, with subtle frameshift and point mutations being a common form of genetic variation. Starkly limited regions of synteny are shared between the large chromosomes of L. borgpetersenii and L. interrogans, probably the result of frequent recombination events between insertion sequences. The L. borgpetersenii genome is approximately 700 kb smaller and has a lower coding density than L .interrogans, indicating it is decaying through a process of insertion sequence-mediated genome reduction. Loss of gene function is not random but is centered on impairment of environmental sensing and metabolite transport and utilization. These features distinguish L. borgpetersenii from L. interrogans, a species with minimal genetic decay and that survives extended passage in aquatic environments before encountering a mammalian host. It is thought that L. borgpetersenii is evolving toward dependence on a strict hostto-host transmission cycle Helicobacter hepaticus: this organism is responsible for chronic hepatitis and liver cancer in mice. It has also been linked to inflammatory bowel disease in immunocompromised mice. H. hepaticus does not colonize the stomach but inhabits the lower bowel. Normally it resides in the lower intestines, but it can cause chronic hepatitis. This organism has a similar urease gene cluster and cytolethal distending toxin as compared to Helicobacter pylori, but lacks other virulence factors such as the vacuolating cytotoxin and the cag pathogenicity island. However, it does contain a pathogenicity island that encodes proteins similar to those found in a type IV secretion system. Xanthomonas oryzae pv. Oryzae: This genus consists of plant-specific yellow-pigmented microbes, some of which are economically important phytopathogens that devastate crops such as citrus plants, rice, beans, grape, and cotton. These organisms are almost exclusively found associated with their plant hosts and are not found free in the soil.Xanthomonas oryzae is a Gram-negative bacterium and is the causative agent of bacterial blight on rice. Bacterial blight is a major disease in tropical Asian countries where high-yielding rice cultivars are often highly susceptible to it. It is a vascular disease resulting in tannish-gray to white lesions along the leaf veins. In severely infested fields, bacterial blight can cause yield losses up to 50%. 2) FREE-LIVING BACTERIA WITH ESPECIALIZED ECOLOGICAL NICHES: BACTERIAL STRAIN GENOME SIZE (bps) MCPs/ GENOME Nitrosococcus oceani ATCC 19707 3481691 1 GRAM TAXONOMY LIFESTYLE NEGATIVE GAMMAPROTEOBACTERIA; Chromatiales MARINE AND FRESHWATER SEA WATER, SEDIMENT METABOLISM NH3-OXIDIZER RESTRICTED NUMBER OF ORGANIC COMPOUNDS AS C AND ENERGY SOURCE PROPIONIC, ORGANIC ACIDS/ SULFATE, FUMARATE PHYSIOLOGY AEROBIC, OBLIGATE CHEMOLITOAUTOTROPHIC, AMMONIA-OXIDIZING AEROBIC, CHEMORGANOTROPHIC Alcanivorax borkumensis SK2 3120143 1 NEGATIVE GAMMAPROTEOBACTERIA; Oceanospirillales Syntrophobacter fumaroxidans MPOB 4990251 1 NEGATIVE DELTAPROTEOBACTERIA, Syntrophobacterales ANAEROBIC SEDIMENT Polaromonas naphthalenivorans CJ2 4410291 1 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales FRESHWATER SEDIMENT NAPHTALENE AS C SOURCE FRESHWATER AND MARINE CO2 AND N2 FIXATION, CHEMOTAXIS TO OBLIGATE NITROGEN PHOTOAUTOTROPH COMPOUNDS Synechococcus elongatus PCC 6301 2696255 1 NEGATIVE CYANOBACTERIA, Chroococcales Erythrobacter litoralis HTCC2594 3052398 2 NEGATIVE ALPHAPROTEOBACTERIA, Sphingomonadales MARINE CIANOBACTERIA L MAT Azoarcus sp. EbN1 4376040 2 NEGATIVE BETAPROTEOBACTERIA; Rhodocyclales SOIL Methylococcus capsulatus str. Bath 3304561 2 NEGATIVE GAMMAPROTEOBACTERIA; Methylococcales Trichodesmium erythraeum IMS101 7750108 3 NEGATIVE CYANOBACTERIA, Oscillatoriales AEROBIC PHOTOTROPHIC AROMATIC DEGRADING CH4 AS C AND ENERGY SOURCE MARINE, NITROGENFIXING ANAEROBIC SYNTROPHIC PROPIONATE-OXIDIZING METHANOTROPH PHOTOAUTOTROPH Zymomonas mobilis subsp. mobilis ZM4 2056416 3 NEGATIVE ALPHAPROTEOBACTERIA, Sphingomonadales Anabaena variabilis ATCC 29413 6365727 3 NEGATIVE CYANOBACTERIA, Nostocales Nitrosomonas europaea ATCC 19718 2812094 3 NEGATIVE BETAPROTEOBACTERIA; Nitrosomonadales TERRESTRIAL, LIMESTONES, NUTRIENT-POOR SOILS PHOTOAUTOTROPH HOT SPRING MICROBIAL MAT ANOXIGENIC PHOTOTROPH SUGAR FERMENTER PHOTOLITOAUTOTROPH NH4-OXIDIZER, CO2 FIXATION Nostoc sp. PCC 7120 6413771 3 NEGATIVE CYANOBACTERIA, Nostocales Roseiflexus castenholzii DSM 13941 5723298 3 NEGATIVE CHLOROFLEXI; Chloroflexaceae Thermosynechococcus elongatus BP-1 2593857 3 NEGATIVE CYANOBACTERIA, Chroococcales LITORAL OCEANIC WATERS PHOTOAUTOTROPH Synechococcus sp. JA-23B'a(2-13) 3046682 3 NEGATIVE CYANOBACTERIA, Chroococcales Synechocystis sp. PCC 6803 3573470 4 NEGATIVE CYANOBACTERIA, Chroococcales FRESHWATER, PHOTOTACTIC Jannaschia sp. CCS1 4317977 4 NEGATIVE ALPHAPROTEOBACTERIA; Rhodobacterales COASTAL AND OPEN OCEAN WATERS, LOWNUTRIENT ENVIRONMENTS Acidothermus cellulolyticus 11B 2443540 5 POSITIVE ACTINOBACTERIA; Actinomycetales ACIDIC HOT SPRING 5 POSITIVE ACTINOBACTERIA; Actinomycetales; Propionibacterineae GROUNDWATER Nocardioides sp. JS614 4985871 OBLIGATE CHEMOLITOAUTOTROPH CO2 AND N2 FIXATION, CHEMOTAXIS TO OXIGENIC NITROGEN PHOTOLITOAUTOTROPH COMPOUNDS PHOTOAUTOTROPH, AND HETEROTROPH IN THE ABSENCE OF LIGHT AEROBIC ANOXIGENIC PHOTOTROPH CELLULOLITIC, SUGARS AS C AND ENERGY SOURCE FERMENTER VINIL CHLORIDE, ETHANE AS C SOURCE AEROBIC HETEROTROPH Thermotoga petrophila RKU-1 1823511 5 NEGATIVE THERMOTOGAE; Thermotogales DEEP SUBTERRANEAN SULFUR REDUCER TO OIL RESERVOIR H2S ANAEROBIC, HETEROTROPHIC INFORMATION: Nitrosococcus oceani ATCC 19707: purple sulfur bacteria, aerobic, obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite; the only gammaproteobacteria capable of ammonia oxidation along with N. halophilus. Detected in many marine environments and natural seawater. In addition to the truly marine environment, it has also been detected in the saline waters of Lake Bonney, a permanently ice-covered lake in Antarctica. Alcanivorax borkumensis SK2: Sea water/sediment samples collected near the isle of Borkum (North Sea), aerobic, use a limited number of organic compounds, including aliphatic hydrocarbons, volatile fatty acids, and pyruvate and its methyl ether as the sole sources of carbon and energy, but cannot use amino acids and carbohydrates; become a predominant part of the microbial community in crude oil-contaminated seawater when nitrogen and phosphorus nutrients are supplemented. Restricted nutritional profile, high halotolerance, the absence of fermentative metabolism, and a low G+C content Syntrophobacter fumaroxidans MPOB: Anaerobic syntrophic propionate-oxidizing bacterium, was isolated from a culture enriched from anaerobic granular sludge. It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure culture with sulfate or fumarate as the electron acceptor. Polaromonas naphthalenivorans CJ2: Isolated from naphthalene-contaminated, freshwater sediment. This organism is capable of aerobic degradation of naphthalene at temperatures of less than 20ºC. Synechococcus elongatus PCC 6301: Unicellular freshwater and marine cyanobacterium, obligate photoautotroph. Synechococcus have a broader distribution in the ocean and are less abundant in oligotrophic (low nutrient) regions. These organisms utilizes photosystem I and II to capture light energy. They are highly adapted to marine environments and some strains have evolved unique motility systems in order to propel themselves towards areas that contain nitrogenous compounds. Erythrobacter litoralis HTCC2594: Organisms in this aerobic phototrophic genus are found in marine environments. Members of this group produce bacteriochlorophyll a, which is normally found in anaerobic organisms. One theory to explain this is that the anoxygenic photosynthetic gene cluster was acquired by these organisms via lateral gene transfer. Although they require an organic carbon substrate for growth, they are able to supplement a significant fraction of their metabolic requirements with photosynthetically derviced energy. This species was isolated from a marine cyanobacterial mat. The presence of the carotenoids bacteriorubixanthinal and erythroxanthin sulfate give this organism a reddish color. Azoarcus sp. EbN1: Strain EbN1 is an aromatic-degrading bacteria found in freshwater and soil habitats. A unique property of strain EbN1 is its capacity to degrade toluene and ethylbenzene via two different, strictly anaerobic pathways. The absence of nitrogen fixation and specific interaction with plants separates EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Methylococcus capsulatus str. Bath: This organism is a methanotroph, and can utilize methane (methanol) as the sole carbon and energy source through the use of monooxygenases. The Methylococci are environmentally important since they are involved in oxidation of methane, a greenhouse gas, and may also be used for bioremediation of polluted sites. Trichodesmium erythraeum IMS101: This filamentous marine cyanobacterium is a nitrogen-fixing organism that contributes a significant amount of the global fixed nitrogen each year. These bacteria are unusual in that nitrogen fixation takes place in a differentiated cell called the diazocyte which is different from the nitrogen-fixing differentiated cell (heterocyst) found in other cyanobacteria. The diazocyte is developed in order to protect the oxygen-sensitive nitrogenases and includes a number of changes including production of more membranes and down-regulation of photosynthetic activity during times of peak nitrogen fixation (noontime). This organism gives the Red Sea its name when large blooms appear and is one of the organisms most often associated with large blooms in marine waters. Zymomonas mobilis subsp. mobilis ZM4: The natural habitat of this organism includes sugar-rich plant saps where the bacterium ferments sugar to ethanol. The high conversion of sugars to ethanol makes this organism useful in industrial production systems, particularly in production of bioethanol for fuel. A recombinant strain of this bacterium is utilized for the conversion of sugars, particularly xylose, which is not utilized by another common sugar-fermenting organism such as yeast, to ethanol. Since xylose is a common breakdown product of cellulose or a waste component of the agricultural industry, it is an attractive source for ethanol production. Zymomonas mobilis was chosen for this process as it is ethanol-tolerant (up to 120 grams of ethanol per litre) and productive (5-10% more ethanol than Saccharomyces). This bacterium ferments using the Enter-Doudoroff pathway, with the result that less carbon is used in cellular biomass production and more ends up as ethanol, another factor that favors this organism for ethanol production. Anabaena variabilis ATCC 29413: These cyanobacteria are bluegreen algae that are capable of fixing carbon and nitrogen. They form long filaments and can be found worldwide in various aquatic environments as well as some terrestrial ones. These bacteria can form a variety of differentiated cell types, including spore-like cells (akinetes), small motile filaments (hormongia) and most importantly, heterocysts that are nitrogen-producing cells. Approximately every tenth cell in a filament becomes a heterocyst and differentiates itself in order to protect the oxygen-sensitive nitrogenase. The heterocyst produces multiple layers outside of its cell wall, shuts down photosystem II in order to inhibit oxygenic photosynthesis and ramps up metabolism in order to use up the oxygen present. Heterocysts donate fixed nitrogen compounds as amino acids to neighboring cells and in return receive a photosynthetically produced carbon source such as sucrose. These organisms produce toxic blooms in aquatic environments that are harmful or fatal to animals and humans due to the various cyanotoxins they produce. Anabaena variabilis is a filamentous heterocyst-forming cyanobacterium that fixes nitrogen and CO2 using the energy of sunlight via oxygen-evolving plant-type photosynthesis. In addition, this organism has been studied extensively for the production of hydrogen using solar energy. This is a wild-type strain which differs from the closely related Anabaena sp. PCC7120 in the heterocyst formation system in that this strain does not have a programmed gene rearrangement at the hupL locus. Nitrosomonas europaea ATCC 19718: This organism is an obligate chemo-lithoautotroph as it only uses ammonia and carbon dioxide and mineral salts for growth, and is an important part of the global biogeochemical nitrogen cycle. It can derive all energy requirements from the oxidation of ammonia to nitrate, driving global nitrogen from the reduced insoluble form to the oxidized and potentially gaseous form (including NO and NO2 which are greenhouse gases). The energy derived from ammonia oxidation is in turn used to drive carbon fixation. This bacterium also provides plants with a readily available form of nitrogen, is important in wastewater treatment, and may be involved in bioremediation of sites contaminated with toxic compounds. Nostoc sp. PCC 7120: This generum of cyanobacteria are typically terrestrially-associated and are especially found in limestone or nutrient-poor soils. They are very similar to Anabaena spp. and historically they have been distinguished on the basis of morphological and life cycle characteristics. Nostoc spp. can grow heterotrophically or photoheterotrophically, and form heterocysts for nitrogen fixation. Roseiflexus castenholzii: It is related to the Chloroflexaceae, a family of anoxygenic phototrophs. However, it differs from other members of that family in that it lacks chlorosomes and bacteriochlorophyll-c. Bacteriochlorophyll-a is the major photosynthetic pigment in Roseiflexus castenholzii. This organism was isolated from a hot spring microbial mat and will be used for comparative genomics with other phototrophic bacteria. Thermosynechococcus elongatus BP1: It is a thermophilic cyanobacterium. This organism is readily transformable making it useful for molecular analyses. Synechococcus sp. JA-2-3B'a(2-13): These unicellular cyanobacteria are also known as blue green algae and along with Prochlorococcus are responsible for a large part of the carbon fixation that occurs in marine environments. Synechococcus have a broader distribution in the ocean and are less abundant in oligotrophic (low nutrient) regions. These organism utilize photosystem I and II to capture light energy. They are highly adapted to marine environments and some strains have evolved unique motility systems in order to propel themselves towards areas that contain nitrogenous compounds. Motility may be due to the presence of spicules (long filaments) that extend from the cell surface and may act like oars during movement. Synechocystis sp. PCC 6803: Cyanobacterium that can grow both using photosynthesis as well as heterotrophically in the absence of light. These organisms serve as models for the uptake of carbon. This cyanobacterium was isolated from a freshwater lake in 1968 and is easily transformed by exogenous DNA. The photosynthetic apparatus is very similar to the one found in plants. This organism also exhibits phototactic movement. Jannaschia sp. strain CCS1: It is a member of the Roseobacter lineage (alpha-Proteobacteria), an ecologically relevant taxon of marine bacteria abundant in coastal and open ocean surface waters. CCS1 is an aerobic anoxygenic phototroph (AAnP), that is, it is incapable of anaerobic photosynthesis, and performs efficient photoinduced electron transfer only under aerobic conditions. However it still uses bacteriochlorophyll a to harvest energy from light without oxygen formation. AAnPs have recently been found in ocean surface waters, where they make up a significant fraction of the marine bacterioplankton community, are responsible for a share of the oceanic photosynthetic electron transport flux, and have important implications for the ocean carbon cycle. Jannaschia CCS1 was isolated from Pacific coastal waters on low-nutrient seawater medium. It is motile, grows slowly, and like other marine AAnPs, produces bacteriochlorophyll a when grown in the dark. Acidothermus cellulolyticus 11B: This organism is a thermotolerant cellulolytic actinomycete that was originally isolated from an acidic hot spring in Yellowstone National Park. A number of thermostable endoglucanases are produced by this organism, which are useful for degrading cellulose in the production of ethanol as a biofuel. An endoglucanase has been patented and is being studied. Nocardioides sp. JS614: Aerobic mesophillic Gram-positive bacterium phylogenetically associated with the Actinobacteria. This bacterium grows quickly and efficiently on media containing vinyl chloride (VC) and ethane (ETH) in aerobic groundwater zones Thermotoga petrophila RKU-1: Motile, anaerobic, heterotrophic, rod-shaped bacterium. It possesses an outer sheath-like structure characteristic of the order Thermotogales. It grows between 47 and 88 degrees Celsius, with an optimum at 80 degrees and at pH between 5.2 and 9, with an optimum at 7.0. It reduces elemental sulfur to hydrogen sulfide. Thermotoga petrophila (strain RKU-1 / ATCC BAA-488 / DSM 13995) was isolated from a deep subterranean oil reservoir in Niigata, Japan. 3) BACTERIA WITH WIDE METABOLIC VERSATILITY: BACTERIAL STRAIN GENOME SIZE (bps) MCPs/ GENOME GRAM TAXONOMY Gluconobacter oxydans 621H 2702173 3 NEGATIVE ALPHAPROTEOBACTERIA, Rhodospiralles Solibacter usitatus Ellin6076 9965640 4 NEGATIVE ACIDOBACTERIA; Solibacterales Nitrobacter hamburgensis X14 4406967 4 NEGATIVE ALPHAPROTEOBACTERIA; Rhizobiales Alkalilimnicola ehrlichii MLHE-1 3275944 5 NEGATIVE Moorella thermoacetica ATCC 39073 2628784 5 POSITIVE FIRMICUTES; Clostridia; Thermoanaerobacterales LIFESTYLE METABOLISM PHYSIOLOGY LIVING IN FLOWERS, FRUITS, FERMENTED JUICES WIDE VARIETY OF CARBOHYDRATES, ALCOHOLS AEROBIC CHEMORGANOTROPH UBIQUITOUS GAMMAPROTEOBACTERIA; ANOXIC LAKE Chromatiales WATERS Roseobacter denitrificans OCh 114 4133097 6 NEGATIVE ALPHAPROTEOBACTERIA; Rhodobacterales Thermotoga maritima MSB8 1860725 6 NEGATIVE THERMOTOGAE; Thermotogales Thiobacillus denitrificans ATCC 25259 2909809 7 NEGATIVE BETAPROTEOBACTERIA; Hydrogenophilales Fervidobacterium nodosum Rt17-B1 1948941 8 NEGATIVE THERMOTOGAE; Thermotogales AEROBIC CHEMORGANOTROPHIC, DESNITRIFICANT FACULTATIVE OXIDATION NITRITE LITOAUTOTROPHIC, TO NITRATE, ORGANIC MIXOTROPH AND COMPONENTS ORGANOTROPH RESPIRATION NITRATE, NITRITE, ANAEROBIC AUTOTROPH ARSENITE SIMPLE AND COMPLEX SUGARS HOT STAGNANT POUNDS MULTIPLE ORGANIC COMPOUNDS ANAEROBE, CO AND CO2 AS ELECTRON ACCEPTOR (FIXING C IN ACETATE) MARINE AND FRESHWATER ORGANIC COMPOUNDS, S2 OXIDIZER, NITRATE REDUCER, O2 AEROBIC ANOXIGENIC PHOTOHETEROTROPH MARINE AND FRESHWATER MANY ORGANICS AS E- DONORS AEROBIC GROUNDWATER OXIDATION OBLIGATE INORGANIC SULFUR CHEMOLITOAUTOTROPH, COUPLED TO NITRATE FACULTATIVE ANAEROBE REDUCTION HOT SPRING WIDE RANGE OF CARBOHYDRATES ANAEROBE, FERMENTER Nitratiruptor sp. SB1552 1877931 8 NEGATIVE DEEP SEA VENT IN DIFFERENT EPSILONPROTEOBACTERIA ECOLOGICAL NICHES Rhodobacter sphaeroides ATCC 17029 chromosome 1 3147721 9 NEGATIVE ALPHAPROTEOBACTERIA; Rhodobacterales Carboxydothermus hydrogenoformans Z2901 2401520 10 POSITIVE FIRMICUTES; Clostridia; Thermoanaerobacterales Pseudoalteromonas atlantica T6c 5187005 10 NEGATIVE Acidiphilium cryptum JF-5 3389227 11 NEGATIVE ALPHAPROTEOBACTERIA; Rhodospirillales; Acetobacteraceae ACIDIC, MINERAL, HYDROTERMAL ENVIRONMENTS Anaeromyxobacter sp. Fw109-5 5277990 12 NEGATIVE DELTAPROTEOBACTERIA; Myxococcales GROUNDWATER FRESHWATER, SEDIMENTS, SLUDGE H2, CO2, AROMATIC HYCROCARBONS AND ALKANES ANAEROBIC SEDIMENTS OXIDIZES MULTIPLE ORGANIC ACIDS AND ALCOHOLS UBIQUITOUS SOIL METABOLICALLY AND FRESHWATER VERSATILE HOT SPRING GAMMAPROTEOBACTERIA; OCEAN, PRIMARY Alteromonadales BIOFILM FORMING Methylibium petroleiphilum PM1 4044195 12 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales Pelotomaculum thermopropionicum SI 3025375 12 POSITIVE Firmicutes; Clostridia; Clostridiales; Peptococcaceae Chromohalobacter salexigens DSM 3043 3696649 13 NEGATIVE GAMMAPROTEOBACTERIA; Oceanospirillales Ralstonia eutropha H16 chromosome 1 4052032 13 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales Saccharophagus degradans 2-40 5057531 13 NEGATIVE H2, S2, ETC. AS EDONORS; NO3-, O2 AS E- ACCEPTORS GAMMAPROTEOBACTERIA; MARINE Alteromonadales PHOTOTROPHIC CO2 AND H2 ALSO HETEROTROPHY, PRODUCER, CO, H20 AS CHEMOTAXIS E- ACCEPTOR IMPLICATION MULTIPLE POLYSACCHARIDES GLUCOSE, MANY METALS AS EACCEPTORS ACETATE, PIRUVATE, LACTATE, EACCEPTORS NITRATE AND Fe (III) WIDE RANGE OF SIMPLE CARBON COMPOUNDS SOIL CHEMOLITOAUTROPH, WIDE METABOLIC VERSATILITY ALSO PHOTOSYNTHETIC ANAEROBIC, MICROAEROPHILIC, PHOTOTROPHIC ANOXIGENIC, HETEROTROPHIC AEROBIC ANAEROBIC RESPIRATION, FERMENTER CHEMORGANOTROPH METABOLICALLY VERSATILE MANY COMPLEX CARBOHYDRATES AEROBIC HETEROTROPH Sulfurimonas denitrificans DSM 1251 2201561 13 NEGATIVE Epsilonproteobacteria; Campylobacterales Pelobacter carbinolicus DSM 2380 3665893 15 NEGATIVE DELTAPROTEOBACTERIA; Desulfuromonadales Ralstonia metallidurans CH34 3928089 16 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales Geobacter metallireducens GS-15 3997420 17 NEGATIVE DELTAPROTEOBACTERIA; Desulfuromonadales Anaeromyxobacter dehalogenans 2CP-C 5013479 18 NEGATIVE Shewanella denitrificans OS217 4545906 19 NEGATIVE COASTAL MARINE SEDIMENTS H2S, S2 / NO2-, NO3- MARINE AND FRESHWATER SEDIMENTS, SYNTROPHIC ETHANOL FERMENTATION, Fe(III) and S2 as acceptors DENITRIFYING CHEMOLITOAUTOTROPH WIDE NUMBER OF HEAVY METALS FRESHWATER, CHEMOTACTIC TO Fe(III) and Mn (IV) DELTAPROTEOBACTERIA; Myxococcales GAMMAPROTEOBACTERIA; AQUATIC AND Alteromonadales MARINE MARINE, FRESHWATER, ANAEROBIC SEDIMENTS Pelobacter propionicus DSM 2379 4008000 20 NEGATIVE DELTAPROTEOBACTERIA; Desulfuromonadales Treponema denticola ATCC 35405 2843201 20 NEGATIVE SPIROCHAETES; ORAL CAVITY Spirochaetales; Spirochaetaceae Desulfotomaculum reducens MI-1 3608104 22 POSITIVE FIRMICUTES; Clostridia; Clostridiales Rhodoferax ferrireducens T118 4712337 24 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales MARINE SEDIMENTS WIDE VARIETY OF METALIC ACCEPTORS MANY HALOGENATED COMPOUNDS, METALS, ORGANICS, NITRITE, NITRATE, ETC. AS ACCEPTORS. NH3, ACETATE, H2, PHENOL, ETC AS DONORS MANY METALS, O2, ORGANIC ACIDS, NITRATE, SULFITE, ETC. AS ELECTRON ACCEPTORS ORGANIC MATTER, Fe(III) WIDE VARIETY OF CARBOHYDRATES AND AMINOACIDS MANY METALS AS ACCEPTORS MULTIPLE ORGANIC ACIDS, Fe(III) STRICT AEROBIC OR MICROAEROPHILIC Shewanella frigidimarina NCIMB 400 4845257 24 NEGATIVE Dechloromonas aromatica RCB 4501104 25 NEGATIVE BETAPROTEOBACTERIA; Rhodocyclales Rhodopseudomonas palustris BisB5 4892717 26 NEGATIVE Desulfovibrio vulgaris DP4 3462887 27 NEGATIVE GAMMAPROTEOBACTERIA; MARINE Alteromonadales HIGH RESPIRATORY FLEXIBILITY SURFACE AND GROUNDWATERS OXIDIZE AROMATIC HYDROCARBONS ALPHAPROTEOBACTERIA; Rhizobiales SOIL, WATER HIGH METABOLIC DIVERSITY DELTAPROTEOBACTERIA; Desulfovibrionales SOIL AND AQUATIC MANY METALS AS ACCEPTORS Shewanella oneidensis MR-1 4969803 27 NEGATIVE GAMMAPROTEOBACTERIA; Alteromonadales WIDE VARIETY OF TERMINAL ELECTRON ACCEPTORS DURING ANAEROBIC RESPIRATION Hahella chejuensis KCTC 2396 7215267 35 NEGATIVE GAMMAPROTEOBACTERIA; COASTAL MARINE Oceanospirillales SEDIMENTS MINERAL, ORGANIC, OTHER ORGANISMS Rhodospirillum rubrum ATCC 11170 4352825 47 NEGATIVE ALPHAPROTEOBACTERIA; Rhodospirillales; PHOTOTROPHIC HETEROTROPH AEROBIC, ANAEROBIC, FERMENTATION, PHOTOSYNTHESIS, NITROGEN FIXATION INFORMATION: Gluconobacter oxydans 621H: It is a member of the Acetobacteraceae family within the alpha proteobacteria and can be isolated from flowers, fruits, and fermented beverages. This organism uses membrane-associated dehydrogenases to incompletely oxidize a wide variety of carbohydrates and alcohols. Oxidation occurs in the periplasm with the products being released into the medium via outer membrane porins and the electrons entering the electron transport chain. Since oxidation occurs in the periplasm, alcohols and carbohydrates do not need to be transported into the cytoplasm and G. oxydans is able to oxidize large amounts of substrates, making it useful for industrial purposes. Among other applications, it has been used to produce 2-ketogluconic for iso-ascorbic acid production, 5-ketogluconic acid from glucose for tartaric acid production, and L-sorbose from sorbitol for vitamin C synthesis. Solibacter usitatus Ellin6076: Aerobic, mesophilic, chemo-organotroph Gram-negative bacterium isolated from soil in ryegrass grass/clover pasture in Australia. S. usitatus is able to use a variety of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. It is capable of nitrate and nitrite reduction, but not N2 fixation or denitrification. It plays an important role in iron redox reactions and important contributions to the terrestrial carbon cycle. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Nitrobacter hamburgensis: It is a rod-shaped, motile, aerobe alpha-proteobacterium. N. hamburgensis is a facultatively lithoautotrophic bacterium that gains energy from the oxidation of nitrite to nitrate (nitrification). It is ubiquitous in nature and has been isolated from several environments, including soil, building sandstone, and sewage sludge. In addition to growing lithoautotrophically, N. hamburgensis is able to grow mixotrophically with NO2 and organic components or heterotrophically solely with organic components. It can be used in biotechnology for efficient transformation of fertilizer nitrogen in agricultural systems, and is a key component of nitrogen removal in wastewater treatment. Alkalilimnicola ehrlichii MLHE-1: An anaerobic, facultatively autotrophic arsenite oxidizing bacterium that respires nitrate or nitrite. The cells are short motile rods. It was isolated from bottom waters of Mono Lake, California USA, a stratified soda lake with high pH and high salt levels. It is a gamma-Proteobacterium located in the Ectothiorhodospira clade of photosynthetic bacteria that occur in soda lakes. However, strain MLHE-1 is not a phototroph, but does grow as an anaerobic chemoautotroph by linking oxidation of arsenite (As III), hydrogen, or sulfide to the reduction of nitrate. It contains Form 1 RuBisCo genes for fixation of CO2 during chemoautotrophic growth, but can also grow as a heterotroph on acetate either with nitrate or air. However, arsenite is only oxidized under anaerobic conditions. This strain is very likely to be helpful to our understanding of As-mobility in subsurface waters. Moorella thermoacetica ATCC 39073: Gram-positive, thermophilic, acetogenic and rod-shaped bacterium. It uses carbon dioxide as a terminal electron acceptor and concomitantly synthesizes biomass and acetate via the acetyl-CoA or Wood-Ljungdahl pathway. This anaerobe can use a wide range of electron donors (sugars, hydrogen, carbon monoxide, alcohols, organic acids and aromatic compounds). Its spores are extremely resistant to high temperatures (55-60 degrees Celsius). Roseobacter denitrificans OCh 114: Purple aerobic anoxygenic phototrophs (AAPs, also known as AAnPs or APBs) are photoheterotrophic organisms that although able to perform photosynthesis, are not able to survive by phototrophy, instead they depend on the respiration of organic compounds for growth. They do not produce oxygen. They also differ from classical purple phototrophic bacteria by their cessation of photosynthetic pigment synthesis upon illumination. Synthesis of the photosynthetic apparatus in aerobic phototrophic bacteria occurs aerobically in darkness, yet the photosystem produced in darkness synthesizes ATP and enhances growth when cells are illuminated. These bacteria may represent an intermediate evolutionary form between the purple phototrophic bacteria and chemotrophic relatives, or may have arisen from an aerobic chemotroph by lateral gene transfer of photosynthesis genes from a purple. Roseobacter denitrificans Och 114 is a marine bacterium that grows photoheterotrophically in the presence of oxygen and light but also anaerobically in the dark using nitrate or trimethylamine N-oxide as electron acceptors. It has a circular chromosome and 4 circular plasmids. The largest plasmid, pTB1, has significant similarity to the Ti plasmids from Agrobacterium, including DNA integration and transfer proteins, suggesting it might be able to transfer genes to other organisms. R. dentrificans lacks the Calvin cyle enzymes ribulose-bis-phosphate carboxylase (RuBisCO) and phosphoribulokinase, and so cannot fix carbon via this cycle. It may instead do so mixotrophically using several different pathways that are encoded in its genome. It is probably able to oxidize inorganic sulfur, and encodes many transport proteins for peptides and amino acids, sugar and carbohydrates, cations and iron. Thermotoga maritima MSB8: Rod-shaped thermophilic marine bacterium that metabolizes many simple and complex carbohydrates including glucose, sucrose, starch, cellulose, and xylan. Thiobacillus denitrificans: It is an obligate chemolithoautotrophic, facultative anaerobe bacterium. It is best known for its ability to couple the oxidation of inorganic sulfur compounds (such as hydrogen sulfide and thiosulfate) to denitrification. It is a natural agent for intrinsic bioremediation of groundwater polluted with nitrate. In addition, it has been used in engineered water treatment systems for nitrate removal. Its ability to carry out nitrate-dependent Fe(II) oxidation under anaerobic conditions could influence metal and radionuclide transport in the subsurface, as ferric iron-containing minerals that may be formed, especially iron(III) oxides, are well-known for their ability to adsorb heavy metals and radionuclides, such as uranium. Fervidobacterium nodosum Rt17-B1: It is a thermophilic, Gram-negative, motile, non-sporulating, glycolytic, obligately anaerobic rod that exists singly, in pairs or in chains. It is a member of the order Thermotogales and was isolated from a New Zealand hot spring. Its optimal growth temperature is 65 to 70 degrees Celsius. It can use a wide range of carbohydrates including glucose, sucrose, starch and lactose. The major end products of glucose fermentation are lactate, acetate, hydrogen, and carbon dioxide and to a lesser extent ethanol. Growth is inhibited by tetracycline, penicillin and chloramphenicol." Nitratiruptor sp. (strain SB155-2): It is a deep-sea vent microaerobic bacterium phylogenetically associated with the epsilonproteobacteria. This strain was isolated in the vicinity of a deep-sea vent occurring in the Iheya North hydrothermal field, in Okinawa, Japan. This rod-shaped bacterium grows chemolithoautotrophically and can utilize a wide spectrum of electron donors and acceptors (i.e. hydrogen, sulfur compounds, nitrate and oxygen). It can occupy different ecological niches, and its metabolic versatility probably enables it to adapt to the geochemical variability in deep-sea hydrothermal environments. Furthermore, fitting to its metal-rich niche, this strain contains a wide array of mineral transport systems including detoxification mechanisms of heavy metals such as arsenate, cadmium, and copper. It probably has some symbiotic relationship with vent animals. Rhodobacter sphaeroides: Purple non-sulfur phototrophic bacterium able to grow under a wide variety of conditions. It is photosynthetic, which provides fundamental insights into light-driven, renewable-energy production and it can also detoxify metal oxides, which may be useful in bioremediation. Each of the three sequenced R. sphaeroides strains (2.4.1, ATCC 17025 and ATCC 17029) has a large ~3.0 Mb chromosome and a small ~0.9 - 1.2 Mb chromosome in addition to differing numbers of plasmids. Comparative optical mapping studies have shown that in terms of size and physical map structure, the large chromosome in these strains is relatively stable, whereas the smaller chromosomes are much more variable. Comparing these genomes will help determine what factors lead to chromosome and genome stability/instability, giving a better understanding of the mechanisms involved in genome evolution and speciation. Carboxydothermus hydrogenoformans Z-2901: It is a hydrogenogen that was isolated from a hot spring in Kunashir Island, Russia. It belongs to the Firmicutes and grows optimally at 78 degrees Celsius. Hydrogenogens are organisms that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Anaerobic species use carbon monoxide thanks to CO dehydrogenase (CODH) complexes. Several homologs of genes involved in sporulation in other Firmicutes have been found in C. hydrogenoformans. Among them, the master switch gene spo0A and all sporulation-specific sigma factors. Although sporulation had not been reported previously for this species, it has been shown to sporulate. Endospore-like structures were found when cultures were stressed. C. hydrogenoformans has been thought to be an autotroph strictly depending on CO for growth, however several aspects of its gene repertoire suggest heterotrophic capabilities. For example, it encodes transporters predicted to import various carbon compounds. It also possesses a cascade of chemotaxis genes and a complete set of flagellar genes. Chemotaxis allows microbes to respond to environmental stimuli by swimming towards nutrients (or away from toxic chemicals), which is a feature not commonly found in autotrophs. Therefore, the presence of a complete array of chemotaxis genes is consistent with its suggested heterotrophic capabilities. Pseudoalteromonas atlantica T6c: is a motile, biofilm-forming, Gram-negative chemoorganotroph that is found in oceans worldwide. It was first isolated in association with marine algae and named Pseudomonas atlantica, but has now been assigned to a new genus, Pseudoalteromonas. P. atlantica is found associated with marine eukaryotic hosts (seaweed, crab) as well as in the water column, and produces a variety of biologically active extracellular compounds. The extracellular compounds identified from P. atlantica include enzymes that hydrolyze agar, alginate, and carrageenan, acidic extracellular polysaccharide (EPS), and proteases. It was shown to be a primary biofilm-forming bacteria, attaching to sterile slides and producing voluminous amounts of EPS. Following biofilm formation by P. atlantica , stalked and/or filamentous bacteria with more limited nutrient utilization capabilities attached to the surface, and these organisms were followed by diatoms, microalgae, and sessile protozoa. These results suggest that P. atlantica colonizes solid surfaces quickly, utilizing substrates that are processed for uptake by its secreted agarases, proteases, etc., and then forms biofilms in which the EPS concentrates nutrients and provides substrates for other marine microorganisms. Acidiphilium cryptum JF-5: It was first isolated from a supposedly pure culture of Thiobacillus ferrooxidans. This organism, a heterotrophic acidophile, has been isolated from acid mine drainage, hydrothermal vent water, and other acidic mineral environments. Acidiphilium species contain bacteriochlorophyll-a, and the genes for the L and M proteins of the photosynthetic reaction center complex have been amplified, indicating that members of this genus are capable of photosynthesis. Acidophilic dissimilatory iron-reducing bacterium (DIRB) of the alpha subdivision of the Proteobacteria. This bacteria is detected in a variety of extreme low pH, radionuclide- and heavy-metal contaminated habitats where Fe(III) reduction is taking place, and may represent a significant proportion of metal-transforming organisms in these environments. Strain JF-5 serves as a model organism for facultative iron-respiring Alphaproteobacterium. It utilizes glucose as an electron donor with the concomitant reduction of soluble and solid-phase Fe(III). Major findings for this bacterium are a novel outer-membrane cytochrome c involved in iron respiration and a Cr(VI) reductase enzyme. Anaeromyxobacter sp. Fw109-5: Mesophilic, iron-reducing delta-Proteobacterium that was recently isolated from subsurface sediments (approximately 15 meters) at the ERSP-FRC in Oak Ridge, TN. The groundwater at the well had a pH of 6.09 and contained approximately 1.4 mM nitrate and 0.9 uM uranium. Optimal growth has been observed from pH 7.0 to 8.0, under anaerobic conditions but slightly microaerophilic conditions are tolerated. Electron donors include acetate, lactate, and pyruvate, and electron acceptors include nitrate and iron(III). It grows very slowly with ethanol, cellobiose and starch but cannot grow with yeast extract and peptone. Anaeromyxobacter have a high GC content (73.5%) and are distantly related to the genus Myxococcus. Based upon SSU rRNA gene sequences, the closest cultivable relative is Anaeromyxobacter dehalogenans 2CP-C with 96.5% sequence identity. Methylibium petroleiphilum PM1: Motile phototrophic methylotrophic Gram-negative bacterium phylogenetically associated with the beta subdivision of the Proteobacteria and representing a new species within the Rubrivivax group (Comamonadaceae family). It is found in many gasoline-contaminated aquifers (freshwater, sewage, and activated sludge) and can grow in the dark under aerobic conditions or photosynthetically under anaerobic conditions. PM1 can also grow on carbon dioxide or on hydrogen. It was isolated by Dr. Scow in 1998 from a sewage treatment plant biofilter that was used for treating discharge from oil refineries in Los Angeles, California. Methylibium petroleiphilum is a model organism for the study of photosynthetic processes due to its genetic tractability. Strain PM1 is capable of degrading the gasoline additive methyl tert-butyl ether (MTBE) and its daughter product tert-butyl alcohol (TBA). Strain PM1 also degrades aromatic hydrocarbons (benzene, toluene, and xylene) and n-alkanes (C5 to C12) present in petroleum products. It is capable of aerobic growth on methanol, formate and succinate, but not on methylamine. Pelotomaculum thermopropionicum SI: Non-halophilic thermophilic anaerobic bacterium phylogenetically associated with the Firmicutes. Pelotomaculum thermopropionicum was isolated from granular sludge from a thermophilic upflow anaerobic sludge blanket (UASB) reactor. It was isolated both in pure culture and in co-culture with methanogens. Pelotomaculum thermopropionicum oxidizes volatile fatty acids and alcohols in syntrophic association with methanogenic archaea. It can utilize propionate, ethanol, lactate, ethylene glycol, 1-butanol, 1-propanol, 1-pentanol and 1,3-propanediol. In pure culture, Pelotomaculum thermopropionicum can ferment pyruvate and fumarate. Fumarate can also be used as an electron acceptor in the presence of propionate, ethanol or lactate as an electron donor. This is the first mesophilic, syntropic propionate-oxidizing species known which is not a member of the delta-proteobacteria. Chromohalobacter salexigens DSM 3043: It is a metabolically versatile, moderately halophilic and halotolerant bacterium, isolated from a solar saltern on Bonaire, Netherlands Antilles. It is a gamma-Proteobacterium, and as such, closely related to Pseudomonas and Escherichia coli . It has resistance functions to heavy metals and can degrade aromatic hydrocarbons. It is an aerobic chemoorganotroph that grows on a wide range of simple carbon compounds at NaCl concentrations between 0.5 M and 4 M, with an optimum at 2-2.5 M Ralstonia eutropha H16: Cupriavidus necator, also known as Ralstonia eutropha is a soil bacterium with diverse metabolic abilities. Strains of this organism are resistant to high levels of copper or are able to degrade chloroaromatic compounds such as halobenzoates and nitrophenols making them useful for bioremediation. Other strains have been studied for their ability to produce polyhydroxybutyrates which have industrial application. Another strain is able to attack other bacteria and fungi when nutrients in the soil are low. Saccharophagus degradans (strain 2-40): Formerly known as Microbulbifer degradans, is a Gram-negative, pleomorphic, aerobic, rod shaped, and motile bacterium. It belongs to a recently discovered group of marine bacteria that degrade and recycle complex carbohydrates. It was originally isolated from the salt marsh cord grass, Spartina alterniflora, in the Chesapeake Bay watershed. Saccharophagus degradans contains degradative surface protuberances, containing what is collectively termed hydrolosomes. The chitinase, agarase and alginase produced by S.degradans are not exported into the extracellular medium but are localized in these surface protuberances. Thanks to these protuberances, it is able to recycle a multitude of ICP (insoluble complex polysaccharides) including agar, chitin, alginic acid, carrageenan, cellulose, B-glucan, laminarin, pectin, pullulan, starch, and xylan. Agricultural, aquacultural, and algalcultural wastes threaten to become an increasingly serious problem. The wastes are mostly recalcitrant complex carbohydrates, namely cellulose, chitin and agar. The degradative protuberances of S. degradans may become important bioremediation tools, using them as concentrated, organized, protective enzyme packets. Sulfurimonas denitrificans: formerly Thiomicrospira denitrificans, is a denitrifying chemolithoautotroph that uses sulfide or thiosulfate and nitrate or nitrite as the electron donor and acceptor. Its genome was sequenced in order to have a representative of the sulfur-oxidizing Epsilonproteobacteria present in the coastal marine sediments in addition to the genomes of the deep-sea hydrothermal vents sulfur-oxidizing Epsilonproteobacteria Nitratiruptor sp. (strain SB155-2) and Sulfurovum sp. (strain NBC37-1) Pelobacter carbinolicus: is commonly isolated from marine and freshwater sediments, and sewage sludge. This organism can make up a significant portion of the anaerobic microbial community in these environments. Pelobacter carbinolicus can ferment ethanol in the presence of hydrogen-utilizing bacteria via interspecies hydrogen transfer. The utilization of hydrogen reduces the hydrogen partial pressure making ethanol fermentation by Pelobacter carbinolicus energetically favorable. Pelobacter carbinolicus is also able to grow using iron and sulfur as terminal electron acceptors. This organism is closely related to the sulfur-reducing Desulfuromonas spp. and iron-reducing Geobacter spp.. Ralstonia metallidurans CH34: This organism, now Cupriavidus metallidurans, is capable of growth in the presence of a large number of heavy metals including silver, cadmium, chromium, cobalt, copper, mercury, nickel, lead, thallium, and zinc. Geobacter metallireducens strain GS-15: was isolated in the Potomac river just downstream from Washington D.C. in 1987. It is able to gain energy through the dissimilatory reduction of iron, manganese, uranium and other metals. In addition, G. metallireducens can oxidize several short chain fatty acids, alcohols and monoaromatic compounds including toluene and phenol with iron as the sole electron acceptor. Therefore, it is a possible agent for bioremediation. Geobacter metallireducens specifically expresses flagella and pili, only when grown on insoluble Fe(III) or Mn(IV) oxide, and is chemotactic towards Fe(II) and Mn(II) under these conditions. These results suggest that it senses when soluble electron acceptors are depleted and then synthesizes the appropriate appendages to search for, and establish contact with, insoluble Fe(III) or Mn(IV) oxide. Anaeromyxobacter dehalogenans 2CP-C: utilizes halogenated compounds, such as 2-chlorophenol, 2,6-dichlorophenol, 2,5-dichlorophenol, and 2-bromophenol, as growthsupporting electron acceptors (halorespiration). Anaeromyxobacter dehalogenans exhibits metabolic versatility, and grows under a variety of redox conditions. Oxidized metal species such as U(VI) and Fe(III) (including ferric oxyhydroxide), anthraquinone disulfonate (AQDS), halogenated phenols, oxygen, nitrate, nitrite, and fumarate are used in terminal electron accepting processes (TEAPs). Also, Anaeromyxobacter dehalogenans demonstrates great electron donor versatility, and couples electron acceptor reduction to the oxidation of a variety of compounds including formate, hydrogen, acetate, succinate, pyruvate, and glucose. A. dehalogenans tolerates high concentrations of reduced products such as phenol or ammonium and has been found to be the predominant metal reducing populations at uranium-contaminated sites that are characterized by changing redox conditions and low pH. A feature that distinguishes A. dehalogenans from other reductively dechlorinating and metal-reducing populations is this organism's ability to both use acetate and hydrogen as a source of reducing equivalents. Sequencing its genome will provide relevant information regarding reductive dehalogenase genes and the organization of reductive dehalogenase operons. Such information is critical for the design of nucleic acid-based tools to detect, monitor and quantify functional genes involved in reductive dechlorination processes at contaminated sites. Shewanella denitrificans: are facultatively anaerobic, Gram-negative bacteria, motile by polar flagella, rod-like, and generally associated with aquatic or marine environments. They are capable of using a variety of compounds as electron acceptors, including oxygen, iron, manganese, uranium, nitrate, nitrite, fumarate, to name but a few. This ability makes Shewanella important for bioremediation of contaminated metals and radioactive wastes. The genus Shewanella comprises 36 recognized and hundreds of uncharacterized cultivable species. A denitrifying estuarine bacterium, Shewanella denitrificans was isolated from the oxic--anoxic interface of an anoxic basin of the central Baltic Sea. It is an unpigmented, polarly flagellated, mesophilic, facultatively anaerobic bacterium, able to use nitrate, nitrite and sulphite as electron acceptors. Pelobacter propionicus DSM 2379: This species is ubiquitous in both marine and fresh water, and in anaerobic sediments. It is able to convert the unsaturated hydrocarbon acetylene to acetate and ethanol via acetylaldehyde as an intermediate. These microorganisms may survive in some sediments as an Fe(III) or elemental sulfur reducer as well as growing fermentatively as an ethanol-oxidizing acetogen. Organisms that can completely oxidize organic acids with Fe(III) serving as the sole electron acceptor are responsible for most of the oxidation of organic matter in anaerobic sediments. Treponema denticola: is a spirochete found in the oral cavity of humans. It is associated with periodontal disease, an inflammation of gum tissue that often precedes bone resorption and tooth loss. Desulfotomaculum reducens: was isolated from heavy metal-contaminated sediment collected at the Mare Island Naval Shipyard on the San Francisco Bay. Desulfotomaculum reducens is able to reduce uranium and chromium making it a potential agent for the bioremediation of heavy metals. Rhodoferax ferrireducens T118: is a Gram-negative, motile, short rod with a single polar flagellum. It grows between pH 6.7 and 7.1, with a temperature range of 4-30 degrees C. The optimal growth temperature is 25 degrees Celsius. Electron donors utilized with Fe(III) as the sole electron acceptor included acetate, lactate, malate, propionate, pyruvate, succinate and benzoate. None of the compounds tested was fermented. Unlike other species in this genus, Rhodoferax ferrireducens (strain DSM 15236 / ATCC BAA-621 / T118) seems not to be a phototroph and not to ferment fructose. Shewanella frigidimarina strain NCIMB 400: is a marine bacterium isolated from the North Sea, off the coast of Aberdeen, UK, which exhibits a high degree of respiratory flexibility. Dechloromonas aromatica strain RCB: is the only organism in pure culture that can oxidize benzene in the absence of oxygen. It can also oxidize aromatics such as toluene, benzoate, and chlorobenzoate. Benzene contamination is a significant problem worldwide. It is widely used in various manufacturing processes and is also a primary component of petroleum-based fuels. Benzene is a highly soluble, mobile, toxic, and stable hydrocarbon especially in ground and surface waters. It is poorly biodegraded in the absence of oxygen. Rhodopseudomonas palustris BisB5: is a phototrophic, purple non-sulfur bacteria commonly found in soils and water. They fix carbon dioxide and nitrogen, produce hydrogen, and degrade diverse biomass-associated aromatic compounds under anaerobic (phototrophic) and aerobic (heterotrophic) conditions. Against the background of general metabolic versatility of the R. palustris species there is considerable strain-to-strain diversity. Desulfovibrio vulgaris subsp. vulgaris (strain DP4:) is an anaerobic bacterium phylogenetically associated with the delta subdivision of the Proteobacteria. Desulfovibrio vulgaris is a sulfate reducer commonly found in a variety of soil and aquatic environments. It respires by electron transfer using the heme group in c-type cytochromes, and can corrode metal by cathodic depolarization using the same process. Its preferred carbon substrates are lactate and pyruvate. The ability of this species to reduce Uranium (VI)ox to Uranium (IV)red makes it a good candidate for bioremediation of sites with uranium-contaminated groundwater. Metal corrosion, a problem that is partly the result of the collective activity of these bacteria, produces billions of dollars of losses each year to the petroleum industry. These organisms are also responsible for the production of poisonous hydrogen sulfide gas in marine sediments and in terrestrial environments such as drilling sites for petroleum products. Shewanella oneidensis MR-1: This organism is a facultative anaerobe that is capable of using a wide variety of terminal electron acceptors during anaerobic respiration which may make it valuable for bioremediation. Since the bacteria can reduce chromium and uranium from the liquid phase to form insoluble compounds, they may be used to eliminate these two environmental pollutants from water. Hahella chejuensis strain KCTC 2396: is a marine red-pigmented gammaproteobacterium belonging to the Oceanospiralles clade. It was originally isolated from the coastal marine sediment of the southernmost island in Korea. It consists of a single circular chromosome and contains 6783 predicted genes. H. chejuensis is a heterotrophic organism living on various resources from mineral to organic materials and even other aquatic organisms. It produces a red pigment, identified as prodigiosin, which has a very efficient lytic activity against the dinoflagellate Cochlodinium polykrikoides. Increases in the population of certain dinoflagellates result in phenomena called algal blooms or red tides, which have become more frequent in recent years throughout the world in the coastal waters. Red tides affect the health of human and marine organisms but also regional economies and marine ecosystems. Hahella chejuensis possesses a complete repertoire of enzyme for central carbon metabolism, including glycolysis, pentose phosphate pathway and TCA cycle as well as those required for biosynthesis of nucleotides and 20 amino acids. Two sets of genes coding for flagellar biosynthesis, type III secretion systems and F0F1-type ATP synthesis have been identified. This multiplicity is more likely to originate from horizontal transfer rather than from a gene duplication inside H. chejuensis genome. Horizontal gene transfer seems to have played an essential role in shaping H. chejuensis as it appears to have at least 69 genomic islands. Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255): is a Gram-negative, motile and spiral-shaped bacterium. It is able to grow under a broad range of conditions including aerobiosis and anaerobiosis. It can use fermentation or photosynthesis for producing energy when it grows anaerobically. It is able to grow on CO as sole source of energy. Its nitrogen fixation system consists of both a Mo-Fe and a Fe-only nitrogenases. 4) BACTERIA THAT INHABIT MULTIPLE AND/OR VARIABLE ENVIRONMENTS: GENOME SIZE (bps) MCPs/ GENOME GRAM Listeria monocytogenes str. 4b F2365 2905187 2 POSITIVE Novosphingobium aromaticivorans DSM 12444 3561584 5 NEGATIVE ALPHAPROTEOBACTERIA; Sphingomonadales WATER, OPORTUNISTIC PATHOGEN Campylobacter jejuni subsp. doylei 269.97 1845106 5 NEGATIVE EPSILONPROTEOBACTERIA; Campylobacterales FOOD CONTAMINANT, PATHOGEN Yersinia pseudotuberculosis IP 31758 4723306 5 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales UBIQUITOUS, FOOD AND WATER PATHOGEN Campylobacter curvus 525.92 1971264 6 NEGATIVE EPSILONPROTEOBACTERIA; Campylobacterales FOOD-BORNE PATHOGEN Burkholderia cenocepacia HI2424 3483902 8 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales SOIL, OPORTUNISTIC PATHOGEN Bordetella bronchiseptica strain RB50 5339179 8 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales OPORTUNISTIC PATHOGEN IN ANIMALS, RARE IN HUMANS, PERSIST IN ENVIRONMENT Leptospira interrogans serovar Lai str. 56601 4332241 8 NEGATIVE SPIROCHAETES; Spirochaetales; Leptospiraceae PATHOGEN, WATER Bacillus amyloliquefaciens FZB42 3918589 8 POSITIVE FIRMICUTES; Bacillales SOIL, PLANT-ASSOCIATED BACTERIAL STRAIN TAXONOMY FIRMICUTES; Bacillales LIFESTYLE SOIL, WATER, FOOD, PATHOGEN METABOLISM Bacillus subtilis subsp. subtilis str. 168 4215606 10 POSITIVE FIRMICUTES; Bacillales SOIL, SPORE-FORMING Bacillus thuringiensis str. Al Hakam 5257091 12 POSITIVE FIRMICUTES; Bacillales SOIL, SPORE-FORMING Yersinia enterocolitica subsp. enterocolitica 8081 4615899 12 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales WATER, NON-PATHOGEN AND OPORTUNISTIC PATHOGEN Citrobacter koseri ATCC BAA-895 4720462 14 NEGATIVE GAMMAPROTEOBACTERIA; Enterobacteriales Burkholderia pseudomallei 1106a 3100794 15 NEGATIVE BETAPROTEOBACTERIA; Burkholderiales SOIL, OPORTUNISTIC PATHOGEN PERIFERY DEEP SEA VENTS, WIDE RANGE OF ENVIRONMENTAL CONDITIONS SOIL, WATER, FOOD, OPORTUNISTIC MENINGITISCAUSATIVE AGENT IN NEONATES Idiomarina loihiensis L2TR 2839318 15 NEGATIVE GAMMAPROTEOBACTERIA; Alteromonadales Bacillus pumilus SAFR-032 3704465 16 POSITIVE FIRMICUTES; Bacillales Clostridium tetani E88 2799251 20 POSITIVE FIRMICUTES; Clostridiales SOIL, ANIMAL, HUMAN INTESTINES NEGATIVE GAMMAPROTEOBACTERIA; Pseudomonadales SOIL, MARSHES AND COASTAL MARINE HABITATS, AS WELL ON PLANTS AND ANIMAL TISSUES. BIOFILM FORMING. NEGATIVE GAMMAPROTEOBACTERIA; Vibrionales MARINE, FREE LIVING THROUGHOUT THE WATER COLUMN, SEDIMENTS, SURFACE OF MARINE Pseudomonas aeruginosa PAO1 Vibrio harveyi ATCC BAA-1116 6264404 3765351 25 25 AMINOACID FERMENTATION WIDE VARIETY OF SOILS, PLANT ROOTS AND ENVIRONMENTAL SURFACES AEROBIC OXIDATION OF MULTIPLE SUGARS, AMINOACIDS, ETC. ORGANISMS Arcobacter butzleri RM4018 2341251 29 NEGATIVE EPSILONPROTEOBACTERIA; Campylobacterales AQUATIC, POULTRY OPORTUNISTIC PATHOGEN, ALSO IN HUMANS Vibrio parahaemolyticus RIMD 2210633 3288558 30 NEGATIVE GAMMAPROTEOBACTERIA; Vibrionales VARIOUS LIFESTYLES: a PLANKTONIC, FREESWIMMING STATE; A SESSILE EXISTENCE ATTACHED TO SHELLFISH IN A COMMENSAL RELATION, TO THE BOTTOMS OF BOATS, OR TO OTHER SURFACES IN THE OCEAN; OR IN HOST ORGANISMS. IT HAS SEVERAL CELL TYPES. Wolinella succinogenes DSM 1740 2110355 31 NEGATIVE EPSILONPROTEOBACTERIA; Campylobacterales BOVINE RUMEN, ORAL CAVITY HUMANS, ORIGIN FROM SOIL Chromobacterium violaceum ATCC 12472 4751080 42 NEGATIVE BETAPROTEOBACTERIA; Neisseriales; ABUNDANT ENVIRONMENTAL, OPORTUNISTIC PATHOGEN Pseudomonas fluorescens Pf-5 7074893 42 NEGATIVE GAMMAPROTEOBACTERIA; Pseudomonadales PLANT COMENSAL RHIZOSPHERE NEGATIVE GAMMAPROTEOBACTERIA; Aeromonadales DIVERSE AQUATIC ENVIRONMENTS, EMERGING HUMAN PATHOGEN Aeromonas hydrophila subsp. hydrophila ATCC 7966 4744448 43 INFORMATION: Listeria monocytogenes str. 4b F2365: This organism, which causes listeriosis, is one of the leading causes of death from food-borne pathogens especially in pregnant women, newborns, the elderly, and immunocompromised individuals. It is found in environments such as decaying vegetable matter, sewage, water, and soil, and it can survive extremes of both temperatures (1-45C) and salt concentration marking it as an extremely dangerous food-born pathogen, especially on food that is not reheated. The bacterium can spread from the site of infection in the intestines to the central nervous system and the fetal-placental unit. Meningitis (inflammation of the membrane surrounding spinal cord and brain), gastroenteritis (inflammation of mucous membranes of stomach and intestine), and septicemia (systemic spread of bacteria and toxins in the blood) can result from infection. This organism is enteroinvasive, and utilizes an actin-based motility system by using a surface protein, ActA, that promotes actin polymerization, to spread intercellularly using the polymerized cytoskeletal protein as a "motor". There are 13 serovars associated with Listeria monocytogenes, and the serovar 4b strains are more commonly associated with invasive disease. Novosphingobium aromaticivorans DSM 12444: Gram-negative, non-spore forming rod displaying a single polar flagellum when it is motile. It is yellow pigmented and obligately aerobic. Unlike typical gram-negative bacteria, it does not have lipopolysaccharide, but rather glycosphingolipid, which is usually a membrane component of eukaryotic cells. The thermoreversible gel formation and solution viscosity properties of these glycosphingolipids (sphingans) make them of technical interest and useful in applications for a wide range of food and pharmaceutical products. The role of sphingans has been proposed to be important in colonization of eukaryotic organisms including plants, marine organisms, and humans by Novosphingobium. N. aromaticivorans strains have been isolated from a wide variety of sources including soil, both marine and fresh waters, marine life, and from plants. Many of the first isolates assigned to this genus (S. paucimobilis) were derived from human clinical specimens or water samples taken from hospital environments and members of this species have been subsequently shown to behave as opportunistic pathogens. More recently, N. aromaticivorans has been linked to the death of coral reefs off the Florida coast. Although there is an emerging role of Novosphingobium species in disease, members of this genus are best known for their ability to degrade a wide variety of aromatic hydrocarbons. Campylobacter jejuni subsp. Doyley: microaerophilic, flagellate, spiral bacterium, Campylobacter species are the leading cause of food-borne gastroenteritis in developed countries. Infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barre syndrome. Strain 269.97 is a representative of the C. jejuni subsp. doylei that causes bacteremia in South Africa. At the Red Cross Children's hospital in Cape Town, South Africa, C. jejuni subsp. doylei is isolated from blood more frequently than C. jejuni subsp. jejuni. Properties: Presence of flagella: Yes Yersinia pseudotuberculosis IP 31758: This organism was first isolated in 1883 by Malassez and Vignal and is termed pseudotuberculosis since it causes lesions in the lung that are similar to those observed during tuberculosis infection. It is ubiquitous in the environment and is a food and waterborne pathogen that affects animals as well as humans by causing gastroenteritis like Yersinia enterocolitica. Campylobacter curvus 525.92: microaerophilic, flagellate, spiral bacterium, Campylobacter species are the leading cause of food-borne gastroenteritis in developed countries. Infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barre syndrome. Like C. concisus, this Campylobacter species has been historically associated with periodontal disease, but has been recently isolated from human patients with gastroenteritis. This strain was isolated in South Africa from the feces of a patient with diarrhea. Burkholderia cenocepacia HI2424: These organisms are commonly found in soil and all are opportunistic pathogens especially in cystic fibrosis patients. Bordetella bronchiseptica: one of the few Bordetella that is capable of persisting in the environment, is rarely found in humans and is often associated with animals. This organism cause respiratory disease most commonly in pigs, rabbits and dogs. This disease in dogs (also called kennel cough) can be severe and a vaccine has been developed. Leptospira interrogans serovar Lai: Leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. Most infections are caused by either Leptospira borgpetersenii or Leptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. L. borgpetersenii uses a host-to-host mode of transmission, whereas L. interrogans is usually acquired from contaminated surface water. Two different strains of L. borgpetersenii serovar Hardjo have been sequenced that have distinct phenotypes and virulence. Strain JB197 was isolated from a beef steer at slaughter in the U.S.A., whereas strain L550 was isolated from a human in Australia who had contracted leptospirosis from infected cattle. These two strains have nearly identical genetic content, with subtle frameshift and point mutations being a common form of genetic variation. Starkly limited regions of synteny are shared between the large chromosomes of L. borgpetersenii and L. interrogans, probably the result of frequent recombination events between insertion sequences. The L. borgpetersenii genome is approximately 700 kb smaller and has a lower coding density than L. interrogans, indicating it is decaying through a process of insertion sequence-mediated genome reduction. Loss of gene function is not random but is centered on impairment of environmental sensing and metabolite transport and utilization. These features distinguish L. borgpetersenii from L. interrogans, a species with minimal genetic decay and that survives extended passage in aquatic environments before encountering a mammalian host. It is thought that L. borgpetersenii is evolving toward dependence on a strict host-to-host transmission cycle Bacillus amyloliquefaciens, strain FZB42: is a plant-associated bacterium, which stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. free-living soil bacteria known to promote plant growth and suppress plant pathogens. Bacillus amyloliquefaciens is able to degrade myo-inositol hexakisphosphate (phytate), making phosphorus more available to plants. This organism also produces antifungal and antibacterial substances, such as bacillomycin D, surfactin, and bacillaene, which protect the plant from pathogenic organisms. In addition, proteases and amylases produced by Bacillus amyloliquefaciens are used in industrial applications. Unlike the closely related B. subtilis 168, it lacks extended phage insertions. It possesses an unexpected potential to produce secondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5 percent of the genome is devoted to the synthesis of antibiotics and siderophores through pathways that do not involve ribosomes. Bacillus subtilis subsp. subtilis str. 168: Gram-positive harmless bacterium found in soil. Its cell envelope consists of a thick peptidoglycan wall and cell membrane. It is capable of producing endospores resistant to adverse environmental conditions such as heat and desiccation and is widely used for the production of enzymes and specialty chemicals. Bacillus thuringiensis: is a Gram-positive, spore-forming bacterium that belongs to the B. cereus group along with Bacillus anthracis and Bacillus cereus. This organism, also known as BT, is famous for the production of an insecticidal toxin. The bacterium was initially discovered as a pathogen of various insects and was first used as an insecticidal agent in the early part of this century. This organism, like many other Bacilli, is found in the soil, where it leads a saprophytic existence, but becomes an opportunistic pathogen of insects when ingested. Bacillus thuringiensis (strain Al Hakam) was collected at a suspected bioweapons facility in Iraq by the United Nations Special Commission. Yersinia enterocolitica subsp. enterocolitica 8081: This species is a food and waterborn pathogen that causes gastroenteritis (inflammation of the mucous membranes of the stomach and intestine) and is able to proliferate at temperatures as low as 4 C. This species is comprised of nonpathogenic strains and pathogenic strains that exclusively contain the plasmid pCD1/pYv. The latter are further subdivided into high and low pathogenic serotypes dependent on the presence or absence of an iron uptake system. Citrobacter koseri: previously known as Citrobacter diversus, Levinea diversus or Levinea malonatica resides in a wide range of environments, including soil, water and food products. It is an occasional inhabitant of human and animal intestines, but is mainly characterized as being a causative agent of neonatal meningitis with an extreme high rate of multiple brain abscess initiations and a concomitant high moratility rate. The bacteria are used in neonatal rat models to study the mechanism of blood-brain barrier penetration, host immune response evasion and its resistance to phagocytotic killing. Burkholderia pseudomallei: is an opportunistic pathogen and a common cause of human pneumonia and fatal bacteremias in endemic areas. Clinical manifestations of B. pseudomallei infection, a disease known as melioidosis, vary greatly from an asymptomatic state, to benign pneumonitis, to acute or chronic pneumonia, or to overwhelming septicemia. Treatment of melioidosis can involve up to nine months of antibiotic therapy, and relapse of the disease is common. The latency period of the organism may vary from two days to 26 years. It is endemic in Southeast Asia and northern Australia, but has also been found in Africa, the Middle East, Europe, Central and South America. Besides humans, melioidosis can affect animals such as sheep, goats, horses, swine, dogs and cats. Transmission occurs by contact with contaminated soil and water, through skin abrasions or inhalation of dust. In northeastern Thailand, B. pseudomallei accounts for 20% of bacterial septicaemias Idiomarina loihiensis: is a gamma-proteobacterium isolated recently from a hydrothermal vent at 1300-m depth on the Loihi submarine volcano in Hawaii. In contrast to obligate anaerobic vent hyperthermophiles, it inhabits partially oxygenated cold waters at the periphery of the vent and can survive a wide range of growth temperatures (from 4 degrees to 46 degrees Celsius) and salinities. I. loihiensis probably relies primarily on amino acid fermentation rather than on saccharolytic pathways for carbon and energy. Bacillus pumilus SAFR-032: This species is a naturally occurring, ubiquitous soil microorganism. Commonly found in a variety of food commodities, some strains have developed an increased tolerance to gamma irradiation. This bacterium colonizes the root zone of some plants, where it inhibits soil-borne fungal diseases and nematodes. It is also undergoing evaluation for commercial production of cellulase, an enzyme used for conversion of cellulolytic materials to soluble sugars or solvents. Bacillus pumilus is generally nonpathogenic in humans. Bacillus pumilus is a ubiquitous Gram-positive, aerobic, rod-shaped endospore-forming bacterium that can be isolated from a wide variety of soils, plants and environmental surfaces and even from the interior of Sonoran desert basalt. B. pumilus spores and vegetative cells show a resistance to UV radiation and H2O2 that is significantly higher than that of other Bacillus species. Isolates of B. pumilus were also recently recovered aboard the International Space Station from hardware surfaces and air particles. It is likely that these isolates were present in spacecraft assembly facilities as metabolically dormant spores. They were found in both unclassified (entrance floors, ante-room, and air-lock) and classified (floors, cabinet tops, and air) locations. As H2O2 is recommended for use in bioreduction of spacecraft components, repeated isolation of H2O2-resistant strains of this species in a clean-room is a concern because their persistence might potentially compromise life-detection missions, which have very strict cleanliness and sterility requirements for spacecraft hardware. Spore-forming microbes recovered from spacecraft surfaces and assembly facilities were exposed to simulated Mars UV irradiation. The effects of UVA (315-400 nm), UVA+B (280400 nm) and full spectrum (200-400 nm), at intensities expected to strike Mars, on the survival of microorganisms showed that spores of Bacillus species isolated from spacecraft associated surfaces were more resistant than a standard dosimetric strain, B. subtilis 168. Among all Bacillus species tested, spores of Bacillus pumilus (strain SAFR-032) showed the highest resistance to all three UV bandwidths as well as the total spectrum. Paradoxically, B. pumilus lacks several DNA repair and oxidative stress response genes found in B. subtilis and B. licheniformis." Clostridium tetani: is an anaerobic spore-forming bacterium whose natural habitat is soil and animal and human intestines. It is the causative agent of tetanus disease which is one of the most dramatic and prevalent diseases of human and vertebrate animals and has been reported for over 24 centuries. It is caused by the tetanus toxin, the second most poisonous substance known. This disease is controlled through immunization with tetanus toxoid (TT), however according to the WHO about 400,000 cases occur each year, mainly of neonatal tetanus. Pseudomonas aeruginosa PAO1: Gram-negative rod-shaped bacterium that grows in soil, marshes and coastal marine habitats, as well on plants and animal tissues. It forms biofilms on wet surfaces such as those of rocks and soil. The emergence of P. aeruginosa as a major opportunistic human pathogen during the past century may be a consequence of its resistance to the antibiotics and disinfectants that eliminate other environmental bacteria. P. aeruginosa is now a significant source of bacteremia in burn victims, urinary-tract infections and hospital-acquired pneumonia in patients. It is also the predominant cause of morbidity and mortality in cystic fibrosis patients. Almost all strains are motile by means of a single polar flagellum, and some strains have two or three flagella. P. aeruginosa is a nonfermentative aerobe that derives its energy from oxidation rather than fermentation of carbohydrates. Although able to use more than 75 different organic compounds, it can grow on media supplying only acetate for carbon and ammonium sulfate for nitrogen. Most strains of P aeruginosa produce one or more pigments, the most common being pyocyanin (a phenazine pigment). Vibrio harveyi: These bacteria are known to form associations with eukaryotes, either as commensals in the intestinal flora of marine animals, as opportunistic pathogens or as primary pathogens of many commercially cultured invertebrate species. Although closely related to the human pathogen V. parahaemolyticus, V. harveyi is not known as a human pathogen. This is one of the first organisms in which quorum sensing (bacterial cell to cell communication via secreted signaling molecules that are used to synchronize community behavior by regulating gene expression) was described. Quorum sensing is known to regulate a number of genes in V. harveyi including those of the lux operon whose products are responsible for the bioluminescence characteristic of this species.. Within the aqueous environment, this free living organism can be found throughout the water column, buried in the sediment, as well as on the exterior surfaces of marine organisms. Unlike the related bacterial species, Vibrio fischeri, which forms a mutualistic association with a squid species, Vibrio harveyi does not form any symbiotic relationship with any other organism. However, there is one well documented example of a relationship with another microorganism causing a phenomenon known as the Milky Sea effect. This occurs when large areas of the ocean are filled with luminescing V. harveyi living in association with colonies of the microalga Phaeocystis. Arcobacter butzleri: formerly named Campylobacter butzleri, is a Gram-negative rod isolated from aqueous environments. It is also present in different breeding animals and in a great variety of retail meats, including chicken, beef, pork, and lamb, with a high prevalence in poultry. A. butzleri can grow at all oxygen concentration and with a temperature range between 15 and 37 degrees Celsius. It has been associated with abortion and enteritis in animals and with diarrhea and bacteremia in adults and children. An important source of human contamination may be food. Vibrio parahaemolyticus is a major causative agent of gastroenteritis, particularly in areas with high seafood consumption. This organism naturally inhabits marine and estuarine environments. It seems suited to various lifestyles: a planktonic, free-swimming state; a sessile existence attached to shellfish in a commensal relation, to the bottoms of boats, or to other surfaces in the ocean; or in host organisms. It has several cell types such as the swimmer cell and the swarmer cell, and it can exist in a viable but non-culturable state. Wolinella succinogenes is most commonly isolated from the bovine rumen and is considered nonpathogenic, however, this organism has also been isolated from the human gingiva and dental root canal infections. It possesses a set of genes for N2 fixation taken from rhizobium, and is a close relative of campilobacter, which suggests a soil-free living evolutionary origin Chromobacterium violaceum: This facultative organism is an abundant environmental bacterium that lives in tropical and subtropical regions in the soil and water. It has exploitable properties including the ability to produce a bactericidal purple pigment, violacein, as well as the ability to produce a bioplastic and to biologically solubilize gold from the environment. It is occasionally pathogenic in immunocompromised individuals or children where it may cause diarrhea, but sometimes causes septicemia and is at times fatal. Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere of many plants and suppresses plant diseases caused by soilborne plant pathogens. It produces several antibiotics and secondary metabolites. Comparisons of the 3 available strains (as of June 2009, SBW25, Pf-5 and Pf0-1) indicate they share only 61% of their genes, most of which cluster near the origin of replication. In fact, the three P. fluorescens strains could be different species. Aeromonas hydrophila: Aeromonas spp. are ubiquitous bacteria found in diverse aquatic environments worldwide, such as bottled water, chlorinated water, well water and heavily polluted waters. Aeromonas hydrophila survives easily in waters polluted by feces and seems resistant to various disinfectants, insecticides and chemicals. High numbers of Aeromonas spp. were recorded in floodwater samples in New Orleans following hurricane Katrina and they were the most common cause of skin and soft tissue infections among the survivors of the 2004 tsunami in Thailand. Aeromonas spp. cause infections in invertebrate and vertebrate such as frogs, birds and domestic animals. Infection in various fish species can result in hemorrhagic disease and furunculosis. Although Aeromonas was originally considered an opportunistic pathogen in immunocompromised humans, increasing cases of intestinal and extraintestinal disease suggest that it is an emerging human pathogen irrespective of the host's immune system. This organism has been included in the Contaminant Candidate List by the Environmental Protection Agency. Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240) was originally isolated from "a tin of milk with a fishy odor". Its genome is comprised of a single circular 4.74 Mb-chromosome. No transposase, resolvase or insertion sequence element was found in the genome. A type II secretion system and genes homologs to the vas genes proposed to encode a prototypic type VI secretion system were identified but a type III secretion system is surprisingly absent. The genes for the polar flagellum are found in four main clusters. It seems well-equipped to counter an attack of antibacterial factors as beta-lactamases, chloramphenicol acetyltransferases and other proteins that could confer resistance to bicyclomicin, fosmidomycin and aminoglycosides are present. A peptide intake transport system may play a role in resistance to antimicrobial peptides and drug efflux transporters may confer further resistance to other classes of antibiotics and toxins. A four-gene arsenical resistance operon that may pump arsenite or antimonite out of the cell has been found. Numerous amino acid and peptide transporters and relatively few sugar uptake systems are present. Both Sec and Tat secretion systems have been identified. Complete multistep pathways for synthesizing all amino acids are predicted. A selenocysteine incorporation system, selABC, is present although only a single selenoprotein, the alpha subunit of format dehydrogenase, is predicted. A. hydrophila possesses a polyhydroxyalkanoic acid storage granule system for nitrogen limitation-induced storage and a glycogen system for carbohydrate storage and mobilization. Many chitin-degrading enzymes have been predicted in addition to the characterized extracellular chitinase Chi192 and chitobiase. 5) BACTERIA WITH COMPLEX BEHAVIOR, LIFE CYCLES OR ABLE TO ACTIVELY ESTABLISH COMPLEX SYMBIOTIC INTERACTIONS: BACTERIAL STRAIN GENOME SIZE (bps) MCPs/ GENOME GRAM TAXONOMY Sinorhizobium meliloti 1021 3654135 9 NEGATIVE Alphaproteobacteria; Rhizobiales SOIL, SIMBIOSIS WITH PLANT ROOTS Sinorhizobium medicae WSM419 3781904 10 NEGATIVE Alphaproteobacteria; Rhizobiales SOIL, PLANT ROOT SIMBIONT, N2 FIXING Bacillus subtilis subsp. subtilis str. 168 4215606 10 POSITIVE FIRMICUTES; Bacillales SOIL, SPORE-FORMING Bacillus thuringiensis str. Al Hakam 5257091 12 POSITIVE FIRMICUTES; Bacillales SOIL, SPORE-FORMING Caulobacter crescentus CB15 4016947 18 NEGATIVE Alphaproteobacteria; Caulobacterales AQUATIC, UNDERGOES DEVELOPMENTAL AND DIFFERENTIATION CYCLES Agrobacterium tumefaciens str. C58 2841580 19 NEGATIVE Alphaproteobacteria; Rhizobiales SOIL, PLANT PATHOGEN Bdellovibrio bacteriovorus strain HD100 3782950 20 NEGATIVE Deltaproteobacteria; Bdellovibrionales BACTERIAL PREDATOR Myxococcus xanthus DK 1622 9139763 21 NEGATIVE Deltaproteobacteria; Myxococcales SOIL, DEVELOPMENTAL CHANGES Azoarcus sp. BH72 4376040 24 NEGATIVE Betaproteobacteria; Rhodocyclales MUTUALISTIC N2-FIXING ENDOPHYTE LIFESTYLE METABOLISM WIDE VARIETY OF ORGANIC COMPOUNDS AS C SOURCE Rhizobium leguminosarum 4381608 27 NEGATIVE Alphaproteobacteria; Rhizobiales Magnetococcus sp. MC-1 4719581 32 NEGATIVE Proteobacteria Pseudomonas stutzeri A1501 4567418 33 NEGATIVE Gammaproteobacteria; Pseudomonadales Bradyrhizobium japonicum USDA 110 9105828 35 NEGATIVE Alphaproteobacteria; Rhizobiales Vibrio fischeri ES114 2897536 43 NEGATIVE Gammaproteobacteria; Vibrionales SOIL-DWELLING, SYMBIOTIC N2FIXING BACTERIUM, IS THE MAIN NODULATOR OF Phaseolus vulgaris AQUATIC ANAEROBIC, POLAR MAGNETO AEROTAXIS, PHOTOTAXIS S2 AND TIOSULFATE AS ELECTRON DONORS, CO2 FIXATION MUTUALISTIC N2-FIXING IN THE RICE ROOTS ROOT N2 FIXING NODULES IN SOYBEAN MARINE, SIMBIONT IN FISH AND SQUIDS, COMPLEX SIGNALS INFORMATION: Sinorhizobium meliloti 1021: This organism, much like other Rhizobia, forms a symbiotic relationship with a leguminous plant, in this case the alfalfa plant (Medicago sativa). The bacterium recognizes plant flavonoid compounds, which turn on nodulation genes. Expression of nodulation genes results in production of a nodulation signal which the plant cell recognizes inducing root nodule formation. The bacterium is endocytosed and remains in a membrane-bound vesicle where it differentiates into a nitrogen-fixing bacteroid. The plant cell provides carbon compounds for the bacterium to grow on. Sinorhizobium medicae WSM419: originally known as Rhizobium meliloti WSM419, is an acid-tolerant strain originally isolated from acidic soil in Sardinia. It is a motile, non-sporeforming, rod-shaped bacteria. It nodulates Medicago spp., is used to inoculate these plants commercially, and is thus studied for its acid-tolerance. It was placed in a new taxon based on phenotypic and phylogenetic studies of the 16S gene. It has one chromosome and three plasmids. Bacillus subtilis subsp. subtilis str. 168: Gram-positive harmless bacterium found in soil. Its cell envelope consists of a thick peptidoglycan wall and and cell membrane. It is capable of producing endospores resistant to adverse environmental conditions such as heat and desiccation and is widely used for the production of enzymes and specialty chemicals. Bacillus thuringiensis: is a Gram-positive, spore-forming bacterium that belongs to the B.cereus group along with Bacillus anthracis and Bacillus cereus. This organism, also known as BT, is famous for the production of an insecticidal toxin. The bacterium was initially discovered as a pathogen of various insects and was first used as an insecticidal agent in the early part of this century. This organism, like many other Bacilli, is found in the soil, where it leads a saprophytic existence, but becomes an opportunistic pathogen of insects when ingested. Bacillus thuringiensis (strain Al Hakam) was collected at a suspected bioweapons facility in Iraq by the United Nations Special Commission. Caulobacter crescentus: also known as Caulobacter vibroides, inhabits aquatic environments and plays an important part in biogeochemical cycling of organic nutrients. This bacterium undergoes an unusual developmental cycle in which a swarming motile cell becomes a stalked cell that is attached to a solid surface. The stalked cell then undergoes asymmetric cell division and produces one flagellated motile daughter cell and one stalked daughter cell. The stalked cell immediately undergoes replication and division, while in the swarmer cell these processes are inhibited. Thus, the asymmetric processes in this organism provide useful models for differentiation and development. Differentiation is managed through a control circuit that is comprised of various switches that regulate, through temporal expression, phosphorylation, and targeted proteolysis, the developmental process. This organism also contains a number of energy-dependent transport system, presumably enabling growth in the substrate-sparse aquatic environments that it lives in. Agrobacterium tumefaciens str. C58: This organism produces tumors (galls) near the top (crown) of dicotyledonous plants and can devastate crops worldwide. Commonly found in the region around plant roots, this organism is similar to bacteria from the Rhizobium genus that form nitrogen-fixing nodules in the roots of various leguminous plants. Both the crown gall and nodule formation genes are contained on plasmids. In the case of Agrobacterium, the DNA is carried on a large conjugative plasmid termed the Ti (tumor-inducing) plasmid. This plasmid is capable of lateral transfer from one Agrobacterium to another, but is also capable of transferring a piece of DNA, the T-DNA (transferred DNA), to the plant cell nucleus. The T-DNA contains genes for expression of various metabolites which the bacterium then uses to grow on. Bdellovibrio bacteriovorus is a tiny and highly motile delta-proteobacterium that preys on other Gram-negative bacteria. Bdellovibrio bacteriovorus attaches itself to the cell wall of its prey and invades the cell where it goes through a full-life cycle. After it reproduces, the offspring burst out of the cell. Despite its small size, it has a relatively large genome encoding more than 3500 proteins. Myxococcus xanthus is a Gram-negative rod-shaped bacterium. Under starvation conditions, it undergoes a developmental process in which roughly 100,000 individual cells aggregate to form a structure called the fruiting body. Inside this structure, rod-shaped cells differentiate into spherical, thick-walled spores. Biochemical changes, such as the synthesis of new proteins and alterations in the cell wall, occur in parallel to the morphological changes. During the aggregation of M. xanthus cells into fruiting bodies, dense ridges of cells appear to move in traveling waves called ripples. Coordinated cell motility, or swarming, also occurs during vegetative growth, facilitating predatory feeding by increasing the extracellular concentration of digestive enzymes secreted by the bacteria. M. xanthus moves across surfaces by means of a poorly understood mechanism known as gliding motility. Azoarcus sp. strain BH72 is a mutualistic N2-fixing endophyte of salt-tolerant Kallar grass (Leptochloa fusca (L.) Kunth), a grass gowing in the Punjab of Pakistan. Endophytes are bacteria that live within the tissues of plants without causing them any harm; Azoarcus resides within the roots of its host. Azoarcus sp. strain BH72 is also capable of endophytic N2 fixation in rice and sugarcane. The bacterium has not been detected in root-free soil, although it is able to be cultured. It does not however excrete significant amounts of nitrogenous compounds in culture. The genome sequence has shown that Azoarcus has very few mobile genetic elements, or phage-related genes, suggesting its adaptation to a fairly stable, lowstress environment. The sec-dependent, SRP-mediated and Tat systems for protein secretion are all present, in addition to a type I, the type IIb secretion systems and an autotransporter. However it is lacking both type III and type IV secretion systems, suggesting it can not export proteins to its host, and indeed it does not seem to encode toxin-producing genes. Type IV pili are present and are known to be important to colonization of grasses. It is unable to metabolize carbohydrates and is lacking cell-wall degrading enzymes, which probably contributes to its ability to colonize its host at very high density without being pathogenic. Rhizobium leguminosarum: a soil-dwelling, symbiotic nitrogen-fixing bacterium, is the main nodulator of Phaseolus vulgaris, the common bean. It contains one chromosome and 6 large plasmids, which contribute approximately one third of the genome. This strain is of considerable agronomic importance. Magnetococcus sp. MC-1: The Gram-negative magnetotactic bacteria Magnetococcus sp. are obligatory microaerophilic cocci phylogenetically associated with the alpha subdivision of the Proteobacteria. They use thiosulfate or sulfide as electron sources, while appearing to grow autotrophically, utilizing CO2 as the carbon source and producing internal sulfur globules. Cells of strain MC-1 are 1-2 microns in diameter and motile with two bundles of flagella located on one side of the cell, a flagellar pattern referred to as bilophotrichous. Each cell usually contains a single chain of membrane-bounded magnetite crystals (magnetosomes). Like all magnetotactic bacteria, cells of strain MC-1 produce only one crystal morphology, in this case, elongated pseudo hexahedral prisms of magnetite. This magnetite morphology is unusual and indicates that the biomineralization processes involved in magnetosome synthesis in this bacterium are under a high degree of genetic. There are typically 5 to 14 crystals per cell. Like other magnetotactic bacteria (e.g., Magnetospirillum magnetotacticum), Magnetococcus sp. use the chain of magnets as a compass to find favorable environmental conditions, the oxic-anoxic interface, by swimming along the Earth's geomagnetic field lines. However, unlike cells of M. magnetotacticum, which swim in both directions under oxic conditions, cells of MC-1 display a polar preference. It has been shown that magnetotaxis works in conjunction with aerotaxis. Cells of M. magnetotacticum appear to use the Earth's magnetic field lines as an axis for alignment and to rely on a temporal sensory mechanism of aerotaxis to find and maintain an optimal position in oxygen gradients; this is referred to as axial magneto-aerotaxis. Cells of MC-1 use the magnetic field directionally and appear to have a novel aerotactic sensory mechanism that seems to function as a two-way switch; this is referred to as polar magneto-aerotaxis. Cells of MC-1 also exhibit a response to short-wavelength light (<500 nm), which causes them to swim persistently parallel to the magnetic field during illumination. Pseudomonas stutzeri (strain A1501) is an aerobic bacterium phylogenetically associated with the gamma subdivision of the Proteobacteria. This strain was isolated from rice roots that had been inoculated with strain A15 in a rice paddy in China. It is considered wild-type, has been studied for the nitrogen-fixation process and is used as an inoculant during rice cultivation. Bradyrhizobium japonicum: a member of rhizobia, has an ability to form root nodules on soybeans (Glycine max). B. japonicum strain USDA 110, which was originally isolated from soybean nodule in Florida, USA in 1957, has been widely used for the purpose of molecular genetics, physiology, and ecology, because this strain is superior at symbiotic nitrogen fixation with soybeans as compared with other strains. Vibrio fischeri ES114: This organism is found in marine environments and was originally named by Bernard Fischer during a sea voyage in the 1800s. It is a symbiont in fish and squids and is responsible for light generation in those organisms, which use it as a defense mechanism to avoid predators. The bioluminescent mechanism is a product of the lux operon, an operon that is used extensivley in molecular biology as a marker. The steps in establishment of the symbiotic relationship are quite complex and involve communication between the bacterium and the host prior to colonization of the light organ by the bacterium.
