Heliothrix oregonensis,gen. nov., sp. nov., a phototrophic filamentous gliding bacterium containing bacteriochlorophyll a

An unusual filamentous, gliding bacterium was found in a few hot springs in Oregon where it formed a nearly unispecific top layer of microbial mats. It contained a bacteriochlorophyll a-like pigment and an abundance of carotenoids. There were no chlorosomes or additional chlorophylls. The organism was aerotolerant and appeared to be photoheterotrophic. It was successfully co-cultured with an aerobic chemoheterotroph in a medium containing glucose and casamino acids. Although it has many characteristics in common with the genus Chloroflexus, the lack of chlorosomes and bacteriochlorophyll c and the aerobic nature of this organism indicate that it should be placed in a new genus. This conclusion is supported by 5S rRNA nucleotide sequence data.     

Chimaereicella alkaliphila gen. nov., sp. nov., a Gram-negative alkaliphilic bacterium isolated from a nonsaline alkaline groundwater

A Gram-negative bacterium designated AC-74(T) was isolated from a highly alkaline groundwater environment (pH 11.4). This organism formed rod-shaped cells, is strictly aerobic, catalase and oxidase positive, tolerates up to 3.0% NaCl, has an optimum growth temperature of 30 degrees C, but no growth occurs at 10 or 40 degrees C, and an optimum pH value of 8.0, but no growth occurs at pH 7.0 or 11.3. The predominant fatty acids are iso-15:0, iso-17:1 omega9c and 16:1 omega7c and or iso-15:2OH. The G+C content of DNA was 43.5mol%. The phylogenetic analyses of the sequences of the 16s RNA genes indicated that strain AC-74(T) belongs to the family "Flexibacteriaceae" and is phylogenetically equidistant ( approximately 94.5%) from the majority of the species of the genus Algoriphagus and from the genus Hongiella. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain AC-74(T), represents a new species of the novel genus for which we propose the name Chimaereicella alkaliphila gen. nov., sp. nov.     

Ruminococcus luti sp. nov., isolated from a human faecal sample

A strain of an unidentified strictly anoxic, gram-postive, non-motile Ruminococcus-like bacterium was isolated from a human faecal sample. The organism used carbohydrates as fermentable substrates, produced acetate, succinate, and hydrogen as the major products of glucose metabolism, and possessed a G + C content of 43.3 mol%. The morphological and biochemical characteristics of the organism were consistent with its assignment to the genus Ruminococcus but it did not correspond to any recognized species of this genus. Comparative 16S rRNA gene sequencing showed the unidentified bacterium represents a previously unrecognised sub-line within the Clostridium coccoides rRNA group of organisms. The nearest relative of the unknown bacterium corresponded to Ruminococcus obeum but a 16S rRNA sequence divergence value of >3% demonstrated it represents a different species. Based on the presented findings a new species, Ruminococcus luti, is described. The type strain of Ruminococcus luti is BInIX(T) (DSM 14534T, CCUG 45635T).     

Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.

On the basis of phenotypical characteristics and analysis of 16S rRNA sequence, a new species belonging to a new genus is described, and the name Marinobacter hydrocarbonoclasticus is proposed. This organism, isolated from Mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. It grows at NaCl concentrations of 0.08 to 3.5 M and uses various hydrocarbons as the sole source of carbon and energy. Its DNA has a guanine-plus-cytosine content of 52.7 mol%. The 16S rRNA analysis shows a clear affiliation between M. hydrocarbonoclasticus and the gamma group of the phylum Proteobacteria. A close phylogenetic relationship appears among the species Marinomonas vaga, Oceanospirillum linum, Halomonas elongata, and Pseudomonas aeruginosa. Because of the impossibility of finding a single most closely related species, we suggest that this bacterium be assigned to a new genus, at least temporarily. The possibility of a revision of this status when new data appear is, however, not excluded. The type strain is M. hydrocarbonoclasticus SP.17 (= ATCC 49840).     

Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources

During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed > 4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN243(T)).     

Thiocapsa halophila sp. nov., a new halophilic phototrophic purple sulfur bacterium

A new phototrophic sulfur bacterium has been isolated from a red layer in a laminated mat occurring underneath a gypsum crust in the mediterranean salterns of Salin-de-Giraud (Camargue, France). Single cells were coccus-shaped, non motile, without gas vacuoles and contained sulfur globules. Bacteriochlorophyll a and okenone were present as major photosynthetic pigments. These properties and the G+C content of DNA (65.9–66.6 mol% G+C) are typical characteristics of the genus Thiocapsa. However, the new isolate differs from known species in the genus, particularly in NaCl requirement (optimum, 7% NaCl; range, 3–20% NaCl) and some physiological characteristics. Therefore, a new species is proposed, Thiocapsa halophila, sp. nov.Dedicated to Prof. Dr. Norbert Pfennig in occasion of his 65th birthday     

Halonatronum saccharophilum gen. nov. sp. nov.: A New Haloalkaliphilic Bacterium of the Order Haloanaerobiales from Lake Magadi

A new alkaliphilic and moderately halophilic chemoorganotrophic anaerobic bacterium (strain Z-7986), which is spore-forming, rod-shaped, and has a gram-negative cell wall pattern, was isolated from the coastal lagoon mud of the highly mineralized Lake Magadi (Kenya). The organism is an obligatorily carbonate- and sodium chloride-dependent motile peritrichously flagellated rod that grows within a 3–17% NaCl concentration range (with an optimum at 7–12% NaCl) and within a pH range of 7.7–10.3 (with an optimum at pH values of 8–8.5). It is a moderate thermophile with a broad temperature optimum at 36–55°C; maximum growth temperature is 60°C. The bacterium catabolizes glucose, fructose, sucrose, maltose, starch, glycogen, N-acetyl-D-glucosamine, and, to a slight degree, peptone and yeast extract. Its anabolism requires yeast extract or casamino acids. Glucose fermentation yields formate, acetate, ethanol, H₂, and CO₂. The bacterium is sulfide-tolerant and capable of the nonspecific reduction of S⁰ to H₂S. The G+C content of the DNA is 34.4 mol %. The analysis of the 16S rRNA sequence revealed that strain Z-7986 belongs to the order Haloanaerobiales and represents a new genus in the family Halobacteroidaceae. We suggest the name Halonatronum saccharophilum gen. nov. sp. nov. The type strain of this species is Z-7986^T (= DSM13868, = Uniqem*211).     

Psychrophilic Planococcus maitriensis sp.nov. from Antarctica

An orange pigmented bacterium, S1, was isolated from a cyanobacterial mat sample collected in the vicinity of Schirmacher Oasis, Maitri, the Indian station, in Antarctica. The bacterium is Gram-positive and possesses all the characteristics of the genus Planococcus. It is non-sporulating, motile and has A4alpha type peptidoglycan, MK-7 and MK-8 as the major menaquinones and anteiso-C(15:0) as the major fatty acid. Based on the phylogenetic characteristics, the bacterium S1 is identified as a close relative of Planococcus citreus with which it shares 98.12% similarity at the 16S rRNA gene level but exhibits a low similarity of 52% at the whole genome level. Apart from the above major differences, S1 also exhibits phenotypic differences with Planococcus citreus and other members of the genus Planococcus. Based on these differences, the bacterium S1 is identified as a new species of the genus Planococcus for which the name Planococcus maitriensis is proposed. The type strain of Planococcus maitriensis is S1(T) (= MTCC 4827; DSM 15305).     

Aureobacterium resistens sp. nov., exhibiting vancomycin resistance and teicoplanin susceptibility

Two similar strains of a coryneform bacterium were isolated from human clinical material. Both strains were resistant to vancomycin but susceptible to teicoplanin. Detailed biochemical, chemotaxonomical, and molecular genetic investigations revealed that both isolates were members of a hitherto undescribed species of the genus Aureobacterium. The name Aureobacterium resistens sp. nov. is proposed for the new bacterium and the type strain is CCUG 38312.     

A new purple sulfur bacterium from stratified freshwater lakes,Amoebobacter purpureus sp. nov.

Six strains of a new purple sulfur bacterium were isolated from the chemocline of four different freshwater lakes. Single cells were spherical to oval, nonmotile and contained gas vacuoles in the central part of the cytoplasm. All strains contained bacteriochlorophyll a and okenone as the major carotenoid. The intracytoplasmic membrane system was of vesicular type. All strains resembled each other in growth conditions and utilization of simple organic carbon sources. The strains were able to grow microaerophilic in the dark, used hydrogen sulfide, elemental sulfur or thiosulfate as electron donor, and lacked assimilatory sulfate reduction. On the basis of all characteristics the new bacterium represents a new species of the genus Amoebobacter, A. purpureus sp. nov.     

Malonomonas rubra gen. nov. sp. nov., a microaerotolerant anaerobic bacterium growing by decarboxylation of malonate

From anoxic marine sediment samples, new anaerobic, microaerotolerant, Gram-negative, non-sporeforming bacteria were isolated which grew in mineral medium with malonate as sole source of carbon and energy. Cells were motile thin rods, often forming large aggregates. Malonate was decarboxylated to acetate with concomitant growth yields of 1.9–2.1 g dry cell matter per mol malonate degraded. Fumarate and malate were fermented to succinate and CO₂. No other substrates were used. No inorganic electron acceptors were reduced. At least 150 mM NaCl was required for growth with either substrate. High amounts of a periplasmic cytochrome c were detected, as well as small amounts of a membrane-bound cytochrome b. All enzymes of the citric acid cycle were found to be present. The DNA base ratio was 48.3 mol% guanine plus cytosine. Since this new bacterium cannot be affiliated with any of the known genera and species, a new genus and species, Malonomonas rubra is proposed.     

Desulfamplus magnetovallimortis gen. nov., sp. nov., a magnetotactic bacterium from a brackish desert spring able to biomineralize greigite and magnetite,that represents a novel lineage in the Desulfobacteraceae

A magnetotactic bacterium, designated strain BW-1^T, was isolated from a brackish spring in Death Valley National Park (California, USA) and cultivated in axenic culture. The Gram-negative cells of strain BW-1^T are relatively large and rod-shaped and possess a single polar flagellum (monotrichous). This strain is the first magnetotactic bacterium isolated in axenic culture capable of producing greigite and/or magnetite nanocrystals aligned in one or more chains per cell. Strain BW-1^T is an obligate anaerobe that grows chemoorganoheterotrophically while reducing sulfate as a terminal electron acceptor. Optimal growth occurred at pH 7.0 and 28 °C with fumarate as electron donor and carbon source. Based on its genome sequence, the G + C content is 40.72 mol %. Phylogenomic and phylogenetic analyses indicate that strain BW-1^T belongs to the Desulfobacteraceae family within the Deltaproteobacteria class. Based on average amino acid identity, strain BW-1^T can be considered as a novel species of a new genus, for which the name Desulfamplus magnetovallimortis is proposed. The type strain of D. magnetovallimortis is BW-1^T (JCM 18010^T–DSM 103535^T).     

Botryozyma nematodophila gen. nov., spec. nov. (Candidaceae)

The new genusBotryozyma with a single species,B. nematodophila is proposed for two isolates from nematodes (Panagrellus zymosiphilus) occurring in grapes with sour-rot. The new genus has typical ascomycetous characteristics and, being unable to produce ascospores, is placed in the family Candidaceae.     

Sedimenticola selenatireducens, gen. nov., sp. nov., an anaerobic selenate-respiring bacterium isolated from estuarine sediment

The respiration of selenate, as a terminal electron acceptor has been known for over a decade, but the microorganisms involved in this respiration are largely unknown. Here we characterize a novel selenate-respiring bacterium, strain AK4OH1, isolated from an estuarine sediment enrichment culture. Strain AK4OH1 has the unique capability to oxidize aromatic acids, such as benzoate, 4-hydroxybenzoate and 3-hydroxybenzoate, coupled to selenate respiration. This novel respiratory coupling has not been described before. Reduction of selenate is followed by stoichiometric accumulation of selenite. The strain grows in agar shake tubes forming bright red colonies due to precipitation of elemental selenium. Strain AK4OH1 is a strictly anaerobic bacterium, which can also respire nitrate and nitrite via denitrification. Analysis of the 16S rRNA gene sequence shows that this strain clusters with another selenate-reducing bacterium and a (per) chlorate reducing bacterium, within the Gammaproteobacteria, along with symbionts of bivalves and tubeworms. Based on its unique physiological capabilities and its 16S rRNA gene sequence phylogeny, we classify this strain AK4OH1 as a new genus and species with the proposed name Sedimenticola selenatireducens.     

Alkanindiges hongkongensis sp. nov. A novel Alkanindiges species isolated from a patient with parotid abscess

A bacterium was isolated from the abscess pus of a 72-year-old patient with Warthin's tumor and parotid abscess. The cells were aerobic, non-motile, Gram-negative but difficult to be destained, non-sporulating, coccobacillus. The bacterium grew poorly on sheep blood agar and MacConkey agar as non-hemolytic colonies of 0.5 mm in diameter after 24h of incubation at 37 degrees C in ambient air. Growth was enhanced by Tween 80. It produces catalase but not cytochrome oxidase. Sequencing of the cloned 16S rRNA PCR products of the bacterium revealed three different 16S rRNA gene sequences, with 12 - 31 bp differences among them. Phylogenetic analysis showed that the bacterium is closely related to Alkanindiges illinoisensis, with 5.0 - 5.9% differences between the 16S rRNA gene sequence of the bacterium and that of A. illinoisensis. Tryptophan auxotrophic strain of Acinetobacter trpE27 transformed with DNA extracted from the bacterium was unable to grow on tryptophan deficient medium, indicating that the bacterium was not a strain of Acinetobacter. The G+C content of the bacterium (mean +/-SD) was 46.9+4.3%. A new species, Alkanindiges hongkongensis sp. nov., is proposed, for which HKU9T is the type strain. Isolates with "small colonies" that are apparently Acinetobacter-like species should be carefully identified. Growth enhancement with aliphatic hydrocarbons should be looked for and 16S rRNA gene sequencing performed in order to find more potential cases of Alkanindiges infections, as well as to define the epidemiology, clinical spectrum, and outcome of infections associated with this genus.     

Improved technique for the isolation of magnetotactic spirilla from a freshwater sediment and their phylogenetic characterization.

An improved technique for the isolation of magnetotactic bacteria was used for the axenic cultivation of microaerophilic magnetotactic spirilla. Magnetotactic bacteria were first separated from non-magnetic contaminants by exploiting their active migration along magnetic field lines by a capillary "racetrack" method. The purified magnetic cells were then inoculated into a two-layer isolation medium with opposing oxygen and sulfide gradients. Several strains of magnetotactic spirilla were isolated from a freshwater sediment sample using this method. Based on their morphology, physiology and comparative analysis of almost complete 16S rRNA gene sequences, all newly isolated strains were identified as members of the genus Magnetospirillum. While five of the isolates were closely related to previously described species (> 99% sequence similarity), two isolates appear to represent a third phylogenetic cluster within the genus Magnetospirillum.     

Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap

Zymobacter palmae gen. nov., sp. nov. was proposed for a new ethanol-fermenting bacterium that was isolated from palm sap in Okinawa Prefecture, Japan. The bacterium is gram-negative, facultatively anaerobic, catalase-positive, oxidase-negative, nonspore-forming and peritrichously flagellated. It requires nicotinic acid for growth. It ferments hexoses, -linked di- and tri-saccarides, and sugar alcohols (fructose, galactose, glucose, mannose, maltose, melibiose, saccharose, raffinose, mannitol and sorbitol). Fifteen percent of maltose in broth medium is effectively fermented, whereas glucose with a concentration higher than 10% delayed growth initiation and decreased growth rates. Maltose is fermented to produce ethanol and CO₂ with a trace amount of acids. Approximately 2 mol of ethanol are produced from 1 mol moiety of hexose of maltose. The organism possesses ubiquinone-9. The G+C content of the DNA is 55.8+-0.4 mol%. Major cellular fatty acids were palmitic and oleic acids and cyclopropanic acid of C_19:0. Characteristic hydroxylated acid was 3-hydroxy dodecanoic acid. The bacterium is distinct from other ethanol-fermenting bacteria belonging to the genera Zymomonas Kluyver and van Niel 1936 and Saccharobacter Yaping et al. 1990 with respect to chemotaxonomic and other phenotypic characters to warrant to compose a new genus and a new species. The type strain is strain T109 (= IAM 14233).Abbreviation IAM IAM Culture Collection, Institute of Applied Microbiology. The University of Tokyo     

Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic,acetate-utilising,butyrate-producing bacterium from human faeces

Two strains of a previously undescribed Eubacterium-like bacterium were isolated from human faeces. The strains are Gram-variable, obligately anaerobic, catalase negative, asporogenous rod-shaped cells which produced acetate, butyrate and lactate as the end products of glucose metabolism. The two isolates displayed 99.9% 16S rRNA gene sequence similarity to each other and treeing analysis demonstrated the faecal isolates are far removed from Eubacterium sensu stricto and that they represent a new subline within the Clostridium coccoides group of organisms. Based on phenotypic and phylogenetic criteria, it is proposed that the two strains from faeces be classified as a new genus and species, Anaerostipes caccae. The type strain of Anaerostipes caccae is NCIMB 13811T (= DSM 14662T).     

Methanothrix soehngenii gen. nov. sp. nov., a new acetotrophic non-hydrogen-oxidizing methane bacterium

A new genus of methanogenic bacteria is described, which was isolated from a mesophilic sewage digester. It is most probably the filamentous bacterium, earlier referred to asMethanobacterium soehngenii, fat rod or acetate organism. The single non-motile, non-sporeforming cells are rod-shaped (0.8×2 m) and are normally combined end to end in long filaments, surrounded by a sheath-like structure. The filaments form characteristic bundles.Methanothrix soehngenii decarboxylates acetate, yielding methane and carbon dioxide. Other methanogenic substrates (H₂–CO₂, formate, methanol, methylamines) are not used for growth or methane formation. Formate is split into hydrogen and carbon dioxide. The temperature optimum for growth and methane formation is 37°C and the optimal pH range is 7.4–7.8. Sulfide and ammonia serve as sulfur and nitrogen source respectively. Oxygen completely inhibits growth and methane formation, but the bacteria do not loose their viability when exposed to high oxygen concentrations. 100 mg/l vancomycin showed no inhibition of growth and methanogenesis. No growth and methane formation was observed in the presence of: 2-bromoethanesulfonic acid, viologen dyes, chloroform, and KCN. The bacterium has a growth yield on acetate of 1.1–1.4 g biomass per mol acetate. The apparent K _S of the acetate conversion system to methane and carbon dioxide is 0.7 mmol/l. The DNA base composition is 51.9 mol% guanine plus cytosine. The nameMethanothrix is proposed for this new genus of filamentous methane bacterium. The type species,Methanothrix soehngenii sp. nov., is named in honor of N. L. Söhngen.     

Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces

Morphological, biochemical, and molecular genetic studies were performed on an unknown anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from dog feces. The unknown bacterium was tentatively identified as a Eubacterium species, based on cellular morphological and biochemical tests. 16S rRNA gene sequencing studies, however, revealed that it was phylogenetically distant from Eubacterium limosum, the type species of the genus Eubacterium. Phylogenetically, the unknown species forms a hitherto unknown sub-line proximal to the base of a cluster of organisms (designated rRNA cluster XVI), which includes Clostridium innocuum, Streptococcus pleomorphus, and some Eubacterium species. Based on both phenotypic and phylogenetic criteria, it is proposed that the unknown bacterium be classified as a new genus and species, Allobaculum stercoricanis. Using a specific rRNA-targeted probe designed to identify Allobaculum stercoricanis, in situ hybridisation showed this novel species represents a significant organism in canine feces comprising between 0.1% and 3.7% of total cells stained with DAPI (21 dog fecal samples). The type strain of Allobaculum stercoricanis is DSM 13633(T)=CCUG 45212(T).