Search

Three highly alkaliphilic bacterial strains designated as A1 T , H1 T and B1 T were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1 T , H1 T and B1 T were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1 T , H1 T and B1 T was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera Malikia (95.1-96.4 %), Macromonas (93.0-93.6 %) and Hydrogenophaga (93.0-96.6 %) in the family Comamonadaceae . Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1 T , H1 T and B1 T against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA-DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov. (type strain A1 T =NBRC 111848 T =DSM 103917 T ), Serpentinimonas barnesii sp. nov. (type strain H1 T = NBRC 111849 T =DSM 103920 T ) and Serpentinimonas maccroryi sp. nov. (type strain B1 T =NBRC 111850 T =DSM 103919 T ) belonging to the family Comamonadaceae . We have designated Serpentinimonas raichei the type species for the genus because it is the dominant species in The Cedars springs.

A novel marine bacterial strain, PV-4(T), isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0-42 degrees C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4(T) was iso-C(15 : 0). Strain PV-4(T) had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4(T) within the genus Shewanella. PV-4(T) exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4(T) showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5 %) and S. marisflavi (8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4(T) (=ATCC BAA-1088(T)=DSM 17748(T)).

A novel thermophilic, acidophilic bacterium, designated strain Pd55T, was isolated from a self-temperature-recording in situ colonization system deployed in a hydrothermal diffusing flow (maximum temperature of 78 degrees C) at the TOTO caldera in the Mariana Arc. Cells of strain Pd55T were motile, short rods with a single polar flagellum. Growth was observed between 30 and 68 degrees C (optimum growth at 50 degrees C; 120 min doubling time) and between (initial) pH 4.2 and 7.0 (optimum at pH 5.2). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as sole energy source and carbon dioxide as sole carbon source. Elemental sulfur served as the sole electron acceptor to support growth. The G+C content of the genomic DNA was 34.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was related to members of the genera Nautilia and Caminibacter, although it appeared to be a novel lineage prior to the divergence between Nautilia and Caminibacter. Strain Pd55T could also be differentiated from Nautilia and Caminibacter species on the basis of its physiological properties. It is, therefore, proposed that strain Pd55T (=JCM 12420T=DSM 16356T) represents the type strain of a novel species in a new genus, Lebetimonas acidiphila gen. nov., sp. nov.

A novel, thermophilic, obligately chemolithoautotrophic, sulfur/thiosulfate-oxidizing bacterium was isolated from subsurface geothermal aquifer water (temperature approximately 70 degrees C) in the Hishikari gold mine, Japan. Cells of the isolate, designated strain C55T, were motile, straight rods with a single polar flagellum. Growth was observed at temperatures between 35 and 62 degrees C (optimum 50-55 degrees C; 60 min doubling time) and pH between 5.2 and 7.7 (optimum pH 6.5-7.0). High growth rate of strain C55T was observed on either thiosulfate or elemental sulfur as a sole energy source, with molecular oxygen as the only electron acceptor. None of the organic compounds tested supported or stimulated growth of strain C55T. The G+C content of the genomic DNA was 66.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C55T was affiliated to the beta-Proteobacteria, but was distantly related to recognized genera. On the basis of its physiological and molecular properties, strain C55T (=JCM12421T=DSM 16629T=ATCC BAA-941T) is proposed as the type strain of Thiobacter subterraneus gen. nov., sp. nov.

A novel thermotolerant bacterium, designated strain I78(T), was isolated from a self-temperature-recording in situ colonization system deployed in a hydrothermal diffusing flow (maximal temperature 78 degrees C) at the TOTO caldera in the Mariana Arc, Western Pacific. Cells were highly motile curved rods with a single polar flagellum. Growth was observed at 15-55 degrees C (optimum 35-40 degrees C; 60 min doubling time) and pH 5.0-8.0 (optimum pH 6.0). The isolate was a microaerobic chemolithomixotroph capable of using thiosulfate, elemental sulfur or sulfide as the sole energy source, and molecular oxygen as the sole electron acceptor. The isolate was able to grow chemolithoautotrophically with carbon dioxide. Various organic substrates such as complex proteinaceous compounds, carbohydrates, organic acids, amino acids and sugars could also support growth as the carbon source instead of carbon dioxide with sulfur oxidation. The G+C content of the genomic DNA was 43.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Thiomicrospira and was most closely related to Thiomicrospira crunogena strain TH-55(T) and Thiomicrospira sp. strain L-12, while DNA-DNA hybridization demonstrated that the novel isolate could be genetically differentiated from previously described strains of Thiomicrospira. On the basis of its physiological and molecular properties the isolate is representative of a novel Thiomicrospira species, for which the name Thiomicrospira thermophila sp. nov. is proposed (type strain, I78(T)=JCM 12397(T)=DSM 16397(T)).

A novel mesophilic sulfur- and thiosulfate-oxidizing bacterium, strain 42BKTT, was isolated from the gas-bubbling sediment at the Iheya North hydrothermal system in the mid-Okinawa Trough, Japan. The isolate was a Gram-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 10-40 degrees C (optimum 28-30 degrees C) and in the pH range 5.0-9.0 (optimum 6.5-7.0). Strain 42BKTT grew chemolithoautotrophically with elemental sulfur or thiosulfate as a sole electron donor and oxygen (optimum 5 % in gas phase) or nitrate as an electron acceptor. The G + C content of the genomic DNA was 48.0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the previously uncultivated Group F within the epsilon-Proteobacteria, which includes phylotypes of vent epibiont and environmental sequences from global deep-sea cold seep and hydrothermal vent fields. On the basis of the physiological and molecular characteristics of this isolate, the type species of a novel genus, Sulfurovum lithotrophicum gen. nov., sp. nov., is proposed. The type strain is 42BKTT (= ATCC BAA-797T = JCM 12117T).

A novel extremely thermophilic, methane-producing archaeon was isolated from a black smoker chimney at the Kairei field in the Central Indian Ridge. Cells of this isolate were irregular cocci with several flagella; motility was not observed. Growth was observed between 55 and 83 degrees C (optimum of 75 degrees C; 30 min doubling time) and between pH 6.0 and 8.5 (optimum of pH 6.7). The isolate was a strictly anaerobic, methanogenic autotroph capable of using hydrogen and carbon dioxide as sole energy and carbon sources. Formate was utilized as an alternative energy source. The G+C content of the genomic DNA was 33.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was most closely related to Methanotorris igneus strain Kol 5T. The isolate, however, could be genetically differentiated from this species by DNA-DNA hybridization analysis and on the basis of its physiological properties. The name Methanotorris formicicus sp. nov. is proposed for this isolate; the type strain is Mc-S-70T (=JCM 11930T=ATCC BAA-687T).

A novel thermophilic bacterium, strain EP1-55-1%T, was isolated from an in-situ colonization system deployed in a superheated, deep-sea, hydrothermal vent emission at the Kairei Field on the Central Indian Ridge in the Indian Ocean. The cells were highly motile rods, each possessing a single polar flagellum. Growth was observed between 35 and 65 degrees C (optimum temperature, 55 degrees C; 70 min doubling time) and between pH 4.9 and 7.2 (optimum, pH 5.9). The isolate was a microaerobic-to-anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Molecular oxygen, nitrate or elemental sulfur (S0) could serve as electron acceptors to support growth. The G+C content of the genomic DNA was 34.6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that strain EP1-55-1%T represents the first strain for which taxonomic properties have been characterized within the previously uncultivated phylogroup classified as belonging to the uncultivated epsilon-Proteobacteria group A; the name Hydrogenimonas thermophila gen. nov., sp. nov. is proposed, with strain EP1-55-1%T (=JCM 11971T=ATCC BAA-737T) as the type strain.

A novel mesophilic, sulfur- and thiosulfate-oxidizing bacterium, strain OK10(T), was isolated from deep-sea sediments at the Hatoma Knoll in the Mid-Okinawa Trough hydrothermal field. Cells of strain OK10(T) were short rods, each being motile by means of a single polar flagellum. The isolate grew at 10-40 degrees C (optimum 25 degrees C) and pH 4.5-9.0 (optimum pH 6.5). It grew chemolithoautotrophically with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Molecular hydrogen did not support growth. The G+C content of the genomic DNA of strain OK10(T) was 35.2 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that the isolate belonged to the epsilon-Proteobacteria. On the basis of its physiological and molecular characteristics, strain OK10(T) (=ATCC BAA-671(T)=JCM 11897(T)) represents the sole species of a new genus, Sulfurimonas, for which the name Sulfurimonas autotrophica is proposed.

A novel anaerobic, heterotrophic thermophile was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. The cells were bent, flexible rods, with a single polar flagellum. Growth was observed between 40 and 70 degrees C (optimum temperature: 60-65 degrees C; doubling time, 40 min) and between pH 5.0 and 7.5(optimum pH 6.5). The isolate was a strictly anaerobic heterotroph capable of using complex organic compounds (yeast extract, tryptone, peptone, casein and Casamino acids), ethanol and various organic acids as energy and carbon sources. Hydrogen could serve as a supplementary energy source. Elemental sulfur (S(0)), nitrate or arsenate was required for growth as an electron acceptor. The G + C content of the genomic DNA was 38.6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that isolate SSM1(T) is closely related to Deferribacter thermophilus BMA(T) (98.1%). However, the novel isolate could be clearly differentiated from D. thermophilus BMA(T) on the basis of its physiological and genetic properties. The name Deferribacter desulfuricans sp. nov. (type strain SSM1(T) = JCM 11476(T) = DSM 14783(T)) is proposed.

A polyphasic taxonomic study was performed on a novel facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotroph recently isolated from subsurface hot aquifer water in a Japanese gold mine. The cells were straight to slightly curved rods, with a single polar flagellum. Growth was observed at 40-70 degrees C (optimum 60-65 degrees C; 80 min doubling time) and at pH 6.4-8.8 (optimum pH 7.5). The isolate was unable to use complex organic compounds, carbohydrates, amino acids or organic acids as sole energy and carbon sources. The G + C content of the genomic DNA was 31.3 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was closely related to an uncultivated group of micro-organisms within the order Aquificales obtained from Icelandic and Japanese hot spring microbial mats, but distantly related to previously identified genera of the Aquificales such as Persephonella, Aquifex and Hydrogenobacter. The name Sulfurihydrogenibium subterraneum gen. nov., sp. nov. is proposed for this novel species; the type strain is HGMK1(T) (= JCM 11477(T) = ATCC BAA-562(T) = DSM 15120(T)).

Two strains of haloalkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria were isolated from the oxygen-sulfide interface water layer of stratified alkaline and saline Mono Lake, California, USA. Strain ALM 1T was a dominant species in enrichment on moderate-saline, carbonate-buffered medium (0.6 M total Na+, pH 10) with thiosulfate as an energy source and nitrate as a nitrogen source. Cells of ALM 1T are open ring-shaped and are non-motile. It has a high growth rate and activity of thiosulfate and sulfide oxidation and very low sulfur-oxidizing activity. Genetic comparison and phylogenetic analysis suggested that ALM 1T (= DSM 14477T = JCM 11371T) represents a new species of the genus Thioalkalimicrobium in the gamma-Proteobacteria, for which the name Thioalkalimicrobium cyclicum sp. nov. is proposed. Another Mono Lake isolate, strain ALM 2T, dominated in enrichment on a medium containing 2 M total Na+ (pH 10). It is a motile vibrio which tolerates up to 4 M Na+ and produces a membrane-bound yellow pigment. Phylogenetic analysis placed ALM 2T as a member of genus Thioalkalivibrio in the gamma-Proteobacteria, although its DNA hybridization with the representative strains of this genus was only about 30%. On the basis of genetic and phenotypic properties, strain ALM 2T (= DSM 14478T = JCM 11372T) is proposed as Thioalkalivibrio jannaschii sp. nov..