bluuebunny/crossref_metadata_2025 huggingface dataset:
Pedobacter terrae sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Tae-Kwang
Published: October 2007

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-57T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. It grew optimally at 25 °C and in trypticase soy broth without NaCl and trypticase soy broth with 0.5 % NaCl. Strain DS-57T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1
ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-57T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae, clustering coherently with Pedobacter suwonensis, Pedobacter roseus and Pedobacter sandarakinus. Strain DS-57T exhibited 16S rRNA gene sequence similarity values of 99.2, 97.9 and 97.2 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively, and values less than 95.6 % with respect to the type strains of other Pedobacter species. Strain DS-57T exhibited levels of DNA–DNA relatedness of 45, 17 and 15 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively. Differential phenotypic properties, together with the phylogenetic distinctiveness and the DNA–DNA relatedness data, were sufficient to allow the classification of strain DS-57T as a species that is separate from recognized Pedobacter species. On the basis of phenotypic properties and phylogenetic distinctiveness, therefore, strain DS-57T represents a novel species of the genus Pedobacter, for which the name Pedobacter terrae sp. nov. is proposed. The type strain is DS-57T (=KCTC 12762T=DSM 17933T).
Molecular systematics support the revival of Mycobacterium salmoniphilum (ex Ross 1960) sp. nov., nom. rev., a species closely related to Mycobacterium chelonae
Authors: Whipps Christopher M. , Butler W. Ray , Pourahmad Fazel , Watral Virginia G. , Kent Michael L.
Published: October 2007

Mycobacterial infections in fish are usually attributed to strains of Mycobacterium marinum, Mycobacterium chelonae and Mycobacterium fortuitum. Bacteria identified as M. chelonae have been isolated numerous times from salmonid fishes. Recently, this bacterium has been associated with salmon mortalities in the aquaculture industry. An M. chelonae-like species from salmon, ‘Mycobacterium salmoniphilum’, was described in 1960. However, the species name lost standing in nomenclature when it was omitted from the 1980 Approved Lists of Bacterial Names because the species could not be distinguished with confidence from M. fortuitum. In the 1980s, mycobacteria isolated from salmon were characterized as a distinct subspecies, ‘Mycobacterium chelonae subsp. piscarium’. Again, the uncertainty of the validity of the species resulted in the subsequent withdrawal of the name. Since then, most studies have considered isolates from salmon to be M. chelonae. Nucleotide sequence analysis of the small-subunit rRNA, hsp65 and rpoB genes was used to examine the taxonomic relatedness of type cultures and authentic isolates in our culture collection available from earlier studies. The M. chelonae-like strains from salmon were phylogenetically distinct from other Mycobacterium strains and members of the M. chelonae complex. Moreover, the cell-wall-bound mycolic acids were not representative of known mycolate patterns for M. chelonae-complex organisms. These results supported the status of the species as a separate taxon and effect the valid publication of the name ‘M. salmoniphilum’ as Mycobacterium salmoniphilum (ex Ross 1960) sp. nov., nom. rev., with the type strain SCT (=ATCC 13578T =DSM 43276T).
Cellulosimicrobium terreum sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Kang So-Jung , Schumann Peter , Oh Tae-Kwang
Published: October 2007

A Gram-positive, yellow-pigmented, non-motile and rod-shaped or coccoid bacterial strain, DS-61T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. The strain grew optimally at pH 6.5–7.5 and 25 °C in the presence of 1.0 % (w/v) NaCl. Strain DS-61Thad peptidoglycan of the type based onl-Lys–l-Thr–d-Asp and contained galactose as the only whole-cell sugar. MK-9(H4) was the predominant menaquinone and anteiso-C15 : 0and iso-C15 : 0were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The DNA G+C content was 72.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-61Tis most closely affiliated to the genusCellulosimicrobium, clustering withCellulosimicrobiumcellulansandCellulosimicrobiumfunkei. The levels of 16S rRNA gene sequence similarity between strain DS-61Tand the type strains ofCellulosimicrobiumcellulansandCellulosimicrobium funkeiwere 97.4–97.6 %. DNA–DNA relatedness data and differential phenotypic properties demonstrated that strain DS-61Tis distinguishable from these two recognizedCellulosimicrobiumspecies. On the basis of phenotypic, phylogenetic and genetic data, strain DS-61Trepresents a novel species of the genusCellulosimicrobium, for which the nameCellulosimicrobium terreumsp. nov. is proposed. The type strain is DS-61T(=KCTC 19206T=DSM 18665T). An emended description of the genus is given.
Halobacillus faecis sp. nov., a spore-forming bacterium isolated from a mangrove area on Ishigaki Island, Japan
Authors: An Sun-Young , Kanoh Kaneo , Kasai Hiroaki , Goto Keiichi , Yokota Akira
Published: October 2007

A Gram-positive, spore-forming, rod-shaped halophilic bacterial strain, IGA7-4T, was isolated from a mangrove area on Ishigaki Island (Japan), and was characterized taxonomically using a polyphasic approach. Strain IGA7-4T was strictly aerobic and non-motile and formed central endospores. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain IGA7-4T is affiliated to the genus Halobacillus, and exhibits sequence similarities of 99.6–98.0 % to the type strains of Halobacillus species. Levels of DNA–DNA relatedness between strain IGA7-4T and the type strains of Halobacillus species were 9.5–46.6 %. The DNA G+C content of strain IGA7-4T was 46.5 mol%. The cell-wall peptidoglycan type (Orn–Asp), major cellular fatty acids (anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0) and quinone type (MK-7) of the isolate support its affiliation to the genus Halobacillus. On the basis of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data, the isolate represents a novel species of the genus Halobacillus, for which the name Halobacillus faecis sp. nov. is proposed. The type strain is IGA7-4T (=MBIC08268T=IAM 15427T=KCTC 13121T).
Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan
Authors: An Sun-Young , Ishikawa Shu , Kasai Hiroaki , Goto Keiichi , Yokota Akira
Published: October 2007

A facultatively anaerobic, moderately alkaliphilic, Gram-positive, spore-forming and rod-shaped bacterial strain, Shu-P-Ggiii25-2T, was isolated from lake sediment in Shizuoka, Japan, and was characterized taxonomically using a polyphasic approach. Analysis of the 16S rRNA gene sequence indicated that the novel isolate clustered with the type strain of Amphibacillus xylanus and it exhibited sequence similarities of 94.9–95.6 % to the type strains of species of the genus Amphibacillus. Isoprenoid quinones and oxidase and catalase activities were not detected for strain Shu-P-Ggiii25-2T. The DNA G+C content was 42.3 mol%, the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid and the major cellular fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. On the basis of phylogenetic position and phenotypic properties, strain Shu-P-Ggiii25-2T represents a novel species of the genus Amphibacillus, for which the name Amphibacillus sediminis sp. nov. is proposed. The type strain is Shu-P-Ggiii25-2T (=MBIC08269T=IAM 15428T=KCTC 13120T). An emended description of the genus Amphibacillus is also given.
Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field
Authors: Kim Myung Kyum , Kim Yu-Jin , Cho Dong-Ha , Yi Tae-Hoo , Soung Nak-Kyun , Yang Deok-Chun
Published: October 2007

A micro-organism, DCY12T, comprising Gram-negative, non-motile, pale-yellow rods was isolated from soil from a ginseng field in South Korea and was investigated to determine its taxonomic status. It grew optimally at 30 °C and at pH 7.0, the G+C content of its DNA was 40.5 mol%, the major components of the fatty acid profile were C16 : 0 and C18 : 1 and the major ubiquinone was Q-8. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate was most closely related to Hydrocarboniphaga effusa AP103T (89.2 %), Nevskia ramosa Soe1 (88.8 %) and Pseudomonas aeruginosa ATCC 10145T (83.2 %). The phenotypic, physiological, metabolic and phylogenetic properties of DCY12T suggest that it represents a novel genus (class Gammaproteobacteria) and species, for which the name Solimonas soli gen. nov., sp. nov. is proposed. The type strain of Solimonas soli is DCY12T (=KCTC 12834T =LMG 24014T).
Streptomyces hainanensis sp. nov., a novel member of the genus Streptomyces
Authors: Jiang Yi , Tang Shu-Kun , Wiese Jutta , Xu Li-Hua , Imhoff Johannes F. , Jiang Cheng-Lin
Published: October 2007

A novel isolate belonging to the genus Streptomyces, strain YIM 47672T, was obtained from soil from Hainan, an island in China. The characterization of this isolate was performed by using a polyphasic approach. The strain formed long spore chains in the aerial mycelia. The cell wall contained l-diaminopimelic acid, traces of meso-diaminopimelic acid and glycine. Whole-cell hydrolysates contained galactose and xylose. The phospholipid was of type II. The 16S rRNA gene sequence similarities for YIM 47672T with respect to the most closely related type strains of species of the genus Streptomyces were less than 96.3 %. Therefore strain YIM 47672T represents a novel member of the genus Streptomyces, for which the name Streptomyces hainanensis sp. nov. is proposed. The type strain is YIM 47672T (=CCTCC AA 205017T=DSM 41900T).
Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins
Authors: Tan Geok Yuan Annie , Robinson Stuart , Lacey Ernest , Brown Roselyn , Kim Wonyong , Goodfellow Michael
Published: October 2007

The taxonomic position of seven soil actinomycetes provisionally assigned to the genusAmycolatopsiswas established in a polyphasic study. The isolates, which had identical 16S rRNA gene sequences, had closest similarity to the type strain ofAmycolatopsis orientalis. A representative isolate, strain GY080T, had chemotaxonomic properties that were typical of the genusAmycolatopsisand could be distinguished from the type strain ofA. orientalisusing DNA–DNA relatedness data. All of the isolates shared a phenotypic profile that distinguished them from representatives of phylogenetically closely related species. Amplified rDNA restriction analysis showed that the isolates formed a homogeneous group that was distinctly separate from single-membered groups consisting of representativeAmycolatopsistype strains, including that ofA. orientalis. Based on the combined genotypic and phenotypic evidence, it is proposed that the seven isolates be classified as representatives of a novel species for which the nameAmycolatopsis regifauciumsp. nov. is proposed. The type strain is GY080T(=DSM 45072T=NCIMB 14277T).
Streptomyces radiopugnans sp. nov., a radiation-resistant actinomycete isolated from radiation-polluted soil in China
Authors: Mao Jun , Tang Qiyong , Zhang Zhidong , Wang Wei , Wei Dong , Huang Ying , Liu Zhiheng , Shi Yuhu , Goodfellow Michael
Published: October 2007

The taxonomic position of an actinomycete isolated from radiation-polluted soil collected in Xinjiang Province, north-west China, was determined by using a polyphasic approach. The isolate, designated strain R97T, had chemical and morphological properties characteristic of streptomycetes. An almost-complete 16S rRNA gene sequence of the isolate was generated and compared with corresponding sequences of representative streptomycetes. The 16S rRNA data not only supported the classification of the strain in the genusStreptomycesbut also showed that it represented a distinct phyletic line that was most closely, albeit loosely, associated with three other thermotolerant organisms, namelyStreptomyces macrosporusNBRC 14748T,Streptomyces megasporusNBRC 14749TandStreptomyces thermolineatusNBRC 14750T. Strain R97Tcould be distinguished from these organisms based on a range of phenotypic properties. It is proposed that R97T(=CGMCC 4.3519T=DSM 41901T) be classified as the type strain of a novel species in the genusStreptomyces,Streptomyces radiopugnanssp. nov. The organism was shown to be resistant to60Co gamma radiation at a dose of 15 kGy.
Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea
Authors: Choi Jeong-Hwa , Im Wan-Taek , Liu Qing-Mei , Yoo Jae-Soo , Shin Jae-Ho , Rhee Sung-Keun , Roh Dong-Hyun
Published: October 2007

A novel Gram-positive, aerobic bacterium, strain JH1T, was isolated from deep-sea sediment of the East Sea, South Korea, and identified by methods of polyphasic taxonomy. The strain was oxidase-positive, motile and coccus-shaped. The genomic DNA G+C content of strain JH1T was 47 mol%. The major fatty acid of strain JH1T was anteiso-C15 : 0 and the predominant menaquinones were MK-7 and MK-8. Similarity of the 16S rRNA gene sequence (1452 nt) of strain JH1T to those of species of the genera Planococcus and Planomicrobium was 96.0–98.2 %. The signature nucleotides in the 16S rRNA gene sequence were compared with those of previously studied type strains of species in the genera Planococcus and Planomicrobium, and suggested that strain JH1T belongs to the genus Planococcus. In addition, phylogenetic analysis showed that strain JH1T was located within the cluster comprising Planococcus antarcticus and Planococcus kocurii. DNA–DNA hybridization showed that it had 9.3 % genomic relatedness with Planococcus antarcticus DSM 14505T and 22.9 % with Planococcus kocurii DSM 20747T. On the basis of the phenotypic, phylogenetic and genomic data, a novel species of the genus Planococcus, Planococcus donghaensis sp. nov., is proposed, with type strain JH1T (=KCTC 13050T=LMG 23779T).
Campylobacter canadensis sp. nov., from captive whooping cranes in Canada
Authors: Inglis G. Douglas , Hoar Bryanne M. , Whiteside Douglas P. , Morck Douglas W.
Published: October 2007

Ten isolates of an unknown Campylobacter species were isolated from cloacal swabs obtained from captive adult whooping cranes (Grus americana). All isolates were identified as Campylobacter based on generic PCR and grouped with other Campylobacter species based on 23S rRNA gene sequence. None of the isolates could be identified by species-specific PCR for known taxa, and all ten isolates formed a robust clade that was very distinct from known Campylobacter species based on 16S rRNA, rpoB and cpn60 gene sequences. The results of 16S rRNA gene nucleotide sequence (≤92 % sequence similarity to recognized Campylobacter species) and genomic DNA (no detectable relatedness) analyses were consistent with novel species status. Cells of the Campylobacter from whooping cranes were uniflagellar and typically sigmoid to allantoid in shape (0.48 μm wide and 2.61 μm long), but also spheroid to coccoid (0.59 μm wide and 0.73 μm long). The bacterium was oxidase-positive, able to reduce nitrite, able to grow at 3 ° and 42 °C, and grew anaerobically, as well as in an atmosphere devoid of H2, and on MacConkey agar. It was not α-haemolytic and was negative for hippurate and indoxyl acetate hydrolysis and alkaline phosphatase. It also was susceptible to cephalotin and was unable to grow on nutrient agar, on a medium containing 3.5 % NaCl or in ambient O2. The bacterium was unable to grow at 25 °C and growth was negative or very restricted at 30 °C. Fluorescent amplified fragment length polymorphism analysis indicated that nine of the recovered isolates were genetically distinct. A species-specific primer set targeting the cpn60 gene was developed. The name Campylobacter canadensis sp. nov. is proposed for the novel species, with the type strain L266T (=CCUG 54429T =LMG 24001T).
Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens
Authors: Kämpfer Peter , Scholz Holger C. , Huber Birgit , Falsen Enevold , Busse Hans-Jürgen
Published: October 2007

Three Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from clinical specimens between 1992 and 2000. On the basis of 16S rRNA gene sequence similarities, these strains (CCUG 30717T, CCUG 43892 and CCUG 38531T) were shown to belong to the Alphaproteobacteria, most closely related to Ochrobactrum grignonense (99.0 and 98.2 % similarity to the type strain). Chemotaxonomic data (major ubiquinone Q-10; major polyamines spermidine, sym-homospermidine and putrescine; major polar lipids phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine; major fatty acids C18 : 1
ω7c and C19 : 0 cyclo ω8c) supported the affiliation of the isolates to the genus Ochrobactrum. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from described Ochrobactrum species. Isolates CCUG 30717T and CCUG 43892 were closely related on the basis of DNA–DNA reassociation experiments and therefore represent one novel species, for which the name Ochrobactrum pseudogrignonense sp. nov. is proposed, with the type strain CCUG 30717T (=CIP 109451T). Isolate CCUG 38531T was different from these strains and also from other Ochrobactrum species. For this strain, the name Ochrobactrum haematophilum sp. nov. is proposed, with the type strain CCUG 38531T (=CIP 109452T).
Ferrimonas senticii sp. nov., a novel gammaproteobacterium isolated from the mucus of a puffer fish caught in Kaneohe Bay, Hawai'i
Authors: Campbell Sonia , Harada Renee M. , Li Qing X.
Published: October 2007

A novel species, strain P2S11T, was isolated from the mucus of a puffer fish caught off the coast of Kaneohe Bay, O'ahu, Hawai'i. A phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was most closely related to Ferrimonas marina DSM 16917T and Ferrimonas balearica DSM 9799T with 93.5 % and 82.9 % sequence similarities, respectively, which established the novel strain as belonging to the genus Ferrimonas. The strain formed off-white coloured colonies on marine agar and cells were Gram-negative, non-motile rods. H2S was produced when strain P2S11T was grown on TSI medium with added salt. Strain P2S11T had a DNA G+C content of 54.9 mol% and the dominant fatty acids were C16 : 1
ω9c, C16 : 0 and C17 : 1
ω8c. On the basis of this polyphasic study, strain P2S11T (=ATCC BAA-1480T=DSM 18821T) represents a novel species of the genus Ferrimonas, for which the name Ferrimonas senticii sp. nov. is proposed.
Nocardioides terrigena sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Soo-Young , Oh Tae-Kwang
Published: October 2007

A Gram-positive, rod- or coccoid-shaped bacterial strain, DS-17T, was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-17T grew optimally at around pH 8.0 and 30 °C in the presence of 0.5–1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-17T belonged to the genus Nocardioides. The chemotaxonomic properties of strain DS-17T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0, C17 : 1
ω8c and C17 : 0 were the major fatty acids. The DNA G+C content was 71.5 mol%. Strain DS-17T exhibited 16S rRNA gene sequence similarity values of 94.5–96.9 % to the type strains of recognized Nocardioides species. Strain DS-17T could be distinguished from recognized Nocardioides species by differences in phenotypic characteristics. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-17T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides terrigena sp. nov. is proposed. The type strain is DS-17T (=KCTC 19217T=JCM 14582T).
Roseospira visakhapatnamensis sp. nov. and Roseospira goensis sp. nov.
Authors: Kalyan Chakravarthy S. , Srinivas T. N. R. , Anil Kumar P. , Sasikala Ch. , Ramana Ch. V.
Published: October 2007

Two Gram-negative, vibrioid, phototrophic, purple non-sulfur strains, JA131T and JA135T, were isolated from marine habitats. Strain JA131T is non-motile but strain JA135T is motile by means of a pair of monopolar flagella. Both strains have an obligate requirement for NaCl for growth. The intracellular photosynthetic membranes of the two novel strains are of the vesicular type. Bacteriochlorophyll a and probably rhodovibrine are present as photosynthetic pigments. Niacin, thiamine and p-aminobenzoic acid are required as growth factors for both novel strains. Based on 16S rRNA gene sequence analysis, morphological and physiological characteristics, strains JA131T and JA135T are significantly different from each other and from other species of the genus Roseospira and thus represent two novel species for which the names Roseospira visakhapatnamensis sp. nov. and Roseospira goensis sp. nov. are proposed, respectively. The type strain of Roseospira visakhapatnamensis sp. nov. is JA131T (=ATCC BAA-1365T=JCM 14190T) and the type strain of Roseospira goensis sp. nov. is JA135T (=ATCC BAA-1364T=JCM 14191T).
Rhodobacter changlensis sp. nov., a psychrotolerant, phototrophic alphaproteobacterium from the Himalayas of India
Authors: Anil Kumar P. , Srinivas T. N. R. , Sasikala Ch. , Ramana Ch. V.
Published: October 2007

A Gram-negative, non-motile, oval to rod-shaped, psychrotolerant, phototrophic, purple non-sulfur bacterium (designated strain JA139T) was isolated from a snow sample from Changla Pass in the Indian Himalayas. Strain JA139T had vesicular-type intracytoplasmic membrane structures and contained bacteriochlorophyll a and most probably spheroidene-like carotenoids. Biotin, niacin and thiamine were required for growth of strain JA139T. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain clustered with species of the genus Rhodobacter but was distinctly separate from all recognized members of the family Rhodobacteraceae. Based on the genotypic and phenotypic differences observed between strain JA139T and recognized Rhodobacter species, strain JA139T is considered to represent a novel species of the genus, for which the name Rhodobacter changlensis sp. nov. is proposed. The type strain is JA139T (=DSM 18774T =CCUG 53722T =JCM 14338T).
Roseomonas terrae sp. nov.
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Hyun Woo , Oh Tae-Kwang
Published: October 2007

A Gram-negative, non-motile, coccobacilli-shaped bacterium, DS-48T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain DS-48T grew optimally at 25 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c and C18 : 1 2-OH as the major fatty acids. The DNA G+C content was 69.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-48T fell within the genus Roseomonas, clustering with Roseomonas lacus TH-G33T (at a bootstrap confidence level of 100 %). The levels of similarity between the 16S rRNA gene sequence of strain DS-48T and those of the type strains of recognized Roseomonas species were in the range 93.2–98.0 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of DS-48T, revealed that this strain differs from recognized Roseomonas species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain DS-48T represents a novel species within the genus Roseomonas, for which the name Roseomonas terrae sp. nov. is proposed. The type strain is DS-48T (=KCTC 12874T=JCM 14592T).
Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment
Authors: Bozal Núria , Montes M. Jesús , Mercadé Elena
Published: October 2007

Two Gram-negative, cold-adapted, aerobic bacteria, designated strains M8Tand M6, were isolated from soil collected from the South Shetland Islands. The organisms were rod-shaped, catalase- and oxidase-positive and motile by means of polar flagella. These two psychrotolerant strains grew between −4 and 30 °C. 16S rRNA gene sequence analysis placed strains M8Tand M6 within the genusPseudomonas. DNA–DNA hybridization experiments between the Antarctic isolate M8Tand type strains of phylogenetically related species, namelyPseudomonas peliandPseudomonas anguilliseptica, revealed levels of relatedness of 33 and 37 %, respectively. Strain M6 showed 99 % DNA similarity to strain M8T. Several phenotypic characteristics, together with data on cellular fatty acid composition, served to differentiate strains M8Tand M6 from related pseudomonads. On the basis of the polyphasic taxonomic evidence presented in this study, it can be concluded that strains M8Tand M6 belong to the same genospecies, representing a novel species of the genusPseudomonas, for which the namePseudomonas guineaesp. nov. is proposed. The type strain is M8T(=LMG 24016T=CECT 7231T).
Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water
Authors: Gomila Margarita , Bowien Botho , Falsen Enevold , Moore Edward R. B. , Lalucat Jorge
Published: October 2007

Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the classBetaproteobacteriaand were related to the genusPelomonas, with 16S rRNA gene sequence similarities higher than 99 % with the only species of the genus,Pelomonas saccharophilaand toPseudomonassp. DSM 2583. The type strains ofMitsuaria chitosanitabidaandRoseateles depolymeranswere their closest neighbours (97.9 and 97.3 % 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG(hydrogenase),cbbL/cbbM(Rubisco) andnifH(nitrogenase)] relevant for the metabolism of the genusPelomonas. DNA–DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain ofPelomonas saccharophilaobtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368Tand LMG 2256T), as well asM. chitosanitabidaIAM 14711TandR. depolymeransCCUG 52219T. Results of DNA–DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from thePelomonas saccharophilatype strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genusPelomonas, for which the namesPelomonas puraquaesp. nov. andPelomonas aquaticasp. nov. are proposed. The type strains ofPelomonas puraquaesp. nov. andPelomonas aquaticasp. nov. are CCUG 52769T(=CECT 7234T) and CCUG 52575T(=CECT 7233T), respectively.
Flavobacterium ceti sp. nov., isolated from beaked whales (Ziphius cavirostris)
Authors: Vela A. I. , Fernandez A. , Sánchez-Porro C. , Sierra E. , Mendez M. , Arbelo M. , Ventosa A. , Domínguez L. , Fernández-Garayzábal J. F.
Published: October 2007

Three isolates of a Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium, isolated from the lung and liver of two beaked whales, were characterized by phenotypic and molecular genetic methods. Based on cellular morphology and biochemical criteria, the isolates were tentatively assigned to the family Flavobacteriaceae, although they did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing showed that the three new isolates shared 100 % sequence similarity. The unknown bacterium was phylogenetically closely related to, but distinct from the type strains of Flavobacterium johnsoniae (93.7 % sequence similarity), Flavobacterium frigidimaris (93.4 %), Flavobacterium aquidurense (93.4 %), Flavobacterium hibernum (93.4 %) and Flavobacterium degerlachei (93.4 %). The novel isolates were readily distinguished from these and other related Flavobacterium species by physiological and biochemical tests. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from whales are classified as a novel species of the genus Flavobacterium, Flavobacterium ceti sp. nov. The type strain is 454-2T (=CECT 7184T =CCUG 52969T).
Fangia hongkongensis gen. nov., sp. nov., a novel gammaproteobacterium of the order Thiotrichales isolated from coastal seawater of Hong Kong
Authors: Lau Ken W. K. , Ren Jianping , Fung Ming-Chiu , Woo Patrick C. Y. , Yuen Kwok-Yung , Chan Kelvin K. M. , Qian Pei-Yuan , Wong Po-Keung , Wu Madeline
Published: October 2007

A Gram-negative, coccobacillus-shaped, aerobic bacterium, designated strain UST040201-002T, was isolated in February 2004 from seawater at the outlet of a sandfilter in Port Shelter, Hong Kong SAR, China. This strain possessed ubiquinone-8; its 16S rRNA gene sequence shared only 91 % similarity with the sequence from Caedibacter taeniospiralis and 89–90 % similarity with sequences from Francisella tularensis, Francisella novicida, Francisella philomiragia and Wolbachia persica. 16S rRNA gene sequence analysis showed that the strain formed a distinct clade with C. taeniospiralis. This subcluster formed a tight coherent group with members of the family Francisellaceae and W. persica. Combined phylogenetic and physiological data suggest that strain UST040201-002T represents a novel genus and species within the order Τhiotrichales. The name Fangia hongkongensis gen. nov., sp. nov. is proposed; the type strain is UST040201-002T (=JCM 14605T=NRRL B-41860T).
Chryseobacterium hominis sp. nov., to accommodate clinical isolates biochemically similar to CDC groups II-h and II-c
Authors: Vaneechoutte Mario , Kämpfer Peter , De Baere Thierry , Avesani Véronique , Janssens Michèle , Wauters Georges
Published: October 2007

A collection of eight clinical strains from Belgian hospitals and three clinical strains of the CCUG collection were characterized biochemically as being similar to CDC groups II-h and II-c; the latter differs from group II-h only by positivity for sucrose acidification. These 11 strains were found to cluster according to 16S rRNA gene sequence similarity at a level of ≥99.5 %, and on the basis of their tDNA-PCR profile. Based on 16S rRNA gene sequence analysis, this collection of strains was related most closely to Chryseobacterium hispanicum (97.2 %), but they differed from the type strain of this species by the following phenotypic characteristics: growth at 37 °C, negativity for xylose acidification, positivity for acetate assimilation–alkalinization on Simmons’ agar base and absence of flexirubin pigments, and by their tDNA-PCR profile. Strain NF802T showed only 57.8 % DNA–DNA relatedness to the type strain of C. hispanicum. Fatty acid composition did not enable differentiation from C. hispanicum. The DNA G+C content of strain NF802T is 36.5 mol%. The name Chryseobacterium hominis sp. nov. is proposed for this taxon, with type strain NF802T (=CCUG 52711T=CIP 109415T).
Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock
Authors: Lang Elke , Swiderski Jolantha , Stackebrandt Erko , Schumann P. , Spröer Cathrin , Sahin Nurettin
Published: October 2007

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain NS11T) was isolated from a lichen-colonized rock surface. On the basis of 16S rRNA gene sequence similarity, strain NS11T was shown to belong to the Betaproteobacteria, and was most closely related to Herminiimonas arsenicoxydans ULPAs1T (98.8 %), Herminiimonas aquatilis CCUG 36956T (98.0 %) and Herminiimonas fonticola S-94T (98.0 %). Major whole-cell fatty acids were C16 : 0, C17 : 0 cyclo and C16 : 1
ω7c. Strain NS11T also contained high proportions of C10 : 0 3-OH and C18 : 1
ω7c. This pattern is typical for members of the genus Herminiimonas. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS11T from the three recognized Herminiimonas species. It is therefore concluded that strain NS11T represents a novel species of the genus Herminiimonas, for which the name Herminiimonas saxobsidens sp. nov. is proposed. The type strain is NS11T (=DSM 18748T=CCM 7436T).
Idiomarina salinarum sp. nov., isolated from a marine solar saltern in Korea
Authors: Yoon Jung-Hoon , Jung Seo-Youn , Jung Yong-Taek , Oh Tae-Kwang
Published: October 2007

A Gram-negative, motile, rod-shaped, Idiomarina-like bacterial strain, ISL-52T, was isolated from a marine solar saltern of the Yellow Sea in Korea and was subjected to a polyphasic taxonomic investigation. Strain ISL-52T grew optimally at pH 7.0–8.0 and at 30–37 °C. It contained Q-8 as the predominant ubiquinone. The major fatty acids (>10 % of total fatty acids) were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1
ω9c. The DNA G+C content was 53.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-52T fell within the genus Idiomarina, joining the type strain of Idiomarina homiensis at a bootstrap resampling value of 100 %. Strain ISL-52T exhibited 16S rRNA gene sequence similarity values of 94.9–96.7 % with respect to the type strains of eight recognized Idiomarina species. The differential phenotypic properties of ISL-52T, together with its phylogenetic distinctiveness, demonstrated that this strain is distinguishable from the recognized Idiomarina species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain ISL-52T represents a novel species of the genus Idiomarina, for which the name Idiomarina salinarum sp. nov. is proposed. The type strain is ISL-52T (=KCTC 12971T=CCUG 54359T).
Pseudidiomarina sediminum sp. nov., a marine bacterium isolated from coastal sediments of Luoyuan Bay in China
Authors: Hu Zong-Yun , Li Yun
Published: October 2007

A strain of heterotrophic, facultatively anaerobic, marine bacterium, designated strain c121T, was isolated from coastal sediment of Luoyuan Bay, in Fujian province, PR China. Analysis of the 16S rRNA gene sequence revealed an affiliation with the genus Pseudidiomarina; the sequence similarity between c121T and Pseudidiomarina taiwanensis PIT1T was 97 %. Cells of the novel strain were non-pigmented, Gram-negative rods, 0.3 μm wide and 1.2–1.8 μm long. Cells grown in broth cultures were non-motile, lacking flagella. Growth of the strain was observed at salinities ranging from 0.5 to 15 % NaCl, and the optimal concentration was about 1–8 %. The temperature range for growth was rather broad and was high for a marine bacterium: the strain grew at 13–42 °C, showed good growth at 20–40 °C and had an optimum between 30 and 40 °C. The major cellular fatty acids were iso-C15 : 0 (24.2 %), C16 : 1
ω7c/iso-C15 : 0 2-OH (15.3 %) and iso-C17 : 1
ω9c (11.9 %). The DNA G+C content was 50.0 mol%. Phylogeny based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain c121T could be classified within a novel species of the genus Pseudidiomarina, for which the name Pseudidiomarina sediminum sp. nov. is proposed, with the type strain c121T (=CICC 10319T =LMG 24046T).
Thermogymnomonas acidicola gen. nov., sp. nov., a novel thermoacidophilic, cell wall-less archaeon in the order Thermoplasmatales, isolated from a solfataric soil in Hakone, Japan
Authors: Itoh Takashi , Yoshikawa Naoto , Takashina Tomonori
Published: October 2007

A novel thermoacidophilic, cell wall-less archaeon, strain IC-189T, was isolated from a solfataric field in Ohwaku-dani, Hakone, Japan. The cells were irregular cocci, sometimes lobed, club-shaped or catenated, and were highly variable in size, ranging from 0.8 to 8.0 μm in diameter. The strain grew at temperatures in the range 38–68 °C (optimally at 60 °C) and at pH 1.8–4.0 (optimally at around pH 3.0). Strain IC-189Twas obligately aerobic and heterotrophic, requiring yeast extract for growth. Yeast extract, glucose and mannose served as carbon and energy sources. The polar lipids consisted mainly of cyclic or acyclic glycerol-bisdiphytanyl-glycerol tetraethers, and the predominant quinone was a menaquinone with seven isoprenoid units (MK-7). The G+C content of total DNA was 56.1 mol%. 16S rRNA gene sequence analysis revealed that strain IC-189Twas a member of the orderThermoplasmatales, but diverged from the hitherto known species of the generaThermoplasma,PicrophilusandFerroplasma(86.2–91.0 % sequence similarity). These phenotypic and phylogenetic properties clearly support a separate taxonomic status for this strain. Therefore, strain IC-189Trepresents a novel genus (orderThermoplasmatales) and species, for which the nameThermogymnomonas acidicolagen. nov., sp. nov. is proposed, with type strain IC-189T(=JCM 13583T=DSM 18835T).
Taxonomic heterogeneity, as shown by siderotyping, of strains primarily identified as Pseudomonas putida
Authors: Meyer Jean-Marie , Gruffaz Christelle , Tulkki Topi , Izard Daniel
Published: October 2007

One hundred and forty-four fluorescent pseudomonad strains isolated from various environments (soil, water, plant rhizosphere, hospital) and received as Pseudomonas putida (83 strains), P. putida biovar A (49 strains), P. putida biovar B (10 strains) and P. putida biovar C (2 strains), were analysed by the pyoverdine-isoelectrofocusing and pyoverdine-mediated iron uptake methods of siderotyping. Both methods demonstrated a great diversity among these strains, which could be subdivided into 35 siderovars. Some siderovars specifically included strains that have subsequently been transferred to well-defined Pseudomonas species, e.g. Pseudomonas monteilii or Pseudomonas mosselii, or which could be related by their siderotype to Pseudomonas jessenii or Pseudomonas mandelii. Other siderovars included strains sharing a high level of DNA-DNA relatedness (>70 %), thus demonstrating that siderotyping could easily circumscribe strains at the species level. However, a group of seven strains, including the type strain, P. putida ATCC 12633T, were allocated into four siderovars, despite sharing DNA–DNA relatedness values of higher than 70 %. Interestingly, the strong genomic relationships between these seven strains were supported by the structural relationships among their pyoverdines, thus reflecting their phylogenetic affinities. These results strongly support the view that pyoverdine-based siderotyping could be used as a powerful tool in Pseudomonas taxonomy.
Desulfatiferula olefinivorans gen. nov., sp. nov., a long-chain n-alkene-degrading, sulfate-reducing bacterium
Authors: Cravo-Laureau Cristiana , Labat Cindy , Joulian Catherine , Matheron Robert , Hirschler-Réa Agnès
Published: October 2007

A novel anaerobic, long-chain alkene-degrading, sulfate-reducing bacterium, strain LM2801T, was isolated from brackish sediment of a wastewater decantation facility of an oil refinery (Berre lagoon, France). Cells of strain LM2801T were Gram-negative, motile, slightly curved or vibrioid rods. Its optimum growth conditions were 30–36 °C, 6–10 g NaCl l−1 and pH 7.5. Strain LM2801T incompletely oxidized long-chain alkenes (from C14 to C23) and fatty acids (C14 to C24). The DNA G+C content was 45.5 mol%. Sequence analyses of the 16S rRNA and dsrAB genes indicated that the strain was a member of the family Desulfobacteraceae within the Deltaproteobacteria. This novel isolate possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus. Therefore, strain LM2801T is described as a member of a new genus, Desulfatiferula gen. nov., of which Desulfatiferula olefinivorans sp. nov. is the type species. The type strain of Desulfatiferula olefinivorans is LM2801T (=DSM 18843T =JCM 14469T).
Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China
Authors: Castillo A. M. , Gutiérrez M. C. , Kamekura M. , Xue Y. , Ma Y. , Cowan D. A. , Jones B. E. , Grant W. D. , Ventosa A.
Published: October 2007

A novel halophilic archaeon, strain EJ-32T, was isolated from water from Lake Ejinor in Inner Mongolia, China. The taxonomy of strain EJ-32T was studied by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain EJ-32T was shown to be phylogenetically related to Halorubrum coriense (97.9 %), Halorubrum trapanicum (97.9 %), Halorubrum sodomense (97.8 %), Halorubrum tebenquichense (97.8 %), Halorubrum xinjiangense (97.6 %), Halorubrum terrestre (97.4 %), Halorubrum distributum (97.1 %) and Halorubrum saccharovorum (96.4 %). Strain EJ-32T was found to be neutrophilic, non-motile and Gram-negative. It grew in medium containing saturation concentrations of NaCl and did not require magnesium for optimal growth. The G+C content of the DNA is 64.0 mol%. Values for DNA–DNA hybridization with respect to phylogenetically related Halorubrum species were ≤49 %, indicating that EJ-32T constitutes a different genospecies. The data show that strain EJ-32T represents a novel species of the genus Halorubrum, for which the name Halorubrum ejinorense sp. nov. is proposed. The type strain is EJ-32T (=CECT 7194T=CGMCC 1.6782T=JCM 14265T).
Runella defluvii sp. nov., isolated from a domestic wastewater treatment plant
Authors: Lu Shipeng , Lee Jung Ro , Ryu Seung Hyun , Chung Bok Sil , Choe Woo-Seok , Jeon Che Ok
Published: October 2007

A long, Gram-negative, rod-shaped bacterium, designated strain EMB13T, was isolated from a wastewater treatment plant in Korea. The isolate was strictly aerobic and non-motile. The strain grew optimally at 30–35 °C and pH 7.5–8.0, and the predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7cand/or iso-C15 : 02-OH), C16 : 1ω5cand iso-C17 : 03-OH. The strain contained a large amount of phosphatidylethanolamine and small amounts of phosphatidylcholine and an unknown phospholipid as the polar lipids. The G+C content of the genomic DNA was 40.1 mol% and the major isoprenoid quinone was menaquinone-7. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB13Tbelonged to the genusRunellaand was most closely related toRunella limosaEMB111T, with a 16S rRNA gene sequence similarity of 97.1 %. DNA–DNA relatedness between strain EMB13TandR. limosaEMB111Twas approximately 25 %. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain EMB13Trepresents a novel species within the genusRunella, for which the nameRunella defluviisp. nov. is proposed. The type strain is EMB13T(=KCTC 12614T=DSM 17976T).
Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. for Brucella strains with cetaceans and seals as their preferred hosts
Authors: Foster Geoffrey , Osterman Bjorn S. , Godfroid Jacques , Jacques Isabelle , Cloeckaert Axel
Published: October 2007

Small Gram-negative cocco-bacilli resembling Brucella strains have been reported from marine mammals since the mid-1990s. Their placement in the genus Brucella has been supported by the following characteristics: they are aerobic, non-motile and catalase-positive, do not produce acid from carbohydrates and have a DNA–DNA relatedness value of >77 % with the six established members of the genus. Twenty-eight European isolates of the genus Brucella from marine mammals were distinguished from the six recognized species by their pattern of utilization of eleven substrates in oxidative metabolism tests and phage lysis. The 28 strains could be further separated into two groups with cetaceans and seals as their respective preferred hosts on the basis of molecular methods and on differences in the metabolism of l-arabinose, d-galactose and d-xylose. The names Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. are proposed for the isolates from cetaceans and seals, respectively. The type strain of Brucella ceti sp. nov. is NCTC 12891T (=BCCN 94-74T) and the type strain of Brucella pinnipedialis sp. nov. is NCTC 12890T (=BCCN 94-73T).
Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater
Authors: Lee Kiyoung , Lee Hong Kum , Choi Tae-Hwan , Cho Jang-Cheon
Published: October 2007

A seawater bacterium, designated IMCC3195T, was isolated from the Antarctic coast. Cells of the novel strain were Gram-negative, rusty-coloured, strictly aerobic, chemoheterotrophic, non-budding and non-motile rods or vibrioids that possessed a thin prostheca. Based on 16S rRNA gene sequence comparisons, the novel strain was most closely related to the generaHyphomonas(89.4–90.9 %),Maricaulis(90.1–90.4 %),Hirschia(89.0 %) andOceanicaulis(87.9 %) of the familyHyphomonadaceae. Phylogenetic analyses also showed the Antarctic isolate to be only distantly related to the genera of stalked bacteria of marine origin in the familyHyphomonadaceae. The DNA G+C content of the novel strain was 60.3 mol% and the predominant cellular fatty acids were C18 : 1ω7c(41.9 %), C17 : 1ω8c(21.4 %) and C17 : 0(14.3 %). The major quinone was Q-10. Several phenotypic and chemotaxonomic characteristics, including optimum temperature and salinity range for growth, cell morphology, pigmentation and fatty acid content, differentiated the novel strain from other related genera in the familyHyphomonadaceae. From the taxonomic evidence collected in this study, it is suggested that strain IMCC3195T(=KCCM 42687T=NBRC 103098T) represents a new genus and novel species in the familyHyphomonadaceae, for which the nameRobiginitomaculum antarcticumgen. nov., sp. nov. is proposed.
Reassessment of the phylogenetic relationships of Thiomonas cuprina
Authors: Kelly Donovan P. , Uchino Yoshihito , Huber Harald , Amils Ricardo , Wood Ann P.
Published: October 2007

The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö5 (=DSM 5495T) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495T =NBRC 102145T) and strain Hö5 maintained frozen in the Universität Regensburg for 23 years (=NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence. This also casts some doubt on the previously published 5S and 23S rRNA gene sequences (GenBank accession nos U67171 and X75567). The correct 16S rRNA gene sequence showed 99.8 % identity to those from Thiomonas delicata NBRC 14566T and ‘Thiomonas arsenivorans’ DSM 16361. The properties of these three species are re-evaluated, and emended descriptions are provided for the genus Thiomonas and the species Thiomonas cuprina.