- Volume 59, Issue 4, 2009

A Gram-positive, rod-shaped, aerobic, non-motile, yellow-pigmented bacterial strain, designated MM2LBT, was isolated from a chironomid egg mass that was sampled in a waste stabilization pond in northern Israel. 16S rRNA gene sequence analysis indicated that the isolate should be placed in the genus Leucobacter (family Microbacteriaceae). Levels of 16S rRNA gene sequence similarity between strain MM2LBT and the type strains of recognized Leucobacter species were 97.1 % or lower. The dominant cellular fatty acids of strain MM2LBT were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which are typical of members of the genus Leucobacter. Strain MM2LBT grew at 17–37 °C, in the presence of 0–7.0 % NaCl and at pH 4.0–9.5. Cell-wall amino acids were alanine, glycine, threonine, 2,4-diaminobutyric acid, glutamic acid and γ-aminobutyric acid in a B-type cross-linked peptidoglycan. The quinone system consisted of menaquinones MK-11, MK-10 and MK-12. The novel isolate was able to grow in medium containing 18 mM Cr(VI). On the basis of phenotypic properties and phylogenetic distinctiveness, strain MM2LBT is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chironomi sp. nov. is proposed. The type strain is MM2LBT (=LMG 24399T=DSM 19883T).

A novel actinomycete strain, designated SCSIO 01066T, was isolated from a marine sediment sample collected from the Nansha Islands in the South China Sea and was subjected to a polyphasic taxonomic study. A phylogenetic tree based on 16S rRNA gene sequences showed that strain SCSIO 01066T had the highest similarity (96.5 %) to members of the genus Streptomyces and was loosely associated with Streptomyces armeniacus JCM 3070T, Streptomyces cacaoi subsp. cacaoi NBRC 12748T and Streptomyces sodiiphilus YIM 80305T. Predominant menaquinones, major fatty acids and morphological properties were also consistent with typical characteristics of the genus Streptomyces; however, the presence of phosphatidylglycerol in the phospholipid pattern differs greatly from those of members of the genus Streptomyces. Additionally, strain SCSIO 01066T showed some physiological differences from its most closely related neighbours. Based on the polyphasic data, a novel species, Streptomyces nanshensis sp. nov., is proposed, with the type strain SCSIO 01066T (=KCTC 19400T=CCTCC AA 208005T).

A novel keratinolytic actinobacterium, strain WCC-2265T, was isolated from bovine hoof keratin ‘baited’ into composting bovine manure from southern Alberta, Canada, and subjected to phenotypic and genotypic characterization. Strain WCC-2265T produced well-developed, non-fragmenting and extensively branched hyphae within substrates and aerial hyphae, from which spherical spores possessing spiny cell sheaths were produced in primarily flexuous or straight chains. The cell wall contained meso-diaminopimelic acid, whole-cell sugars were galactose, glucose, madurose and ribose, and the major menaquinones were MK-9(H6), MK-9(H8), MK-9(H4) and MK-9(H2). These characteristics suggested that the organism belonged to the genus Actinomadura and a comparative analysis of 16S rRNA gene sequences indicated that it formed a distinct clade within the genus. Strain WCC-2265T could be differentiated from other species of the genus Actinomadura by DNA–DNA hybridization, morphological and physiological characteristics and the predominance of iso-C16 : 0, iso-C17 : 0 and 10-methyl C17 : 0 fatty acids. The broad range of phenotypic and genetic characters supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura keratinilytica sp. nov. is proposed; the type strain is strain WCC-2265T (=DSM 45195T=CCUG 56181T).

A Gram-positive, aerobic, rod-shaped and non-motile bacterium, designated strain KP02T, was isolated from soil from a ginseng field in Daejeon, South Korea. On the basis of 16S rRNA gene sequence similarity, this strain was shown to be related to ‘Pseudoclavibacter alba’ NBRC 15616 (95.5 %), ‘Pseudoclavibacter faecalis’ NBRC 15706 (93.9 %), Pseudoclavibacter helvolus DSM 20419T (93.7 %) and ‘Pseudoclavibacter bifida’ IAM 14848 (93.0 %). Chemotaxonomic data revealed that strain KP02T possessed MK-9 and MK-8 as major menaquinones and anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0 as predominant fatty acids. The genomic DNA G+C content of strain KP02T was 64.4 mol%. The physiological and biochemical tests suggested that strain KP02T represents a novel species. Based on these data, strain KP02T (=KCTC 19255T=JCM 15058T) should be classified as the type strain of a novel Pseudoclavibacter species, for which the name Pseudoclavibacter soli sp. nov. is proposed.

Eighteen isolates of a nonchromogenic, slowly growing, non-tuberculous species of the genus Mycobacterium were cultured from respiratory specimens obtained over the last eight years from 17 patients in the Netherlands. These isolates were grouped because they revealed a unique 16S rRNA gene sequence and were related to Mycobacterium xenopi. None of the 17 patients met the American Thoracic Society diagnostic criteria for non-tuberculous mycobacterial disease, which distinguishes the novel isolates from the related species, M. xenopi. A polyphasic taxonomic approach, including identification by biochemical and phenotypical analysis, hsp65 gene sequencing and PCR restriction enzyme pattern analysis, and sequence analyses of the rpoB gene and 16S–23S internal transcribed spacer supported the separate species status of the novel isolates. The name Mycobacterium noviomagense sp. nov. is proposed for the novel strains. The type strain is NLA000500338T (=DSM 45145T=CIP 109766T). A more distinctive taxonomy of NTM is a prerequisite for the assessment of their clinical relevance.

Four Gram-positive, non-motile, non-spore-forming bacterial strains, LC4T, LC6T, LC10T and LC13T, were isolated from a filtration substrate made from trass, a volcanic rock, and their taxonomic positions were investigated by a polyphasic taxonomic approach. The novel strains grew over a temperature range of 5–40 °C, at pH values of 6–11 and in the presence of 3–7 % (w/v) NaCl. A phylogenetic tree based on 16S rRNA gene sequences showed the novel strains formed a distinct evolutionary lineage within the genus Arthrobacter. Chemotaxonomic analyses demonstrated that the major menaquinone was MK-9(H2), a menaquinone typical of the Arthrobacter globiformis group. The major fatty acid was anteiso-C15 : 0 and the major amino acid present in the cell-wall peptidoglycan was l-lysine. These observations supported the affiliation of the novel strains to the genus Arthrobacter. On the basis of their morphological, physiological and genotypic characteristics, the new isolates are considered to represent four novel species of the genus Arthrobacter, for which the names Arthrobacter niigatensis sp. nov. (type strain LC4T=IAM 15382T=CCTCC AB 206012T), Arthrobacter alkaliphilus sp. nov. (type strain LC6T=IAM 15383T=CCTCC AB 206013T), Arthrobacter echigonensis sp. nov. (type strain LC10T=IAM 15385T=CCTCC AB 206017T) and Arthrobacter albidus sp. nov. (type strain LC13T=IAM 15386T=CCTCC AB 206018T) are proposed.

An alkaliphilic actinobacterium, designated strain CAAS 252T, was isolated from the black liquor treatment system of a cotton pulp mill in Wuhan, China. Cells of strain CAAS 252T were Gram-positive, non-motile, non-endospore-forming, short rod-shaped, and grew optimally at 42 °C and pH 9–10 in the presence of 3 % (w/v) NaCl. Strain CAAS 252T contained MK-7, MK-8 and MK-9 as the major menaquinones and anteiso-C17 : 0, anteiso-C15 : 0 and C16 : 0 as the predominant cellular fatty acids and had a peptidoglycan type of A4α, Lys–Gly-d-Asp. The DNA G+C content was 60.2 mol%. Based on analysis of 16S rRNA gene sequences (94.7–96.8 % similarity), DNA–DNA hybridization (<70 % relatedness) and chemotaxonomic characteristics, strain CAAS 252T belonged to the genus Nesterenkonia, but differed from all recognized species. Therefore, it is proposed that strain CAAS 252T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia alba sp. nov. is proposed. The type strain is CAAS 252T (=CCTCC AB 207011T=DSM 19423T).

A novel, Gram-positive bacterial strain, F12T, was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected from seawater off the coast of Japan. According to 16S rRNA gene sequence analysis, this strain represents a novel, deep-rooting lineage within the class Actinobacteria and clusters with uncultured bacteria and Acidimicrobium ferrooxidans. Compared to species with validly published names, the highest 16S rRNA gene sequence similarity (89.8 %) was to Acidimicrobium ferrooxidans DSM 10331T. Phylogenetic analyses showed that strain F12T represents a distinct phylogenetic lineage related closely to the genus Acidimicrobium. Strain F12T contained MK-9(H6) as the major menaquinone, whilst 17 : 0, 17 : 1ω8c, 15 : 0 and 16 : 0 were the major cellular fatty acids. The cell-wall peptidoglycan of strain F12T was composed of meso-diaminopimelic acid as the diagnostic diamino acid, alanine and glutamic acid (1 : 2 : 1). The cell-wall sugars detected were rhamnose, mannose, arabinose, galactose and xylose. The G+C content of the DNA was 74.4 mol%. From the taxonomic data obtained in this study, the name Iamia majanohamensis gen. nov., sp. nov. is proposed for the isolate, with type strain F12T (=NBRC 102561T=DSM 19957T). The name Iamiaceae fam. nov. is also proposed for the distinct phyletic line represented by the genus Iamia.

A mesophilic, methylotrophic methanogen, strain MobMT, was isolated from a natural gas field in Japan. Strain MobMT grew on methanol and methylamines, but not on H2/CO2, formate, acetate or dimethyl sulfide. The cells were motile, irregular cocci (diameter, 0.9–1.2 μm) and occurred singly, in pairs, as tetracocci or (occasionally) as aggregates. Strain MobMT grew at 9–37 °C (optimally at 30 °C) and at pH 6.1–7.8 (optimally at pH 6.5). Sodium and magnesium were required for growth, at 0.1–1.0 M Na+ (optimally at 0.35 M) and 10–400 mM Mg2+ (optimally at 15–25 mM). The G+C content of the genomic DNA was 42.4 mol%. 16S rRNA gene sequencing revealed that the isolate is a member of the genus Methanolobus, but distinct from its closest neighbours, Methanolobus tindarius DSM 2278T (sequence similarity, 98.0 %) and Methanolobus vulcani DSM 3029T (98.1 %). On the basis of phenotypic and phylogenetic features of MobMT, it is clear that this strain represents a novel species of the genus Methanolobus, for which the name Methanolobus profundi sp. nov. is proposed. The type strain is MobMT (=DSM 21213T=NBRC 104158T).

A novel methane-producing archaeon, designated strain HASUT, was isolated from a lotus field. Cells were Gram-negative, non-motile, irregular cocci, 2–3 μm in diameter, and occurred singly. Growth was observed at 15–40 °C (optimum, 37 °C) and pH 6.5–7.5 (optimum, pH 7.0). The G+C content of the genomic DNA was 60.9 mol%. Strain HASUT utilized ethanol, 1-propanol, 1-butanol, hydrogen and formate for growth and methane production. It converted ethanol to methane and acetate. Based on comparative 16S rRNA gene sequence analysis, strain HASUT was shown to be affiliated with the genus Methanofollis. It was related most closely to the type strain of Methanofollis liminatans (96.1 % 16S rRNA gene sequence similarity). Based on phylogenetic analysis and phenotypic characteristics, strain HASUT is considered to represent a novel species of the genus Methanofollis, for which the name Methanofollis ethanolicus sp. nov. is proposed. The type strain is HASUT (=NBRC 104120T=JCM 15103T=DSM 21041T).

An aerobic, gliding, yellow-pigmented bacterium lacking flagella and showing strong tyrosinase activity, designated strain EM41T, was isolated from seawater on the eastern coast of Jeju Island in Korea. Growth was observed at 15–35 °C (optimum, 25–30 °C) and at pH 6.5–9.0 (optimum, pH 7.0–8.5). Cells were Gram-negative, negative for flexirubin pigments and catalase- and oxidase-positive. The G+C content of the genomic DNA was 33.5 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Comparative 16S rRNA gene sequence analysis showed that strain EM41T formed a distinct phyletic line within the genus Cellulophaga with a 100 % bootstrap value and was most closely related to Cellulophaga pacifica KMM 3664T (97.0 % sequence similarity). The level of DNA–DNA relatedness between strain EM41T and C. pacifica KMM 3664T was about 17.8 %. On the basis of phenotypic and genotypic data, strain EM41T is considered to represent a novel species of the genus Cellulophaga, for which the name Cellulophaga tyrosinoxydans sp. nov. is proposed. The type strain is EM41T (=KCTC 22297T=DSM 21164T).

The type strains of the species Chryseobacterium arothri (DSM 19326T) and Chryseobacterium hominis (NF802T) were compared in order to clarify the taxonomic relationship of the two species. The 16S rRNA gene sequences of the two strains shared 99.9 % identity. DNA–DNA pairing studies between the two strains showed 100 % (reciprocal, 76.0 %) relatedness. Phenotypic data, including fatty acid patterns and substrate utilization profiles, showed no pronounced differences between the type strains of the two species. On the basis of these results, we propose the reclassification of Chryseobacterium arothri Campbell et al. 2008 as a later heterotypic synonym of Chryseobacterium hominis Vaneechoutte et al. 2007 .

A marine bacterial strain, designated A71T, was isolated from marine algae collected from the South Sea, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A71T belonged to the family Flavobacteriaceae and was closely related to Aequorivita antarctica SW49T (96.5 % sequence similarity). Cells of strain A71T were Gram-negative, aerobic, oxidase-negative, catalase-positive, yellow/orange-pigmented and non-motile. The major fatty acids were iso-C15 : 0 (20.6 %), iso-C17 : 1 ω9c (13.3 %), anteiso-C15 : 0 (13.1 %), iso-C17 : 0 3-OH (12.7 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 6.6 %). The DNA G+C content was 36.9 mol%. Several phenotypic characteristics served to differentiate the isolate from recognized members of the genus Aequorivita. Data from this polyphasic study clearly demonstrated that strain A71T represents a novel species of the genus Aequorivita. The name Aequorivita capsosiphonis sp. nov. is proposed, with strain A71T (=KCTC 22183T =JCM 15070T) as the type strain. In addition, an emended description of the genus Aequorivita is presented.

Four strains of anaerobic Gram-negative bacilli isolated from the human mouth were characterized using a variety of phenotypic and genotypic tests. The strains were found to comprise a homogeneous group and 16S rRNA gene sequence analysis revealed them to be distinct from but related to a loose cluster of Prevotella species including Prevotella buccalis, Prevotella nanceiensis and Prevotella marshii. A novel species, Prevotella micans sp. nov., is proposed to accommodate these strains. Prevotella micans is saccharolytic and produces acetic, isovaleric and succinic acids and minor amounts of isobutyric acid as end products of fermentation. The G+C content of the DNA of the type strain is 46 mol%. The type strain of Prevotella micans is E7.56T (=DSM 21469T =CCUG 56105T).

Two novel aerobic, dark-orange-pigmented, Gram-negative bacterial strains, designated KMM 3531T and KMM 3953, were isolated from the green alga Ulva fenestrata. Analysis of the 16S rRNA gene sequences showed that the strains represented a novel lineage within the family Flavobacteriaceae. The most closely related genera with validly published names were Costertonia, Flagellimonas, Kriegella, Maribacter, Muricauda and Zobellia, with 16S rRNA gene sequence similarities of 93.3–91.8 %. Cells of strains KMM 3531T and KMM 3953 were rod-shaped, motile by gliding and grew at temperatures up to 49 °C. They produced acid from carbohydrates and possessed oxidase, catalase, β-galactosidase and agarase activities. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, summed feature 3 (comprising C16 : 1 ω7c and/or iso-С15 : 0 2-OH), iso-C17 : 1 ω9c and iso-C15 : 0 3-OH. The DNA G+C content was 47–49 mol%. On the basis of phenotypic and genotypic characteristics, strains KMM 3531T and KMM 3953 represent a novel genus and species, for which the name Pseudozobellia thermophila gen. nov., sp. nov. is proposed. The type strain is KMM 3531T (=DSM 19858T=JCM 11733T=KCTC 22016T).

The accurate taxonomic position of Donghaeana dokdonensis DSW-6T was investigated. Phylogenetic analysis revealed that the 16S rRNA gene sequences of the strain studied and of Persicivirga xylanidelens SW256T shared 98.2 % similarity. On the basis of phylogenetic evidence, phenotypic data and DNA–DNA reassociation values, it is proposed that strain DSW-6T be reclassified as Persicivirga dokdonensis comb. nov. Emended descriptions of the genus Persicivirga and of P. xylanidelens are also proposed.

Two pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9T and SPM-10T) were isolated from a permafrost soil collected from the Adventdalen valley, Spitsbergen, northern Norway. A third isolate (strain M5-H2) was recovered from the same soil sample after the sample had been exposed to simulated Martian environmental conditions. The three strains were characterized taxonomically by using a polyphasic approach. Phylogenetic, chemotaxonomic, physiological and morphological analyses demonstrated that the three isolates were most closely related to members of the genus Spirosoma. 16S rRNA gene sequence data indicated that the three isolates could be divided into two clusters: (i) strain SPM-9T and (ii) strains SPM-10T and M5-H2. This grouping was confirmed by DNA–DNA hybridization experiments. Strains SPM-9T and SPM-10T exhibited 92 % 16S rRNA gene sequence similarity to both Spirosoma linguale LMG 10896T and Spirosoma rigui WPCB 118T. The major fatty acids present in all three isolates were summed feature 3 (comprising iso-C15:0 2-OH and/or C16 : 1 ω7c; 43.0–48.2 % of the total), C16 : 1 ω5c (19.1–21.3 %), C16 : 0 (6.7–7.3 %), iso-C17 : 0 3-OH (4.7–6.0 %) and iso-C15 : 0 (2.6–5.7 %). On the basis of their phenotypic and genotypic characteristics, the new strains are assigned to two novel species of the genus Spirosoma, for which the names Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov. are proposed. The type strain of Spirosoma spitsbergense is SPM-9T (=NCIMB 14407T=DSM 19989T) and the type strain of Spirosoma luteum is SPM-10T (=NCIMB 14406T=DSM 19990T). An emended description of the genus Spirosoma is also proposed.