- Volume 62, Issue 2, 2012

The taxonomic position of a streptomycete isolated from soil collected from Cockle Park Experimental Farm, Northumberland, UK, was determined by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Streptomyces. 16S rRNA gene sequence analysis supported classification of the strain in the genus Streptomyces and showed that it formed a distinct phyletic line loosely associated with members of the Streptomyces yeochonensis clade. It was related most closely to Streptomyces paucisporeus 1413T (98.6 %16S rRNA gene sequence similarity), but could be distinguished from the latter based on the low level of DNA–DNA relatedness (40 %). It was readily distinguished from the type strains of all species assigned to the S. yeochonensis clade based on a combination of phenotypic properties. Strain BK168T ( = KACC 20908T = NCIMB 14704T) should therefore be classified as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces cocklensis sp. nov. is proposed. The organism produces the antibiotic dioxamycin.

Three strains, K08-0182T, K08-0178 and K08-0195 were isolated from the paste of ground plant roots collected in Kanagawa Prefecture, Japan. These strains contained meso-diaminopimelic acid and lysine as the diamino acids in cell-wall peptidoglycan, and MK-9(H6) and MK-9(H8) as the predominant menaquinones. The G+C contents of the DNA were 72–73 mol%. Taken together, these characteristics combined with 16S rRNA gene sequence analyses revealed that the isolated strains belong to the genus Actinoallomurus. DNA–DNA hybridization values showed that the three strains belonged to a novel species of the genus Actinoallomurus. Therefore strains K08-0182T, K08-0178 and K08-0195 are proposed as representatives of a novel species, Actinoallomurus radicium sp. nov. The type strain is K08-0182T ( = DSM 45523T  = NBRC 107678T  = JCM 17294T).

A novel actinomycete strain, designated RP-AC37T, was isolated from rhizosphere soil collected on Mara Island of Jeju, Republic of Korea. Cells were aerobic, Gram-positive, oxidase-negative, catalase-positive, non-mycelium-forming and motile rods (0.6–0.7×1.9–2.4 µm). Phylogenetic analysis based on 16S rRNA gene sequences showed that the organism formed a distinct clade within the radiation occupied by the suborder Frankineae. 16S rRNA gene similarity values were less than 93.2 % to members of the suborder Frankineae and related taxa. The diamino acid isomer in the cell-wall peptidoglycan was ll-diaminopimelic acid. The major whole-cell sugars were glucose, galactose and xylose. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The cellular fatty acids were straight-chain, unsaturated and saturated, with a significant amount of tuberculostearic acid (10-methyl-C18 : 0). The DNA G+C content was 73.2 mol%. The combination of morphological, chemotaxonomic and phylogenetic data clearly separate the isolate from members of known genera of the suborder Frankineae and related taxa, suggesting that the isolate represents a novel species in a new genus in this suborder, for which the name Motilibacter peucedani gen. nov., sp. nov. is proposed; the type strain is RP-AC37T ( = KCTC 19630T = DSM 45328T).

A Gram-positive, aerobic, rod- or coccus-shaped, non-motile bacterium, designated DMZ1T, was isolated from soil of the Demilitarized Zone, South Korea. Strain DMZ1T grew optimally at 30 °C, at pH 7–8 and with 1 % (w/v) NaCl. The isolate showed high 16S rRNA gene sequence similarity with Knoellia aerolata 5317S-21T (98.2 %). The cell-wall sugars were glucose and ribose. The peptidoglycan amino acids were meso-diaminopimelic acid, glutamic acid and glycine. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and five unknown phospholipids. The isolate did not contain mycolic acids. The DNA G+C content was 72.6 mol%. The isolate showed <28 % DNA–DNA relatedness with members of the genus Knoellia. Phylogenetic, phenotypic and genotypic analysis indicated that strain DMZ1T represents a novel species of the genus Knoellia, for which the name Knoellia locipacati sp. nov. is proposed. The type strain is DMZ1T ( = KACC 15114T  = JCM 17313T).

A Gram-positive, aerobic, non-spore-forming actinobacterial strain, designated strain TL1T, was isolated from pig manure in Wuhan, China. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinone was MK-8(H4). The major fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0 and C17 : 1ω8c. The genomic DNA G+C content was 70.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TL1T was most closely related to the type strains of Knoellia sinensis (98.5 %), Knoellia subterranea (98.2 %) and Knoellia aerolata (96.9 %). DNA–DNA relatedness values of strain TL1T with the type strains of K. sinensis and K. subterranea were 27.3 and 34.0 %, respectively. Comparison of phenotypic, chemotaxonomic and phylogenetic characteristics among strain TL1T and related organisms revealed that the isolate represents a novel species of the genus Knoellia, for which the name Knoellia flava sp. nov. is proposed; the type strain is TL1T ( = CGMCC 1.10749T = KCTC 19810T).

A Gram-stain-positive, aerobic, non-motile, psychrophilic bacterium, designated strain Cr6-08T, was isolated from alpine glacier cryoconite. Growth of strain Cr6-08T occurred at 1–25 °C. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Cr6-08T is most closely related to members of the genus Arthrobacter. Strain Cr6-08T possessed chemotaxonomic properties consistent with those of the genus Arthrobacter, such as peptidoglycan type A3α (l-Lys–l-Ala4), MK-9(H2) as major menaquinone and anteiso- and iso-branched compounds (anteiso-C15 : 0 and iso-C15 : 0) as major cellular fatty acids. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown glycolipid and three unknown polar lipids. The genomic DNA G+C content of strain Cr6-08T was 57.3 mol%. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain Cr6-08T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter cryoconiti sp. nov. is proposed. The type strain is Cr6-08T ( = DSM 23324T  = LMG 26052T  = CGMCC 1.10698T).

A Gram-positive, aerobic actinobacterium with high chromate [Cr(VI)]-reducing ability, designated strain Q5-1T, was isolated from manganese mining soil in Hunan Province, central-south China. The organism formed branching hyphae and contained ll-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipid profile was characterized by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The major fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-8(H4). The genomic DNA G+C content was 71.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q5-1T was closely related to Intrasporangium calvum DSM 43043T ( = NRRL B-3866T) and Humihabitans oryzae KV-657T ( = NRRL B-24470T) with similarities of 96.6 and 96.4 %, respectively. Comparison of phenotypic, biochemical and chemotaxonomic characters of strain Q5-1T and phylogenetically related strains revealed that the isolate represents a novel species of the genus Intrasporangium, for which the name Intrasporangium chromatireducens sp. nov. is proposed. The type strain is Q5-1T ( = KCTC 19811T = CCTCC AA 2010019T = CGMCC 1.10750T = NRRL B-59521T). An emended description of the genus Intrasporangium is also proposed.

A Gram-positive, non-motile, rod-shaped, psychrophilic actinomycete, designated strain Cr7-14T, was isolated from alpine glacier cryoconite. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Cr7-14T was related to members of the genus Nocardioides and shared highest 16S rRNA gene sequence similarities with the type strains of Nocardioides furvisabuli (98.6 %), Nocardioides ganghwensis (98.2 %), Nocardioides oleivorans (98.1 %) and Nocardioides exalbidus (97.6 %). The predominant cellular fatty acids of strain Cr7-14T were C17 : 1ω8c (39.5 %) and iso-C16 : 0 (32.4 %). The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were galactose and rhamnose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, four unknown glycolipids and two unknown polar lipids. The genomic DNA G+C content was 71.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species, Nocardioides alpinus sp. nov., is proposed, with Cr7-14T ( = DSM 23325T = LMG 26053T = CGMCC 1.10697T) as the type strain.

A moderately halophilic and alkalitolerant bacterium, designated strain HN30T, was isolated from garden soil in Japan. Cells of strain HN30T were motile, endospore-forming, aerobic, rod-shaped and Gram-positive, and contained A1γ meso-diaminopimelic acid-type murein. Growth occurred in 7–23 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 6.5–10.0 (optimum, pH 8.0–8.5) and at 20–40 °C (optimum, 30 °C). The isoprenoid quinone was menaquinone-7. The polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The DNA G+C content of strain HN30T was 47 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN30T was most closely related to Geomicrobium halophilum BH1T (93 % sequence similarity). 16S rRNA gene sequence similarities with other recognized species were less than 89 %. Phylogenetic and phenotypic characteristics indicated that strain HN30T represents a novel species in a new genus, for which the name Natribacillus halophilus gen. nov., sp. nov. is proposed; the type strain is HN30T ( = JCM 15649T = DSM 21771T).

Bacillus sporothermodurans is an industrially important micro-organism because of its ability to produce endospores which resist ultra-high temperature (UHT) and industrial sterilization processes. It was described by Pettersson et al. (1996) [Pettersson, B., Lembke, F., Hammer, P., Stackebrandt, E. & Priest, F. G. (1996). Int J Syst Bacteriol 46, 759–764] based on seven genetically homogeneous isolates all from UHT milk. Bacillus oleronius, the closest phylogenetic neighbour of B. sporothermodurans, was described by Kuhnigk et al. (1995) [Kuhnigk, T., Borst, E.-M., Breunig, A., König, H., Collins, M. D., Hutson, R. A. & Kämpfer, P. (1995). Can J Microbiol 41, 699–706] based on a single strain, isolated from the hindgut of the termite Reticulitermes santonensis. A polyphasic study of a heterogeneous collection of B. sporothermodurans and B. oleronius strains isolated from various sources and geographical origins led to an emended description of both species. Additional data presented are the results of fatty acid, quinone and/or cell wall (polar lipid) analyses. DNA–DNA hybridization confirmed 3 subgroups of strains obtained after SDS-PAGE analysis of cellular proteins as B. sporothermodurans. One named B. sporothermodurans strain (R-7489) was reclassified as a Bacillus fordii strain. The phenotypic profiles of both species were rather heterogeneous, sometimes different from the original descriptions and did not differ in a large number of characteristics, although B. oleronius generally gave stronger reactions in its positive tests than did B. sporothermodurans; the variable and weak reactions for both organisms with some substrates blurred the distinction between the two. However, differences in polar lipid, SDS-PAGE and menaquinone profiles clearly allow distinction between the two species.

Twelve independent isolates of a Gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13 % similarity). DNA–DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbours. The partial sequences of the 23S rRNA gene for the novel strains and their nearest neighbours also provide support for the novel species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α l-Lys–Gly–d-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids are iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062T  = DSM 23544T  = CCUG 59649T  = LMG 26022T) is proposed.

In the early 1980s, a facultatively anaerobic, non-motile, short rod, designated 202T, was isolated from a chicken crop and identified as a homofermentative lactic acid bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain was affiliated with the genus Lactobacillus, clustering within the Lactobacillus acidophilus–delbrueckii group. In this analysis, strain 202T appeared to be most closely related to the type strains of Lactobacillus intestinalis and Lactobacillus amylolyticus, with gene sequence similarities of 96.1 and 96.2 %, respectively. Strain 202T was found to differ from these two species, however, when investigated by multilocus sequence analysis, and it also differed in terms of some of its metabolic properties. On the basis of these observations, strain 202T is considered to represent a novel species in the genus Lactobacillus, for which the name Lactobacillus gigeriorum sp. nov. is proposed; the type strain is 202T ( = CRBIP 24.85T = DSM 23908T).

A Gram-staining-variable, motile, endospore-forming and rod-shaped bacterial strain, IDS-20T, was isolated from a marine solar saltern in Korea and subjected to a polyphasic taxonomic investigation. Strain IDS-20T grew optimally at 37 °C, at pH 7.5–8.0 and in the presence of 4–5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IDS-20T belongs to the genus Virgibacillus. Strain IDS-20T exhibited 93.4–96.6 % 16S rRNA gene sequence similarity to the type strains of species of the genus Virgibacillus. Strain IDS-20T had MK-7 as the predominant menaquinone and a cell-wall peptidoglycan based on meso-diaminopimelic acid. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0 and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified phospholipids. The DNA G+C content was 39.5 mol%. The phylogenetic distinctiveness and differential phenotypic characteristics of strain IDS-20T demonstrated that this strain can be distinguished from recognized species of the genus Virgibacillus. On the basis of the data presented, strain IDS-20T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus campisalis sp. nov. is proposed. The type strain is IDS-20T ( = KCTC 13727T  = CCUG 59308T).

A Gram-positive, aerobic, motile rod, designated strain CCBAU 05776T, was isolated from the inner tissues of a healthy soybean (Glycine max L.) root collected from an agricultural field in the countryside of Shijiazhuang city, Hebei Province, China. Phylogenetic analysis of the 16S rRNA gene indicated that this strain was most closely related to Bacillus muralis LMG 20238T and Bacillus simplex NBRC 15720T with similarity of 96.5 % and 96.3 %, respectively, lower than the suggested threshold (97.0 %) for separating bacterial species. In phenotypic characterization, the novel strain differed from the two most related species in that it did not hydrolyse casein or starch but could grow on MacConkey agar. It grew between 15 and 45 °C and tolerated up to 7 % NaCl (w/v). Strain CCBAU 05776T grew in media with pH 5.5 to 10 (optimal growth at pH 7.0–8.0). The predominant cellular fatty acids were iso-C15 : 0 (40.81 %) and C16 : 1ω7c alcohol (10.61 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C was 40.8 mol% (T m). DNA–DNA relatedness of the novel isolate with B. muralis and B. simplex was 42.4 % and 32.7 %, respectively. Based upon the consensus of phylogenetic and phenotypic analyses, strain CCBAU 05776T represents a novel species within the genus Bacillus, for which the name Bacillus endoradicis sp. nov. is proposed. The type strain is CCBAU 05776T ( = LMG 25492T  = HAMBI 3097T).

A novel Legionella species was identified based on analysis of 16S rRNA and mip (macrophage infectivity potentiator) gene sequences, cellular fatty acids, isoprenoid quinones, biochemical reactions, antigens and quantitative DNA–DNA hybridization. Strain CDC-1796-JAP-ET was isolated from well water at the Nagasaki Municipal Medical Center, Japan. Two strains, CDC-3041-AUS-E and CDC-3558-AUS-E, were isolated from water samples during an outbreak of legionellosis in South Australia. Strain CDC-5427-OH-H was isolated from a 66-year-old female patient diagnosed with Legionnaires’ disease in the US. Cells from these four strains were Gram-negative, non-fluorescent, rod-shaped, and positive for alkaline phosphatase, esterase, leucine arylamidase, catalase, gelatinase, β-lactamase and tyrosine browning assay. Phylogenetic analysis of 16S rRNA and mip genes revealed that the four strains formed a distinct cluster within the genus Legionella. The bacteria contained branched-chain fatty acids and quinones that are typical of members of the genus Legionella. Slide agglutination tests demonstrated no cross-reaction with 52 previously described members of the Legionellaceae. DNA–DNA hybridization studies indicated that DNAs from the four strains were highly related (78–84 %) but they showed 29 % relatedness to Legionella oakridgensis ATCC 33761T and less than 10 % to strains of other Legionella species tested. These characterizations suggest that the isolates represent a novel species, for which the name Legionella nagasakiensis sp. nov. is proposed; the type strain is CDC-1796-JAP-ET ( = ATCC BAA-1557T = JCM 15315T).

Three Gram-negative, microaerophilic bacteria, strains ASB1T, ASB2 and ASB3, with a corkscrew-like morphology isolated from the gastric mucosa of cats were studied using a polyphasic taxonomic approach. The isolates grew on biphasic culture plates under microaerobic conditions at 37 °C and exhibited urease, oxidase and catalase activities. They were also able to grow in colonies on dry agar plates. Based on 16S rRNA gene sequence analysis, ASB1T, ASB2 and ASB3 were identified as members of the genus Helicobacter and showed 98 to 99 % sequence similarity to strains of Helicobacter felis, Helicobacter bizzozeronii, ‘Candidatus Helicobacter heilmannii’, Helicobacter cynogastricus, Helicobacter baculiformis and Helicobacter salomonis, six related Helicobacter species previously detected in feline or canine gastric mucosa. Sequencing of the partial hsp60 gene demonstrated that ASB1T, ASB2 and ASB3 constitute a separate taxon among the feline and canine Helicobacter species. The urease gene sequences of ASB1T, ASB2 and ASB3 showed approximately 91 % similarity to those of ‘Candidatus Helicobacter heilmannii’. Protein profiling, the absence of alkaline phosphatase activity and several other biochemical characteristics also allowed strains ASB1T, ASB2 and ASB3 to be differentiated from other Helicobacter species of feline or canine gastric origin. The results of this polyphasic taxonomic study show that the cultured isolates constitute a new taxon corresponding to ‘Candidatus Helicobacter heilmannii’, which was previously demonstrated in the stomach of humans, wild felidae, cats and dogs. The name Helicobacter heilmannii sp. nov. is proposed for these isolates; the type strain is ASB1T ( = DSM 23983T = LMG 26292T).

During a study of the diversity and phylogeny of rhizobia in the root nodules of Kummerowia striata grown in north-western China, four strains were classified in the genus Rhizobium on the basis of their 16S rRNA gene sequences. The 16S rRNA gene sequences of three of these strains were identical and that of the other strain, which was the only one isolated in Yangling, differed from the others by just 1 bp. The16S rRNA gene sequences of the four strains showed a mean similarity of 99.3 % with the most closely related, recognized species, Rhizobium vitis. The corresponding recA and glnA gene sequences showed similarities with established species of Rhizobium of less than 86.5 % and less than 89.6 %, respectively. These low similarities indicated that the four strains represented a novel species of the genus Rhizobium. The strains were also found to be distinguishable from the closest related, established species (R. vitis) by rep-PCR DNA fingerprinting, analysis of cellular fatty acid profiles and from the results of a series of phenotypic tests. The level of DNA–DNA relatedness between the representative strain CCNWSX 0483T and Rhizobium vitis IAM 14140T was only 40.13 %. Therefore, a novel species, Rhizobium taibaishanense sp. nov., is proposed, with strain CCNWSX 0483T ( = ACCC 14971T = HAMBI 3214T) as the type strain. In nodulation and pathogenicity tests, none of the four strains of Rhizobium taibaishanense sp. nov. was able to induce any nodule or tumour formation on plants. As no amplicons were detected when DNA from the strains was run in PCR with primers for the detection of nodA, nifH and virC gene sequences, the strains probably do not carry sym or vir genes.