- Volume 57, Issue 12, 2007

A Gram-positive, aerobic, non-motile, mesophilic strain, djl-6T, able to degrade carbendazim, was isolated from a carbendazim-contaminated soil sample from Jiangsu province, China. The taxonomic position of this isolate was analysed by using a polyphasic approach. Chemotaxonomic analysis including peptidoglycan type, diagnostic sugar composition, fatty acid profile, menaquinones, polar lipids and mycolic acids showed that the characteristics of strain djl-6T were in good agreement with those of the genus Rhodococcus. DNA–DNA hybridization showed that it had low genomic relatedness with Rhodococcus baikonurensis DSM 44587T (31.8 %), Rhodococcus erythropolis DSM 43066T (23.8 %) and Rhodococcus globerulus DSM 43954T (17.7 %), the three type strains to which strain djl-6T was most closely related based on 16S rRNA gene sequence analysis (99.78, 99.25 and 98.91 % similarity, respectively). Based on the phenotypic properties and DNA–DNA hybridization data, strain djl-6T (=CGMCC 1.6580T =KCTC 19205T) is proposed as the type strain of a novel Rhodococcus species, Rhodococcus qingshengii sp. nov.

In the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91F2T was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological and chemotaxonomic characteristics of this strain, which are different from those of all species of Saccharothrix as well as the other genera within the suborder, it was concluded that this strain represents a new genus, for which the name Umezawaea gen. nov. is proposed. Pseudosporangia are produced on the aerial mycelium, the whole-cell sugar pattern consists of galactose, mannose and ribose, phosphatidylethanolamine, phosphatidylinositol and lyso-phosphatidylethanolamine are the predominant phospholipids and MK-9(H4) is the predominant menaquinone. The type species of the proposed new genus is Umezawaea tangerina gen. nov., comb. nov., with the type strain MK27-91F2T (=NRRL B-24463T =DSM 44720T =FERM P-16053T =JCM 10302T =NBRC 16184T).

A yellow-pigmented, Gram-positive, aerobic, non-motile, non-spore-forming, irregular rod-shaped bacterium (strain TAN 31504T) was isolated from the bacteriophagous nematode Caenorhabditis elegans. Based on 16S rRNA gene sequence similarity, DNA G+C content of 69.5 mol%, 2,4-diaminobutyric acid in the cell-wall peptidoglycan, major menaquinone MK-11, abundance of anteiso- and iso-fatty acids, polar lipids diphosphatidylglycerol and phosphatidylglycerol and a number of shared biochemical characteristics, strain TAN 31504T was placed in the genus Leucobacter. DNA–DNA hybridization comparisons demonstrated a 91 % DNA–DNA relatedness between strain TAN 31504T and Leucobacter chromiireducens LMG 22506T indicating that these two strains belong to the same species, when the recommended threshold value of 70 % DNA–DNA relatedness for the definition of a bacterial species by the ad hoc committee on reconciliation of approaches to bacterial systematics is considered. Based on distinct differences in morphology, physiology, chemotaxonomic markers and various biochemical characteristics, it is proposed to split the species L. chromiireducens into two novel subspecies, Leucobacter chromiireducens subsp. chromiireducens subsp. nov. (type strain L-1T=CIP 108389T=LMG 22506T) and Leucobacter chromiireducens subsp. solipictus subsp. nov. (type strain TAN 31504T=DSM 18340T=ATCC BAA-1336T).

A novel, yellow-pigmented actinobacterium was isolated from a small stone collected in Jeju, Republic of Korea. The cells of the organism, designated strain R-Ac013T, were Gram-positive, aerobic, non-motile cocci that occurred singly or in pairs. The strain showed growth at 10–37 °C and pH 4.1–11.1, and tolerated 2 % NaCl. On the basis of the 16S rRNA gene sequence, the organism was phylogenetically related to members of the genera Tetrasphaera (94.6–97.1 % sequence similarity), Terrabacter (96.5 %), Knoellia (96.4 %), Terracoccus (96.4 %), Oryzihumus (96.4 %), Janibacter (96.1–96.4 %) and Intrasporangium (96.2 %). The chemotaxonomic results for the organism were as follows: ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, acetyl-type murein, MK-8(H4) as the major menaquinone, a DNA G+C content of 74.1 mol%, and a polar lipid profile that comprised diphosphatidylglycerol and phosphatidylinositol. The fatty acid profile consisted of iso- and anteiso-methyl-branched, straight-chain saturated and monounsaturated types, the major components being iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. The combination of the phenotypic and phylogenetic data revealed that this strain represents a novel genus and species of the family Intrasporangiaceae, for which the name Lapillicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain is strain R-Ac013T (=KCTC 19200T=DSM 18607T).

A study was conducted to determine the taxonomic status of six actinomycete strains isolated from root nodules of Lupinus angustifolius. The strains were filamentous, Gram-positive and produced single spores at the tip of the hyphae. Phylogenetic, chemotaxonomic and morphological analyses demonstrated that all six strains belonged to the genus Micromonospora. According to the 16S rRNA gene sequence data, the strains were divided into two clusters that are moderately related to Micromonospora mirobrigensis, Micromonospora matsumotoense and Micromonospora purpureochromogenes. Fatty acid patterns also supported the division of the strains, and significant differences between the two groups were found in the amounts of iso-15 : 0, iso-16 : 0, iso-16 : 1 and iso-17 : 0. Furthermore, the two groups showed physiological differences which included utilization of arabinose, trehalose, alanine and sucrose and xylan hydrolysis. Finally, DNA–DNA hybridization and ribotyping studies confirmed that each group represents a novel species. Based on the genotypic and phenotypic data, the novel species Micromonospora lupini sp. nov. (type strain Lupac 14NT =DSM 44874T =LMG 24055T) and Micromonospora saelicesensis sp. nov. (type strain Lupac 09T =DSM 44871T =LMG 24056T) are proposed.

A novel actinomycete was isolated from radiation-polluted soil collected from Xinjiang in north-western China. The isolate, strain R24T, was found to have chemical and morphological properties associated with members of the genus Lechevalieria. An almost-complete 16S rRNA gene sequence of the isolate was aligned with corresponding sequences from representatives of the genus Lechevalieria and related taxa, using three tree-making algorithms, and was shown to form a distinct phyletic line in the Lechevalieria phylogenetic tree. DNA–DNA relatedness and phenotypic data served to distinguish strain R24T from members of the three Lechevalieria species with validly published names. The genotypic and phenotypic data show that the isolate should be classified as a novel species within the genus Lechevalieria. The name proposed for this taxon is Lechevalieria xinjiangensis sp. nov. The type strain is R24T (=CGMCC 4.3525T=DSM 45081T).

An aerobic, Gram-positive, non-motile, non-spore-forming, rod–coccus-shaped bacterium, strain 5317S-21T, was isolated from an air sample from Suwon city, Republic of Korea. The isolate was able to grow within a pH range of 5.0–9.0 and a temperature range of 5–35 °C and it tolerated up to 2 % (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The predominant isoprenoid quinone was MK-8(H4). The major polar lipids were phosphatidylinositol, phosphatidylethanolamine and diphosphatidylglycerol; phosphatidylglycerol and several unknown phospholipids were also detected. Mycolic acids were absent. The only whole-cell sugar was glucose. The major cellular fatty acids were iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. 16S rRNA gene sequence analysis indicated that strain 5317S-21T was related phylogenetically to members of the genus Knoellia, with 97.4 % sequence similarity to the type strains of Knoellia sinensis and Knoellia subterranea. The G+C content of the genomic DNA of strain 5317S-21T was 73 mol%. Levels of DNA–DNA relatedness between strain 5317S-21T and the type strains of Knoellia sinensis and Knoellia subterranea were 37 and 41 %, respectively. It was concluded that strain 5317S-21T represents a novel species of the genus Knoellia, for which the name Knoellia aerolata sp. nov. is proposed. The type strain is 5317S-21T (=KACC 20583T =DSM 18566T).

The taxonomic status of a mycolic acid-containing actinomycete, isolated from a natural cave on Jeju Island, Republic of Korea, was investigated by means of a polyphasic approach. The isolate, designated strain N2-11T, produced yellow- to orange-coloured vegetative hyphae and white- to pinkish white-coloured aerial mycelia, both of which fragmented into irregular rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the organism belonged to the family Nocardiaceae, occupying a distinct position between Nocardia harenae and a Nocardia carnea cluster. The results of chemotaxonomic analyses were consistent with the affiliation of the organism with the genus Nocardia. On the basis of 16S rRNA gene sequence similarities, the closest phylogenetic neighbours were the type strains of N. carnea (98.3 %), Nocardia flavorosea (98.0 %), Nocardia sienata (97.9 %) and Nocardia testacea (97.8 %), but the organism could be clearly distinguished from its phylogenetic relatives with reference to a broad range of physiological markers. On the basis of phenotypic and molecular genetic data presented in this study, strain N2-11T represents a novel species of the genus Nocardia, for which the name Nocardia speluncae sp. nov. is proposed. The type strain is N2-11T (=JBRI 2006T =KCTC 19223T =DSM 45078T).

The taxonomic position of a novel actinobacterium (designated SBS-12T), which was isolated from beach sand on Jeju Island, Republic of Korea, was determined following a polyphasic taxonomic characterization. Cells of the organism were Gram-positive, catalase-positive, oxidase-negative and non-motile rods. The organism contained ll-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as predominant menaquinone, and had a polar lipid profile containing phosphatidylglycerol and phosphatidylinositol, iso-C16 : 0 as the major fatty acid and a DNA G+C content of 73.1 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism occupies a distinct phylogenetic position within the radiation including representatives of the family Nocardioidaceae. High levels of 16S rRNA gene sequence similarity were found with Nocardioides kribbensis (97.2 %), Nocardioides aquiterrae (96.9 %), Nocardioides pyridinolyticus (96.6 %) and Nocardioides aquaticus (96.3 %). The combination of morphological and chemotaxonomic characteristics was consistent with classification in the genus Nocardioides, but the isolate can be differentiated from all Nocardioides species with validly published names by a range of physiological properties. The name Nocardioides marinisabuli sp. nov. is proposed for this novel organism, with the type strain SBS-12T (=JBRI 2003T=KCCM 42681T=DSM 18965T).

A thermophilic, methylotrophic methanogen, strain ZC-1T, was isolated from the Shengli oilfield, China. Cells of strain ZC-1T were motile cocci, 0.7–1.0 μm in diameter and always occurred in clusters of two to four cells. Lysis-susceptibility experiments and analysis of transmission electron micrographs of strain ZC-1T suggested the presence of a proteinaceous cell wall. Strain ZC-1T used methanol, methylamine and trimethylamine as substrates for methanogenesis. Optimal growth, with a doubling time of around 5 h, occurred at pH 6.0–6.5, 65 °C, 0.3–0.5 M NaCl and 0.05–0.20 M MgCl2. The DNA G+C content of this organism was 56 mol%. Analysis of 16S rRNA gene sequence and the inferred amino acid sequence of the mcrA gene of strain ZC-1T indicated that it is related specifically to members of the family Methanosaetaceae (90.6 and 76.6 % sequence similarity, respectively). However, strain ZC-1T failed to grow with acetate as substrate for methanogenesis, which is a special characteristic of the family Methanosaetaceae. Based on these phenotypic and phylogenic characteristics, strain ZC-1T is proposed to represent a novel genus and species, for which the name Methermicoccus shengliensis gen. nov., sp. nov. is proposed. The type strain is ZC-1T (=CGMCC 1.5056T=DSM 18856T). Methermicoccaceae fam. nov. is also proposed.

A Gram-negative, non-motile, rod-shaped bacterium, strain ISL-6T, phenotypically resembling members of the genus Salegentibacter, was isolated from a marine solar saltern of the Yellow Sea in Korea and subjected to a polyphasic taxonomic investigation. Strain ISL-6T grew optimally at pH 7.0–8.0 and 30 °C and in the presence of 8 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 37.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-6T belonged to the genus Salegentibacter. Strain ISL-6T exhibited 16S rRNA gene sequence similarity values of 92.0–98.6 % with respect to the type strains of recognized Salegentibacter species. Low DNA–DNA relatedness values, differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain ISL-6T is distinguishable from the recognized Salegentibacter species. Therefore strain ISL-6T represents a novel species of the genus Salegentibacter, for which the name Salegentibacter salarius sp. nov. is proposed. The type strain is ISL-6T (=KCTC 12974T =CCUG 54355T).

A Gram-negative, aerobic, light-orange-coloured, marine bacterium (designated SST-19T) was isolated from beach sediment in Jeju, Korea, and its taxonomic position was determined by means of a polyphasic approach. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain SST-19T was positioned within the family ‘Saprospiraceae’, class Sphingobacteria, and formed a consistent cluster with Lewinella persica ATCC 23167T (94.7 % sequence similarity). The levels of 16S rRNA gene sequence similarity between the isolate and recognized members of the family ranged from 84 to 89 %, with Lewinella cohaerens ATCC 23123T, Lewinella nigricans ATCC 23147T, Haliscomenobacter hydrossis DSM 1100T and Saprospira grandis ATCC 23119T showing values of 89.0 , 88.4 , 86.4 and 84.1 %, respectively. Strain SST-19T required seawater for growth and its cells were unbranched, flexible rods or filaments with gliding motility. The cellular fatty acids consisted mainly of saturated, unsaturated and iso-branched fatty acids, the major components being C16 : 1 ω7c and/or iso-C15 : 0 2-OH (24.1 %), C18 : 0 (13.5 %), iso-C15 : 0 (11.1 %) and C16 : 0 (10.9 %). The G+C content of the DNA was found to be 51.3 mol%. On the basis of the results from phenotypic and phylogenetic analyses, the isolate represents a novel species of the genus Lewinella, for which the name Lewinella agarilytica sp. nov. is proposed. The type strain is SST-19T (=JBRI 2009T=KCTC 12774T=JCM 14216T).

A novel gliding, heterotrophic, Gram-negative, yellow–orange-pigmented, aerobic, oxidase- and catalase-positive bacterium, designated strain KMM 6151T, was isolated from the Pacific red alga Polysiphonia japonica. Analysis of the 16S rRNA gene sequence of the strain revealed that it formed a distinct lineage within the genus Maribacter, family Flavobacteriaceae, with sequence similarities in the range 94.6–96.9 %. On the basis of phenotypic, genotypic and phylogenetic data, strain KMM 6151T represents a novel species of the genus Maribacter, for which the name Maribacter polysiphoniae sp. nov. is proposed. The type strain is KMM 6151T (=KCTC 22021T=LMG 23671T).

A Gram-negative, yellow-pigmented bacterium capable of gliding motility, designated strain WPCB118T, was isolated from fresh water collected from the Woopo wetland (Republic of Korea). Cells were rod-shaped and sometimes filamentous. The major fatty acids were iso-C15 : 0 2-OH and/or C16 : 1 ω7c (45.6 %), C16 : 1 ω5c (18.5 %), iso-C15 : 0 (9.5 %) and C16 : 0 (8.8 %). The predominant menaquinone and polar lipid were MK-7 and phosphatidylethanolamine, respectively. The DNA G+C content was 53.3 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WPCB118T had an evolutionary lineage within the radiation encompassing the members of the family ‘Flexibacteraceae’, its closest neighbour being Spirosoma linguale LMG 10896T (93.7 % gene sequence similarity). Data from this polyphasic study indicated that strain WPCB118T could not be assigned to any recognized species. Strain WPCB118T represents a novel species of the genus Spirosoma, for which the name Spirosoma rigui sp. nov. is proposed. The type strain is WPCB118T (=KCTC 12531T=NBRC 101117T).

A Gram-negative, psychrotolerant, chemoheterotrophic, aerobic, non-gliding, non-motile, yellow-pigmented bacterium, designated IMCC3228T, was isolated from coastal seawater of the Antarctic. On the basis of 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Sejongia (95.3–96.1 %) and Chryseobacterium (94.2–95.9 %) in the family Flavobacteriaceae. Phylogenetic trees generated using several treeing algorithms based on 16S rRNA gene sequences showed that this Antarctic marine isolate formed a distinct phyletic line within the genus Sejongia. The DNA G+C content of the strain was 35.0 mol% and the major respiratory quinone was MK-6. Several phenotypic and chemotaxonomic characteristics, including temperature and NaCl optima for growth, oxidase activity and the proportions of major cellular fatty acids, served to differentiate the strain from the recognized species of the genus Sejongia. Therefore strain IMCC3228T represents a novel species of the genus Sejongia, for which the name Sejongia marina sp. nov. is proposed. The type strain is IMCC3228T (=KCCM 42689T=NBRC 103143T).

A seawater bacterium, designated IMCC3101T, was isolated from Antarctic coastal seawater. The strain was Gram-negative, chemoheterotrophic, obligately aerobic, pigmented dark yellow (flexirubin-type pigments) and devoid of gliding and flagellar motility. On the basis of 16S rRNA gene sequence comparisons, the most closely related species was Ulvibacter litoralis (96.6 %). Phylogenetic trees generated by using 16S rRNA gene sequences confirmed that the strain belonged to the genus Ulvibacter in the family Flavobacteriaceae. The DNA G+C content was 37.0 mol% and the major respiratory quinone was MK-6. Several phenotypic characteristics, including cell and colony morphology, the absence of gliding motility and the temperature range for growth, serve to differentiate the strain from the only species in the genus Ulvibacter with a validly published name (U. litoralis). Therefore, strain IMCC3101T represents a novel species of the genus Ulvibacter, for which the name Ulvibacter antarcticus sp. nov. is proposed. The type strain is IMCC3101T (=KCCM 42686T=NBRC 102682T).

Three strains of anaerobic Gram-negative bacilli isolated from human oral sites were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed the strains to constitute a novel group within the genus Prevotella, most closely related to Prevotella oris and Prevotella salivae. A novel species, Prevotella maculosa sp. nov., is proposed to accommodate these strains. Prevotella maculosa is saccharolytic and produces acetic and succinic acids as end products of fermentation. The G+C content of the DNA of the type strain is 48 mol%. The type strain of Prevotella maculosa is W1609T (=DSM 19339T =CCUG 54766T).

Two strains, MKG-38T and FYK2402M69T, were isolated from a marine sediment sample and a sea snail, respectively, both collected on the Pacific coast of Japan. Phylogeny of these new isolates based on 16S rRNA gene sequences indicated that they are members of the genus Lewinella. Morphological, physiological and biochemical properties of these two isolates, together with the type strains of the three previously described species of the genus Lewinella, were characterized. The new isolates were Gram-negative, aerobic, rod-shaped, chemo-organotrophic and able to degrade starch and CM-cellulose. A comparative polyphasic study showed that these two isolates represent two novel species of the genus Lewinella, for which the names Lewinella marina sp. nov. (type strain, MKG-38T=NBRC 102633T=NCIMB 14312T) and Lewinella lutea sp. nov. (type strain, FYK2402M69T=NBRC 102634T=NCIMB 14313T) are proposed. Emended descriptions of the genus Lewinella ( Sly et al. 1998 ) and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica are also proposed.