- Volume 59, Issue 11, 2009

Strain DCY24T, a Gram-reaction-positive, aerobic, rod-shaped, motile bacterium, was isolated from soil of a ginseng field in South Korea. According to 16S rRNA gene sequence analysis, it was closely related to Nocardioides aromaticivorans DSM 15131T (95.1 % similarity), Nocardioides simplex KCTC 9106T (95.0 %), Nocardioides nitrophenolicus DSM 15529T (94.8 %) and Nocardioides kongjuensis DSM 19082T (94.7 %). Chemotaxonomic data revealed that strain DCY24T possessed MK-8(H4) as the predominant menaquinone, ll-2,6-diaminopimelic acid as the diagnostic diamino acid, phosphatidylglycerol and diphosphatidylglycerol as predominant polar lipids and iso-C16 : 0, iso-C17 : 0 and C18 : 1 ω9c as predominant fatty acids. The DNA G+C content was 71.0 mol%. Based on evidence from this polyphasic study, strain DCY24T (=KCTC 19265T =LMG 24128T) should be classified as the type strain of a novel Nocardioides species, for which the name Nocardioides humi sp. nov. is proposed.

The taxonomic position of an actinomycete, designated strain IMMIB L-21T, was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA–DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21T (=DSM 45234T=CCUG 56587T).

The taxonomic position of a Gram-positive, non-motile, non-spore-forming coryneform, isolated from activated sludge and designated strain CAU 212T, was investigated using a polyphasic approach. Cellular morphology, biochemical tests and chemotaxonomic investigations revealed that strain CAU 212T had the characteristics of the genus Corynebacterium. Comparative 16S rRNA gene sequence analysis showed that the organism formed a hitherto-unknown subline within the genus Corynebacterium. Sequence divergence values of more than 4.3 % from recognized Corynebacterium species, together with phenotypic differences, showed that the bacterium represents a previously unrecognized member of the genus Corynebacterium, for which the name Corynebacterium doosanense sp. nov. is proposed. The type strain is CAU 212T (=KCTC 19568T=CCUG 57284T).

A novel actinomycete strain, designated YIM 61105T, was isolated from a leaf of Maytenus austroyunnanensis from the tropical rainforest in Xishuangbanna, Yunnan Province, south-west China. A 16S rRNA gene sequence analysis revealed that the organism belonged to the phylogenetic cluster of the genus Nonomuraea and was most closely related to Nonomuraea candida HMC10T (98.2 %), ‘Nonomuraea aegyptia’ S136 (97.9 %), Nonomuraea kuesteri GW 14-1925T (97.5 %) and Nonomuraea turkmeniaca DSM 43926T (97.4 %). The 16S rRNA gene sequence similarities to other Nonomuraea species were less than 97.4 %. The main chemotaxonomic properties of strain YIM 61105T, such as the principal amino acid of the peptidoglycan, the predominant menaquinone and the polar lipid profile, supported its classification within the genus Nonomuraea. Strain YIM 61105T was also readily differentiated from closely related species on the basis of a broad range of phenotypic properties and DNA–DNA hybridization values. Thus, this isolate is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea antimicrobica sp. nov. is proposed. The type strain is YIM 61105T (=DSM 45220T=CCTCC AA 208016T).

Two novel Gram-positive-staining, acidophilic strains were isolated from soil samples. Both show typical features of filamentous actinomycetes. On the basis of 16S rRNA gene sequence analysis, the strains are members of the family Micromonosporaceae. The two strains contain hydroxydiaminopimelic acid, glycine, alanine and glutamic acid in the peptidoglycan. Fatty acid profiles clearly differentiate the two strains: cyclohexyl C17 : 0, i-C16 : 0 and ai-C17 : 0 are predominant in Delta1T, while the major components for Delta3T are ai-C17 : 0 and i-C16 : 0. The two strains also differ in their major menaquinones, MK-9(H8, H4, H6) for Delta1T and MK-9(H8, H6) for Delta3T, and in phospholipid patterns; Delta1T displays phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, methyl phosphatidylethanolamine and an unknown aminophospholipid, while Delta3T also contains minor amounts of several unknown phospholipids in addition to these phospholipids. The whole-cell sugars of both strains are galactose, arabinose and xylose. The G+C content of the DNA is 72.7 mol% for Delta1T and 71.9 mol% for Delta3T. On the basis of chemotaxonomic, physiological and phylogenetic data, we propose Rugosimonospora gen. nov. to accommodate the two strains, with the description of Rugosimonospora acidiphila gen. nov., sp. nov. (the type species; type strain Delta1T =DSM 45227T =NBRC 104874T) and Rugosimonospora africana sp. nov. (type strain Delta3T =DSM 45228T =NBRC 104875T).

A psychrotrophic Arthrobacter strain, GP3T, was isolated from Adélie penguin guano from Antarctica and characterized. The 16S rRNA gene sequence of the novel strain showed the highest similarity (97.8 %) with that of Arthrobacter psychrolactophilus B7T. The novel strain showed a morphological change from rod to coccus. The growth temperature range of strain GP3T was 0–25 °C, with optimal growth at 20 °C. The strain grew over a salinity range of between 0 and 3 % (w/v) NaCl and the optimal pH for growth was pH 6–8. Strain GP3T contained anteiso-C15 : 0 as the major fatty acid. The major menaquinone was MK-9(H2). The cell-wall peptidoglycan type was of the A3α variant. The DNA G+C content of strain GP3T was 58.5 mol%. Strain GP3T was able to hydrolyse chitin, Tween 80, starch, cellulose and lactose, but not gelatin, lecithin or urea. In addition to these physiological characteristics, DNA–DNA hybridization studies clearly differentiated strain GP3T from A. psychrolactophilus. The combined results of phylogenetic, physiological and chemotaxonomic studies indicated that strain GP3T represents a novel species of the genus Arthrobacter. The name Arthrobacter psychrochitiniphilus sp. nov. (type strain GP3T=JCM 13874T=CGMCC 1.6355T) is proposed in recognition of the strain's strong chitin-utilizing ability.

Two motile actinomycetes, designated strains 03-723T and 03-8772T, which had potent inhibitory activity against Enterococcus faecium peptide deformylase and several clinical Gram-positive, antibiotic-resistant strains, were isolated from two soil samples collected from Sichuan Province and Xinjiang Uyghur Autonomous Region in China, respectively. The taxonomic status of these two organisms was established by using a polyphasic approach. The taxonomic data were consistent with the assignment of the strains to the genus Actinoplanes. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that the two isolates formed a branch with the type strains of Actinoplanes lobatus, Actinoplanes auranticolor, Actinoplanes capillaceus, Actinoplanes campanulatus and Actinoplanes philippinensis in the clade of Actinoplanes species. This branching pattern was also supported by the tree constructed with the maximum-parsimony method. Levels of 16S rRNA gene sequence similarity between strains 03-723T and 03-8772T and their phylogenetic neighbours ranged from 98.0 to 98.8 % and 97.4 to 98.1 %, respectively. However, the two strains shared low levels of DNA–DNA relatedness with the type strains of closely related Actinoplanes species and were readily distinguished by using a combination of phenotypic properties. Therefore, it is proposed that strains 03-723T and 03-8772T represent two novel species of the genus Actinoplanes, for which the names Actinoplanes sichuanensis sp. nov. (type strain 03-723T=KCTC 19460T=CCM 7526T) and Actinoplanes xinjiangensis sp. nov. (type strain 03-8772T=KCTC 19461T=CCM 7527T) are proposed.

A novel aerobic, non-motile, Gram-positive, pink–orange-pigmented, coccoid marine bacterium, designated strain SJ2T, was isolated from the Gwangalli coast of Korea. The taxonomic position of strain SJ2T was determined based on 16S rRNA gene sequence analysis, fatty acid patterns and physiological reaction profiles. The full-length 16S rRNA gene sequence of strain SJ2T showed highest similarity to those of the type strains of Kocuria carniphila and Kocuria marina. Strain SJ2T exhibited mean levels of DNA–DNA relatedness of 17 and 35 % to the type strains of K. carniphila and K. marina, respectively. Based on these results, strain SJ2T is considered to represent a novel species of the genus Kocuria, for which the name Kocuria gwangalliensis sp. nov. is proposed. The type strain is SJ2T (=KCCM 42914T =LMG 24672T).

Three strains of anaerobic, pleomorphic, Gram-positive-staining bacilli, which were isolated from human carious dentine, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. The strains were saccharolytic and produced acetic and propionic acids in large amounts, and succinic acid in moderate amounts, as the end products of fermentation. 16S rRNA gene and RpoB protein sequence analyses revealed that the strains constituted a novel group within the genus Propionibacterium, most closely related to Propionibacterium australiense but sharing only 8 % DNA–DNA relatedness with the type strain of that species. Therefore, a novel species, Propionibacterium acidifaciens sp. nov., is proposed to accommodate these strains. The DNA G+C content of the type strain is 70 mol%. The type strain is C3M_31T (=DSM 21887T =CCUG 57100T).

Slowly growing, scotochromogenic bacteria of a novel Mycobacterium species were isolated from lymph node samples in two children and pulmonary samples in two elderly patients from different regions in the Netherlands as well as from a surface water sample in Zambia. Its 16S rRNA gene, 16S–23S internal transcribed spacer (ITS), hsp65 and rpoB gene sequences are unique in comparison with other mycobacteria. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that these micro-organisms are most closely related to Mycobacterium scrofulaceum ATCC 19981T (8 differences; 0.6 % divergence). The hsp65 sequence shows 96 % similarity to that of Mycobacterium saskatchewanense MB54784 and the rpoB sequence shows 95 % similarity to that of Mycobacterium chimaera CIP 107892T. The 16S–23S ITS sequence places these micro-organisms within the Mycobacterium avium complex, as a novel ITS sequevar. This is not supported by analysis of the 16S rRNA, hsp65 or rpoB gene sequences. Their scotochromogenicity, combined with mostly positive urease, positive semiquantitative catalase and negative tellurite reduction tests, set these isolates apart from related species. The mycolic acid patterns, obtained by HPLC, are similar to that of Mycobacterium scrofulaceum, though the peak heights and distribution present minor differences. We propose the name Mycobacterium mantenii sp. nov. for this novel species. The type strain, isolated from a lymph node biopsy sample, is strain 04-1474T (=NLA000401474T =CIP 109863T =DSM 45255T).

A Gram-positive, non-motile, rod- or coccoid-shaped bacterial strain, designated MN8T, was isolated from sludge of domestic wastewater in Korea, and its taxonomic position was investigated by use of a polyphasic study. Strain MN8T grew optimally at pH 6.5–7.5 and 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MN8T fell within the cluster comprising Nocardioides species, clustering with Nocardioides simplex KCTC 9106T, Nocardioides aromaticivorans H-1T, Nocardioides kongjuensis A2-4T and Nocardioides nitrophenolicus NSP41T, with which it shared 98.4–99.0 % 16S rRNA gene sequence similarity. The chemotaxonomic properties of strain MN8T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 and C18 : 1 ω9c. The DNA G+C content was 71.5 mol%. Strain MN8T exhibited levels of DNA–DNA relatedness of 13–31 % to the type strains of phylogenetically related Nocardioides species and could be differentiated from these species based on differences in phenotypic characteristics. On the basis of the data presented, strain MN8T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides caeni sp. nov. is proposed. The type strain is MN8T (=KCTC 19600T=CCUG 57506T).

A Gram-positive-staining, non-motile and rod-shaped bacterium, strain ON10T, was isolated from soil around a wastewater treatment plant in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain ON10T grew optimally at pH 6.5–7.0 and 30 °C in the presence of 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ON10T clustered with the clade comprising Terrabacter species, with which it exhibited 16S rRNA gene sequence similarity values of 98.4–98.8 %. The cell-wall peptidoglycan type was based on ll-diaminopimelic acid and the cell-wall sugars were glucose, mannose, arabinose and xylose. The predominant menaquinone was MK-8(H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid. The major fatty acids were iso-C15 : 0 and iso-C14 : 0. The DNA G+C content was 71.6 mol%. Strain ON10T exhibited DNA–DNA relatedness levels of 17–28 % to the type strains of Terrabacter species and could also be differentiated from these species by differences in phenotypic characteristics. On the basis of the data obtained, strain ON10T was considered to represent a novel species of the genus Terrabacter, for which the name Terrabacter terrigena sp. nov. is proposed. The type strain is ON10T (=KCTC 19602T=CCUG 57508T).

An rpoB sequence-based evaluation of 100 Mycobacterium avium complex (MAC) clinical isolates led to the identification of five respiratory tract isolates that were potential representatives of three novel MAC species. Distinctive phenotypic features of isolates 62863 and 5356591T included a pseudomycelium morphology and both esterase and acid phosphatase activities. These two isolates exhibited sequence similarities of 99.8 % for the 16S rRNA gene, 86.3 and 86.1 % for 16S–23S rRNA gene internal transcribed spacer (ITS-1) sequence, 96.7 and 97.8 % for rpoB and 97.6 and 97.4 % for hsp65, respectively, with the type strain of Mycobacterium chimaera, the most closely related species. Isolates 3256799 and 5351974T lacked α-mannosidase and β-glucosidase activities. They exhibited sequence similarities of 99.6 % for the 16S rRNA gene, 90.1 and 90.4 % for ITS-1, 97.8 % for rpoB and 98.0 and 98.1 % for hsp65, respectively, with the type strain of M. chimaera, the most closely related species. Isolate 4355387T lacked urease and α-glucosidase activities, but it exhibited valine arylamidase, cystine arylamidase and acid phosphatase activities. It had sequence similarities of 99.3 % for the 16S rRNA gene, 51.8 % for ITS-1, 97.1 % for rpoB and 97.8 % for hsp65 with the type strain of Mycobacterium colombiense, the most closely related species. A phylogenetic tree based on concatenated 16S rRNA gene, ITS-1, rpoB and hsp65 sequences showed the uniqueness of these five isolates as representatives of three novel species, with bootstrap values ≥95 % in all nodes. On the basis of these phenotypic and genetic characteristics, these five isolates are proposed as representatives of three novel MAC species: Mycobacterium marseillense sp. nov., with strain 5356591T (=CCUG 56325T =CIP 109828T =CSUR P30T) as the type strain; Mycobacterium timonense sp. nov., with strain 5351974T (=CCUG 56329T =CIP 109830T =CSUR P32T) as the type strain; and Mycobacterium bouchedurhonense sp. nov., with strain 4355387T (=CCUG 56331T =CIP 109827T =CSUR P34T) as the type strain.

A novel Gram-positive bacterium, designated Kis4-28T, was isolated from the intestinal tract of a fish, and its taxonomic position was investigated by a polyphasic approach. The sample was collected from the coast of Tokyo Bay, Japan. Cells of strain Kis4-28T were rod-shaped, non-motile and non-sporulating. The peptidoglycan type of the isolate was A4α; lysine was the diagnostic diamino acid. The only menaquinone detected was MK-8(H4), and the major fatty acids were anteiso-C15 : 0 and C16 : 0. Galactose was detected as a major cell-wall sugar. The polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 70.7 mol%. 16S rRNA gene sequence analysis revealed that strain Kis4-28T and the type strain of Salana multivorans formed a monophyletic cluster with a 16S rRNA gene sequence similarity of 96.2 %. Strain Kis4-28T was clearly distinguishable from the genus Salana in terms of its chemotaxonomic characteristics. On the basis of the genotypic and phenotypic characteristics, a new genus and species is proposed for strain Kis4-28T, with the name Serinibacter salmoneus gen. nov., sp. nov. The type strain of Serinibacter salmoneus is Kis4-28T (=NBRC 104924T =DSM 21801T). In addition, on the basis of 16S rRNA gene sequence analysis of the genus Serinibacter and related genera, emended descriptions of the families Beutenbergiaceae and Bogoriellaceae are proposed to accommodate the genera Beutenbergia, Salana and Serinibacter, and the genera Bogoriella and Georgenia, respectively.

The novel actinomycete strain Ap1T was isolated from rhizosphere soil of the argan tree (Argania spinosa L.) in the south of Morocco. Strain Ap1T has been reported as a novel producer of the pentaene polyene macrolide isochainin, which strongly inhibits the growth of pathogenic yeasts and phytopathogenic fungi. Strain Ap1T shows a greyish-white aerial mycelium with chains of smooth-surfaced spores of the Spiralis type and a cell wall containing ll-diaminopimelic acid. Based on chemotaxonomy and morphological features, strain Ap1T was identified as a member of the genus Streptomyces. 16S rRNA gene sequence similarities based on almost-complete 16S rRNA gene sequences showed that strain Ap1T is closely associated with members of the Streptomyces violaceoruber species group (S. violaceoruber, S. coelescens, S. violaceorubidus, ‘S. caesius’, ‘S. lividans’, S. violaceolatus and S. humiferus) and others (Streptomyces aurantiogriseus, S. lienomycini, S. chattanoogensis, S. rubrogriseus and S. tendae). However, protein profiling, DNA–DNA hybridization and BOX-PCR fingerprinting proved a relationship above the species level. In addition, the phenotype also allowed for the differentiation of strain Ap1T from its closest neighbours. As a result of this polyphasic approach, we conclude that strain Ap1T represents a novel species of the genus Streptomyces, for which the name Streptomyces marokkonensis sp. nov. is proposed. The type strain is Ap1T (=R-22003T =LMG 23016T =DSM 41918T).

Actinobacteria often constitute a large fraction of the bacterioplankton in freshwater systems. Cultivation-independent methods have revealed that the so-called acI lineage frequently represents the most numerous taxon among assemblages of freshwater Actinobacteria and even among total freshwater bacterioplankton. Bacteria affiliated with this uncultivated lineage have been detected in freshwater habitats located in various continents and climatic zones but have never been found among terrestrial or offshore marine systems. So far, this ecologically important lineage of freshwater Actinobacteria is not represented by a recognized taxon. In this study, we established a stable mixed culture containing a strain affiliated with the acI lineage from a freshwater lake in Austria. The proportion of the strain in the culture could be increased by manipulation of the medium composition by more than one order of magnitude, however all subsequent attempts to isolate this strain into pure culture were unsuccessful. Some of the phenotypic traits of this acI strain were determined and its taxonomic position within the Actinobacteria was analysed. Phylogenetic analysis of this organism's 16S rRNA gene revealed a distant relationship with cultivated organisms and recognized species (89 % gene sequence similarity with the latter). Furthermore, this analysis did not support a clear assignment of the strain to any of the recognized families within the phylum Actinobacteria. It is suggested that a candidate taxon, ‘Candidatus Planktophila limnetica’ is established to represent this strain.

A novel actinomycete, strain S187T, was isolated from a marine sediment sample collected from Xinghai Bay, Dalian, China. Growth occurred on ISP medium 2 containing 0–9 % NaCl and at pH 6.0–9.0 and 10–45 °C. The cell wall of strain S187T contained the isomer ll-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H6) (40.8 %), MK-9(H8) (38.2 %) and MK-9(H2) (8.8 %). The major fatty acids were iso-C16 : 0 (29.6 %), anteiso-C15 : 0 (14.0 %) and anteiso-C17 : 0 (11.6 %). Cells contained phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylinositol mannosides and one unknown phospholipid. The G+C content of the genomic DNA was 72.01 mol%. The 16S rRNA gene sequence of the isolate had similarities of 98.1 and 97.5 % with those of Streptomyces flavofuscus NRRL B-8036T (=DSM 41426T) and Streptomyces albiaxialis DSM 41799T, respectively, showing that the novel strain should be assigned to the genus Streptomyces. DNA–DNA hybridizations with the two above-mentioned Streptomyces species showed 31.4 and 46.9 % relatedness, respectively. Moreover, the three strains differed in some physiological and biochemical properties. Thus, on the basis of phenotypic and genotypic analyses, it is proposed that strain S187T represents a novel species of the genus Streptomyces, for which the name Streptomyces xinghaiensis sp. nov. is proposed; the type strain is S187T (=NRRL B-24674T=CCTCC AA 208049T=KCTC 19546T).