- Volume 58, Issue 6, 2008

A Gram-positive, non-motile, cream-coloured, curved or straight rod-shaped bacterial strain, DS-10T, was isolated from soil of Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-10T grew optimally at 25 °C and pH 7.0–8.0 in the presence of 0.5–1.0 % (w/v) NaCl. Strain DS-10T had peptidoglycan type B2γ [d-Glu–d-Dab (diaminobutyric acid)] and galactose and ribose as whole-cell sugars. Strain DS-10T contained MK-11, MK-12 and MK-10 as predominant menaquinones. Major cellular fatty acids (>10 % of total) were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The DNA G+C content was 71.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-10T belonged to the genus Agromyces. Similarity values between the 16S rRNA gene sequence of strain DS-10T and those of the type strains of recognized Agromyces species ranged from 95.8 to 99.3 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DS-10T could be differentiated from recognized Agromyces species. On the basis of the data presented, strain DS-10T is considered to represent a novel species of the genus Agromyces, for which the name Agromyces terreus sp. nov. is proposed. The type strain is DS-10T (=KCTC 19216T =JCM 14581T).

A Gram-positive, aerobic, non-mycelium-forming actinomycete, designated strain SSWW-21T, was isolated from a living seaweed sample on the coast of Jeju, Republic of Korea. Cells of the organism were rod-shaped or coccoid depending on culture age. Short rods were observed in young cultures, whereas older cultures predominantly consisted of coccoid cells. Rod-shaped cells were motile by means of flagella, but coccoid cells were non-motile. Budding-like cell division was observed. The temperature and pH for growth were 4–30 °C and pH 6.1–10.1. Growth occurred in the presence of up to 2 % NaCl. Phylogenetic analyses showed that the organism formed a distinct clade within the family Microbacteriaceae. Comparative 16S rRNA gene sequence analyses showed that strain SSWW-21T was related most closely to the type strains of Okibacterium fritillariae (96.8 % similarity), Leifsonia poae (96.8 %) and Agreia bicolorata (96.6 %). Levels of 16S rRNA gene sequence similarity between the new isolate and members of other genera within the family Microbacteriaceae were in the range 93.1–96.3 %. The cell-wall peptidoglycan of strain SSWW-21T was of the B-type (2,4-diaminobutyric acid as the diagnostic diamino acid). The acyl type of the muramic acid was acetyl. The predominant menaquinone was MK-11. The polar lipid profile contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were not present. The major cellular fatty acids were saturated branched-chain components (anteiso-C15 : 0 and anteiso-C17 : 0). The G+C content of the DNA was 69.8 mol%. On the basis of the phenotypic and phylogenetic data presented, strain SSWW-21T is considered to represent a novel species of a new genus within the family Microbacteriaceae, for which the name Phycicola gilvus gen. nov., sp. nov. is proposed. The type strain of Phycicola gilvus is SSWW-21T (=KCTC 19185T =DSM 18319T).

A novel actinomycete, designated strain YIM 46034T, was isolated from an evergreen broadleaved forest at Menghai, in southern Yunnan Province, China. Phenotypic characterization and 16S rRNA gene sequence analysis indicated that the strain belonged to the family Micromonosporaceae. Strain YIM 46034T showed more than 3 % 16S rRNA gene sequence divergence from recognized species of genera in the family Micromonosporaceae. Characteristic features of strain YIM 46034T were the production of two types of spores, namely motile spores, which were formed in sporangia produced on substrate mycelia, and single globose spores, which were observed on short sporophores of the substrate mycelia. The cell wall contained meso-diaminopimelic acid, glycine, arabinose and xylose, which are characteristic components of cell-wall chemotype II of actinomycetes. Phosphatidylethanolamine was the major phospholipid (phospholipid type II). Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain YIM 46034T is considered to represent a novel species of a new genus in the family Micromonosporaceae, for which the name Planosporangium flavigriseum gen. nov., sp. nov. is proposed. The type strain of Planosporangium flavigriseum is YIM 46034T (=CCTCC AA 205013T =DSM 44991T).

A Gram-positive, non-motile, moderately halophilic, alkalitolerant actinobacterium, designated strain YIM 70179T, was isolated from a saline soil sample collected from Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan type of strain YIM 70179T was A4α, l-Lys–Gly–l-Glu. Cells of the isolate contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown glycolipid, MK-8 as major menaquinone and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as major fatty acids. The DNA G+C content was 68.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 70179T fell within the radiation of species of the genus Nesterenkonia. Levels of 16S rRNA gene sequence similarity between strain YIM 70179T and the type strains of recognized Nesterenkonia species were below 97 %, except to Nesterenkonia halobia DSM 20541T (99.6 %), but these two strains exhibited a low level of DNA–DNA relatedness (18.4 %). Based on genetic and phenotypic evidence, it is proposed that strain YIM 70179T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia halophila sp. nov. is proposed. The type strain is YIM 70179T (=DSM 16378T =KCTC 19048T).

The taxonomic status of six strains received as Streptomyces hygroscopicus was established using a polyphasic approach. The organisms had phenotypic and morphological properties consistent with their classification in the genus Streptomyces. Almost complete 16S rRNA gene sequences of the strains were determined and aligned with corresponding sequences of representatives of the genus Streptomyces and phylogenetic trees were inferred using four tree-making algorithms. All of the strains fell within the Streptomyces violaceusniger 16S rRNA gene clade and four of them were considered to merit species status using a combination of genotypic and phenotypic data. These organisms were designated Streptomyces himastatinicus sp. nov. (type strain ATCC 53653T=DSM 41914T), Streptomyces mordarskii sp. nov. (type strain NRRL B-1346T=DSM 40771T), Streptomyces rapamycinicus sp. nov. (type strain NRRL 5491T=ATCC 29253T) and Streptomyces ruanii sp. nov. (type strain ISP 5276T=DSM 40276T). DNA–DNA relatedness and phenotypic data showed that the two remaining strains, ‘Streptomyces hygroscopicus subsp. enhygrus’ NRRL 3664 and Streptomyces hygroscopicus subsp. hygroscopicus NRRL 3111 belong to the same species as the type strain of Streptomyces rutgersensis subsp. castelarensis. This taxon is designated Streptomyces castelarensis sp. nov., comb. nov. (type strain ATCC 15191T=DSM 40830T) following the proposal that Streptomyces rutgersensis subsp. rutgersensis is a heterotypic synonym of Streptomyces albidoflavus.

A Gram-positive, aerobic, non-motile actinobacterium strain, designated YIM 45607T, was isolated from a rhizosphere soil sample in Kunming, south-west China. Chemotaxonomically, the isolate contained chemical markers that supported its assignment to the genus Rhodococcus. On the basis of 16S rRNA gene sequence similarity analysis, strain YIM 45607T formed a new subline within the genus Rhodococcus, with Rhodococcus equi as its closest phylogenetic neighbour (98.2 % 16S rRNA gene sequence similarity to the type strain). However, DNA–DNA hybridization demonstrated that strain YIM 45607T was different from R. equi DSM 20307T (35.4 % relatedness). Based on polyphasic analysis, strain YIM 45607T could be clearly distinguished from other species of the genus Rhodococcus. The isolate therefore represents a novel species of Rhodococcus, for which the name Rhodococcus kunmingensis sp. nov. is proposed. The type strain is strain YIM 45607T (=KCTC 19149T =DSM 45001T).

During the course of phylogenetic analyses based on 16S rRNA gene sequences for all currently described taxa within the family Pseudonocardineae, it became evident that Kibdelosporangium albatum DSM 44149T was misplaced within the genus Kibdelosporangium and is phylogenetically most closely related to the genus Kutzneria. Chemotaxonomic analyses revealed that Kibdelosporangium albatum differed from Kutzneria in containing arabinose as well as galactose and mannose as diagnostic whole-cell sugars. The polar lipid pattern was distinct from both Kibdelosporangium and Kutzneria species in containing phosphatidylethanolamine containing 2-hydroxy fatty acids, lyso-phosphatidylethanolamine and lyso-phosphatidylmethylethanolamine as well as phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. These data preclude the inclusion of this strain within the genus Kutzneria or Kibdelosporangium and a new genus is proposed, to be named Allokutzneria gen. nov. The type species of this new genus is Allokutzneria albata gen. nov., comb. nov., the type strain of which is R761-7T (=NRRL B-24461T =DSM 44149T =ATCC 55061T).

A new actinobacterial strain, RS16T, was isolated from sandy soil collected in Zamora, Spain, and was studied to determine its taxonomic position. A neighbour-joining tree based on 16S rRNA gene sequence analysis revealed that the novel isolate formed an independent branch between Promicromonospora sukumoe DSM 44121T and Promicromonospora citrea DSM 43110T. Levels of 16S rRNA gene sequence similarity between the novel isolate and its phylogenetic neighbours ranged from 98.7 to 98.9 %. Chemotaxonomic properties, such as the predominant menaquinone and polar lipids, supported the assignment of the novel isolate to the genus Promicromonospora, however, a significant number of physiological differences were found between the novel isolate and the other recognized species of the genus Promicromonospora. On the basis of these results, it is proposed that strain RS16T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora kroppenstedtii sp. nov. is proposed. The type strain is RS16T (=DSM 19349T=LMG 24382T).

A novel aerobic, Gram-negative bacterium, designated strain CM41_14bT, was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 μm long and 0.7 μm wide and formed pale-orange colonies on marine agar medium. The G+C content of the genomic DNA was 39 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain within the genus Balneola (phylum Bacteroidetes). On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species for which the name Balneola alkaliphila sp. nov. is proposed. The type strain is CM41_14bT (=DSM 19538T=CIP 109603T=OOB 103T).

A Gram-negative, non-motile, aerobic bacterium, designated strain KOPRI 20941T, was isolated from a sample of marine sediment from Ny Ålesund, Spitsbergen, Norway. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate nested within the genus Maribacter and showed the highest sequence similarity (98.1 %) with respect to Maribacter orientalis KMM 3947T. Chemotaxonomic data (DNA G+C content of 36 mol%; MK-6 as the major respiratory quinone and iso-C17 : 0 3-OH, C16 : 1 ω7c/iso-C15 : 0 2-OH and iso-C15 : 0 as the major fatty acids) supported the affiliation of strain KOPRI 20941T to the genus Maribacter. The results of phylogenetic analyses, physiological and biochemical tests and a DNA–DNA reassociation test (<54 % relatedness) allowed genotypic and phenotypic differentiation of the strain from the recognized species of the genus Maribacter. Therefore strain KOPRI 20941T represents a novel species of the genus Maribacter, for which the name Maribacter arcticus sp. nov. is proposed. The type strain is KOPRI 20941T (=KCTC 22053T=JCM 14790T).

A Gram-negative, non-spore-forming, non-motile, yellow-pigmented, strictly aerobic bacterial strain, designated En5T, was isolated from the East Sea of Korea and was subjected to a polyphasic taxonomy study. Strain En5T grew optimally at 30 °C, in the presence of 1–3 % (w/v) NaCl and at pH 5.3–7.6. The major respiratory lipoquinone was MK-6 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c. The DNA G+C content of strain En5T was 30.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain En5T formed a distinct evolutionary lineage within the family Flavobacteriaceae and shared 93 % sequence similarity with the type strains of both Galbibacter mesophilus and Zhouia amylolytica. On the basis of its phenotypic and phylogenetic properties, strain En5T is suggested to represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Joostella marina gen. nov., sp. nov. is proposed. The type strain is En5T (=KCTC 12518T=DSM 19592T=CGMCC 1.6973T).

The taxonomic position of a novel Gram-negative strain, designated SY1T, isolated from a farm-soil sample obtained from Jiangsu Province, PR China, was characterized by using a polyphasic approach. The cells were non-motile, non-spore-forming rods. The organism grew optimally at 30–37 °C and at pH 6.0–8.0. Based on 16S rRNA gene sequence analysis, strain SY1T is a member of the genus Sphingobacterium; Sphingobacterium multivorum JCM 21156T was the nearest relative (98.5 % sequence similarity). The predominant fatty acids of strain SY1T were iso-C15 : 0 (32.9 %), C16 : 0 (10.9 %) and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 24.1 %). The DNA G+C content was 38.5 mol%. The low level of DNA–DNA relatedness (2.2 %) to S. multivorum JCM 21156T in combination with differential morphological and biochemical properties demonstrated that strain SY1T (=KCTC 22131T=CGMCC 1.6855T) should be classified as representing a novel species of the genus Sphingobacterium for which the name Sphingobacterium siyangense sp. nov. is proposed.

The presence of symbiotic bacteria in flies belonging to the subfamily Tephritinae, which predominantly infest the flower heads of composite flowers (Asteraceae), was investigated. Twenty-five species of flies, collected mainly in northern Italy, were examined. The bacteria adhered to the midgut epithelium in a space external to the peritrophic membrane and therefore not in direct contact with the gut contents. Specific, unique and live, but unculturable bacteria were consistently found in the majority of the fly species and their presence was also shown to be persistent in flies reared under microbiologically controlled conditions and devoid of any residual culturable intestinal bacteria. Sequencing of the small subunit rRNA gene from the novel bacteria indicated that they belonged to the family Enterobacteriaceae. Three main strongly supported clades were delineated by phylogenetic trees, the first of which featured a coherent set of sequences displaying gene sequence similarities lower than 96 % compared with recognized taxa. The second and third clades featured cases with higher gene sequence similarities to culturable bacteria, including Erwinia persicina and Ewingella americana, respectively. Relative rate tests were supportive of a fast genetic evolution for the majority of the bacterial symbionts of the subfamily Tephritinae. In agreement with the interpretation suggested in 1929 after pioneering observations made by H. J. Stammer, a symbiotic relationship between the novel bacteria and the tephritid flies is postulated. The origin of this apparently polyphyletic relationship is discussed and a novel candidate organism is proposed for the first clade under the designation ‘Candidatus Stammerula tephritidis’.

Phenotypic and phylogenetic studies were performed on a novel sulfate-reducing bacterium, strain D41T, isolated as part of a methanogenic syntrophic culture from a gas condensate-contaminated aquifer undergoing intrinsic bioremediation. The bacterium was a Gram-negative, non-spore-forming, curved rod, motile by a single polar flagellum, which oxidized several alcohols incompletely, including methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 2-butanol, 3-methyl-1-butanol (isoamyl alcohol), ethylene glycol, 1,2-propanediol, 1,3-propanediol, 1,4-butanediol, phenylethanol and benzyl alcohol. Additionally, the strain oxidized H2/CO2, formate, lactate, pyruvate, maleate, malate and fumarate. Sulfate, thiosulfate and sulfite were used as electron acceptors. The DNA G+C content was 63 mol%. Based on phylogenetic and phenotypic evidence, the novel species Desulfovibrio carbinoliphilus sp. nov. is proposed. The type strain is D41T (=ATCC BAA-1241T =DSM 17524T).

A Gram-negative, coccoid to rod-shaped, strictly aerobic bacterium, strain CL-GR66T, was isolated from coastal seawater collected off Korea. The strain grew optimally in the presence of 3–5 % sea salts, at a temperature of 30 °C and at pH 7. The polar lipid profile of strain CL-GR66T comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids, an unidentified glycolipid and an unidentified lipid. The major fatty acids were C18 : 1 ω7c (71.4 %), 11-methyl C18 : 1 ω7c (11.3 %), C16 : 0 (6.4 %), C18 : 0 (4.6 %) and C12 : 1 3-OH (3.0 %). Ubiquinone 10 was the major quinone. The DNA G+C content was 67.9 mol%. 16S rRNA gene sequence analysis revealed that strain CL-GR66T belonged to the Roseobacter clade within the family Rhodobacteraceae. Strain CL-GR66T was related most closely to the type strain of Marinovum algicola (95.5 % 16S rRNA gene sequence similarity), and sequence similarities between strain CL-GR66T and other type species of the Roseobacter clade ranged from 91.8 to 95.4 %. Phylogenetic analyses of 16S rRNA gene sequences showed that strain CL-GR66T was not associated with any known genus in the family Rhodobacteraceae. The distinct phylogenetic position of strain CL-GR66T, its phylogenetic distance from genera of the family Rhodobacteraceae, together with phenotypic data, suggest that the organism represents a novel species of a new genus, for which the name Ponticoccus litoralis gen. nov., sp. nov. is proposed. The type strain of Ponticoccus litoralis is CL-GR66T (=KCCM 90028T =DSM 18986T).

A Gram-negative, motile, rod-shaped, non-sporulating, aerobic bacterial strain (Esp-1T) was isolated from oil-contaminated soil of Panipat Oil Refinery, India, and its taxonomic position was determined using a polyphasic approach. Strain Esp-1T grew in the presence of 2 % NaCl at 30 °C and was characterized chemotaxonomically by having C16 : 0 as the major fatty acid followed by C17 : 0 cyclo and C18 : 1 ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Esp-1T formed a cluster together with Pseudomonas knackmussii DSM 6978T (98.9 % sequence similarity), Pseudomonas delhiensis MTCC 7601T (98.5 %), Pseudomonas nitroreducens DSM 14399T (98.5 %), Pseudomonas citronellolis DSM 50332T (98.7 %), Pseudomonas multiresinivorans ATCC 700690T (98.9 %) and Pseudomonas jinjuensis DSM 16612T (97.8 %). DNA–DNA hybridization values of strain Esp-1T with P. knackmussii DSM 6978T, P. delhiensis MTCC 7601T, P. jinjuensis DSM 16612T, P. citronellolis DSM 50332T, P. multiresinivorans ATCC 700690T and P. nitroreducens DSM 14399T were 32.9, 30.2, 20.6, 23.4, 23.4 and 20.0 %, respectively. Low levels of DNA–DNA hybridization and phenotypic and chemotaxonomic results are sufficient to delineate strain Esp-1T from other closely related species of Pseudomonas. Phenotypic and chemotaxonomic data confirm that strain Esp-1T represents a novel species, for which the name Pseudomonas panipatensis sp. nov. is proposed. The type strain of Pseudomonas panipatensis sp. nov. is Esp-1T (=MTCC 8990T=CCM 7469T).

Two Gram-negative, cold-adapted, moderately halophilic, aerobic bacteria, designated strains M3BT and M3T, were isolated from marine sediment collected from the South Shetland Islands, Antarctica. The organisms were rod-shaped, catalase- and oxidase-positive, and motile by means of polar flagella. These two psychrotolerant strains required Na+ and grew at NaCl concentrations of 1–15 % and temperatures between 4 and 42 °C. 16S rRNA gene sequence analysis placed strains M3BT and M3T within the genus Marinobacter. DNA–DNA hybridization experiments between the Antarctic isolate M3BT and type strains of phylogenetically related species, namely Marinobacter lipolyticus, Marinobacter flavimaris, Marinobacter sediminum, Marinobacter algicola, Marinobacter maritimus and Marinobacter koreensis, revealed levels of relatedness lower than 32 %. Strain M3T showed 99 % DNA relatedness to strain M3BT. The DNA G+C contents of M3BT and M3T were 57.1 and 57.4 mol%, respectively, and their major isoprenoid quinone was ubiquinone-9. Several phenotypic characteristics, together with data on cellular fatty acid composition, served to differentiate strains M3BT and M3T from strains of related Marinobacter species. On the basis of the polyphasic taxonomic evidence presented in this study, it can be concluded that strains M3BT and M3T belong to the same genospecies and represent a novel species of the genus Marinobacter, for which the name Marinobacter guineae sp. nov. is proposed. The type strain is M3BT (=LMG 24048T=CECT 7243T).