- Volume 59, Issue 1, 2009

A pink-pigmented, aerobic, facultatively methylotrophic bacterial strain, CBMB27T, isolated from leaf tissues of rice (Oryza sativa L. ‘Dong-Jin’), was analysed using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species Methylobacterium oryzae, Methylobacterium fujisawaense and Methylobacterium mesophilicum; strain CBMB27T showed sequence similarities of 98.3, 98.5 and 97.3 %, respectively, to the type strains of these three species. DNA–DNA hybridization experiments revealed low levels (<38 %) of DNA–DNA relatedness between strain CBMB27T and its closest relatives. The sequence of the 1-aminocyclopropane-1-carboxylate deaminase gene (acdS) in strain CBMB27T differed from those of close relatives. The major fatty acid of the isolate was C18 : 1 ω7c and the G+C content of the genomic DNA was 66.8 mol%. Based on the results of 16S rRNA gene sequence analysis, DNA–DNA hybridization, and physiological and biochemical characterization, which enabled the isolate to be differentiated from all recognized species of the genus Methylobacterium, it was concluded that strain CBMB27T represents a novel species in the genus Methylobacterium for which the name Methylobacterium phyllosphaerae sp. nov. is proposed (type strain CBMB27T =LMG 24361T =KACC 11716T =DSM 19779T).

A novel Gram-negative, aerobic, motile, short rod-shaped bacterium, designated J64T, was isolated from black sand collected from Soesoggak, Jeju Island, Korea. Cells grew at 4–37 °C, at pH 5.5–10.0 and with 0–10 % NaCl. The strain was found to be oxidase- and catalase-positive. Phylogenetic analyses showed that strain J64T belongs to the genus Pseudomonas, forming a monophyletic group with Pseudomonas pachastrellae, Pseudomonas pertucinogena and ‘Pseudomonas denitrificans’. The 16S rRNA gene sequence similarity between strain J64T and type strains of all Pseudomonas species with validly published names was below 96.6 %. Low levels of DNA–DNA relatedness were found with respect to type strains of P. pachastrellae and P. pertucinogena, supporting the classification of strain J64T within a novel species of the genus Pseudomonas. Strain J64T contained C18 : 1 ω7c (37.2 %), C16 : 0 (20.4 %), summed feature 3 (17.4 %; comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c) and C12 : 0 (7.6 %) as major cellular fatty acids. On the basis of the phenotypic and phylogenetic data, strain J64T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sabulinigri sp. nov. is proposed. The type strain is J64T (=KCTC 22137T =JCM 14963T).

A Gram-negative, non-motile, rod-shaped bacterial strain, designated SMK-117T, belonging to the Alphaproteobacteria, was isolated from a tidal flat of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain SMK-117T grew optimally at pH 7.0–8.0 and 30 °C in the presence of 2 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences showed that strain SMK-117T clustered with Maritimibacter alkaliphilus HTCC2654T, with which it exhibited a sequence similarity of 95.3 %. Strain SMK-117T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified phospholipids. The DNA G+C content was 63.5 mol%. Strain SMK-117T was differentiated from members of the genera Maritimibacter and Oceanicola on the basis of differences in the fatty acid and polar lipid profiles. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain SMK-117T represents a novel genus and species, for which the name Lutimaribacter saemankumensis gen. nov., sp. nov. is proposed. The type strain of Lutimaribacter saemankumensis is SMK-117T (=KCTC 22244T =CCUG 55760T).

Two Gram-negative strains of heterotrophic, aerobic, marine bacteria, designated PIM1T and PIN1T, were isolated from seawater samples collected from the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods and non-motile. The two isolates required NaCl for growth and grew optimally at 30–35 °C and 2–5 % NaCl. They grew aerobically and were not capable of anaerobic growth by fermentation of glucose or other carbohydrates. The cellular fatty acids were predominantly iso-branched, with iso-C15 : 0 (17.0–21.4 %), iso-C17 : 0 (18.2–21.0 %) and iso-C17 : 1 ω9c (15.7–16.6 %) as the most abundant components. The predominant isoprenoid quinone was Q-8 (95.2–97.1 %). Strains PIM1T and PIN1T had DNA G+C contents of 46.6 and 46.9 mol%, respectively. Phylogeny based on 16S rRNA gene sequences and DNA–DNA hybridization, together with data from physiological, morphological and chemotaxonomic characterizations, indicated that the two isolates should be classified as representatives of two novel species of the genus Pseudidiomarina of the family Idiomarinaceae, for which the names Pseudidiomarina marina sp. nov. (type strain PIM1T=BCRC 17749T=JCM 15083T) and Pseudidiomarina tainanensis sp. nov. (type strain PIN1T=BCRC 17750T=JCM 15084T) are proposed. In addition, based on the characterization data obtained in this study, it is proposed that Idiomarina homiensis and Idiomarina salinarum should be reclassified as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively.

A Gram-negative, non-spore-forming, rod-shaped bacterium, designated strain E3T, which was motile with a polar flagellum, was isolated from coastal surface seawater near Tianjin city, China. The taxonomy of strain E3T was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain E3T forms non-pigmented colonies with a butyrous–mucoid consistency on marine 2216 agar. It grows optimally at 30 °C, in the presence of 2.0 % (w/v) NaCl and at pH 7.6. Strain E3T is positive for catalase and oxidase and hydrolysis of lipid and reduces nitrate to N2 gas. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E3T belongs to the Gammaproteobacteria and is grouped in the genus Glaciecola, with highest sequence similarity to the type strains of Glaciecola chathamensis (94.6 %), G. agarilytica (94.4 %) and G. mesophila (94.4 %). Strain E3T contained summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 34.5 %), C18 : 1 ω7c (17.3 %) and C16 : 0 (17 %) as the major fatty acids and phosphatidylethanolamine and phosphatidylglycerol as the main phospholipids. The DNA G+C content was 40.8 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain E3T is considered to represent a novel species of the genus Glaciecola, for which the name Glaciecola lipolytica sp. nov. is proposed. The type strain is E3T (=CGMCC 1.7001T =JCM 15139T).

The aim of the present study was to re-examine the taxonomic position and structure of taxon K (also known as group K) within the Burkholderia cepacia complex (Bcc). For this purpose, a representative set of strains was examined by a traditional polyphasic taxonomic approach, by multilocus sequence typing (MLST) analysis and by analysis of available whole-genome sequences. Analysis of the recA gene sequence revealed three different lineages, designated recA-I, recA-II and recA-III. DNA–DNA hybridization experiments demonstrated that recA-I and recA-II isolates each represented a single novel species. However, DNA–DNA hybridization values of recA-II strains towards recA-III strains and among recA-III strains were at the threshold level for species delineation. By MLST, recA-I isolates were clearly distinguished from the others and represented a distinct lineage referred to as MLST-I, whereas recA-II and recA-III isolates formed a second MLST lineage referred to as MLST-II. A divergence value of 3.5 % was obtained when MLST-I was compared with MLST-II. The internal level of concatenated sequence divergence within MLST-I and MLST-II was 1.4 and 2.7 %, respectively; by comparison with the level of concatenated sequence divergence in established Bcc species, these data demonstrate that the MLST-I and MLST-II lineages represent two distinct species within the Bcc. The latter conclusion was supported by comparison of the whole-genome average nucleotide identity (ANI) level of MLST-I and MLST-II strains with strains of established Bcc species and by a whole-genome-based phylogenetic analysis. We formally propose to classify taxon K bacteria from the MLST-I and MLST-II lineages as Burkholderia contaminans sp. nov. (with strain J2956T =LMG 23361T =CCUG 55526T as the type strain) and Burkholderia lata sp. nov. (with strain 383T =ATCC 17760T =LMG 22485T =CCUG 55525T as the type strain), respectively. The MLST approach was confirmed as a valuable instrument in polyphasic taxonomic studies; more importantly, the cumulative data for about 1000 Bcc isolates analysed demonstrate that the 3 % concatenated sequence divergence level correlates with the 70 % DNA–DNA hybridization or 95 % whole-genome ANI threshold levels for species delineation.

The taxonomic status of 24 haemolytic, non-glucose acidifying Acinetobacter strains that did not belong to any previously described species was investigated by means of a polyphasic approach. Using AFLP fingerprinting, amplified rDNA restriction analysis and phenotypic characterization, the strains were classified into two phenetically coherent groups (comprising 15 and 9 strains) that were distinct from each other and from all known Acinetobacter species. Confirmation that these groups formed two separate lineages within the genus Acinetobacter was obtained from comparative analysis of partial sequences of the gene encoding the β-subunit of RNA polymerase in all strains and also from 16S rRNA gene sequence analysis of representative strains. Previously published DNA–DNA reassociation data for some of the strains used also supported the species rank for both groups, for which the names Acinetobacter beijerinckii sp. nov. and Acinetobacter gyllenbergii sp. nov. are proposed. The strains of A. beijerinckii sp. nov. originated from human and animal specimens and from various environmental sources, whereas those of A. gyllenbergii sp. nov. were isolated exclusively from human clinical specimens. The phenotypic characteristics most useful for the differentiation of these species from other Acinetobacter species that comprise haemolytic strains were the inability of A. beijerinckii sp. nov. to grow on l-arginine and the ability of A. gyllenbergii sp. nov. to grow on azelate. The type strain of A. beijerinckii sp. nov. is NIPH 838T (=LUH 4759T=CCUG 51249T=CCM 7266T=58aT) and the type strain of A. gyllenbergii sp. nov. is NIPH 2150T (=RUH 422T=CCUG 51248T=CCM 7267T=1271T).

A Gram-negative, coccoid- or rod-shaped bacterium was isolated from black sand collected from Soesoggak beach, Jeju Island, Korea. The isolate, designated J3T, grew at 15–45 °C, at pH 5.5–10.0 and in 0–8 % NaCl. It was oxidase- and catalase-positive. Strain J3T reduced nitrate to nitrite, but did not reduce nitrite to nitrogen gas. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain J3T was closely related to Nitratireductor aquibiodomus NL21T and belonged to the genus Nitratireductor. Major cellular fatty acids were C18 : 1 ω7c (82.0 %), C19 : 0 ω8c cyclo (4.3 %) and C18 : 0 (4.0 %), a profile that is typical of members of the genus Nitratireductor and distinct from those of other genera in the family Phyllobacteriaceae. Differences in physiological characteristics and fatty acid profiles, as well as low DNA–DNA hybridization values, further established that strain J3T was distinct from N. aquibiodomus NL21T. Thus, strain J3T (=KCTC 22119T =JCM 14935T) should be classified as the type strain of a novel species in the genus Nitratireductor, for which the name Nitratireductor basaltis sp. nov. is proposed.

Strain 78-123T was isolated from a sample of a bird's nest situated on the bank of Qiongtailan River in the region of Tuomuer Peak of Tianshan Mountain in the Xin-jiang Uygur Autonomous Region in north-western China. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain 78-123T was related to members of the genus Pseudomonas. 16S rRNA gene sequence similarity between strain 78-123T and Pseudomonas mendocina ATCC 25411T, Pseudomonas pseudoalcaligenes JCM 5968T and Pseudomonas alcaliphila AL15-21T was 97.1, 97.4 and 97.5 %, respectively. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C18 : 1 ω7c and C12 : 0. The G+C content was 60.4 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, the novel species Pseudomonas tuomuerensis sp. nov. is proposed, with the type strain 78-123T (=CGMCC 1.1365T =JCM 14085T).

In an ongoing attempt to analyse the diversity of culturable micro-organisms from oil-contaminated soil, two yellow-pigmented, Gram-negative, halophilic bacterial strains (SM16T and SM117T) were isolated. These two strains were characterized using a polyphasic approach. Strains SM16T and SM117T showed a range of phenotypic and chemotaxonomic properties that were consistent with those of members of the genus Novosphingobium. Both strains contained sphingoglycolipids, thus confirming that they belong to the Alphaproteobacteria. Furthermore, the polar lipid profile consisted of phosphatidylglycerol, phosphatidyldimethylethanolamine and phosphatidylethanolamine, with minor amounts of phosphatidyldimethylethanolamine, phosphatidylcholine and phosphatidylmonomethylethanolamine. Spermidine was the major polyamine in the cell wall, a characteristic feature of members of the genus Novosphingobium. Fatty acid analysis revealed the presence of C18 : 1 ω7c, C16 : 0 and C14 : 0 2-OH in both isolates, a characteristic feature of sphingomonads. 16S rRNA gene sequence similarities with the type strains of the most closely related species of the genus Novosphingobium (Novosphingobium pentaromativorans and Novosphingobium resinovorum) were less than 98.8 % for both strains. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains SM16T and SM117T fall in the clade represented by the genus Novosphingobium. Strains SM16T and SM117T shared 98.8 % similarity in their 16S rRNA gene sequences and their mean level of DNA–DNA relatedness was 8.5 %. Strains SM16T and SM117T differed from each other with respect to their morphological, physiological and chemotaxonomic properties. Thus, these results indicate that strains SM16T and SM117T belong to separate species of the genus Novosphingobium, for which the names Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov. are proposed; the type strains are SM16T (=CCM 7472T =MTCC9019T) and SM117T (=CCM 7473T =MTCC9020T), respectively.

A hexachlorocyclohexane (HCH)-degrading bacterial strain (RL-3T) was isolated from an HCH dump site located in the northern part of India. Resting cell assays and analytical GC studies confirmed the ability of strain RL-3T to degrade HCH isomers. Southern blot hybridization studies revealed the presence of lin genes, which are involved in the HCH degradation pathway, in this bacterium. The 16S rRNA gene sequence of strain RL-3T showed that it was most closely related to Sphingobium cloacae JCM 10874T (97.3 %) and Sphingobium fuliginis MTCC 7295T (96.4 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain RL-3T between S. cloacae JCM 10874T and S. fuliginis MTCC 7295T. The DNA G+C content of strain RL-3T was 62 mol%. The DNA–DNA relatedness values of strain RL-3T with S. cloacae JCM 10874T and S. fuliginis CCM 7327T were 8.65 and 7.47 %, respectively. SGL1 was the major sphingolipid and spermidine was the major polyamine in strain RL-3T. The major fatty acids in strain RL-3T were C18 : 1 ω7c (56.6 %), C16 : 0 (14 %) and C14 : 0 2-OH (7.4 %). Ubiquinone Q-10 was the major respiratory quinone. Phylogenetic distinctiveness, DNA–DNA relatedness values, biochemical and physiological characterization and unique phenotypic characteristics suggest that strain RL-3T represents a novel species of the genus Sphingobium, for which the name Sphingobium ummariense sp. nov. is proposed. The type strain is RL-3T (=MTCC 8599T=CCM 7431T).

Anamorphic basidiomycetous yeast strains M9962T and M9963 were isolated from water samples collected from a small stream in Ohwakudani, Hakone, a hot-spring area in Japan. These belonged to a single species and were phylogenetically closely related to Bullera lagerstroemiae, although the ability to form ballistoconidia was not observed. Based on sequence analyses of the D1/D2 domain of the LSU rDNA and ITS regions and differences in G+C content, the name Cryptococcus tepidarius sp. nov. Takashima, Sugita, Toriumi et Nakase (Trichosporonales, Tremellomycetes, Basiomycota) is proposed for these isolates, with strain M9962T (=SP-5T =JCM 11965T =CBS 9427T) as the type strain. The strains grew in YM broth at 47 °C and in YM broth with the pH adjusted to 1.5 by HCl, indicating that the species is thermotolerant and acid-tolerant.

During a survey of the mycobiota in the stone chamber of the Takamatsu-zuka tumulus in the village of Asuka, Nara Prefecture, Japan, we isolated 19 yeast strains assigned to the genus Candida from various samples, taken mainly from mouldy spots where the colour of the murals had changed to black, white or another tone, and from viscous gels (biofilms) on plaster walls. The 26S rDNA D1/D2 domain sequence-based phylogeny clearly indicates two groups of isolates. Polyphasic characterization, including morphological, physiological and chemotaxonomic characteristics, and sequence analysis of the 26S rDNA D1/D2 domain and ITS regions suggest that each group is assignable to one of two novel species within the Candida membranifaciens clade. Proposed herein are the names Candida tumulicola sp. nov. (originally T6517-9-5T; holotype JCM 15403T; isotypes CBS 10917T, NBRC 104392T) and Candida takamatsuzukensis sp. nov. (originally T4922-1-1T; holotype JCM 15410T; isotypes CBS 10916T, NBRC 104391T). The 26S rDNA D1/D2 domain sequence divergence indicates that C. tumulicola differs from Candida friedrichii NBRC 10277T, the type strain of the nearest species, in 15 nucleotides (3 %), whereas C. takamatsuzukensis differs from Candida insectorum NBRC 10283T and Pichia mexicana NBRC 10544T, the type strains of the nearest species, in 20 nucleotides (4 %). Both novel species are also clearly distinguishable from the species closest to them by various physiological characteristics.