- Volume 58, Issue 9, 2008

A Gram-negative, rod-shaped, moderately halophilic bacterium, designated strain YIM 91118T, motile with a single polar flagellum, was isolated from Xinjiang province in north-west China and subjected to a polyphasic taxonomic study. Strain YIM 91118T grew optimally at 37 °C, pH 7.0–8.0 and 10 % NaCl (w/v). Its major cellular fatty acids were iso-C15 : 0, iso-C17 : 0, C16 : 0 and iso-C17 : 1 ω9c. The predominant lipoquinone was Q-8. The DNA G+C content was 63.2 mol%. All of these chemotaxonomic data supported the assignment of the new isolate to the genus Microbulbifer. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 91118T belongs to the genus Microbulbifer and it formed a distinct subclade with Microbulbifer maritimus KCCM 41774T. The levels of 16S rRNA gene sequence similarity to the type strains of Microbulbifer species were in the range 93.5–95.0 %. The mean level of DNA–DNA relatedness between strain YIM 91118T and M. maritimus KCCM 41774T was 45.8 %. On the basis of phenotypic properties, phylogeny and genomic data, strain YIM 91118T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer halophilus sp. nov. is proposed. The type strain is YIM 91118T (=CCTCC AB 206094T =KCTC 12848T). Furthermore, it is necessary to emend the description of the genus Microbulbifer.

A yellow-pigmented bacterial strain, designated RIB1-20T, isolated from fresh water was investigated by means of a polyphasic taxonomic approach. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses with the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Luteimonas, its two closest neighbours being Luteimonas composti CC-YY255T (96.1 % sequence similarity) and Luteimonas mephitis B1953/27.1T (95.8 %). Strain RIB1-20T was clearly distinguished from both of those type strains using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain RIB1-20T represents a novel species of the genus Luteimonas, for which the name Luteimonas aquatica sp. nov. is proposed. The type strain is RIB1-20T (=BCRC 17731T =LMG 24212T).

A Gram-negative, moderately halophilic bacterium, designated YIM 91125T, was isolated from a salt lake in Xinjiang province, north-west China. The isolate grew at salinities in the range 1–20 % (w/v) and at 4–45 °C. Optimal growth occurred at 37 °C, pH 7.5 and 5–10 % (w/v) NaCl. Cells were short rods motile by means of single polar flagella. The major fatty acids were C18 : 1 ω7c, C16 : 0, C19 : 0 cyclo ω8c and C12 : 0 3-OH. The DNA G+C content was 60.8 mol%. The predominant respiratory quinone was Q-9. A comparison of 16S rRNA gene sequences revealed its relationship to Halomonas species, its closest neighbours being Halomonas pantelleriensis (95.9 % similarity to the type strain) and Halomonas muralis (95.4 % similarity). On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain YIM 91125T represents a novel member of the genus Halomonas, for which the name Halomonas lutea sp. nov. is proposed. The type strain is YIM 91125T (=KCTC 12847T =CCTCC AB 206093T).

Strain CPCC 100056T, which was isolated from a soil sample collected from the Qinghai–Tibet plateau, China, was subjected to a polyphasic taxonomic study. The organism was coccobacillus-shaped, non-motile and formed vinaceous colonies on ISP2 agar medium. The respiratory quinone was ubiquinone-10. The major fatty acids were C18 : 1 ω7c and C16 : 1 ω7c and/or C16 : 1 ω6c. The G+C content of the genomic DNA was 67.3 mol%. A comparison of sequences in GenBank revealed that strain CPCC 100056T exhibited highest 16S rRNA gene sequence similarity (84.5–95.5 %) with Roseomonas species. Strain CPCC 100056T could be distinguished from all Roseomonas species with validly published names by differences in phenotypic and genotypic properties. In view of the combined phenotypic, chemotaxonomic and phylogenetic data, strain CPCC 100056T should be classified as a representative of a novel species in the genus Roseomonas, Roseomonas vinacea sp. nov.; the type strain is CPCC 100056T (=KCTC 22045T =CCM 7468T).

A Gram-negative, strictly aerobic, non-motile, club-shaped bacterial strain, designated CL-ES2T, was isolated from coastal water from the east coast of Korea. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain CL-ES2T was related to the genera Phaeobacter (95.0–96.6 % similarity to the type strains), Leisingera (96.1 %) and Marinovum (95.6 %) in the family Rhodobacteraceae. However, strain CL-ES2T did not form a robust clade with any species of the Roseobacter clade, instead forming a distinct subline. The optimum temperature and pH for growth were 25 °C and pH 7. Strain CL-ES2T was able to grow with sea salts at concentrations in the range 2–6 %, with optimum growth occurring at 3–4 %. The major fatty acid was C18 : 1 ω7c (75.2 %). The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and three unidentified lipids. The isoprenoid quinone was Q-10. The G+C content of the DNA was 47.0 mol%. On the basis of the data from the polyphasic analysis, strain CL-ES2T represents a novel genus and species, for which the name Pelagicola litoralis gen. nov., sp. nov. is proposed. The type strain of Pelagicola litoralis is CL-ES2T (=KCCM 42274T =DSM 18290T).

Strain A34T, an obligately halophilic, Gram-negative, non-motile, rod-shaped bacterium, was isolated from seawater obtained from Semarang Port in Indonesia. It possesses a pink pigment and degrades short-chain alkanes. It is positive for catalase and oxidase and reduces nitrate to nitrite. Analyses of 16S rRNA gene sequences revealed a clear affiliation of this strain with the family ‘Rhodobacteraceae’ in the class Alphaproteobacteria, with its closest relatives being Salipiger mucosus A3T (94.9 % sequence similarity) and Palleronia marisminoris B33T (93.4 %). The DNA G+C content was 69.1 mol%. The major cellular fatty acids of strain A34T were C18 : 1 ω7c (56.2 %), C19 : 0 cyclo ω8c (26.0 %) and C16 : 0 (9.1 %), while the predominant respiratory lipoquinone was ubiquinone-10. Based on the physiological and phylogenetic data, it is proposed that strain A34T should be classified in a new genus and species, for which the name Tranquillimonas alkanivorans gen. nov., sp. nov. is proposed. The type strain of Tranquillimonas alkanivorans is strain A34T (=JCM 14836T =DSM 19547T).

An aerobic, Gram-negative bacterial isolate, strain DSM 19503T, was isolated from haemolymph serum of the blacklip abalone Haliotis rubra. Cells of strain DSM 19503T were vibrioid to spiral, motile and were able to pass through sterile filters with a pore size of 0.2 μm, indicating the small width of the bacterium. The isolate was psychrophilic, with the ability to grow at 2–8 °C. Oxidase activity was present, whereas catalase activity was absent. The nearly complete 16S rRNA gene sequence of strain DSM 19503T was obtained and phylogenetic sequence analysis showed that it formed a distinct genus in the family Oceanospirillaceae with highest sequence similarity of 92.9 % to Oleispira antarctica RB-8T. The cellular fatty acid composition was dependent on the growth medium used for cultivation. During growth on seawater agar, the fatty acid composition was most similar to that of Oleispira antarctica DSM 14852T, with mainly C16 : 0 (90.3 %). In contrast, Columbia blood agar/NaCl-grown cells exhibited mainly C10 : 0 3-OH (11.8 %), C12 : 1 cis5 (8.2 %), C16 : 1 cis9 (29.6 %), C16 : 0 (19.3 %) and C18 : 1 cis9 (13.1 %) fatty acids. On the basis of phenotypic, chemotaxonomic and genotypic data, strain DSM 19503T is considered to represent a novel species in a new genus for which the name Oceaniserpentilla haliotis gen. nov., sp. nov. is proposed. The type strain of Oceaniserpentilla haliotis is DSM 19503T (=LMG 24225T).

A Gram-negative, non-motile, facultatively anaerobic, denitrifying bacterial strain, designated Ho-11T, was isolated from sludge of a leachate treatment plant and was characterized taxonomically by using a polyphasic approach. The G+C content of the genomic DNA was 63.5 mol%. Strain Ho-11T contained ubiquinone Q-8 as the major respiratory lipoquinone and putrescine as the predominant polyamine. The major fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 29.3 %), C16 : 0 (28.0 %) and summed feature 7 (C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t; 19.8 %). Comparative 16S rRNA gene sequence analysis showed that strain Ho-11T belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. 16S rRNA gene sequence similarities between strain Ho-11T and the type strains of the two recognized species of the genus, Castellaniella denitrificans DSM 11046T and Castellaniella defragrans DSM 12141T, were 97.8 and 97.4 %, respectively. Levels of similarity between strain Ho-11T and all other recognized species of the family Alcaligenaceae were below 95.6 %. Strain Ho-11T exhibited relatively low levels of DNA–DNA relatedness with respect to C. denitrificans DSM 11046T (33 %) and C. defragrans DSM 12141T (28 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain Ho-11T (=KCTC 12197T=LMG 23411T) should be classified in the genus Castellaniella as the type strain of a novel species, for which the name Castellaniella caeni sp. nov. is proposed.

A Gram-negative, flagellated, heterotrophic, catalase-negative, rod-shaped bacterium previously identified as an earthworm symbiont was isolated from nephridia of the earthworm Eisenia foetida. Comparisons of 16S rRNA gene sequences indicated its relatedness to the betaproteobacterial genus Acidovorax and the novel isolates shared 92–94 % sequence similarity with recognized species of this genus. Gene sequence phylogenies revealed that the group of earthworm symbionts formed a cohesive and independent clade. The DNA G+C content was 67.0±0.2 mol%. Major fatty acids were C16 : 0, C16 : 1 ω7c and C17 : 0 cyclo. While capable of growing in fully aerated media, all isolates favoured low oxygen concentrations and all required biotin or a mix of amino acids in order to grow on defined mineral media. Based on phylogenies inferred from three housekeeping gene sequences (gap, recA and rpoC), DNA–DNA hybridization values, the unique ecology and the distinct physiology of the novel strains, the new genus Verminephrobacter gen. nov. is proposed for the earthworm nephridial symbionts. The name Verminephrobacter eiseniae sp. nov. is proposed for the type species with strain EF01-2T (=ATCC BAA-1489T=DSM 19286T) as the type strain of the type species.

During a study of endophytic nitrogen-fixing bacteria present in the wild rice species Oryza alta, eight novel isolates were obtained from surface-sterilized roots and classified in the genus Rhizobium on the basis of almost-complete 16S rRNA gene sequence analysis. These strains can nodulate Phaseolus vulgaris and Glycine max. The highly similar protein patterns, DNA fingerprint patterns of insertion sequence-based PCR (IS-PCR) and DNA–DNA hybridizations showed that these novel isolates were members of the same species. The closest phylogenetic relatives of the representative strain Alt 505T of the novel group were Rhizobium etli CFN 42T and Rhizobium indigoferae CCBAU 71714T, with 96.2 and 96.0 % 16S rRNA gene sequence similarity, respectively. Low DNA–DNA relatedness with the type strains of R. etli, R. indigoferae, Rhizobium hainanense, Rhizobium mongolense and Rhizobium galegae and differences in IS-PCR fingerprinting patterns, SDS-PAGE of proteins, antibiotic resistance, phenotypic tests and comparison of cellular fatty acids with Rhizobium species indicated that the novel group of isolates were distinct from previously described species. Based on these results, we propose to place them in a novel species, as Rhizobium oryzae sp. nov. The type strain is Alt 505T (=LMG 24253T =CGMCC 1.7048T).

Two rhizobial strains, Br3407T and Br3405, were isolated from nitrogen-fixing nodules on the roots of Mimosa caesalpiniifolia, a legume tree native to Brazil. On the basis of 16S rRNA gene sequence similarities, both strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA–DNA hybridizations, pulsed-field gel electrophoresis of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia sabiae sp. nov. is proposed. The type strain is strain Br3407T (=LMG 24235T =BCRC 17587T).

Six acetic acid bacterial isolates, obtained during a study of the microbial diversity of spontaneous fermentations of Ghanaian cocoa beans, were subjected to a polyphasic taxonomic study. (GTG)5-PCR fingerprinting grouped the isolates together, but they could not be identified using this method. Phylogenetic analysis based on 16S rRNA gene sequences allocated the isolates to the genus Acetobacter and revealed Acetobacter lovaniensis, Acetobacter ghanensis and Acetobacter syzygii to be nearest neighbours. DNA–DNA hybridizations demonstrated that the isolates belonged to a single novel genospecies that could be differentiated from its phylogenetically nearest neighbours by the following phenotypic characteristics: no production of 2-keto-d-gluconic acid from d-glucose; growth on methanol and d-xylose, but not on maltose, as sole carbon sources; no growth on yeast extract with 30 % d-glucose; and weak growth at 37 °C. The DNA G+C contents of four selected strains were 56.8–58.0 mol%. The results obtained prove that the isolates should be classified as representatives of a novel Acetobacter species, for which the name Acetobacter fabarum sp. nov. is proposed. The type strain is strain 985T (=R-36330T =LMG 24244T =DSM 19596T).

A denitrifying bacterium, designated strain FST, was isolated from anoxic digested sludge on oestradiol [17β-oestra-1,3,5(10)-triene-3,17-diol] or testosterone (17β-hydroxyandrost-4-en-3-one) as the sole source of carbon and energy with nitrate as the electron acceptor. Strain FST represents the first known bacterium to grow anaerobically on both oestradiol (C-18) and testosterone (C-19). Steroidal hormones were degraded completely by nitrate reduction to dinitrogen monoxide, which was further reduced to dinitrogen in stationary-phase cultures. Gram-negative cells were slightly curved rods, 0.3–0.5×0.6–1.6 μm in size, motile, non-fermentative, non-spore-forming and catalase- and oxidase-positive, showing optimal growth at pH 7.0, 28 °C and 0.1 % (w/v) NaCl. Beside steroidal hormones, the bacterium utilized only a narrow range of organic substrates with nitrate as the electron acceptor, including several fatty acids and glutamate. No aerobic or anaerobic growth occurred on liquid or solid complex media. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain FST has no known close relatives and represents a distinct lineage within the Gammaproteobacteria. Together with the genera Nevskia, Hydrocarboniphaga, Solimonas and Sinobacter (less than 88 % 16S rRNA gene sequence similarity to strain FST), it forms a phylogenetic cluster separated from the families Chromatiaceae, Ectothiorhodospiraceae and Xanthomonadaceae. The quinone system of strain FST consisted exclusively of ubiquinone Q-8. The dominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. Spermidine in combination with putrescine and traces of sym-homospermidine were the basic polyamines. The major fatty acids detected in testosterone- or heptanoate-grown cells were C15 : 0 and C17 : 1 ω8c, minor hydroxylated fatty acids were C11 : 0 3-OH and C12 : 0 3-OH. The G+C content of the DNA was 61.9 mol%. Based on the high 16S rRNA gene sequence divergence and different phenotypic properties from previously described gammaproteobacteria in combination with chemotaxonomic data, strain FST is considered to represent a new genus and species, for which the name Steroidobacter denitrificans gen. nov., sp. nov. is proposed. The type strain of Steroidobacter denitrificans is FST (=DSM 18526T =JCM 14622T).

A Gram-negative, non-spore-forming, rod-shaped bacterial strain, K106T, was isolated from wastewater collected from a textile dye works in Korea. Strain K106T grew optimally at pH 7.0–7.5 and 30–37 °C in the presence of 0–1.0 % (w/v) NaCl. A phylogenetic tree based on 16S rRNA gene sequences showed that strain K106T joined the type strain of Chelatococcus asaccharovorans with a bootstrap resampling value of 99.9 %. The predominant ubiquinone of strain K106T was Q-10. The fatty acid profile of strain K106T was similar to that of C. asaccharovorans DSM 6462T. Major polar lipids of strain K106T and C. asaccharovorans DSM 6462T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two aminolipids and two unidentified phospholipids. sym-Homospermidine, spermidine and putrescine were major polyamines. The DNA G+C content was 68.3 mol%. Strain K106T exhibited 16S rRNA gene sequence similarity of 96.6 % to the type strain of C. asaccharovorans. DNA–DNA relatedness data and differential phenotypic properties, particularly differences in cell morphology and the ability to utilize nitrilotriacetate, demonstrated that strain K106T can be differentiated from C. asaccharovorans. On the basis of phenotypic, phylogenetic and genetic data, strain K106T represents a novel species of the genus Chelatococcus, for which the name Chelatococcus daeguensis sp. nov. is proposed. The type strain is K106T (=KCTC 12979T =CCUG 54519T).

A Gram-negative, strictly aerobic, rod-shaped bacterium, designated strain BD-c54T, was isolated from BTEX (benzene, toluene, ethylbenzene and xylenes)-contaminated soil in Sacheon, Korea. Growth of strain BD-c54T was observed at 15–35 °C (optimum 25–30 °C) and pH 6.0–9.5 (optimum pH 7.0–8.0). The predominant fatty acids were iso-C15 : 0, iso-C17 : 1 ω9c, iso-C11 : 0 3-OH, iso-C16 : 0, iso-C11 : 0 and iso-C17 : 0. The strain contained large amounts of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and a small amount of an unknown amino-group-containing polar lipid as polar lipids. The major quinone was ubiquinone-8 (Q-8) and the G+C content of the genomic DNA was 67.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain BD-c54T formed a tight phylogenetic lineage with Pseudoxanthomonas yeongjuensis GR12-1T within the genus Pseudoxanthomonas and was most closely related to P. yeongjuensis GR12-1T and [Stenotrophomonas] dokdonensis DS-16T, with 98.3 and 96.6 % 16S rRNA gene sequence similarity, respectively. The DNA–DNA relatedness between strain BD-c54T and P. yeongjuensis GR12-1T was 24.5 %. On the basis of chemotaxonomic data and molecular properties, strain BD-c54T represents a novel species within the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas sacheonensis sp. nov. is proposed. The type strain is BD-c54T (=KCTC 22080T =DSM 19373T). In addition, the transfer of Stenotrophomonas dokdonensis to Pseudoxanthomonas as Pseudoxanthomonas dokdonensis comb. nov. and an emended description of the genus Pseudoxanthomonas are proposed.

The novel species Metschnikowia shivogae is described to accommodate three isolates recovered from insects of morning glory flowers at two localities in East Africa. The isolates differ slightly in rDNA ITS and D1/D2 large-subunit sequences and one isolate featured a two-base heterogeneity that might be the result of recombination between two variant rDNAs. M. shivogae is a sister species to Metschnikowia aberdeeniae and shares the same habitat. The reproductive boundaries of M. aberdeeniae, which were not clear in the past, have now been elucidated further. The type strain of Metschnikowia shivogae sp. nov. is strain SUB 04-310.1T (h +; =CBS 10292T =NRRL Y-27924T) and the allotype is strain UWOPS 07-203.2 (h −; =CBS 10770 =NRRL Y-48447).

A high-throughput screening effort, designed to isolate bacteriocin-producing lactic acid bacteria (LAB) from malted cereals, resulted in the isolation of four bacteriocin-producing strains that could not be assigned conclusively to recognized species. The four isolates (UCC128T, UCC125, UCC126 and UCC127) were found to share identical (100 %) 16S rRNA gene sequences and were therefore deemed to belong to the same species. The strains were Gram-positive, catalase-negative, non-motile homofermentative LAB. The closest recognized relative to strain UCC128T identified based on comparative 16S rRNA gene sequence analysis was Lactobacillus mali DSM 20444T (97 % similarity). The strains were characterized phenotypically to identify specific growth requirements. DNA–DNA hybridization between strain UCC128T and L. mali DSM 20444T revealed a level of relatedness of only 39.4 %. This indicates that strain UCC128T does not belong to the species L. mali. The four bacteriocin-producing strains are therefore considered to represent a novel species of the genus Lactobacillus, for which the name Lactobacillus hordei sp. nov. is proposed. The type strain is UCC128T (=DSM 19519T=LMG 24241T).

It is proposed that Clostridium proteoclasticum be reclassified as Butyrivibrio proteoclasticus comb. nov. on the basis of phylogenetic position, DNA G+C content and physiological traits. Phylogenetic analyses based on 16S rRNA gene sequences from an extensive range of taxa within clostridial rRNA subcluster XIVa grouped C. proteoclasticum together with isolates of the genus Butyrivibrio, though this species was genetically distinct from the extant Butyrivibrio species examined. The DNA G+C content of C. proteoclasticum was originally erroneously reported as 28 mol%. However the genome sequence of the type strain of C. proteoclasticum, strain B316T, and HPLC analysis estimate the DNA G+C content as 40 mol%, which is within the range reported for strains of Butyrivibrio. C. proteoclasticum was distinguishable from other species of the genus Butyrivibrio as the 16S rRNA gene from strain B316T shared less than 97 % sequence similarity with sequences from the type strains of Butyrivibrio species. C. proteoclasticum was also able to convert linoleic acid to stearic acid, in contrast to other species of Butyrivibrio. Physiological characteristics, including carbon source utilization, volatile fatty acid production and proteinase activities, were assessed for a panel of representative strains of the genera Butyrivibrio and Pseudobutyrivibrio and C. proteoclasticum. These data, together with the phylogenetic analyses, support the reclassification of Clostridium proteoclasticum as a separate species within the genus Butyrivibrio, Butyrivibrio proteoclasticus comb. nov. (type strain B316T=ATCC 51982T=DSM 14932T).

A Gram-positive, rod-shaped, motile, spore-forming bacterium, strain SA-7-6T, was isolated from desert soil in China and was subjected to a polyphasic taxonomic study. The strain grew optimally at pH 7.5 and 37 °C. The G+C content of the genomic DNA of strain SA-7-6T was 53.7 mol%. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0. Strain SA-7-6T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. 16S rRNA gene sequence analysis showed that the new isolate shared highest similarity with Paenibacillus glycanilyticus JCM 11221T (96.6 %) and Paenibacillus daejeonensis KCTC 3745T (96.6 %). Based on morphological, physiological, chemotaxonomic and phylogenetic characteristics, strain SA-7-6T is considered to represent a novel species of the genus Paenibaillus, for which the name Paenibacillus tarimensis sp. nov. is proposed. The type strain is SA-7-6T (=CCTCC AB 206108T=DSM 19409T).