Major Hydroxy Fatty Acid Research Articles

Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae.

Three novel bacterial strains (UCM-2T, UCM-G28T, and UCM-G35T) were obtained while isolating soil bacteria for the development of antibiotics. Cells of these strains were Gram-negative, non-spore forming, motile by means of a single flagellum, and rod shaped. In all strains, the predominant isoprenoid quinone was ubiquinone-8 (Q-8). Cells contained C16:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 8 (C18:1ω7c and/or C18:1ω6c), and C17:0 cyclo as the major fatty acids, and C10:0 3-OH as the major hydroxy fatty acid. The polar lipid profiles of the three novel strains were dominated by diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G + C contents of strains UCM-2T, UCM-G28T, and UCMG35T were 67.5, 65.9, and 66.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA sequences showed that strain UCM-2T was most closely related to Variovorax soli NBRC 106424T, whereas strains UCM-G28T and UCM-G35T were most similar to Variovorax ginsengisoli Gsoil 3165T. Values indicating DNA-DNA hybridization between the novel isolates and closely related species in the genus Variovorax were lower than the 70% cut-off point. These phenotypic, chemotaxonomic, and phylogenetic data indicate that the three isolates should be classified as new members of the genus Variovorax, for which the names Variovorax ureilyticus sp. nov., Variovorax rhizosphaerae sp. nov., and Variovorax robiniae sp. nov. are proposed. The type strains are UCM-2T (= KACC 18899T = NBRC 112306T), UCMG28T (= KACC 18900T = NBRC 112307T), and UCM-G35T (= KACC 18901T = NBRC 112308T), respectively.

Novosphingobium bradum sp. nov., isolated from a spring.

A bacterial strain designated STM-24T was isolated from a spring in Taiwan and characterized using the polyphasic taxonomic approach. Cells of strain STM-24T were Gram-staining- negative, aerobic, poly-β-hydroxybutyrate accumulating, non-motile, rod shaped and forming light yellow-coloured colonies. Growth occurred at 15-30 °C (optimum, 20 °C), at pH 5.0-9.0 (optimum, pH 6.0) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain STM-24T belonged to the genus Novosphingobium and was most closely related to Novosphingobium piscinae SLH-16T with sequence similarity of 98.4 %. The major fatty acids (>10 %) of strain STM-24T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major 2-hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine and several uncharacterized lipids. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 69.1mol%. The DNA-DNA hybridization value for strain STM-24T with N.piscinae SLH-16T, Novosphingobium taihuense JCM 12465T and Novosphingobium subterraneum DSM 12447T was less than 55 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain STM-24T represents a novel species in the genus Novosphingobium, for which the name Novosphingobium bradum sp. nov. is proposed. The type strain is STM-24T (=BCRC 80925T=LMG 29291T=KCTC 42984T).

Novosphingobium piscinae sp. nov., isolated from a fish culture pond.

A bacterial strain designated SLH-16T was isolated from a fish culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain SLH-16T were Gram-stain-negative, aerobic, motile rods that were covered by large capsules and formed yellow colonies. Growth occurred at 20-40 °C (optimum, 37-40 °C), at pH 4.0-9.0 (optimum, pH 5.0-6.0) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SLH-16T belonged to the genus Novosphingobium and was related most closely to Novosphingobium taihuense T3-B9T with sequence similarity of 97.3 %. The major fatty acids (>10 %) of strain SLH-16T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major 2-hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine and several uncharacterized lipids. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.2 mol%. The DNA-DNA hybridization value for strain SLH-16T and the type strain of N. taihuense was less than 43.2 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain SLH-16T represents a novel species in the genus Novosphingobium, for which the name Novosphingobium piscinae sp. nov. is proposed. The type strain is SLH-16T ( = BCRC 80888T = LMG 28418T = KCTC 42194T).

Novel environmental species isolated from the plaster wall surface of mural paintings in the Takamatsuzuka tumulus: Bordetella muralis sp. nov., Bordetella tumulicola sp. nov. and Bordetella tumbae sp. nov.

Ten strains of Gram-stain-negative, non-spore-forming, non-motile coccobacilli were isolated from the plaster wall surface of 1300-year-old mural paintings inside the stone chamber of the Takamatsuzuka tumulus in Asuka village (Asuka-mura), Nara Prefecture, Japan. Based on 16S rRNA gene sequence analysis of the isolates, they belonged to the proteobacterial genus Bordetella (class Betaproteobacteria) and could be separated into three groups representing novel lineages within the genus Bordetella. Three isolates were selected, one from each group, and identified carefully using a polyphasic approach. The isolates were characterized by the presence of Q-8 as their major ubiquinone system and C16 : 0 (30.0-41.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.1-27.0 %) and C17 : 0 cyclo (10.8-23.8 %) as the predominant fatty acids. The major hydroxy fatty acids were C12 : 0 2-OH and C14 : 0 2-OH. The DNA G+C content was 59.6-60.0 mol%. DNA-DNA hybridization tests confirmed that the isolates represented three separate novel species, for which the names Bordetella muralis sp. nov. (type strain T6220-3-2bT = JCM 30931T = NCIMB 15006T), Bordetella tumulicola sp. nov. (type strain T6517-1-4bT = JCM 30935T = NCIMB 15007T) and Bordetella tumbae sp. nov. (type strain T6713-1-3bT = JCM 30934T = NCIMB 15008T) are proposed. These results support previous evidence that members of the genus Bordetella exist in the environment and may be ubiquitous in soil and/or water.

Sphingomonas chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge.

Strain Y1(T), a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from activated sludge. This strain is able to degrade several commonly used chloroacetamide herbicides, such as butachlor, acetochlor and alachlor. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y1(T) is a member of the genus Sphingomonas and shows high sequence similarities with S. starnbergensis 382(T) (95.7 %), S. sanxanigenens NX02(T) (95.7 %) and S. haloaromaticamans A175(T) (95.3 %), and shows low (<95 %) sequence similarities to all other Sphingomonas species. Chemotaxonomic analysis revealed that strain Y1(T) possesses Q-10 as the predominant ubiquinone, C14:0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain Y1(T) were found to be C18:1 ω7c (38.2 %), C16:1 ω6c/C16:1 ω7c (28.5 %), C16: 0 (10.7 %) and C14:0 2-OH (14.3 %). The main polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipids (SGL1-SGL3), phosphatidyl dimethylethanolamine and aminophospholipid. The DNA G+C content was found to be 66 ± 0.4 mol%. Based on phylogenetic analysis, phenotypic characteristics and chemotaxonomic data, strain Y1(T) is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas chloroacetimidivorans sp. nov. is proposed. The type strain is Y1(T) (=CCTCC AB 2011178(T) = KACC 16607(T)).

Agaribacter marinus gen. nov., sp. nov., an agar-degrading bacterium from surface seawater.

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 8-8(T), was isolated from surface seawater at Muroto, Kochi, Japan. The strain exhibited agar-degrading activity. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Alteromonadaceae and clustered distantly with members of the genus Glaciecola (≤ 94.0% similarity). The DNA G+C content was 41.8 mol%. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c and the major hydroxy fatty acid was C12 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid; lysophosphatidylethanolamine and unidentified polar lipids were found as minor components. The major quinone was Q-8. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 8-8(T) represents a novel species of a new genus, for which the name Agaribacter marinus gen. nov., sp. nov. is proposed. The type strain of Agaribacter marinus is 8-8(T) ( = NBRC 110023(T) = LMG 28167(T)).

Novosphingobium kunmingense sp. nov., isolated from a phosphate mine.

A yellow-pigmented, Gram-stain-negative, strictly aerobic, rod-shaped, round-ended bacterium, designated strain 18-11HK(T), was isolated from a phosphate mine situated in the suburb of Kunming in Yunnan province in south-western China. The taxonomic status of this strain was evaluated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, strain 18-11HK(T) was shown to belong to the genus Novosphingobium, showing the highest levels of sequence similarity with respect to 'Novosphingobium ginsenosidimutans' FW-6 (97.2%), Novosphingobium subterraneum DSM 12447(T) (96.7%), Novosphingobium aromaticivorans DSM 12444(T) (96.7%) and Novosphingobium tardaugens DSM 16702(T) (96.3%). Strain 18-11HK(T) had a genomic DNA G+C content of 65.3 mol% and Q-10 as the predominant respiratory quinone. DNA-DNA hybridizations of strain 18-11HK(T) with N. subterraneum DSM 12447(T), N. aromaticivorans DSM 12444(T) and N. tardaugens DSM 16702(T) showed low relatedness values of 29.6, 33.5 and 32.3%, respectively. The predominant fatty acids of strain 18-11HK(T) were summed feature 8 (C18 : 1ω7c and/or C18: 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0, and the major 2-hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile revealed the presence of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and some unidentified lipids. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain 18-11HK(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium kunmingense sp. nov. is proposed. The type strain is 18-11HK(T) ( = CGMCC 1.12274(T) = DSM 25975(T)).

Prosthecate sphingomonads: proposal of Sphingomonas canadensis sp. nov.

Two stalked, aerobic, catalase- and oxidase-positive rod-shaped isolates, VKM B-1508 ( = CB 258) and FWC47(T), were analysed using a polyphasic approach. While the morphology and the 16S rRNA gene sequence of strain VKM B-1508 were 100% identical to the ones of Sphingomonas leidyi DSM 4733(T), the morphology of FWC47(T) was different, and the closest recognized species were Sphingomonas oligophenolica S213(T) ( = DSM 17107(T)) and Sphingomonas leidyi DSM 4733(T) with 97.2% and 97.0% 16S rRNA gene sequence similarity, respectively. DNA-DNA hybridization studies supported the differentiation of strain FWC47(T) from S. oligophenolica and S. leidyi. Strain FWC47(T) grew optimally at 28-30 °C, and pH 6.0-8.0. The major respiratory quinone was Q10 and the major polyamine was sym-homospermidine. The major fatty acids were C(17:1)ω6c and C(18:1)ω7c and C(15:0) 2-OH was the major 2-hydroxy fatty acid. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethylamine and unidentified sphingoglycolipids. The G+C content of the genomic DNA of strain FWC47(T) was 67.1 mol%. Strain FWC47(T) differed from S. leidyi by its ability to assimilate l-alanine, maltose and sucrose, by the presence of β-galactosidase and α-chymotrypsin, and the lack of valine arylamidase and β-glucosidase activities. Contrary to S. leidyi, FWC47(T) did not reduce nitrate and could not use fructose, acetate and N-acetyl-glusosamine. In the genus Sphingomonas, the dimorphic life cycle involving a prosthecate sessile and a flagellated swarmer cell was hitherto only known from Sphingomonas leidyi. Therefore, strain FWC47(T) represents an additional distinct prosthecate species in this genus for which the name Sphingomonas canadensis is proposed. The type strain is FWC47(T) ( =LMG 27141(T) =CCUG 62982(T)).

Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake

A novel type of freshwater bacterium was isolated from the prealpine mesotrophic Starnberger See (Bavaria, southern Germany). Cells of strain 382(T) were Gram-negative and rod-shaped, motile and creamy-white. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew at pH values of 6-9 (optimum, pH 7) and temperatures of 10-37 °C (optimum, 28 °C). The genomic G+C content of strain 382(T) was 64.1 mol%. Based on 16S rRNA gene sequence analyses, strain 382(T) belongs to the family Sphingomonadaceae and clusters within the genus Sphingomonas. Sphingomonas histidinilytica UM 2(T) and Sphingomonas wittichii DSM 6014(T) were the closest relatives, as indicated by the highest 16S rRNA gene sequence similarities (97.1 % and 96.8 %, respectively). Sphingomonas paucimobilis DSM 1098(T) (the type species of the genus Sphingomonas) exhibited 95.3 % sequence similarity. This affiliation of strain 382(T) to the genus Sphingomonas is confirmed by the presence of Q-10 as the major respiratory quinone, two sphingoglycolipids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain 382(T) were C18 : 1ω7c (39 %), C16 : 1ω7c (21 %), C16 : 0 (10 %) and C14 : 0 2-OH (10 %). Based on the phylogenetic distance from other species of the genus Sphingomonas and its unusually high C16 : 1ω7c content, strain 382(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas starnbergensis is proposed. The type strain is 382(T) ( = DSM 25077(T) = LMG 26763(T)).

Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae , and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.

Two novel chemo-organoheterotrophic members of the Sphingomonadaceae were isolated from alpine and pre-alpine lakes. Cells stained gram-negative, were motile and rod-shaped, and formed yellow, circular, convex colonies on different agar media. Strains 301(T) and 469(T) were strictly aerobic, catalase- and oxidase-positive, and grew at temperatures between 10 and 40 °C (optimum, 28 °C), and at pH values between 5 and 10 (optimum, pH 7). Both strains contained Q-10 as the dominant quinone, sphingoglycolipids and 2-hydroxymyristic acid, whereas 3-hydroxy fatty acids were absent. Major fatty acids of strain 301(T) were C(18 : 1)ω7c (53.3 %) and C(16 : 1)ω7c (22.9 %), with C(14 : 0) 2-OH (10.8 %) as the major 2-hydroxy fatty acid. Fatty acids of strain 469(T) were dominated by C(18 : 1)ω7c (34.4 %), C(16 : 1)ω7c (32.0 %) and C(14 : 0) 2-OH (15.2 %) as the major 2-hydroxy fatty acid. The genomic DNA G+C contents of strains 301(T) and 469(T) were 63.4 and 64.6 mol%, respectively. 16S rRNA gene sequence comparison indicated that both strains belonged to the genus Sphingobium. This classification was supported by the presence of spermidine as the major polyamine. The phylogenetically closest relatives of strain 301(T) were Sphingobium amiense DSM 16289(T), Sphingobium vermicomposti DSM 21299(T), Sphingobium yanoikuyae DSM 7462(T) and Sphingobium scionense DSM 19371(T) (98.8, 98.0, 97.9 and 97.4 % sequence similarity, respectively). DNA-DNA hybridization of genomic DNA yielded similarities in the range 43.2-12.1 % between strain 301(T) and the type strains of these four Sphingobium species. Closest relatives of strain 469(T) were Sphingomonas suberifaciens DSM 7465(T) and Sphingobium scionense DSM 19371(T) (97.1 and 96.5 % 16S rRNA gene sequence similarity, respectively). The degree of DNA-DNA hybridization between strain 469(T) and Sphingomonas suberifaciens DSM 7465(T) was 17.9 %. Based on the results of the molecular analyses and their phenotypic characteristics, strains 301(T) and 469(T) represent two novel species of the genus Sphingobium. The name Sphingobium limneticum sp. nov. is proposed for strain 301(T)( = DSM25076(T) = LMG 26659(T)). The name Sphingobium boeckii sp. nov. is proposed for strain 469(T) ( = DSM 25079(T) = LMG 26901(T)). The polyphasic analysis also suggests that Sphingomonas suberifaciens should be reclassified as Sphingobium suberifaciens comb. nov. with Ca1(T) ( = EY 2404(T) = ATCC 49355(T) = CIP 105429(T) = DSM 7465(T) = ICMP 12535(T) = NBRC 15211(T) = JCM 8521(T) = LMG 17323(T) = NCPPB 3629(T)) as the type strain.

Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas

'Caulobacter leidyi' DSM 4733(T) has been shown to be affiliated with the family Sphingomonadaceae instead of the Caulobacteraceae, and due to its poor characterization has been omitted from the current edition of Bergey's Manual of Systematic Bacteriology and removed to limbo. We isolated a novel sphingoglycolipid-containing dimorphic prosthecate bacterium, designated strain 247, from a pre-alpine freshwater lake. Strain 247 and 'Caulobacter leidyi' DSM 4733(T) were characterized in detail. The rod-shaped cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive, and formed a stalk or polar flagellum. Both strains grew optimally at 28-30 °C, and pH 6.0-8.0. The major fatty acids were C(18 : 1)ω7c, C(16 : 0) and 11-methyl C(18 : 1)ω7c. C(14 : 0) 2-OH represents the major 2-hydroxy fatty acid. Q-10 was the major respiratory quinone and the major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, three glycolipids, two phosphoaminolipids and two unidentified sphingoglycolipids. The major polyamine was sym-homospermidine. The G+C content of genomic DNA of strains 247 and DSM 4733(T) was 67.6 mol% and 67.0 mol%, respectively. According to 16S rRNA gene sequence analysis and DNA-DNA hybridization, strains DSM 4733(T) and 247 were phylogenetically closely related (99.6 % 16S rRNA gene sequence similarity, 82.9 % DNA-DNA hybridization value) and affiliated to the genus Sphingomonas. The closest recognized species was Sphingomonas aquatilis DSM 15581(T) (98.1 % sequence similarity). In addition, the presence of cystine arylamidase, absence of β-galactosidase, and the inability to utilize l-arabinose, galactose and sucrose distinguished strains DSM 4733(T) and 247 from most other members of the family Sphingomonadaceae. So far, the dimorphic life cycle that involves a prosthecate and a flagellated stage is unique for strains DSM 4733(T) and 247 among all members of the family Sphingomonadaceae. Therefore, Caulobacter leidyi is reclassified as Sphingomonas leidyi, with the type strain DSM 4733(T) ( = ATCC 15260(T) = CIP 106443(T) = VKM B-1368(T)) and strain 247 (DSM 25078 = LMG 26658) as an additional strain of this species.

Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil

In the present study, a yellow-pigmented, Gram-negative, short rod-shaped novel bacterium that was capable of degrading a wide range of polycyclic aromatic hydrocarbons (naphthalene, phenanthrene and pyrene) was isolated from agricultural soil located in Yunlin County, Taiwan. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus Sphingomonas as an independent lineage adjacent to a subclade containing Sphingomonas fennica K101(T), Sphingomonas histidinilytica UM2(T), Sphingomonas wittichii RW1(T) and Sphingomonas haloaromaticamans A175(T). 16S rRNA gene sequence analysis of strain CC-Nfb-2(T) showed highest sequence similarity to S. fennica K101(T) (96.2%), S. histidinilytica UM2(T) (96.1%), S. wittichii RW1(T) (95.9%), S. haloaromaticamans A175(T) (95.7%), and Sphingobium ummariense RL-3(T) (94.7%); lower sequence similarities were observed with strains of all other Sphingomonas species. The strain contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and diphosphatidylglycerol. The predominant fatty acids were summed feature 8 (C(18:1)ω7c and/or C(18:1)ω6c) C(16:0) and 11-methyl C(18:1)ω7c; C(14:0) 2-OH was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus Sphingomonas. The serine palmitoyl transferase gene (spt) was also detected and sphingolipid synthesis was confirmed. The predominant isoprenoid quinone system was ubiquinone (Q-10) and the isolate contained sym-homospermidine as the major polyamine. The DNA G+C content of the isolate was 62.8±0.8 mol%. On the basis of chemotaxonomic, phenotypic and phylogenetic data, strain CC-Nfb-2(T) represents a novel species within the genus Sphingomonas, for which the name Sphingomonas formosensis sp. nov. is proposed; the type strain is CC-Nfb-2(T) (=BCRC 80272(T)=DSM 24164(T)).

Sphingomonas rubra sp. nov., isolated from bioreactor wastewater

A Gram-reaction-negative, rod-shaped, motile, neutrophilic bacterium, designated strain BH3(T), was isolated from wastewater of a sequential batch reactor treating wastewater taken from a leather plant. The isolate grew in 0-8 % (w/v) NaCl, at pH 6-9 and at 4-45 °C. Chemotaxonomic analysis showed that strain BH3(T) had characteristics typical of members of the genus Sphingomonas, such as the presence of sphingolipids, Q-10 and 2-hydroxymyristic acid and the absence of 3-hydroxy fatty acids. The presence of C(18 : 1)ω7c (39.2 %) and C(16 : 0) (11.2 %) as major fatty acids, C(14 : 0) 2-OH (20.6 %) as the major 2-hydroxy fatty acid and homospermidine as the major polyamine indicated that strain BH3(T) belonged to the genus Sphingomonas sensu stricto. The genomic DNA G+C content of strain BH3(T) was 65.6 mol%. 16S rRNA gene sequence similarities between the isolate and closely related members of the genus Sphingomonas sensu stricto ranged from 92.6 to 97.3 %, the highest sequence similarities being to Sphingomonas melonis DSM 14444(T) (97.3 %) and Sphingomonas aquatilis DSM 15581(T) (97.3 %). Based on its phenotypic characteristics and the results of DNA-DNA hybridization studies and 16S rRNA gene sequence comparisons, strain BH3(T) represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas rubra sp. nov. is proposed. The type strain is BH3(T) ( = CGMCC 1.9113(T) = JCM 16230(T)).

Sphingobium faniae sp. nov., a pyrethroid-degrading bacterium isolated from activated sludge treating wastewater from pyrethroid manufacture

A bacterial strain capable of degrading pyrethroid, designated JZ-2(T), was isolated from activated sludge treating pyrethroid-contaminated wastewater. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JZ-2(T) belongs to the genus Sphingobium. It showed the highest levels of 16S rRNA gene sequence similarity to Sphingobium cloacae JCM 10874(T) (98.3 %) and Sphingobium ummariense CCM 7431(T) (97.1 %), and 94.8-96.9 % similarity to the type strains of other members of the genus Sphingobium. Strain JZ-2(T) contained C(18 : 1)omega7c as the predominant fatty acid, C(14 : 0) 2-OH as the major 2-hydroxy fatty acid, ubiquinone Q-10 as the main respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and two sphingoglycolipids as the predominant polar lipids and spermidine as the major polyamine. DNA-DNA hybridization results showed that strain JZ-2(T) had low genomic relatedness with S. cloacae JCM 10874(T) (34 %) and S. ummariense CCM 7431(T) (23 %). Based on the phenotypic, genotypic and phylogenetic data presented, strain JZ-2(T) is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium faniae sp. nov. is proposed. The type strain is JZ-2(T) (=CGMCC 1.7749(T) =DSM 21829(T)).

Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica

A Sphingomonas-like bacterium, strain KC7(T), was isolated from a marine crustacean specimen obtained from the Sea of Japan and subjected to a polyphasic study. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus Sphingomonas as an independent lineage adjacent to a subclade containing Sphingomonas trueperi LMG 2142(T), Sphingomonas pituitosa EDIV(T) and Sphingomonas azotifigens NBRC 15497(T). Strain KC7(T) shared highest 16S rRNA gene sequence similarity (96.1 %) with S. trueperi LMG 2142(T), Sphingomonas dokdonensis DS-4(T) and S. azotifigens NBRC 15497(T); similarities to strains of other recognized Sphingomonas species were lower (96.0-93.9 %). The strain contained sphingoglycolipid and the predominant fatty acids were C(16 : 1), C(16 : 0) and C(18 : 1); 2-OH C(14 : 0) was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus Sphingomonas sensu stricto. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain KC7(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas japonica sp. nov. is proposed. The type strain is KC7(T) (=KMM 3038(T) =NRIC 0738(T) =JCM 15438(T)).

Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea

A Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046(T), was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046(T) belongs to the family Xanthomonadaceae in the Gammaproteobacteria. The greatest sequence similarity was found with respect to Dyella koreensis KCTC 12359(T) (97.7 %), Dyella japonica IAM 15069(T) (97.4 %), Frateuria aurantia DSM 6220(T) (96.7 %), Fulvimonas soli LMG 19981(T) (96.2 %) and Luteibacter rhizovicinus DSM 16549(T) (96.0 %). The phylogenetic distances from other recognized species within the family Xanthomonadaceae, including Dyella yeojuensis KACC 11405(T), were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA-DNA hybridization experiments showed that the levels of DNA-DNA relatedness between strain Gsoil 3046(T) and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C(17 : 1)omega9c, iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 0) as the major cellular fatty acids and iso-C(13 : 0) 3-OH and iso-C(11 : 0) 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046(T) to the genus Dyella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046(T) represents a novel species in the genus Dyella, for which the name Dyella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3046(T) (=KCTC 12599(T)=DSM 18387(T)).

Paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in Tokyo Bay

Two novel marine, Gram-negative, non-motile, catalase- and oxidase-positive, aerobic bacteria were isolated from coastal seawater in Tokyo Bay. Analysis of almost-complete 16S rRNA gene sequences showed that the two isolates are members of the genus Paracoccus, sharing highest 16S rRNA gene sequence similarity (96.5 %) with Paracoccus aminophilus NBRC 16710(T). The DNA-DNA reassociation values between P. aminophilus NBRC 16710(T) and these isolates were only 10-20 %, in contrast to the high DNA relatedness between the two isolates (89 %). At least 1 % (w/v) NaCl was required for growth. Cellular fatty acid profiles revealed C(18 : 1)omega7c as the major component and C(10 : 0) 3-OH as the major hydroxy fatty acid. Ubiquinone-10 was detected as the major respiratory quinone. The G+C content of the genomic DNA of both strains was 69 mol%. On the basis of DNA-DNA hybridization data and physiological and chemotaxonomic characteristics, it is proposed that these strains should be placed in a novel species, Paracoccus marinus sp. nov. The type strain is KKL-A5(T) (=NBRC 100637(T) =CIP 108500(T)); KKL-B9 (=NBRC 100640) is a reference strain.

Chitinophaga terrae sp. nov., isolated from soil

A novel strain, designated KP01(T), belonging to the class Sphingobacteria (phylum Bacteroidetes) was isolated from soil in South Korea and was characterized taxonomically using a polyphasic approach. The strain was found to comprise Gram-negative, aerobic, non-motile, non-spore-forming rods. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Chitinophaga but was clearly separated from established Chitinophaga species. The 16S rRNA gene sequence similarities between KP01(T) and type strains of established Chitinophaga species ranged from 90.3 to 95.7 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C(15 : 0) and C(16 : 1) omega 5c; major hydroxy fatty acid, C(17 : 0) iso 3-OH) supported the affiliation of strain KP01(T) with the genus Chitinophaga. Therefore strain KP01(T) represents a novel species, for which the name Chitinophaga terrae sp. nov. is proposed. The type strain is KP01(T) (=KCTC 12836(T) =LMG 24015(T)).

Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea

Two novel strains belonging to the phylum Bacteroidetes [formerly the Cytophaga-Flexibacter-Bacteroides (CFB) group], designated Gsoil 040(T) and Gsoil 052(T), were isolated from the soil of a ginseng field in Pocheon province, South Korea. A polyphasic approach was used to characterize the taxonomic position of the novel strains. Both strains were Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolates belong to the genus Chitinophaga but are clearly separated from the recognized species of this genus; gene sequence similarities between the novel isolates and type strains of recognized species ranged from 91.2 to 96.5 %. One exception was found; strain Gsoil 052(T) and the type strain of Chitinophaga filiformis had a gene sequence similarity of 99.6 % but had a DNA-DNA relatedness value of 38 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C(15 : 0) and C(16 : 1)omega5c; major hydroxy fatty acid, iso-C(17 : 0) 3-OH and major polyamine, homospermidine) supported the affiliation of both strains Gsoil 040(T) and Gsoil 052(T) to the genus Chitinophaga. The results of physiological and biochemical tests enabled the genotypic and phenotypic differentiation of the novel strains from the other recognized species of the genus Chitinophaga. Therefore, it is suggested that the new isolates represent two novel species, for which the names Chitinophaga ginsengisoli [corrected] sp. nov. [type strain Gsoil 040(T) (=KCTC 12654(T)=DSM 18108(T))] and Chitinophaga ginsengisoli sp. nov. [type strain Gsoil 052(T) (=KCTC 12592(T)=DSM 18017(T))] are proposed.

Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest

An aerobic bacterium, designated strain E1HC-02(T), was isolated from the decaying leaf litter of a slash pine forest located in southeast Queensland, Australia. Cells of strain E1HC-02(T) were short irregular rods (0.5-1.0 x 0.2-0.4 microm) which stained Gram-positive and possessed a cell-wall ultrastructure which appeared to be made of protein subunits. The novel strain grew optimally in 1 % trypticase soy broth (TSB) at 25 degrees C and at a pH of 9.1. Strain E1HC-02(T) metabolized a range of carbohydrates, organic acids and amino acids. The G+C content of the DNA was 71+/-1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis of strain E1HC-02(T) showed that it was a member of the family Microbacteriaceae, phylum Actinobacteria. The cell wall contained a type B2beta peptidoglycan, the dominant cellular fatty acid was 18 : 1omega7c and the major hydroxy fatty acid was 2-OH 14 : 0. The major menaquinones were MK-8 (76 %) and MK-7 (24 %) and the glycolipids present were disphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. The chemotaxonomic properties of strain E1HC-02(T) were distinctly different to all of the 17 genera of the family Microbacteriaceae and hence strain E1HC-02(T) is designated as representing a novel species of a new genus, Frondicola australicus gen. nov., sp. nov. The type strain of the type species is E1HC-02(T) (=JCM 13598(T)=DSM 17894(T)).