- Volume 59, Issue 4, 2009

Thirty six Gram-positive, rod-shaped, non-spore-forming, non-motile bacterial strains were isolated from the non-salted pickle solution used in producing sunki products, a traditional Japanese pickle. The novel strains were discriminated and separated into four groups by amplified fragment length polymorphism profiling, and by analysis based on recA gene sequences. The strains were classified into four species groups belonging to the Lactobacillus buchneri species group, which consists of L. buchneri, Lactobacillus diolivorans, Lactobacillus hilgardii, Lactobacillus kefiri, Lactobacillus parabuchneri and Lactobacillus parakefiri. The phenotypic and genotypic features of the four groups demonstrated that they represented four novel species, for which the names Lactobacillus kisonensis sp. nov. (type strain YIT 11168T=NRIC 0741T=JCM 15041T=DSM 19906T), Lactobacillus otakiensis sp. nov. (type strain YIT 11163T=NRIC 0742T=JCM 15040T=DSM 19908T), Lactobacillus rapi sp. nov. (type strain YIT 11204T=NRIC 0743T=JCM 15042T=DSM 19907T) and Lactobacillus sunkii sp. nov. (type strain YIT 11161T=NRIC 0744T=JCM 15039T=DSM 19904T) are proposed.

Gram-positive, catalase-negative, chain-forming, coccus-shaped organisms were isolated both from intraperitoneally grown vesicles of the fox tapeworm Echinococcus multilocularis and the oropharynges of laboratory-kept Mongolian jirds (Meriones unguiculatus). The strains displayed no haemolytic activity on Columbia sheep blood agar, pyrrolidonyl arylamidase activity was negative and the organisms reacted weakly with Lancefield group D antiserum. On the basis of phenotypic characteristics, the strains were tentatively identified as members of the genus Streptococcus. Comparative 16S rRNA gene sequencing studies confirmed their assignment to the genus Streptococcus and revealed that Streptococcus hyointestinalis DSM 20770T was their closest phylogenetic neighbour (96.5 % sequence similarity). The levels of 16S rRNA gene sequence similarity between the isolates and representatives of species of the genus Streptococcus were only 95.7–96.2 %. On the basis of the phenotypic and molecular data presented, the isolates from Mongolian jirds represent a novel species of the genus Streptococcus, for which the name Streptococcus merionis sp. nov. is proposed. The type strain is WUE3771T (=DSM 19192T=CCUG 54871T).

A novel lactic acid bacterium, strain MIC1-18T, was isolated from crude oil collected at an oil–water well in Akita, Japan. Cells of strain MIC1-18T were found to be facultatively anaerobic, mesophilic, neutrophilic, Gram-negative, non-sporulating, motile by means of peritrichous flagella and oval rods, 1.8–2.5 μm long. Optimum growth was observed at 30 °C, pH 7.0 and 3 % (w/v) NaCl. Strain MIC1-18T produced acid from l-arabinose, ribose, glucose, fructose, mannose, N-acetylglucosamine, amygdalin, arbutin, salicin, cellobiose, maltose, sucrose, trehalose, gentiobiose and 5-ketogluconate. l-Lactic acid was the major end product from glucose. The major cellular fatty acid was C16 : 1 ω7c. The cell-wall murein type was A4α containing Lys–Glu. The G+C content of the genomic DNA was 37.8 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that strain MIC1-18T was accommodated as a member of the lactic acid bacteria of the low-G+C content Gram-positive bacteria; the closest neighbour of this organism was Atopococcus tabaci CCUG 48253T, with only 90.0 % sequence similarity. On the basis of the phenotypic features and phylogenetic position, a novel genus and species, Lacticigenium naphtae gen. nov., sp. nov., are proposed for strain MIC1-18T (=NBRC 101988T=DSM 19658T).

A novel Gram-positive-staining, catalase- and oxidase-positive, non-motile, non-spore-forming coccus, designated YIM-Y21T, was isolated from a salt mine in Yunnan, south-west China. The strain was moderately halophilic, facultatively alkaliphilic and obligately aerobic. Colonies were white. Growth occurred with 1.0–30.0 % NaCl (optimum, 10.0 % NaCl), at pH 6.0–10.0 (optimum, pH 8.5) and at 5–40 °C (optimum, 25 °C). The major amino acid constituents of the cell wall were glycine and lysine. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. MK-6 was the predominant respiratory quinone, with MK-7 present in minor amounts. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 46.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM-Y21T was most closely related to the type strains of the nine recognized species of the genus Salinicoccus. The sequence similarities between the isolate and the type strains of members of this genus were in the range of 90.6–93.8 %, which indicated that strain YIM-Y21T is a representative of a novel species within the genus Salinicoccus. Together with the phenotypic characteristics and chemotaxonomic differences, these results support the proposal of a novel species of the genus Salinicoccus, Salinicoccus albus sp. nov., with YIM-Y21T (=CCTCC AA 207024T =DSM 19776T =KCTC 13192T) as the type strain.

A single Leptospira strain (designated Bejo-Iso9T) was isolated from a soil sample taken in Johor, Malaysia. The isolate showed motility and morphology typical of the genus Leptospira under dark-field microscopy. Cells were found to be 10–13 μm in length and 0.2 μm in diameter, with a wavelength of 0.5 μm and an amplitude of approximately 0.2 μm. Phenotypically, strain Bejo-Iso9T grew in Ellinghausen–McCullough–Johnson–Harris medium at 13, 30 and 37 °C, and also in the presence of 8-azaguanine. Serologically, strain Bejo-Iso9T produced titres towards several members of the Tarassovi serogroup, but was found to be serologically unique by cross-agglutinin absorption test and thus represented a novel serovar. The proposed name for this serovar is Malaysia. Phylogenetic analysis of 16S rRNA gene sequences placed this novel strain within the radiation of the genus Leptospira, with sequence similarities within the range 90.4–99.5% with respect to recognized Leptospira species. DNA–DNA hybridization against the three most closely related Leptospira species was used to confirm the results of the 16S rRNA gene sequence analysis. The G+C content of the genome of strain Bejo-Iso9T was 36.2 mol%. On the basis of phenotypic, serological and phylogenetic data, strain Bejo-Iso9T represents a novel species of the genus Leptospira, for which the name Leptospira kmetyi sp. nov. is proposed. The type strain is Bejo-Iso9T (=WHO LT1101T=KIT Bejo-Iso9T).

A Gram-positive-staining, spherical-shaped and faintly pink-pigmented bacterial strain, X-82T, was isolated from soil samples collected from a desert in Xinjiang, China. The organism was found to be resistant to UV radiation but sensitive to gamma radiation and desiccation. The optimum growth pH, NaCl concentration and temperature were pH 7.0, 0–1 % NaCl and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X-82T is member of a novel species belonging to the genus Deinococcus, with Deinococcus hopiensis KR-140T as its closest relative (93.5 % similarity). The DNA G+C content (60 mol%), quinone type (MK-8), major cellular fatty acids (16 : 1ω7c, 16 : 0 and 17 : 1 iso ω9c), the presence of peptidoglycan with l-ornithine and the dominant polar lipid (phosphoglycolipids and glycolipids) support the affiliation of strain X-82T with the genus Deinococcus. A novel species is proposed, for which the name Deinococcus xinjiangensis sp. nov. is proposed, with the type strain X-82T (=CCTCC AB 207226T =NRRL B-51287T).

During studies of moderately halophilic strains of Ectothiorhodospira from steppe soda lakes, we found a novel group of bacteria related to Ectothiorhodospira haloalkaliphila with salt optima at 50–80 g NaCl l−1. Phylogenetic analysis using 16S rRNA gene sequences of strains from soda lakes in Mongolia, Egypt and Siberia revealed separation of the group of new isolates from other Ectothiorhodospira species, including the closely related Ect. haloalkaliphila. DNA–DNA hybridization studies demonstrated that the new isolates form a homogeneous group at the species level, but at the same time are distinct from related species such as Ect. haloalkaliphila, Ect. vacuolata, Ect. shaposhnikovii and Ect. marina. The new isolates are considered to be strains of a novel species, for which the name Ectothiorhodospira variabilis sp. nov. is proposed, with the type strain WN22T (=VKM B-2479T =DSM 21381T). Photosynthetic pigments of the novel species are bacteriochlorophyll a and carotenoids of the spirilloxanthin series with spirilloxanthin and derivatives thereof, together with small amounts of lycopene and rhodopin. Gas vesicles are formed by most of the strains, particularly in media containing yeast extract (0.5 g l−1) and acetate (0.5–2.0 g l−1). Sequence analysis of nifH (nitrogenase) and cbbL (RuBisCO) confirmed the assignment of the strains to the genus Ectothiorhodospira and in particular the close relationship to Ect. haloalkaliphila. The novel species Ect. variabilis is found in soda lakes separated by great geographical distances and is an alkaliphilic and halophilic bacterium that tolerates salt concentrations up to 150–200 g NaCl l−1.

Four unusual Gram-negative, catalase-positive, oxidase-positive, coccus-shaped bacteria isolated from one sheep and three pigs were characterized using phenotypic and molecular genetic methods. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Moraxella, although the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing studies demonstrated that the isolates represent a novel subline within the genus Moraxella. The most closely related species in phylogenetic terms was Moraxella cuniculi, with 16S rRNA gene sequence similarity of 97.9 % to the type strain CCUG 2154T, although the DNA–DNA relatedness value was only 29 %. The novel isolates were readily distinguished from all recognized Moraxella species by means of physiological and biochemical tests. On the basis of molecular genetic and phenotypic evidence, therefore, the four isolates represent a novel species of the genus Moraxella, for which the name Moraxella pluranimalium sp. nov. is proposed. The type strain is 248-01T (=CECT 7295T =CCUG 54913T).

The taxonomic position of a novel bacterial strain, YC6269T, isolated from the rhizosphere of rice (Oryza sativa L.) managed under no-tillage practice in Jinju, South Korea, was studied using polyphasic approach. Cells of the strain were Gram-negative, rod-shaped and facultatively anaerobic. The novel strain grew at a temperature of 15–42 °C (optimum at 28 °C). Growth of the strain occurred between pH 5.5 and 11.0, with an optimum at pH 7.0–8.0. The G+C content of the total DNA was 67.4 mol%. The 16S rRNA gene sequence of the strain was most closely related to species of the genus Lysobacter, Lysobacter yangpyeongensis DSM 17635T (98.6 %), Lysobacter niabensis GH34-4T (97.2 %), Lysobacter enzymogenes DSM 2043T (96.9 %), Lysobacter daejeonensis DSM 17634T (96.3 %) and Lysobacter niastensis GH41-7T (96.2 %). The novel strain showed <96.0 % similarity with other species of the genus Lysobacter. Chemotaxonomic data (major quinone, Q-8; major polar lipids, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine, and major fatty acids, C15 : 0 iso, C16 : 0 iso, C17 : 0 iso and C17 : 1 iso ω9c) supported the affiliation of strain YC6269T to the genus Lysobacter. Phylogenetic analysis based on the 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain YC6269T from recognized species of the genus Lysobacter. Strain YC6269T, therefore, represents a novel member of the genus Lysobacter, for which the name Lysobacter oryzae sp. nov. is proposed. The type strain is YC6269T (=KCTC 22249T=DSM 21044T).

A short-rod-shaped, Gram-negative, motile bacterial strain, designated CS-6T, was isolated from a water sample collected from a spring located inside Nature Valley, Hsinchu County, Taiwan, and was characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Aquabacterium in the class Betaproteobacteria. The closest neighbours were Aquabacterium parvum B6T (96.7 % sequence similarity), Aquabacterium commune B8T (96.6 %) and Aquabacterium citratiphilum B4T (95.9 %). The predominant fatty acids were 18 : 1ω7c (30.5 %), 16 : 0 (27.9 %) and summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH) (22.7 %). The DNA–DNA relatedness of the strain with respect to recognized species of the genus Aquabacterium was less than 70 %. The isolate was also distinguishable from members of the genus Aquabacterium on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data, therefore, that strain CS-6T represents a novel species of the genus Aquabacterium, for which the name Aquabacterium fontiphilum sp. nov. is proposed. The type strain is CS-6T (=LMG 24215T=BCRC 17729T).

Two marine heterotrophic bacteria, A5K-61T and A5K-106T, were isolated from marine animals. 16S rRNA gene sequence analysis data showed that the isolates were affiliated with the genus Thalassomonas; highest 16S rRNA gene sequence similarity values were found with Thalassomonas viridans DSM 13754T (97.5 and 98.1 %, respectively). DNA–DNA hybridization values of strains A5K-61T and A5K-106T with T. viridans DSM 13754T (22.2–49.1 %) were clearly below 70 %, the generally accepted limit for species delineation. The isolates produced a brown diffusible pigment. The major respiratory quinone was Q-8 and the predominant cellular fatty acids were C16 : 1 ω7c and C16 : 0. Based on DNA–DNA hybridization data, some biochemical characteristics and 16S rRNA gene sequence comparison, the isolates represent two novel species of the genus Thalassomonas, for which the names Thalassomonas actiniarum sp. nov. (type strain A5K-106T =MBIC08328T =NCIMB 14418T =NBRC 104231T) and Thalassomonas haliotis sp. nov. (type strain A5K-61T =MBIC08329T =NCIMB 14417T =NBRC 104232T) are proposed.

A novel gammaproteobacterium, designated Gsoil 3054T, was isolated from soil of a ginseng field in Pocheon province, South Korea, and was characterized using a polyphasic approach to determine its taxonomic position. The strain was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Rhodanobacter; it was most closely related to Rhodanobacter fulvus Jip2T and Rhodanobacter thiooxydans LCS2T (97.9 and 97.2 % 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data, i.e. Q-8 as the predominant ubiquinone and iso-C15 : 0, 10-methyl C16 : 0 and iso-C17 : 0 as major fatty acids, also supported classification of strain Gsoil 3054T in the genus Rhodanobacter. However, DNA–DNA hybridization values of Gsoil 3054T with R. fulvus Jip2T and R. thiooxydans LCS2T were 45 and 31 %, respectively. Moreover, physiological and biochemical tests enabled strain Gsoil 3054T to be differentiated phenotypically from other established species of Rhodanobacter. Therefore, the isolate represents a novel species, for which the name Rhodanobacter ginsenosidimutans sp. nov. is proposed; the type strain is Gsoil 3054T (=KACC 12822T =DSM 21013T =KCTC 22231T =LMG 24457T).

Eleven strains of halophilic, facultative anaerobes isolated from healthy and diseased Dentex dentex and Sparus aurata (bony fishes) cultured in Spanish Mediterranean fisheries have been studied by a polyphasic approach that included a wide phenotypic characterization, DNA–DNA hybridization and phylogenetic analysis using 16S rRNA, recA and rpoD gene sequences. All strains were phylogenetically related to Enterovibrio species and Vibrio calviensis. On the basis of sequence analysis and DNA–DNA hybridization data, eight of the strains were identified as Enterovibrio coralii. The remaining three strains formed a tight, independent clade in all sequence analyses and showed less than 70 % DNA–DNA hybridization with strains of the closest Enterovibrio species, from which they could be differentiated by several phenotypic traits. We conclude that these three strains represent a novel species in the genus Enterovibrio and we thus propose the name Enterovibrio nigricans sp. nov., with strain DAl 1-1-5T (=CECT 7320T =CAIM 661T) as the type strain. In addition, we propose the reclassification of Vibrio calviensis Denner et al. 2002 as Enterovibrio calviensis comb. nov. (type strain RE35/F12T =CIP 107077T =DSM 14347T =CECT 7414T) and we provide an emended description of the genus Enterovibrio.

Strain NX02T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil, and its taxonomic position was investigated using a polyphasic approach. Chemotaxonomic analysis revealed that strain NX02T possessed Q-10 as the predominant ubiquinone, sym-homospermidine as the major polyamine and C18 : 1 ω7c, C16 : 0 and C14 : 0 2-OH as the major fatty acids. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified glycolipid. The DNA G+C content was 66.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NX02T belongs to the α-4 subgroup of the Proteobacteria, exhibiting the highest sequence similarity with respect to Sphingomonas azotifigens NBRC 15497T (95.9 %), Sphingomonas pituitosa DSM 13101T (95.8 %) and Sphingomonas dokdonensis KCTC 12541T (95.8 %). On the basis of these results, strain NX02T represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas sanxanigenens sp. nov. is proposed. The type strain is NX02T (=DSM 19645T =CGMCC 1.6417T).

This investigation was based on 23 isolates from several European countries collected over the past 30 years, and included characterization of all isolates. Published data on amplified fragment length polymorphism typing of isolates representing all biovars as well as protein profiles were used to select strains that were then further characterized by polyamine profiling and sequencing of 16S rRNA, infB, rpoB and recN genes. Comparison of 16S rRNA gene sequences revealed a monophyletic group within the avian 16S rRNA group of the Pasteurellaceae, which currently includes the genera Avibacterium, Gallibacterium and Volucribacter. Five monophyletic subgroups related to Gallibacterium anatis were recognized by 16S rRNA, rpoB, infB and recN gene sequence comparisons. Whole-genome similarity between strains of the five subgroups and the type strain of G. anatis calculated from recN sequences allowed us to classify them within the genus Gallibacterium. In addition, phenotypic data including biochemical traits, protein profiling and polyamine patterns clearly indicated that these taxa are related. Major phenotypic diversity was observed for 16S rRNA gene sequence groups. Furthermore, comparison of whole-genome similarities, phenotypic data and published data on amplified fragment length polymorphism and protein profiling revealed that each of the five groups present unique properties that allow the proposal of three novel species of Gallibacterium, for which we propose the names Gallibacterium melopsittaci sp. nov. (type strain F450T =CCUG 36331T =CCM 7538T), Gallibacterium trehalosifermentans sp. nov. (type strain 52/S3/90T =CCUG 55631T =CCM 7539T) and Gallibacterium salpingitidis sp. nov. (type strain F150T =CCUG 15564T =CCUG 36325T =NCTC 11414T), a novel genomospecies 3 of Gallibacterium and an unnamed taxon (group V). An emended description of the genus Gallibacterium is also presented.

A rod-shaped, phototrophic, purple sulfur bacterium was isolated in pure culture from brackish water near Bheemli, Visakhapatnam, India, in a medium that contained 2 % NaCl (w/v). Strain JA144T was Gram-negative and motile. It did not require salt, but tolerated up to 3 % NaCl (w/v). Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids that probably belonged to the rhodopinal series were present as photosynthetic pigments. Strain JA144T was able to grow photolithoautotrophically, photolithoheterotrophically and photoorganoheterotrophically. It did not require vitamins. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA144T clustered with species of the genus Allochromatium belonging to the class Gammaproteobacteria. Highest sequence similarities of strain JA144T were found with the type strains of Allochromatium vinosum (96.7 % similarity), Allochromatium renukae (96.3 %), Allochromatium minutissimum (95.6 %) and Allochromatium warmingii (89.2 %). Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA144T is sufficiently different from other Allochromatium species to represent a novel species, Allochromatium phaeobacterium sp. nov.; the type strain is JA144T (=JCM 14796T=DSM 19781T).

A polyphasic taxonomic study was performed on a pink-coloured unknown bacterium isolated from discarded road tar. Comparative analysis of the 16S rRNA gene sequence demonstrated that the isolate belongs phylogenetically to the genus Azospirillum with Azospirillum lipoferum, A. melinis and A. rugosum as its closest phylogenetic relatives (96.7, 96.6 and 96.6 % similarity to the respective type strains). The generic assignment was confirmed on the basis of chemotaxonomic data, which revealed a fatty acid profile characteristic for the genus Azospirillum, consisting of straight-chain saturated and unsaturated fatty acids, with C18 : 1 ω7c as the major unsaturated non-hydroxylated fatty acid, and C16 : 0 3-OH as the major hydroxylated fatty acid, and a ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone. On the basis of both the phenotypic and molecular genetic evidence, it is proposed that the unknown isolate should be classified within a novel species of the genus Azospirillum, for which the name Azospirillum picis sp. nov. is proposed. The type strain is IMMIB TAR-3T (=CCUG 55431T =DSM 19922T).

A strictly anaerobic Fe(III)-reducing bacterium, designated strain Red1T, was isolated from the production water of the Redwash oilfield, USA. The cells were motile rods (1–5×0.5–0.6 μm) that stained Gram-negative and possessed polar flagella. Strain Red1T obtained energy from the reduction of Fe(III), Mn(IV), nitrate, elemental sulfur and trimethylamine N-oxide in the presence of a wide range of electron donors, including a variety of organic acids, alcohols, biological extracts and hydrogen. Strain Red1T was incapable of fermentative growth. The novel isolate grew optimally at 40 °C (temperature range for growth, 30–50 °C) and at pH 7 (pH range, 6–9) with 2 % (w/v) NaCl (NaCl range, 0.1–10 %, w/v). The DNA G+C content was 52.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Red1T was a member of the order Desulfuromonadales within the class Deltaproteobacteria and most closely related to Geoalkalibacter ferrihydriticus Z-0531T (95.8 %), Desulfuromonas palmitatis SDBY1T (92.5 %) and ‘Desulfuromonas michiganensis’ BB1 (92.4 %). On the basis of phenotypic and phylogenetic differences, the novel strain is proposed to represent a novel species, Geoalkalibacter subterraneus sp. nov. (type strain Red1T=JCM 15104T=KCTC 5626T).

A bacterial isolate, strain XM415T, obtained from soil of Tibet in China was characterized using a polyphasic taxonomic approach. Strain XM415T was aerobic, Gram-negative, gliding, rod-shaped, oxidase-negative and catalase-positive. Strain XM415T showed the highest 16S rRNA gene sequence similarity with Lysobacter niastensis GH41-7T (96.0 %). Ubiquinone Q-8 and branched fatty acids, such as iso-C16 : 0 (24.0 %), iso-C15 : 0 (22.6 %), iso-C17 : 1 ω9c (6.7 %), iso-C14 : 0 (6.1 %) and iso-C11 : 0 3-OH (5.2 %), were predominant in strain XM415T as well as in all type strains of recognized Lysobacter species. The DNA G+C content of XM415T was 63.5 mol%. The genotypic and phenotypic data show that strain XM415T represents a novel species of the genus Lysobacter, for which the name Lysobacter ximonensis sp. nov. is proposed. The type strain is XM415T (=CCTCC AB 207091T =NRRL B-51263T).