- Volume 55, Issue 5, 2005

Four strains (3001T, 2, 12 and 13), which were isolated as chitosanase-producing bacteria from soil from Matsue city (Japan), were studied phenotypically, genotypically and phylogenetically. Based on sequence analysis of 16S rRNA genes, DNA G+C content (67·4–69·2 mol%), quinone type (UQ-8), major fatty acid composition (3-OH 10 : 0, 3-OH 14 : 0) and other phylogenetic studies, strains 3001T, 12 and 13 were found to occupy a separate position in the ‘Betaproteobacteria’. Roseateles depolymerans, Rubrivivax gelatinosus and Ideonella dechloratans were their closest neighbours (93–95 % 16S rRNA gene sequence similarity). The 16S rRNA gene sequence and other characteristics suggested that strain 2 belonged to the genus Flavobacterium. DNA–DNA hybridization experiments supported the conclusion that strains 3001T, 12 and 13 were of the same species (72–78 % DNA hybridization) and only distantly related to I. dechloratans and R. gelatinosus. It is proposed that strains 3001T, 12 and 13 represent a novel genus and species for which the name Mitsuaria chitosanitabida gen. nov., sp. nov. is proposed. The type strain of Mitsuaria chitosanitabida is 3001T (=IAM 14711T=ATCC BAA-476T).

The type strains of Jannaschia cystaugens (LMG 22015T) and Thalassobacter stenotrophicus (CECT 5294T) were analysed by means of genomic DNA–DNA hybridization, comparison of 16S rRNA gene sequences and phenotypic properties determined under the same methodological conditions. J. cystaugens LMG 22015T showed DNA–DNA relatedness levels of 72 % when hybridized with the genomic DNA of T. stenotrophicus CECT 5294T. Sequence comparisons revealed that the 16S rRNA genes of the two strains had a similarity of 99·8 %. The cellular fatty acid and polar lipid compositions of the two strains and their DNA mol% G+C contents were almost identical. Bacteriochlorophyll a (Bchl a) and polyhydroxybutyrate were produced by both strains under the same culture conditions. Their closest phylogenetic neighbours were Jannaschia helgolandensis and Jannaschia rubra; however, the low sequence similarity values (95·7–95·9 %) and several important differences in phenotypic traits (ionic requirements, Bchl a production and polar lipids) support the distinction between the genera Thalassobacter and Jannaschia. Thus, we propose the unification of J. cystaugens (LMG 22015T) and T. stenotrophicus (CECT 5294T) as Thalassobacter stenotrophicus (type strain, CECT 5294T=DSM 16310T). An emended description of the genus Thalassobacter is also presented.

Three strains of Sphingomonas paucimobilis, B90A, UT26 and Sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains do not fall in a clade that includes the type strain, Sphingomonas paucimobilis ATCC 29837T, but form a coherent cluster with [Sphingomonas] chungbukensis IMSNU 11152T followed by Sphingobium chlorophenolicum ATCC 33790T. The three strains showed low DNA–DNA relatedness values with Sphingomonas paucimobilis ATCC 29837T (8–25 %), [Sphingomonas] chungbukensis IMSNU 11152T (10–17 %), Sphingobium chlorophenolicum ATCC 33790T (23–54 %) and Sphingomonas xenophaga DSM 6383T (10–28 %), indicating that they do not belong to any of these species. Although the three strains were found to be closely related to each other based on 16S rRNA gene sequence similarity (99·1–99·4 %), DNA–DNA relatedness (19–59 %) and pulsed-field gel electrophoresis (PFGE) patterns indicated that they possibly represent three novel species of the genus Sphingobium. The three strains could also be readily distinguished by biochemical tests. The three strains showed similar polar lipid profiles and contained sphingoglycolipids. The strains differed from each other in fatty acid composition but contained the predominant fatty acids characteristic of other Sphingobium species. A phylogenetic study based on 16S rRNA gene sequences showed that [Sphingomonas] chungbukensis IMSNU 11152T formed a cluster with members of the genus Sphingobium. Based on these results, it is proposed that strains B90A, UT26 and Sp+, previously known as Sphingomonas paucimobilis, are the type strains of Sphingobium indicum sp. nov. (=MTCC 6364T=CCM 7286T), Sphingobium japonicum sp. nov. (=MTCC 6362T=CCM 7287T) and Sphingobium francense sp. nov. (=MTCC 6363T=CCM 7288T), respectively. It is also proposed that [Sphingomonas] chungbukensis be transferred to Sphingobium chungbukense comb. nov.

Bacterial strain PETP02T was isolated from nodules of Trifolium pratense growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene sequence showed that this strain represents a member of the genus Phyllobacterium. However, divergence found with the 16S rRNA gene sequence of the single recognized species of this genus, Phyllobacterium myrsinacearum, indicated that strain PETP02T belongs to a different species. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain represents a novel species of the genus Phyllobacterium, for which the name Phyllobacterium trifolii sp. nov. is proposed. The type strain is PETP02T (=LMG 22712T=CECT 7015T). This strain was strictly aerobic and used several carbohydrates as carbon source. It was not able to reduce nitrate. Aesculin hydrolysis was negative. It did not produce urease, arginine dihydrolase, gelatinase or β-galactosidase. The DNA G+C content was 56·4 mol%. The nodD gene of this strain showed a sequence closely related to those of strains able to nodulate Lupinus. Infectivity tests showed that this strain is able to produce nodules in both Trifolium repens and Lupinus albus.

A Gram-negative, rod-shaped, non-spore-forming bacteria was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, this strain, designated LMG 22951T, was shown to belong to the ‘Alphaproteobacteria’ and to be related to Devosia neptuniae (97·4 %) and Devosia riboflavina (97·0 %). The results of DNA–DNA hybridization, analysis of fatty acid composition, SDS-PAGE, physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22951T from the two recognized Devosia species. LMG 22951T therefore represents a novel species within this genus, for which the name Devosia limi is proposed. The type strain is LMG 22951T (=DSM 17137T).

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, Slu-01T, was isolated from activated sludge from a wastewater treatment plant in Daejeon, South Korea. After 3 days on R2A medium, strain Slu-01T developed colourless colonies (0·7–1·2 mm). The non-motile rods (0·7–1·0×1·0–2·0 μm) were slightly curved and occurred singly and in pairs. No filamentous cells were found. On the basis of 16S rRNA gene sequence similarity, strain Slu-01T was shown to belong to the family Caulobacteraceae and was most closely related to Phenylobacterium immobile (96·6 %) and Phenylobacterium lituiforme (96·5 %). The genomic DNA G+C content of strain Slu-01T was 68·1 mol%, within the range of 67·3–68·4 mol% for the genus Phenylobacterium. Chemotaxonomic data (major ubiquinone, Q-10; major fatty acids C18 : 1 ω7c, C16 : 0, C15 : 0 and C17 : 0) and 16S rRNA gene sequence analysis supported the affiliation of strain Slu-01T to the genus Phenylobacterium. However, DNA–DNA hybridization data and phenotypic properties showed that strain Slu-01T could be distinguished from the two other Phenylobacterium species with validly published names. Thus, it is suggested that strain Slu-01T represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium koreense is proposed. The type strain is Slu-01T (=KCTC 12206T=IAM 15119T).

Halomonas almeriensis sp. nov. is a Gram-negative non-motile rod that was isolated from a saltern in the Cabo de Gata-Níjar wildlife reserve in Almería, south-east Spain. It is moderately halophilic, capable of growth at concentrations of 5–25 % w/v sea-salt mixture, the optimum being 7·5 % w/v. It is chemo-organotrophic and strictly aerobic, produces catalase but not oxidase, does not produce acid from any sugar and does not synthesize hydrolytic enzymes. The most notable difference between this micro-organism and other Halomonas species is that it is very fastidious in its use of a carbon source. It forms mucoid colonies due to the production of an exopolysaccharide. Its G+C content is 63·5 mol%. A comparison of 16S rRNA gene sequences confirmed its relationship to Halomonas species. The most closely related species is Halomonas halmophila with 95·8 % similarity between their 16S rRNA gene sequences. DNA–DNA hybridization with H. halmophila is 10·1 %. Its major fatty acids are 18 : 1ω7c, 16 : 0, 16 : 1ω7c/15 : 0 iso 2-OH, 12 : 0 3-OH, 12 : 0, 11-methyl 18 : 1ω7c and 10 : 0. The proposed name is Halomonas almeriensis sp. nov., with strain M8T (=CECT 7050T=LMG 22904T) as the type strain.

A moderately halophilic, Gram-negative bacterium, strain BH539T, which was isolated from a solar saltern at Taean in Korea, was considered to be a member of the genus Halomonas. Strain BH539T grew at salinities of 1–25 % (w/v) and at temperatures of 10–45 °C. Cells were short rods that were motile by means of several flagella. Their major fatty acids were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The genomic DNA G+C content was about 65 mol% and the predominant ubiquinone was Q-9. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate formed a branch of the species Cobetia marina. However, 23S and 16S rRNA gene sequence similarities revealed that strain BH539T was related more closely to the type strains of the genus Halomonas. Phylogenetic analyses based on 23S rRNA gene sequences also indicated that the strain formed a phyletic line within the genus Halomonas. Therefore, it was concluded that strain BH539T should be classified within the genus Halomonas, rather than Cobetia. On the basis of physiological and molecular properties, strain BH539T represents a novel species of the genus Halomonas, for which the name Halomonas taeanensis sp. nov. is proposed. The type strain is BH539T (=KCTC 12284T=DSM 16463T).

A marine bacterium, designated strain GW14-5T, capable of degrading high-molecular-mass polycyclic aromatic hydrocarbons was isolated from the sediments of Gwangyang Bay, Republic of Korea, after enrichment culture for 2 years with a mixture of benzo[a]pyrene and pyrene. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate forms a phyletic lineage that is distinct from the seven known orders within the ‘Alphaproteobacteria’. 16S rRNA gene sequence similarity of strain GW14-5T to all recognized bacterial species was not greater than 92 %. The dominant fatty acids of the isolate were i-17 : 1 (46·2 %), i-15 : 0 (15·1 %) and i-17 : 0 (12·6 %). The major respiratory quinone was MK-5, and the DNA G+C content was 39·3 mol%. Cells of strain GW14-5T were Gram-negative, motile, catalase-positive, oxidase-positive and weakly halophilic. Glucose, N-acetylglucosamine and maltose were utilized as sole carbon sources. The strain was positive for β-glucosidase activity. Optimal growth of strain GW14-5T was at pH 7·0 and 37–40 °C and required the presence of 2 % (w/v) NaCl. On the basis of this evidence, strain GW14-5T represents a novel genus and species in the ‘Alphaproteobacteria’ for which the name Kordiimonas gwangyangensis gen. nov., sp. nov. is proposed. The novel order Kordiimonadales is proposed for the distinct phyletic line represented by the genus Kordiimonas. The type strain is GW14-5T (=KCCM 42021T=JCM 12864T).

Recent studies on the occurrence of (per)chlorate-reducing bacteria have resulted in the characterization of strains capable of dissimilatory (per)chlorate reduction. Phylogenetic analysis has shown that these bacteria are members of the Proteobacteria. Strains have been isolated from polluted and pristine sites, but only strains from polluted sites have been characterized in detail and deposited in culture collections. Herein we describe the isolation and characterization of perchlorate-reducing bacterium strain MA-1T and chlorate-reducing bacterium strain ASK-1, respectively isolated from a pristine and a chlorate-polluted site. Both isolates are members of the Proteobacteria. The 16S rRNA gene sequence similarity of MA-1T to Dechloromonas agitata DSM 13637T is 97·6 %, but the relatedness in DNA–DNA reassociation is only 37 %. Therefore, we propose to classify strain MA-1T (=DSM 15637T=ATCC BAA-776T) as the type strain of a novel species, Dechloromonas hortensis sp. nov. Strain ASK-1 and a previously described strain GR-1 show 100 and 99 % 16S rRNA gene sequence similarity to Pseudomonas chloritidismutans DSM 13592T and Dechlorosoma suillum DSM 13638T, respectively. DNA–DNA hybridization studies indicated that strains ASK-1 and GR-1 are related at the species level to P. chloritidismutans DSM 13592T (79 %) and Dechlorosoma suillum DSM 13638T (85 %), respectively. As suggested previously, Dechlorosoma suillum appears to be a later heterotypic synonym of Azospira oryzae. Although strain ASK-1 is identified as P. chloritidismutans, its morphology and growth requirements are different from those of the type strain.

A novel Gram-negative coccus/coccobacillus, strain Ben 114T, growing in tetrads, clusters or aggregates, was isolated from activated sludge by micromanipulation. 16S rRNA gene sequence analysis revealed that it belonged to the ‘Alphaproteobacteria’, with no close relatives among cultured bacterial isolates. On the basis of phylogenetic data, this organism is considered to belong to a new genus, Defluvicoccus, represented by the species Defluvicoccus vanus sp. nov., a name chosen because of the distinctive staining properties of this organism; only the cell wall stained strongly with a wide range of stains, giving the cell a hollow and empty appearance. No intracellular polyphosphate granules could be detected after staining, but poly-β-hydroxyalkanoate inclusions were detected using Nile blue A staining. Because of its taxonomic distance from its closest relatives among the ‘Alphaproteobacteria’, namely members of the genera Azospirillum, Phaeospirillum, Rhodospirillum, Rhodocista, Magnetospirillum and Rhodospira, D. vanus is considered to represent a new phylogenetic lineage within subgroup 1 of the ‘Alphaproteobacteria’, the D. vanus subgroup. The type strain is Ben 114T (=NCIMB 13612T=CIP 107350T).

Strain HHS 11T was isolated from a water sample collected from the snout of Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Dyadobacter. HHS 11T possessed 96 and 95 % 16S rRNA gene sequence similarity with respect to Dyadobacter crusticola and Dyadobacter fermentans, respectively. Furthermore, strain HHS 11T differs from D. crusticola and D. fermentans in a number of phenotypic characteristics. These data suggest that strain HHS 11T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter hamtensis sp. nov. is proposed. The type strain is HHS 11T (=JCM 12919T=MTCC 7023T).

A Gram-negative, rod-shaped, urea-dissolving and non-spore-forming bacterium, designated strain NiVa 51T, was isolated from water of the River Torsa in Hasimara, Jalpaiguri district, West Bengal, India. On the basis of 16S rRNA gene sequence similarity, strain NiVa 51T was shown to belong to the γ-Proteobacteria and to be related to Serratia marcescens subsp. sakuensis (98·35 %) and S. marcescens subsp. marcescens (98·30 %); however, strain NiVa 51T exhibited only 43·7 % similarity to S. marcescens by DNA–DNA hybridization. The G+C content of the genomic DNA of the isolate was 60 mol%. Both biochemical characteristics and fatty acid analysis data supported the affiliation of strain NiVa 51T to the genus Serratia. Furthermore, strain NiVa 51T was found to utilize urea as nitrogen source. The results of DNA–DNA hybridization as well as physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NiVa 51T from recognized Serratia species. Strain NiVa 51T therefore represents a novel species, for which the name Serratia ureilytica sp. nov. is proposed, with type strain NiVa 51T (=LMG 22860T=CCUG 50595T).

One whitish and four pinkish strains of Gram-negative, non-motile, aerobic bacteria were isolated from sea-water and sediment samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean). Analysis of 16S rRNA gene sequences revealed that these strains belonged to the ‘Alphaproteobacteria’, having highest sequence similarity of about 94–97 % with species of the genus Loktanella. None of the strains degraded gelatin, casein, chitin, agar, DNA or starch and they had limited ability to utilize carbon sources. The four pinkish strains, Fg36T, Fg1, Fg116 and Fg117, degraded Tween 80. Sea-water strain R10SW5T grew at 3–6 % NaCl and a temperature range of 8–35 °C, whilst strains Fg36T, Fg1, Fg116 and Fg117 grew at NaCl concentrations of 1–12 % and a temperature range of 4–35 °C. Phosphatidylglycerol (58/79 %), diphosphatidylglycerol (11/6 %) and phosphatidylcholine (28/22 %) were the major phospholipids. The predominant fatty acids were 16 : 0 (12·2/8·6 %) and 18 : 1ω7 (76·6/68·4 %). The DNA G+C content of strain R10SW5T was 59·1 mol% and those of the four pinkish strains ranged from 60·5 to 61·8 mol%. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, Loktanella agnita sp. nov. and Loktanella rosea sp. nov., are proposed. The type strains are R10SW5T (=KMM 3788T=CIP 107883T) and Fg36T (=KMM 6003T=CIP 107851T=LMG 22534T), respectively.

A Gram-positive, coryneform bacterium, strain 1-19T, was isolated from coastal sediment from the Eastern China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the organism formed a robust clade with the type species of the genus Sanguibacter and displayed less than 97 % gene sequence similarity. Phenotypic characteristics supported the assignment of this organism to the genus Sanguibacter. A range of biochemical features distinguished it from all other Sanguibacter species with validly published names. On the basis of a polyphasic taxonomical analysis, it is proposed that this bacterium is a novel species of Sanguibacter, for which the name Sanguibacter marinus sp. nov. is proposed. The type strain is 1-19T (=CGMCC 1.3457T=JCM 12547T).

A taxonomic study was carried out to clarify the taxonomy of representatives of a group of marine actinomycetes previously designated MAR 1 and considered to belong to the family Micromonosporaceae. The organisms had phenotypic properties consistent with their assignment to this taxon. The strains formed a distinct taxon in the 16S rRNA Micromonosporaceae gene tree and shared a range of phenotypic properties that distinguished them from members of all of the genera with validly published names classified in this family. The name proposed for this novel taxon is Salinispora gen. nov. The genus contains two species recognized using a range of genotypic and phenotypic criteria, including comparative 16S–23S rRNA gene spacer region and DNA–DNA relatedness data. The names proposed for these taxa are Salinispora arenicola sp. nov., the type species, and Salinispora tropica sp. nov.; the type strains of these novel species have been deposited in service culture collections as strain CNH-643T (=ATCC BAA-917T=DSM 44819T) and strain CNB-440T (=ATCC BAA-916T=DSM 44818T), respectively.

A Gram-positive bacterium, designated strain AG019T, was isolated by micromanipulation from aerobic granules obtained from a laboratory-scale sequencing batch reactor. This isolate grew axenically as cocci clustered predominantly in tetrads, and was morphologically similar to the dominant organisms observed in the biomass. The morphology also resembled that of the tetrad-forming organisms commonly seen in activated sludge samples. Strain AG019T was found to be an oxidase-negative, catalase-positive, non-motile aerobe that does not reduce nitrate and grows at temperatures between 15 and 40 °C, with an optimum at 37 °C. The pH range for growth was 5·0–9·0, with an optimum at pH 7·5. Strain AG019T contained a peptidoglycan with directly cross-linked meso-diaminopimelic acid (type A1γ) and lacked mycolic acids. The G+C content of the DNA was 75 mol%. Menaquinone MK-8(H2) was the major isoprenoid quinone. The bacterium stained positively for intracellular polyphosphate granules but not for poly-β-hydroxyalkanoates. It produced capsular material and showed autoaggregation ability. Phenotypic and 16S rRNA gene analyses showed that the bacterium differed sufficiently from its closest phylogenetic relatives, namely members of the suborder Frankineae, which includes the genera Geodermatophilus, Blastococcus, Frankia, Sporichthya, Acidothermus and Microsphaera, that it is proposed that it be placed in a novel genus, Quadrisphaera, as Quadrisphaera granulorum gen. nov., sp. nov. The type strain is AG019T (=ATCC BAA-1104T=DSM 44889T).

A novel moderately halophilic bacterium, strain G-19.1T, has been isolated from a phenol enrichment of samples collected in hypersaline habitats of southern Spain. This enrichment culture was a part of a screening programme to isolate halophilic bacteria able to degrade various aromatic compounds. Strain G-19.1T has been characterized as a potential phenol-degrader over a wide range of saline conditions. Strain G-19.1T was found to be an aerobic, Gram-positive, endospore-forming, non-pigmented, moderately halophilic rod that grew optimally in media containing 7·5–10 % NaCl at pH 7·0. The DNA G+C content was 42·4 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences indicated that the closest relatives were Halobacillus species (96·2–97·0 %), although this novel isolate constitutes a separate line of descent within the radiation of Gram-positive rods. The cell-wall peptidoglycan contained meso-diaminopimelic acid, indicating that this strain does not share the main characteristic that differentiates members of the genus Halobacillus (which contain Orn–d-Asp) from other related genera. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. On the basis of phenotypic, genotypic and phylogenetic analyses, this isolate should be classified in a novel genus and species, for which the name Thalassobacillus devorans gen. nov., sp. nov. is proposed. The type strain is strain G-19.1T (=DSM 16966T=CECT 7046T=CCM 7282T).

An aerobic bacterium was isolated from saline soil located in Qinghai, north-west China. The bacterium, designated YIM 70157T, was investigated using a polyphasic taxonomic approach. The Gram reaction of the organism was positive. Comparative 16S rRNA gene sequence analysis demonstrated the isolate to be a member of the genus Marinococcus, the closest phylogenetic neighbour of the unknown bacterium being Marinococcus halophilus DSM 20408T with a similarity of 99·4 %. The peptidoglycan type of YIM 70157T was A1γ, with meso-diaminopimelic acid as diagnostic diamino acid. The major fatty acids were ai-C15 : 0, ai-C17 : 0 and i-C16 : 0. The menaquinones were MK-7 and MK-6. The phospholipids were diphosphatidylglycerol and phosphatidylinositol. The G+C content of total DNA was 48·5 mol%. On the basis of phylogenetic and phenotypic evidence and DNA–DNA hybridization data, this isolate should be classified as a novel species of Marinococcus, for which the name Marinococcus halotolerans sp. nov. is proposed. The type strain is YIM 70157T (=DSM 16375T=KCTC 19045T).