Youhei Fukui

Vibrio porteresiae sp. nov., a diazotrophic bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka)

Two facultatively anaerobic, nitrogen-fixing bacteria (strains MSSRF30(T) and MSSRF31) were isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka). These strains were determined to be nitrogen-fixers using the acetylene reduction assay and by PCR detection of a nifH gene amplicon. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strains were most closely related to Vibrio fluvialis LMG 7894(T) (96.8 % gene sequence similarity), Vibrio furnissii LMG 7910(T) (96.8 % sequence similarity) and Vibrio tubiashii CIP 102760(T) (96.7 % sequence similarity). Further multilocus sequence analysis using recA, pyrH, rpoA and nifH genes also showed low levels of sequence similarities (83-93 %) with all species of the genus Vibrio with validly published names. A multigene phylogenetic tree using concatenated sequences of the four genes (16S rRNA, rpoA, recA and pyrH) showed that strains MSSRF30(T) and MSSRF31 occupied a distinct phylogenetic position, forming a long branching that was not clustered with any other recognized Vibrio species. The fatty acid profile also suggested that the novel strains belonged to the genus Vibrio. The results of physiological and biochemical tests, genomic fingerprinting and DNA-DNA hybridization analyses clearly differentiated both novel strains from their closest phylogenetic neighbours, Vibrio cholerae IID6019, Vibrio mimicus LMG 7896(T), V. fluvialis LMG 7894(T) and V. furnissii LMG 7910(T). Several phenotypic traits enabled the differentiation of strain MSSRF30(T) from other species of the genus Vibrio. The DNA G+C content of strain MSSRF30(T) was 44.4+/-3.1 mol%. Based on genotypic, phenotypic, chemotaxonomic, phylogenetic and DNA-DNA hybridization analyses, the name Vibrio porteresiae sp. nov. (type strain MSSRF30(T)=LMG 24061(T)=DSM 19223(T)) is proposed for this novel taxon.

Polaribacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis, and emended descriptions of the genus Polaribacter and two Polaribacter species

Three Gram-negative, non-motile, strictly aerobic strains, designated LNM-20(T), LCM-1 and LAM-13, were isolated from thalli of the marine red alga Porphyra yezoensis. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates were associated with the genus Polaribacter in the family Flavobacteriaceae and were most closely related to Polaribacter dokdonensis DSW-5(T) (96.2 % 16S rRNA gene sequence similarity) and Polaribacter gangjinensis K17-16(T) (95.0 %). The DNA G+C content of the isolates was 28.6-29.2 mol%. DNA-DNA hybridization analysis showed that the isolates belonged to a single species distinct from both of their closest relatives. The only isoprenoid quinone detected was menaquinone-6. The main polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids were iso-C15 : 0, iso-C15 : 1ω10c and iso-C15 : 0 3-OH. The phenotypic features of strain LNM-20(T) differed from those of their closest relatives in several regards (colony colour, growth with 1 % NaCl and on TSA plus 2.5 % NaCl, hydrolysis of Tweens 40 and 80, and oxidization of five carbon compounds). On the basis of phylogenetic, chemotaxonomic and phenotypic analysis, the isolates represent a novel species in the genus Polaribacter, for which the name Polaribacter porphyrae sp. nov. is proposed. The type strain is LNM-20(T) ( = LMG 26671(T)  = NBRC 108759(T)). Emended descriptions of the genus Polaribacter and P. dokdonensis and P. gangjinensis are also proposed.

Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine

A novel Gram-positive, motile, endospore-forming, aerobic bacterium was isolated from the NASA Phoenix Lander assembly clean room that exhibits 100 % 16S rRNA gene sequence similarity to two strains isolated from a deep subsurface environment. All strains are rod-shaped, endospore-forming bacteria, whose endospores are resistant to UV radiation up to 500 J m(-2). A polyphasic taxonomic study including traditional phenotypic tests, fatty acid analysis, 16S rRNA gene sequencing and DNA-DNA hybridization analysis was performed to characterize these novel strains. The 16S rRNA gene sequencing convincingly grouped these novel strains within the genus Paenibacillus as a separate cluster from previously described species. The similarity of 16S rRNA gene sequences among the novel strains was identical but only 98.1 to 98.5 % with their nearest neighbours Paenibacillus barengoltzii ATCC BAA-1209(T) and Paenibacillus timonensis CIP 108005(T). The menaquinone MK-7 was dominant in these novel strains as shown in other species of the genus Paenibacillus. The DNA-DNA hybridization dissociation value was <45 % with the closest related species. The novel strains had DNA G+C contents of 51.9 to 52.8 mol%. Phenotypically, the novel strains can be readily differentiated from closely related species by the absence of urease and gelatinase and the production of acids from a variety of sugars including l-arabinose. The major fatty acid was anteiso-C(15 : 0) as seen in P. barengoltzii and P. timonensis whereas the proportion of C(16 : 0) was significantly different from the closely related species. Based on phylogenetic and phenotypic results, it was concluded that these strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus phoenicis sp. nov. is proposed. The type strain is 3PO2SA(T) ( = NRRL B-59348(T)  = NBRC 106274(T)).

Vibrio neonatus sp. nov. and Vibrio ezurae sp. nov. Isolated from the Gut of Japanese Abalones

Five alginolytic, facultative anaerobic, non-motile bacteria were isolated from the gut of Japanese abalones (Haliotis discus discus, H. diversicolor diversicolor and H. diversicolor aquatilis). Phylogenetic analyses based on 16S rRNA gene and gap gene sequences indicated that these strains are closely related to V. halioticoli. DNA-DNA hybridizations, FAFLP fingerprintings, and phylogenies of gap and 16S rRNA gene sequences showed that the five strains represent two species different from all currently described vibrios. The names Vibrio neonatus sp. nov. (IAM 15060T = LMG 19973T = HDD3-1T; mol% G+C of DNA is 42.1-43.9), and Vibrio ezurae sp. nov. (IAM 15061T = LMG 19970T = HDS1-1T; mol% G+C of DNA is 43.6-44.8) are proposed to encompass these new taxa. The two new species can be differentiated from V. halioticoli on the basis of several features, including beta-galactosidase activity, assimilation of glycerol, D-mannose and D-gluconate.

Vibrio jasicida sp. nov., a member of the Harveyi clade, isolated from marine animals (packhorse lobster, abalone and Atlantic salmon)

Six isolates of a facultatively anaerobic bacterium were recovered in culture from marine invertebrates and vertebrates, including packhorse lobster (Jasus verreauxi), abalone (Haliotis sp.) and Atlantic salmon (Salmo salar), between 1994 and 2002. The bacteria were Gram-negative, rod-shaped and motile by means of more than one polar flagellum, oxidase-positive, catalase-positive and able to grow in the presence of 0.5-8.0% NaCl (optimum 3.0-6.0%) and at 10-37 °C (optimum 25-30 °C). On the basis of 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) using five loci (2443 bp; gyrB, pyrH, ftsZ, mreB and gapA), the closest phylogenetic neighbours of strain TCFB 0772(T) were the type strains of Vibrio communis (99.8 and 94.6 % similarity, respectively), Vibrio owensii (99.8 and 94.1%), Vibrio natriegens (99.4 and 88.8%), Vibrio parahaemolyticus (99.4 and 90.3%), Vibrio rotiferianus (99.2 and 94.4%), Vibrio alginolyticus (99.1 and 89.3%) and Vibrio campbellii (99.1 and 92.3%). DNA-DNA hybridization confirmed that the six isolates constitute a unique taxon that is distinct from other known species of Vibrio. In addition, this taxon can be readily differentiated phenotypically from other Vibrio species. The six isolates therefore represent a novel species, for which the name Vibrio jasicida sp. nov. is proposed; the novel species is represented by the type strain TCFB 0772(T) ( = JCM 16453(T)  = LMG 25398(T)) (DNA G+C content 45.9 mol%) and reference strains TCFB 1977 ( = JCM 16454) and TCFB 1000 ( = JCM 16455).

Algimonas porphyrae gen. nov., sp. nov., a member of the family Hyphomonadaceae, isolated from the red alga Porphyra yezoensis.

Three Gram-negative, stalked, motile bacteria, designated 0C-2-2(T), 0C-17 and LNM-3, were isolated from the red alga Porphyra yezoensis. 16S rRNA gene sequence analysis revealed that the three novel strains belonged to the family Hyphomonadaceae, and were closely related to Litorimonas taeanensis G5(T) (96.5 % 16S rRNA gene sequence similarity) and Hellea balneolensis 26III/A02/215(T) (94.3 %). The DNA G+C contents of the novel isolates (58.5-60.2 mol%) were clearly distinguished from those of L. taeanensis G5(T) (47.1 mol%) and H. balneolensis DSM 19091(T) (47.9 mol%). The G+C content of L. taeanensis G5(T) obtained in this study was quite different from a previous report (63.6 mol%). DNA-DNA hybridization experiments showed that the novel strains constituted a single species. Eleven phenotypic features of the three isolates differed from those of both related genera. The predominant respiratory quinone was ubiquinone-10 and the major fatty acid was C(18 : 1)ω7c. On the basis of this polyphasic taxonomic analysis, the novel strains represent a novel genus and species, for which the name Algimonas porphyrae gen. nov., sp. nov. is proposed. The type strain of Algimonas porphyrae is 0C-2-2(T) (= LMG 26424(T) = NBRC 108216(T)).

Sulfitobacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis.

Gram-stain-negative, aerobic, halophilic bacteria, designated SCM-1(T), LCM10-1 and CTBL-B-147, were isolated from modified half-strength SWM-III medium, PES medium and thalli after laboratory cultivation of a red alga, Porphyra yezoensis. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolates were affiliated to the genus Sulfitobacter of the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the new isolates with the closest related species, Sulfitobacter mediterraneus CH-B427(T), was 98.8%. The DNA G+C contents of the new isolates were in the range of 61.4-62.3 mol%. DNA-DNA relatedness values of strain SCM-1(T) with other type strains of the genus Sulfitobacter were less than 15.9%. The new isolates contained Q-10 as the predominant ubiquinone, phosphatidylcholine, phosphatidylglycerol, an unidentified amino lipid and an unidentified lipid as the main polar lipids, and C(18 : 1)ω7c, C(19 : 1)ω7c and C(16 : 0) as the major fatty acids (>10% of the total). Strain SCM-1(T) could be differentiated from Sulfitobacter mediterraneus JCM 21792(T) by 35 morphological and phenotypic characteristics. On the basis of the phylogenetic, genetic and phenotypic properties of the new isolates, the name Sulfitobacter porphyrae sp. nov. is proposed, with strain SCM-1(T) ( = LMG 27110(T) = NBRC 109054(T)) as the type strain.

Maritalea porphyrae sp. nov., isolated from a red alga (Porphyra yezoensis), and transfer of Zhangella mobilis to Maritalea mobilis comb. nov.

Three Gram-negative, motile, aerobic bacteria were isolated from cultures of the marine red alga Porphyra yezoensis. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strains were closely related to Maritalea myrionectae CL-SK30(T) (97.9% 16S rRNA gene sequence similarity) and Zhangella mobilis E6(T) (96.2 %). 16S rRNA gene sequence similarity between Z. mobilis E6(T) and M. myrionectae CL-SK30(T) was 97.9%. The DNA G+C contents of the isolates (49.4-50.0 mol%) were similar to those of M. myrionectae DSM 19524(T) (52.3 mol%) and Z. mobilis JCM 15144(T) (50.3 mol%). From these results, it was difficult to differentiate the genus Zhangella from the genus Maritalea. DNA-DNA hybridization demonstrated that the isolates belonged to a single species. The isolates could also be distinguished from M. myrionectae and Z. mobilis on the basis of chemotaxonomic and phenotypic features, including fatty acid composition (particularly C(16:1)ω7c), growth with 6-9% (w/v) NaCl, carbon utilization, oxidation patterns and so on. A novel species of the genus Maritalea is proposed to accommodate the three isolates, with the name Maritalea porphyrae sp. nov. The type strain is LCM-3(T) (=LMG 25872(T)=NBRC 107169(T)). Furthermore, it is proposed that Zhangella mobilis should be transferred from the genus Zhangella to the genus Maritalea, with the name Maritalea mobilis comb. nov. (type strain E6(T)=CGMCC 1.7002(T)=JCM 15144(T)).

Algimonas ampicilliniresistens sp. nov., isolated from the red alga Porphyra yezoensis, and emended description of the genus Algimonas.

Three strains (14A-2-7(T), 14A-3-1 and 14A-3) of Gram-stain-negative, prosthecate, motile bacteria were isolated from an algal medium supplemented with 10 mg ampicillin l(-1) (w/v), in which the red alga Porphyra yezoensis had been cultured. Based on the 16S rRNA gene sequence analysis, the three isolates formed a cluster with the genus Algimonas of the family Hyphomonadaceae. The sequences of the three isolates had high similarity with those of Algimonas porphyrae 0C-2-2(T) (97.6 % similarity) and Litorimonas taeanensis G5(T) (95.6 % similarity). The DNA G+C contents of the three isolates ranged from 54.3 to 55.0 mol%, which were more similar to that of A. porphyrae 0C-2-2(T) (58.5 mol%) than to that of L. taeanensis G5(T) (47.1 mol%). The DNA-DNA relatedness showed that the three isolates were representatives of the same species (88.1-94.0 % relatedness) and that strain 14A-2-7(T) was a representative of a different species from A. porphyrae 0C-2-2(T) and L. taeanensis G5(T) (1.2-8.6 % relatedness). The phenotypic characteristics of strain 14A-2-7(T) differed by 20 results and 30 results from A. porphyrae 0C-2-2(T) and L. taeanensis G5(T), respectively. The three isolates contained ubiquinone-10 as the predominant quinone and C18 : 1ω7c as the major fatty acid. Based on the polyphasic taxonomic analysis, the three isolates represent a novel species of the genus Algimonas, for which the name Algimonas ampicilliniresistens sp. nov. is proposed. The type strain is 14A-2-7(T) ( = LMG 26421(T) = NBRC 108219(T)). An emended description of the genus Algimonas is also proposed.

Streptomyces abietis sp. nov., a cellulolytic bacterium isolated from soil of a pine forest.

Cellulolytic bacteria A191(T), A192 and A193 isolated from the soil of Sakhalin fir forest in Hokkaido, Japan were studied phenotypically, genotypically and phylogenetically. Analysis of their 16S rRNA gene and gyrB sequences and DNA base composition suggested that these isolates were conspecific and members of the genus Streptomyces. However, levels of 16S rRNA gene and gyrB sequence similarity between the isolates and the type strains of their closest relatives in the genus Streptomyces were no higher than 97.9 and 95.0 %, respectively, implying that these isolates were distinctive. Moreover, the results of DNA-DNA hybridization experiments and physiological characterization clearly differentiated these isolates from their closest neighbours. It is therefore concluded that these isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces abietis is proposed. The type strain is A191(T) ( = NBRC 109094(T) = DSM 42080(T)).