Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae.

Flexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa. Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes. Levels of DNA-DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species, Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin, as well as by α-glucosidase and ß-glucosidase activity. On the basis of these results, NBRC 15981T is proposed as representing a novel species of the genus Marivirga, named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).

Nonlabens marinus [corrected] sp. nov., a novel member of the Flavobacteriaceae isolated from the Pacific Ocean.

Two aerobic, Gram-negative, orange pigmented and irregular rod-shaped bacteria, designated S1-05 and S1-08(T), were isolated from seawater from the Pacific Ocean. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the genus Nonlabens of the family Flavobacteriaceae. The strains S1-05 and S1-08(T) shared 100 % pairwise sequences similarity with each other and showed less than 96.8 % similarity with the cultivated members of the genus Nonlabens. The novel isolates are phenotypically and physiologically different from strains described previously. The strains were found to be non-motile, oxidase positive, catalase positive and hydrolyzed gelatin and aesculin. The G+C contents of the DNA were determined to 41.4 and 41.7 mol% and MK-6 the predominant menaquinone. Anteiso-C15:0 and iso-C15:0 were found to be the major two cellular fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strains S1-05 and S1-08(T) represent a novel species within the genus Nonlabens, for which the name Nonlabens marina sp. nov. is proposed. The type strain of N. marina is S1-08(T) (=KCTC 23432(T) = NBRC 107738(T)).

Salinirepens amamiensis gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from seawater, and emended descriptions of the genera Fluviicola and Wandonia.

The taxonomic position of bacterial strain AM11-6(T), isolated from seawater in Japan, was determined by using a polyphasic taxonomic approach. The strain was a strictly aerobic and Gram-staining-negative slender rod, motile by gliding. The major respiratory quinone was menaquinone-6 and the predominant cellular fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH, C(14 : 0) and iso-C(15 : 1) G. The polar lipid pattern indicated the presence of an unidentified phospholipid, several glycolipids and an unidentified polar lipid. The G+C content of the genomic DNA was 36.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AM11-6(T) clustered with members of the genera Wandonia and Fluviicola in the family Cryomorphaceae of the phylum Bacteroidetes. The strain required NaCl and MgCl(2) for growth and could be differentiated from members of other genera in the family Cryomorphaceae by fatty acid composition and other phenotypic characters. On the basis of these results, we describe the novel genus and species, Salinirepens amamiensis gen. nov., sp. nov. The type strain of Salinirepens amamiensis is AM11-6(T) (= NBRC 101268(T) = NCIMB 14607(T)). Emended descriptions of the genera Fluviicola and Wandonia are also proposed.

Persicobacter psychrovividus sp. nov., isolated from shellfish, and emended descriptions of the genus Persicobacter and Persicobacter diffluens.

The taxonomic position of three bacterial strains, Asr22-19T, NBRC 101035 and NBRC 101041, isolated from shellfish in Japan, was determined by using a polyphasic taxonomic approach. The strains were facultatively anaerobic, motile by gliding and Gram-staining-negative slender rods. Their major respiratory quinone was menaquinone-7 and their predominant cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH, C16:0 3-OH, and C16:0. The G+C content of the genomic DNA was 42.0-42.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains clustered with the genus Persicobacter in the family 'Flammeovirgaceae'. DNA-DNA relatedness values were higher than 68% among strains Asr22-19T, NBRC 101035 and NBRC 101041, and were lower than 28% between strain Asr22-19T and Persicobacter diffluens NBRC 15940T. The three novel strains could be differentiated from Persicobacter diffluens by several phenotypic characteristics. On the basis of these results, the novel species Persicobacter psychrovividus sp. nov. (type strain Asr22-19T=NBRC 101262T=CIP 109100T) is proposed and emended descriptions are given for the genus Persicobacter and for Persicobacter diffluens.

Silvimonas iriomotensis sp. nov. and Silvimonas amylolytica sp. nov., new members of the class Betaproteobacteria isolated from the subtropical zone in Japan.

The taxonomic positions of two bacterial strains, ir6-1(T) and ir6-4(T), isolated from soil collected in Iriomote Island in Japan, were determined by using a polyphasic taxonomic approach. The strains were facultatively anaerobic, motile and Gram-stain-negative rods and their optimum pH for growth was pH 4.0. Their major respiratory quinone was ubiquinone-8 and the predominant cellular fatty acids were C(14 : 0), C(16 : 0), C(16 : 1)omega7c and C(18 : 1)omega7c. The G+C content of the genomic DNA of ir6-1(T) and ir6-4(T) was 59.9 and 57.5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains clustered with the genus Silvimonas in the class Betaproteobacteria. DNA-DNA similarities were lower than 53 % among ir6-1(T), ir6-4(T) and Silvimonas terrae NBRC 100961(T), and these strains could be differentiated from each other by several phenotypic characters. Based on these results, we propose the emendation of the genus Silvimonas and inclusion of two novel species, Silvimonas iriomotensis sp. nov. (type strain ir6-1(T)=NBRC 103188(T) =CGMCC 1.8859(T) =KCTC 22513(T)) and Silvimonas amylolytica sp. nov. (ir6-4(T) =NBRC 103189(T) =CGMCC 1.8860(T) =KCTC 22514(T)).

Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan.

A polyphasic study was performed to determine the taxonomic position of strain EK05(T) isolated from a root-outgrowth of Entada koshunensis, a legume available in Okinawa, Japan. Phylogenetic analysis of the 16S rRNA gene showed that the strain belongs to the genus Bradyrhizobium. Subsequent multilocus sequence analysis with ITS, glnII, recA, gyrB, and atpD sequences revealed that the isolate represents a distinct evolutionary lineage within the genus Bradyrhizobium. DNA-DNA hybridization indicated that strain EK05(T) shares <61% DNA relatedness with the type strains of all six recognized species of Bradyrhizobium, confirming that this strain is a novel species within the genus. Phylogenetic trees based on symbiotic loci, nifH and nodC, also placed strain EK05(T) clearly in a novel branch. On the basis of its phylogenetic distinctiveness, we propose Bradyrhizobium iriomotense sp. nov. for strain EK05(T). The type strain is EK05(T) (= NBRC 102520(T) = LMG 24129(T)).

Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov.

Two strains, MKG-38(T) and FYK2402M69(T), were isolated from a marine sediment sample and a sea snail, respectively, both collected on the Pacific coast of Japan. Phylogeny of these new isolates based on 16S rRNA gene sequences indicated that they are members of the genus Lewinella. Morphological, physiological and biochemical properties of these two isolates, together with the type strains of the three previously described species of the genus Lewinella, were characterized. The new isolates were Gram-negative, aerobic, rod-shaped, chemo-organotrophic and able to degrade starch and CM-cellulose. A comparative polyphasic study showed that these two isolates represent two novel species of the genus Lewinella, for which the names Lewinella marina sp. nov. (type strain, MKG-38(T)=NBRC 102633(T)=NCIMB 14312(T)) and Lewinella lutea sp. nov. (type strain, FYK2402M69(T)=NBRC 102634(T)=NCIMB 14313(T)) are proposed. Emended descriptions of the genus Lewinella (Sly et al. 1998) and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica are also proposed.

Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau.

The taxonomic positions of two bacterial strains, MBIC01146(T) and MBIC01099, isolated from marine environments of Japan and Palau, respectively, were determined by using a polyphasic approach. The bacteria were aerobic, motile, Gram-negative rods and formed star-shaped aggregations. The G+C content of the genomic DNA ranged from 58.5 to 58.7 mol%. The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were C(16 : 0), C(18 : 1)omega6c and C(18 : 1)omega7c. 16S rRNA gene sequence analyses based on both neighbour-joining and maximum-parsimony methods revealed that strains MBIC01146(T) and MBIC01099 were positioned within the cluster comprising Ruegeria atlantica and Silicibacter lacuscaerulensis within subgroup alpha-3 of the Proteobacteria. The phenotypic and chemotaxonomic characteristics of the novel strains were similar to those of Ruegeria atlantica; however, DNA-DNA hybridization tests showed that the isolates represented an independent species. The isolates could be differentiated from Ruegeria atlantica based on several characteristics. Therefore, strains MBIC01146(T) and MBIC01099 are considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria mobilis sp. nov. is proposed. The type strain is MBIC01146(T) (=NBRC 101030(T)=CIP 109181(T)). An emended description of Ruegeria atlantica Uchino et al. 1999 is also given.

Labrys okinawensis sp. nov. and Labrys miyagiensis sp. nov., budding bacteria isolated from rhizosphere habitats in Japan, and emended descriptions of the genus Labrys and Labrys monachus.

Three strains, MAFF 210191(T), G24103(T) and G24116, assumed to be members of two novel species, were isolated from several rhizosphere habitats in different parts of Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates formed a distinct monophyletic group together with the two known species of the genus Labrys, suggesting that the isolates have a close affiliation with this genus. In this study, a polyphasic approach was used to characterize and compare the three isolates with the two species of the genus Labrys, Labrys monachus and Labrys methylaminiphilus. All three isolates were aerobic, Gram-negative, motile and non-sporulating and they ranged in shape from spherical to short rods. The cells multiplied by budding and utilized a wide variety of monosaccharides, disaccharides and sugar alcohols as sole carbon and energy sources, but they did not utilize C(1) compounds, salicin or d-melezitose. The strains were inhibited by dl-alpha-alanine and glycine (both at 10 mM). The major cellular fatty acids were C(19 : 0) cyclo omega8c, C(16 : 0), C(18 : 0) and C(18 : 1)omega7c. The three isolates shared <12 % and <11 % DNA-DNA relatedness with L. monachus DSM 5896(T) and L. methylaminiphilus DSM 16812(T), respectively. The G+C content of the isolates (61-62 mol%) was also significantly lower than those of the two previously characterized species. In spite of many morphological, physiological and chemotaxonomic similarities among the three isolates, strain MAFF 210191(T) could be differentiated from strains G24103(T) and G24116 on the basis of 16S rRNA gene sequence divergence, DNA-DNA relatedness (<46 %) and gelatin hydrolysis. Two novel species are therefore proposed, namely Labrys okinawensis sp. nov., with the type strain MAFF 210191(T) (=DSM 18385(T)), and Labrys miyagiensis sp. nov., with the type strain G24103(T) (=NBRC 101365(T)=NCIMB 14143(T)) and also including strain G24116 (=NBRC 101366=NCIMB 14144). Emended descriptions of the genus Labrys and Labrys monachus are also presented.

Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov.

The taxonomic positions of five bacterial strains isolated from the Yaeyama Islands of Japan and 'Microscilla arenaria' NBRC 15982 were determined using a polyphasic taxonomic approach. 16S rRNA gene sequence analyses placed all of the strains close to the genus Flammeovirga. DNA-DNA hybridization studies, biochemical and physiological characterizations and chemotaxonomic analyses suggested that 'M. arenaria' NBRC 15982 and the five novel isolates represented two separate species of the genus Flammeovirga. Emendation of the genus Flammeovirga Nakagawa et al. 1997 and the species Flammeovirga aprica (Reichenbach 1989) Nakagawa et al. 1997 is proposed. In addition, 'Microscilla arenaria' Lewin 1969 is proposed as Flammeovirga arenaria nom. rev., comb. nov. (with the type strain NBRC 15982(T)=CIP 109101(T)) and the novel isolates are proposed as Flammeovirga yaeyamensis sp. nov. (type strain IR25-3(T)=NBRC 100898(T)=CIP 109099(T)).

Sandarakinotalea sediminis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae.

Four Gram-negative, orange-coloured, aerobic, heterotrophic bacteria were isolated from sediment samples collected on the Pacific coast of Japan near the cities of Toyohashi and Katsuura. 16S rRNA gene sequence analysis indicated that these strains form a distinct lineage within the family Flavobacteriaceae. The four isolates shared 99.9-100 % 16S rRNA gene sequence similarity with each other and showed 88-90.9 % similarity with their neighbours in the family Flavobacteriaceae. The four strains also shared high DNA-DNA reassociation values of 67-99 % with each other. All the strains grew at 37 degrees C but not at 4 degrees C, and degraded gelatin, starch and DNA. The major fatty acids were i-C15:0, a-C15:0, i-C16:0 and i-C17:0 3-OH. However, two common fatty acids of members of the Flavobacteriaceae, i-C15:1 and a-C15:1, were absent in these strains. The DNA G+C contents of the four strains were in the range 35-37 mol%. On the basis of the polyphasic evidence, it was concluded that these strains should be classified as a novel genus and a novel species in the family Flavobacteriaceae, for which the name Sandarakinotalea sediminis gen. nov., sp. nov. is proposed. The type strain of Sandarakinotalea sediminis is CKA-5T (=NBRC 100970T=LMG 23247T).