Actimicrobium antarcticum gen. nov., sp. nov., of the family Oxalobacteraceae, isolated from Antarctic coastal seawater.

A Gram-negative, non-motile, catalase- and oxidase- positive, strictly aerobic, and short rod-shaped bacterium that was designated strain KOPRI 25157(T) was isolated from coastal seawater sample in Antarctica. The temperature and pH ranges for growth on R2A agar were 10-20°C, and 5.0-10.0, respectively. Phylogenetic analyses of the 16S rRNA gene sequence of strain KOPRI 25157(T) showed it to belong to the family Oxalobacteraceae of the class Betaproteobacteria, and it formed a distinct clade from other recognized members of the family. DNA G + C content was 65.9 mol%. Major ubiquinone was Q-8. Predominant cellular fatty acids were C(16:1) ω7c/15 iso 2OH (56.4%) and C(16:1) (30.5%). Major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and unknown lipid. On the basis of these data, it is proposed that strain KOPRI 25157(T) is the representative of a novel genus, for which the name Actimicrobium gen. nov. is proposed in the family Oxalobacteraceae. The type strain for Actimicrobium antarcticum sp. nov. is KOPRI 25157(T) (=JCM 16673(T)=KCTC 23040(T)).

High abundance and role of antifungal bacteria in compost-treated soils in a wildfire area.

Compost has been widely used in order to promote vegetation growth in post-harvested and burned soils. The effects on soil microorganisms were scarcely known, so we performed the microbial analyses in a wildfire area of the Taebaek Mountains, Korea, during field surveys from May to September 2007. Using culture-dependent and -independent methods, we found that compost used in burned soils influenced a greater impact on soil fungi than bacteria. Compost-treated soils contained higher levels of antifungal strains in the genera Bacillus and Burkholderia than non-treated soils. When the antifungal activity of Burkholderia sp. strain O1a_RA002, which had been isolated from a compost-treated soil, was tested for the growth inhibition of bacteria and fungi isolated from burned soils, the membrane-filtered culture supernatant inhibited 19/37 fungal strains including soil fungi, Eupenicillium spp. and Devriesia americana; plant pathogens, Polyschema larviformis and Massaria platani; an animal pathogen, Mortierella verticillata; and an unidentified Ascomycota. However, this organism only inhibited 11/151 bacterial strains tested. These patterns were compatible with the culture-independent DGGE results, suggesting that the compost used in burned soils had a greater impact on soil fungi than bacteria through the promotion of the growth of antifungal bacteria. Our findings indicate that compost used in burned soils is effective in restoring soil conditions to a state closer to those of nearby unburned forest soils at the early stage of secondary succession.

Vitellibacter aestuarii sp. nov., isolated from tidal-flat sediment, and an emended description of the genus Vitellibacter.

A Gram-reaction-negative, aerobic, yellowish-orange-pigmented bacterial strain, designated JC2436(T), was isolated from tidal-flat sediment of Oi Island in Korea. Comparative 16S rRNA gene sequence analysis indicated its close affiliation to Vitellibacter vladivostokensis, with 96 % sequence similarity to the type strain. Cells grew with 2-6 % NaCl and at 10-41 degrees C. Orange flexirubin pigments were present. The major isoprenoid quinone was MK-6, the DNA G+C content was 48.7 mol% and the predominant fatty acids (>10 %) were iso-C(15 : 0) and iso-C(17 : 0) 3-OH. The data obtained from this polyphasic study support the classification of this isolate within a novel species in the genus Vitellibacter, for which the name Vitellibacter aestuarii sp. nov. is proposed. The type strain is JC2436(T) (=IMSNU 14137(T) =KACC 13727(T) =KCTC 22361(T) =JCM 15496(T)).

Marinifilum fragile gen. nov., sp. nov., isolated from tidal flat sediment.

A facultatively anaerobic, moderately halophilic, Gram-negative, filamentous bacterium, designated JC2469T, was isolated from tidal flat sediment in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the phylum Bacteroidetes and its closest taxonomic relative was Cytophaga fermentans NCIMB 2218T (89.6% sequence similarity). Cells appeared as filaments during exponential growth, but became fragmented to rods at stationary phase. Spherical cells were also observed in aged cultures. Strain JC2469T contained iso-C15:0 (56.2%) and MK-7 as the predominant fatty acid and respiratory quinone, respectively. On the basis of evidence from this polyphasic study, the isolate showed substantial differences from other genera. The phylogenetic and physiological data of the present study strongly suggest that the isolate represents a novel genus and species, for which the name Marinifilum fragile gen. nov., sp. nov. is proposed. The type strain of Marinifilum fragile is JC2469T (=IMSNU 14138T=KCTC 22488T=JCM 15579T).

Proposal to transfer Flavobacterium oceanosedimentum Carty and Litchfield 1978 to the genus Curtobacterium as Curtobacterium oceanosedimentum comb. nov.

Flavobacterium oceanosedimentum Carty & Litchfield 1978(AL) had been described as a novel species in the genus Flavobacterium on the basis of phenotypic characteristics, although the organism shows a high G+C content, a property never found in the other members of the genus. In this study, we re-evaluated the taxonomic position of F. oceanosedimentum using a polyphasic approach. The 16S rRNA gene sequence of F. oceanosedimentum ATCC 31717(T) indicated that it is closely related to the genus Curtobacterium in the class Actinobacteria, showing 96.5-99.9% similarity values to Curtobacterium spp. Phylogenetic analysis based on the gene encoding the gyrase subunit B (gyrB) and DNA-DNA hybridization suggest that F. oceanosedimentum represents a separate species in the genus Curtobacterium, which is also supported by comparative analysis of cellular fatty acid profiles and a large array of phenotypic traits. We therefore propose to transfer F. oceanosedimentum to the genus Curtobacterium as Curtobacterium oceanosedimentum comb. nov.

Pedobacter koreensis sp. nov., isolated from fresh water.

A motile, rod-shaped bacterium, designated strain WPCB189(T), was isolated from fresh water collected from the Woopo wetland (Republic of Korea). The cells were found to be Gram-negative, aerobic and catalase- and oxidase-positive. A phylogenetic analysis based on 16S rRNA gene sequences showed that this isolate forms a lineage within the genus Pedobacter, showing sequence similarities of 89.7-96.4 % with respect to recognized species of the genus, and represents a novel member of this genus. The major fatty acids were iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (summed feature 3, 29.7 %), iso-C(15 : 0) (26.4 %) and iso-C(17 : 1) 3-OH (10.1 %). The DNA G+C content was 38.0 mol%. On the basis of data obtained from this polyphasic taxonomic study, strain WPCB189(T) represents a novel species of the genus Pedobacter, for which the name Pedobacter koreensis sp. nov. is proposed. The type strain is WPCB189(T) (=KCTC 12536(T)=NBRC 101153(T)).

Reclassification of Flavobacterium resinovorum Delaporte and Daste 1956 as Novosphingobium resinovorum comb. nov., with Novosphingobium subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001 as a later heterotypic synonym.

The taxonomic status of Flavobacterium resinovorum Delaporte and Daste 1956 (Approved Lists 1980) was investigated using a polyphasic approach. The 16S rRNA gene sequence of F. resinovorum NCIMB 8767(T) was almost identical to that of the type strain of Novosphingobium subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001, with 99.85 % sequence similarity. The DNA-DNA relatedness value between the type strains of these species was 100 %. Phenotypic comparison based on API 20E, API NE and API ZYM kits demonstrated that the type strains of F. resinovorum and N. subarcticum were also indistinguishable based on their biochemical properties. On the basis of genotypic and phenotypic evidence, it is therefore proposed to reclassify Flavobacterium resinovorum as Novosphingobium resinovorum comb. nov., with the type strain NCIMB 8767(T) =ATCC 33545(T) =DSM 7478(T) =LMG 8367(T), and that Novosphingobium subarcticum is a later heterotypic synonym of Novosphingobium resinovorum.

Pseudomonas segetis sp. nov., isolated from soil.

A Gram-negative, aerobic bacterium, designated strain FR1439T, was isolated from the soil of Dokdo in the Republic of Korea. The cells of strain FR1439T were catalase- and oxidase-positive, motile and rod-shaped. Phylogenetic analysis of the 16S rRNA gene sequence revealed that it represents a distinct line of descent within the genus Pseudomonas. The levels of DNA-DNA relatedness between strain FR1439T and type strains of phylogenetically related species, namely Pseudomonas flavescens, Pseudomonas mendocina, Pseudomonas pseudoalcaligenes and Pseudomonas straminea, ranged from 28 to 37%. Several phenotypic characteristics, together with the cellular fatty acid composition, can be used to differentiate strain FR1439T from related pseudomonads. On the basis of the polyphasic taxonomic evidence presented in this study, strain FR1439T represents a novel species, for which the name Pseudomonas segetis sp. nov. is proposed. The type strain is FR1439T (=IMSNU 14101T=CIP 108523T=KCTC 12331T).

Hymenobacter rigui sp. nov., isolated from wetland freshwater.

A non-motile, rod-shaped and pinkish-red-pigmented bacterium, designated strain WPCB131(T), was isolated from freshwater of Woopo wetland, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter with sequence similarities of 93.2-95.5 % to known Hymenobacter species. No other taxa in the phylum Bacteroidetes showed more than 90 % sequence similarity to the isolate. Cells were Gram-negative, oxidase-negative and catalase-positive. Optimum growth was observed at pH 6 and 30 degrees C. The major fatty acids were iso-C(15 : 0) (34.8 %), C(16 : 1)omega5c (15.0 %), anteiso-C(17 : 1) B/iso-C(17 : 1) I (14.4 %) and C(16 : 1)omega7c/iso-C(15 : 0) 2-OH (13.8 %). The DNA G+C content of strain WPCB131(T) was 65 mol%. The isolate could be readily distinguished from other Hymenobacter species using a combination of phenotypic characters. On the basis of the polyphasic evidence presented in this study, it is proposed that strain WPCB131(T) (=IMSNU 14116(T)=KCTC 12533(T)=NBRC 101118(T)) represents a novel species, Hymenobacter rigui sp. nov.

Paenibacillus elgii sp. nov., with broad antimicrobial activity.

Two novel spore-forming bacteria with broad antimicrobial activity were isolated from roots of Perilla frutescens. The isolates, SD17(T) and SD18, were facultatively anaerobic and showed variable Gram reaction. Growth was observed between 20 and 45 degrees C. DNA G+C content of SD17(T) was 51.7 mol%, and the major fatty acid was anteiso-C(15 : 0) (54.1 %). 16S rRNA gene sequence similarity of SD17(T) ranged from 98.6 to 91.3 % with other Paenibacillus species. The phylogenetic tree showed that isolate SD17(T) formed a significant monophyletic clade with Paenibacillus koreensis KCTC 2393(T) and Paenibacillus ehimensis IFO 15659(T). DNA-DNA relatedness values for strain SD17(T) with Paenibacillus koreensis KCTC 2393(T) and Paenibacillus ehimensis IFO 15659(T) were 17.4 and 19.8 %, respectively. These isolates thus merit species status within Paenibacillus, for which the name Paenibacillus elgii sp. nov. is proposed. The type strain is SD17(T) (=KCTC 10016BP(T)=NBRC 100335(T)).