Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field.

A taxonomic study was carried out on Gsoil 142(T), a bacterial strain isolated from the soil collected in a ginseng field in Pocheon province, South Korea. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this bacterium to the Gammaproteobacteria, and it was most closely related to Hydrocarboniphaga effusa ATCC BAA 332(T) (94.4%, 16S rRNA gene sequence similarity), Nevskia ramosa DSM 11499(T) (94.1%) and Alkanibacter difficilis MN154.3(T) (92.0%). Strain Gsoil 142(T) was a gram-negative, strictly aerobic, motile, and rod-shaped bacterium. The G+C content of the genomic DNA was 69.9% and predominant ubiquinone was Q-8. Major fatty acids were summed feature 8 (C(18:1) omega7c and/or omega6c, 36.3%), summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1) omega7c, 20.6%) and C(16:0) (17.4%). The major polar lipids detected in strain Gsoil 142(T) were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown glycolipid. On the basis of polyphasic evidence, it is proposed that strain Gsoil 142(T) should be placed in a novel genus and species, for which the name Panacagrimonas perspica gen. nov., sp. nov. is proposed. The type strain is Gsoil 142(T) (= KCTC 12982(T) = LMG 23239(T)).

Dokdonella ginsengisoli sp. nov., isolated from soil from a ginseng field, and emended description of the genus Dokdonella.

A Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 191T, was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 191T belongs to the family Xanthomonadaceae and is related to Dokdonella fugitiva LMG 23001T (97.8% sequence similarity) and Dokdonella koreensis KCTC 12396T (96.9%). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17:1omega9c (30.6%), iso-C17:0 (21.6%) and iso-C15:0 (13.0%), supporting the affiliation of strain Gsoil 191T to the genus Dokdonella. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain Gsoil 191T and its closest phylogenetic neighbours were below 40%. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Gsoil 191T from recognized species of the genus Dokdonella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 191T represents a novel species of the genus Dokdonella, for which the name Dokdonella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 191T (=KCTC 12564T=DSM 17954T=CCUG 52462T).

Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea.

A novel gammaproteobacterium, designated Gsoil 3054(T), 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 Jip2(T) and Rhodanobacter thiooxydans LCS2(T) (97.9 and 97.2 % 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data, i.e. Q-8 as the predominant ubiquinone and iso-C(15 : 0), 10-methyl C(16 : 0) and iso-C(17 : 0) as major fatty acids, also supported classification of strain Gsoil 3054(T) in the genus Rhodanobacter. However, DNA-DNA hybridization values of Gsoil 3054(T) with R. fulvus Jip2(T) and R. thiooxydans LCS2(T) were 45 and 31 %, respectively. Moreover, physiological and biochemical tests enabled strain Gsoil 3054(T) 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 3054(T) (=KACC 12822(T) =DSM 21013(T) =KCTC 22231(T) =LMG 24457(T)).

Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.

A Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046(T), was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046(T) belongs to the family Xanthomonadaceae in the Gammaproteobacteria. The greatest sequence similarity was found with respect to Dyella koreensis KCTC 12359(T) (97.7 %), Dyella japonica IAM 15069(T) (97.4 %), Frateuria aurantia DSM 6220(T) (96.7 %), Fulvimonas soli LMG 19981(T) (96.2 %) and Luteibacter rhizovicinus DSM 16549(T) (96.0 %). The phylogenetic distances from other recognized species within the family Xanthomonadaceae, including Dyella yeojuensis KACC 11405(T), were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA-DNA hybridization experiments showed that the levels of DNA-DNA relatedness between strain Gsoil 3046(T) and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C(17 : 1)omega9c, iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 0) as the major cellular fatty acids and iso-C(13 : 0) 3-OH and iso-C(11 : 0) 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046(T) to the genus Dyella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046(T) represents a novel species in the genus Dyella, for which the name Dyella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3046(T) (=KCTC 12599(T)=DSM 18387(T)).

Nevskia soli sp. nov., isolated from soil cultivated with Korean ginseng.

A Gram-negative bacterium, designated strain GR15-1(T), was isolated from a field cultivated with Korean ginseng. Cells were strictly aerobic, motile with multipolar flagella and rod-shaped. The strain grew optimally at 25-28 degrees C and pH 6.0-7.0. The predominant fatty acids of strain GR15-1(T) were C(18 : 1)omega7c, C(16 : 0) and summed feature 2 (C(14 : 0) 3-OH and/or iso-C(16 : 1) I). The major isoprenoid quinone was ubiquinone 8. The G+C content of the genomic DNA was 63.9 mol%. Phylogenetic analysis showed that strain GR15-1(T) formed a phyletic cluster with Nevskia ramosa Soe1(T), with a 16S rRNA gene sequence similarity of 96.8 %. Based on phenotypic, chemotaxonomic and phylogenetic features, strain GR15-1(T) represents a novel species within the genus Nevskia, for which the name Nevskia soli sp. nov. is proposed. The type strain is GR15-1(T) (=KACC 11703(T) =DSM 19509(T)).

Pseudoxanthomonas spadix sp. nov., isolated from oil-contaminated soil.

A bacterial isolate from a sample of oil-contaminated soil was characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constituted a distinct phyletic line within the genus Pseudoxanthomonas, displaying >3.7 % sequence divergence with respect to recognised Pseudoxanthomonas species. The genus assignment was confirmed by a chemotaxonomic analysis, which revealed the presence of a fatty acid profile characteristic of members of the genus Pseudoxanthomonas (straight-chain saturated, unsaturated and branched-chain fatty acids of the iso/anteiso type and 3-hydroxylated fatty acids) and the presence of a ubiquinone with eight isoprene units (Q-8) as the predominant respiratory quinone. The novel isolate was distinguishable from other members of the genus Pseudoxanthomonas on the basis of a combination of phenotypic properties. The genotypic and phenotypic data show that the strain represents a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas spadix sp. nov. is proposed. The type strain is IMMIB AFH-5(T) (=DSM 18855(T)=CCUG 53828(T)).

Suppression of damping-off disease in host plants by the rhizoplane bacterium Lysobacter sp. strain SB-K88 is linked to plant colonization and antibiosis against soilborne Peronosporomycetes.

We previously demonstrated that xanthobaccin A from the rhizoplane bacterium Lysobacter sp. strain SB-K88 suppresses damping-off disease caused by Pythium sp. in sugar beet. In this study we focused on modes of Lysobacter sp. strain SB-K88 root colonization and antibiosis of the bacterium against Aphanomyces cochlioides, a pathogen of damping-off disease. Scanning electron microscopic analysis of 2-week-old sugar beet seedlings from seeds previously inoculated with SB-K88 revealed dense colonization on the root surfaces and a characteristic perpendicular pattern of Lysobacter colonization possibly generated via development of polar, brush-like fimbriae. In colonized regions a semitransparent film apparently enveloping the root and microcolonies were observed on the root surface. This Lysobacter strain also efficiently colonized the roots of several plants, including spinach, tomato, Arabidopsis thaliana, and Amaranthus gangeticus. Plants grown from both sugar beet and spinach seeds that were previously treated with Lysobacter sp. strain SB-K88 displayed significant resistance to the damping-off disease triggered by A. cochlioides. Interestingly, zoospores of A. cochlioides became immotile within 1 min after exposure to a SB-K88 cell suspension, a cell-free supernatant of SB-K88, or pure xanthobaccin A (MIC, 0.01 microg/ml). In all cases, lysis followed within 30 min in the presence of the inhibiting factor(s). Our data indicate that Lysobacter sp. strain SB-K88 has a direct inhibitory effect on A. cochlioides, suppressing damping-off disease. Furthermore, this inhibitory effect of Lysobacter sp. strain SB-K88 is likely due to a combination of antibiosis and characteristic biofilm formation at the rhizoplane of the host plant.

A clp gene homologue belonging to the Crp gene family globally regulates lytic enzyme production, antimicrobial activity, and biological control activity expressed by Lysobacter enzymogenes strain C3.

Lysobacter enzymogenes strain C3, a biological control agent for plant diseases, produces multiple extracellular hydrolytic enzymes and displays antimicrobial activity against various fungal and oomycetous species. However, little is known about the regulation of these enzymes or their roles in antimicrobial activity and biocontrol. A study was undertaken to identify mutants of strain C3 affected in extracellular enzyme production and to evaluate their biocontrol efficacy. A single mini-Tn5-lacZ(1)-cat transposon mutant of L. enzymogenes strain C3 that was globally affected in a variety of phenotypes was isolated. In this mutant, 5E4, the activities of several extracellular lytic enzymes, gliding motility, and in vitro antimicrobial activity were reduced. Characterization of 5E4 indicated that the transposon inserted in a clp gene homologue belonging to the Crp gene family of regulators. Immediately downstream was a second open reading frame similar to that encoding acetyltransferases belonging to the Gcn5-related N-acetyltransferase superfamily, which reverse transcription-PCR confirmed was cotranscribed with clp. Chromosomal deletion mutants with mutations in clp and between clp and the acetyltransferase gene verified the 5E4 mutant phenotype. The clp gene was chromosomally inserted in mutant 5E4, resulting in complemented strain P1. All mutant phenotypes were restored in P1, although the gliding motility was observed to be excessive compared with that of the wild-type strain. clp mutant strains were significantly affected in biological control of pythium damping-off of sugar beet and bipolaris leaf spot of tall fescue, which was partially or fully restored in the complemented strain P1. These results indicate that clp is a global regulatory gene that controls biocontrol traits expressed by L. enzymogenes C3.