Fodinicola feengrottensis gen. nov., sp. nov., an actinomycete isolated from a medieval mine.

A filamentous, Gram-positive actinobacterium was isolated from acidic rocks in a medieval alum slate mine and was investigated by means of a polyphasic taxonomic approach. A 16S rRNA gene sequence similarity study indicated that strain HKI 0501(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genus Cryptosporangium (family 'Kineosporiaceae') and the other by members of the genera Frankia and Acidothermus (family Frankiaceae and family Acidothermaceae, respectively). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and xylose as the characteristic cell-wall sugar. The muramic acid in the peptidoglycan was found to be N-acetylated. The major menaquinones were MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)) and the fatty acid profile was characterized by the predominance of iso-C(16 : 0), 10-methyl C(17 : 0), C(17 : 1) cis9 and 10-methyl iso-C(18 : 0). The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol and several unknown phospholipids and glycolipids. Mycolic acids were absent. The DNA G+C content was 65 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain HKI 0501(T) represents a novel genus and species, for which the name Fodinicola feengrottensis gen. nov., sp. nov. is proposed. The type strain of Fodinicola feengrottensis is HKI 0501(T) (=DSM 19247(T) =JCM 14718(T)).

Nesterenkonia halophila sp. nov., a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil.

A Gram-positive, non-motile, moderately halophilic, alkalitolerant actinobacterium, designated strain YIM 70179(T), was isolated from a saline soil sample collected from Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan type of strain YIM 70179(T) was A4alpha, l-Lys-Gly-l-Glu. Cells of the isolate contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown glycolipid, MK-8 as major menaquinone and anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0) as major fatty acids. The DNA G+C content was 68.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 70179(T) fell within the radiation of species of the genus Nesterenkonia. Levels of 16S rRNA gene sequence similarity between strain YIM 70179(T) and the type strains of recognized Nesterenkonia species were below 97 %, except to Nesterenkonia halobia DSM 20541(T) (99.6 %), but these two strains exhibited a low level of DNA-DNA relatedness (18.4 %). Based on genetic and phenotypic evidence, it is proposed that strain YIM 70179(T) represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia halophila sp. nov. is proposed. The type strain is YIM 70179(T) (=DSM 16378(T) =KCTC 19048(T)).

Brevibacterium album sp. nov., a novel actinobacterium isolated from a saline soil in China.

A novel Gram-positive, rod-shaped actinobacterium, designated strain YIM 90718(T), was isolated from a saline soil in Xinjiang province, north-west China, and subjected to polyphasic taxonomy. The peptidoglycan type was A1gamma and the cell-wall sugars contained galactose. Phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinone was MK-8(H(2)). The major fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0). All of these chemotaxonomic data assigned the new isolate YIM 90718(T) consistently to the genus Brevibacterium. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 90718(T) formed a distinct phyletic lineage in the genus Brevibacterium and showed the highest sequence similarity (96.2 %) to Brevibacterium samyangense SST-8(T) and low similarity (<95.5 %) to other species of the genus Brevibacterium. On the based of the polyphasic evidence, a novel species, Brevibacterium album sp. nov., is proposed, with the type strain YIM 90718(T) (=DSM 18261(T) =KCTC 19173(T) =CCTCC AB 206112(T)).

Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China.

A previously unknown Gram-positive, obligately aerobic actinomycete, YIM 28A4(T), was isolated from a sample of saline soil collected from the Qaidam Basin in Qinghai Province, north-west China, and was investigated using a polyphasic taxonomic approach. The strain grew well on most of the media tested, producing white to pale-yellow substrate mycelium, white aerial mycelium and straight to flexuous hyphae. The substrate mycelium was well developed and fragmented with age; the aerial mycelium produced long, straight spore chains. The spore chains were composed of non-motile, smooth-surfaced, rod-shaped spores. No diffusible pigments were produced on any of the media tested. The strain grew in the presence of 0-10 % (w/v) NaCl and at pH 6.0-8.0, with optimum growth occurring at 3 % (w/v) NaCl and pH 7.0. It grew at 10-37 degrees C, the optimum growth temperature being 28 degrees C. Whole-cell hydrolysates of strain YIM 28A4(T) contained meso-diaminopimelic acid and no diagnostic sugars. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinones were MK-10, MK-10(H(2)), MK-11 and MK-11(H(2)). The major cellular fatty acids were iso-C(16 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 67.1 mol%. The morphological and chemotaxonomic characteristics of the isolate matched those described for Nocardiopsis species. A phylogenetic analysis based on 16S rRNA gene sequence comparisons confirmed that strain YIM 28A4(T) was a member of the genus Nocardiopsis and most closely related to the type strains Nocardiopsis aegyptia DSM 44442(T) and Nocardiopsis halotolerans DSM 44410(T), showing 98.1 and 97.8 % 16S rRNA gene sequence similarity, respectively. Strain YIM 28A4(T) can be differentiated from these type strains by using phenotypic, phylogenetic and DNA-DNA hybridization data. On the basis of the polyphasic evidence, strain YIM 28A4(T) represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis quinghaiensis sp. nov. is proposed. The type strain is YIM 28A4(T) (=DSM 44739(T) =CGMCC 4.3494(T)).

Biostraticola tofi gen. nov., spec. nov., a novel member of the family Enterobacteriaceae.

Bacterial strain BF36T, isolated from the biofilm of a tufa deposit in a hard water rivulet, was characterized by a polyphasic taxonomic approach. Cells of these organisms were Gram-negative, motile, nonpigmented, rod-shaped, non-endospore-forming, and facultatively anaerobic. Cells, organized in loose consortia, were coated by a massive slime layer. Phylogenetic analyses using 16S rRNA gene sequences showed that strain BF36T was a member of the family Enterobacteriaceae, class Gammaproteobacteria, displaying a moderate degree of relationship (96.5% sequence similarity) to Sodalis glossinidius and "Sodalis pallipedes," intracellular symbionts of the tsetse fly Glossinis morsitans morsitans. Dendrograms of relationship generated by different algorithms consistently grouped isolate BF36T with Sodalis glossinidius, Pragia fontium, Budvicia aquatica, Serratia rubideae, and Brenneria spp (94.7-95.8% similarity) which also share many common metabolic properties. Differences between strain BF36T and Sodalis glossinidius DSM 13495T are seen in motility and in the pattern of substrates utilized. Membership to the family was also confirmed by a fatty acid profile consisting of major amounts of C16:0)and C16:1omega7, by the presence of isoprenoids of the ubiquinone Q8 and menaquinone MK8 types and a DNA G + C content of 54.2 mol%. The decision to classify strain BF36T into a new genus Biostraticola gen. nov. is based on its distant phylogenetic position as compared to any other representative of the family and the significant phenotypic differences to its nearest phylogenetic neighbor, Sodalis glossinidius. BF36T represents the type species, for which the name Biostraticola tofi sp. nov. is proposed. The type strain is BF36T (DSM 19580T; CIP109699T).

Rudanella lutea gen. nov., sp. nov., isolated from an air sample in Korea.

An orange-coloured bacterial strain, designated 5715S-11(T), was isolated from an air sample in Suwon, Republic of Korea. The strain was strictly aerobic, Gram-negative, non-spore-forming, non-flagellated and rod-shaped, frequently forming filaments. Growth of the strain was observed at 4-40 degrees C (optimum, 30 degrees C), pH 6.0-8.0 (optimum, pH 7.0) and 0-2 % (w/v) NaCl. Phylogenetically, strain 5715S-11(T) was shown to be a member of the family Spirosomaceae within the phylum Bacteroidetes. Its closest relatives were Spirosoma linguale LMG 10896(T) (87.9 % 16S rRNA gene sequence similarity) and Larkinella insperata LMG 22510(T) (86.2 % 16S rRNA gene sequence similarity). Predominant cellular fatty acids were summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH), C(16 : 1)omega5c and iso-C(15 : 0). Major polar lipids were phosphatidylethanolamine and unknown aminolipids and polar lipids. On the basis of the evidence from this polyphasic study, strain 5715S-11(T) is considered to represent a novel species of a new genus, for which the name Rudanella lutea gen. nov., sp. nov. is proposed. The type strain of Rudanella lutea is 5715S-11(T) (=KACC 12603(T) =DSM 19387(T)).

Jannaschia pohangensis sp. nov., isolated from seashore sand in Korea.

A Gram-negative, aerobic bacterium, H1-M8(T), was isolated from seashore sand in Korea and then characterized using a polyphasic approach. Cells were short rods (0.7-1.0 x 1.5-2.0 microm) and were motile (each cell having at least one flagellum). Colonies were light-brown, non-pigmented, circular and convex with clear margins. Growth of the strain was observed at 5-35 degrees C, pH 6.0-9.0 and NaCl concentrations up to 8.4 % (w/v). Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation between the novel strain and members of the genus Jannaschia. The sequence similarities between H1-M8(T) and type strains of the genus Jannaschia ranged from 97.0 to 97.8 %. However, DNA-DNA hybridizations between the isolate and type strains of other related species produced low values (21-38 %). The major isoprenoid quinone was Q-10 and the predominant cellular fatty acids were 18 : 1omega7c (68.2 %) and 18 : 0 (10.5 %). The G+C content of the DNA was 63.6 mol%. On the basis of physiological, biochemical and chemotaxonomic traits and data from the comparative 16S rRNA sequence analysis, strain H1-M8(T) represents a novel species of the genus Jannaschia, for which the name Jannaschia pohangensis sp. nov. is proposed. The type strain is H1-M8(T) (=KACC 11609(T) =DSM 19073(T)).

Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine.

Three actinomycetes (strains HKI 0478(T), HKI 0479 and HKI 0480) isolated from the surfaces of rocks in the Feengrotten medieval alum slate mine (Thuringia, Germany) were examined in a polyphasic taxonomic study. The following morphological and chemotaxonomic features supported their classification as members of the genus Kribbella: the presence of ll-diaminopimelic acid in the cell-wall peptidoglycan; glucose together with minor amounts of mannose and ribose as the whole-cell sugars; polar lipids comprising phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospho- and glycolipids; fatty acid profiles characterized by the predominance of anteiso-C(15 : 0), iso-C(16 : 0) and C(16 : 0) 9-methyl; and the presence of MK-9(H(4)) as the main menaquinone. The isolates had almost identical 16S rRNA gene sequences (99.9-100 %) and were most closely related to the type strains of Kribbella jejuensis (98.9 % sequence similarity), Kribbella swartbergensis and Kribbella solani (both 98.8 %). A wide range of genotypic and phenotypic markers as well as the low levels of DNA-DNA relatedness between strain HKI 0478(T) and the type strains of K. jejuensis (41.3 %), K. swartbergensis (18.6 %) and K. solani (14.2 %) distinguished the novel strains from their closest phylogenetic neighbours. On the basis of these results, strain HKI 0478(T) represents a novel member of the genus Kribbella, for which the name Kribbella aluminosa sp. nov. is proposed. The type strain is HKI 0478(T) (=DSM 18824(T) =JCM 14599(T)).

Terrabacter aerolatus sp. nov., isolated from an air sample.

A Gram-positive, strictly aerobic, motile, rod- or coccoid-shaped bacterium, strain 5516J-36(T), was isolated from an air sample from Jeju region, Korea, and its taxonomic position was investigated by a polyphasic approach. The organism grew optimally at 30 degrees C and pH 7.0-8.0. Comparative 16S rRNA gene sequencing studies demonstrated that this strain was highly related phylogenetically to Terrabacter terrae PPLB(T) and Terrabacter tumescens DSM 20308(T), showing 98.9 % sequence similarity to both strains. However, the DNA-DNA reassociation values between 5516J-36(T) and the type strains of Terrabacter terrae and Terrabacter tumescens were low (51 and 48 %, respectively). The peptidoglycan type was A3gamma, the predominant menaquinone was MK-8(H(4)), the polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and an unidentified phosphoglycolipid and the whole-cell sugars were glucose, ribose, rhamnose, xylose and galactose. Mycolic acids were absent. The major fatty acids (>5 % of total fatty acids) were iso-C(15 : 0), iso-C(16 : 0), iso-C(14 : 0), iso-C(17 : 0) and anteiso-C(15 : 0). The DNA G+C content was 71.7 mol%. On the basis of the above data, it is proposed that strain 5516J-36(T) represents a novel species, Terrabacter aerolatus sp. nov. The type strain of Terrabacter aerolatus is 5516J-36(T) (=KACC 20556(T) =DSM 18562(T)).

Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia.

A Gram-positive, motile, short-rod-shaped strain, designated YIM 004(T), was isolated from a forest-soil sample collected from Lijiang, Yunnan Province, China, and was investigated using a polyphasic taxonomic approach. The isolate contained chemotaxonomic markers that corresponded to those of its phylogenetic neighbour, Georgenia muralis, i.e. it possessed peptidoglycan type A4 alpha with lysine as the diagnostic cell-wall diamino acid, the predominant menaquinone was MK-8(H(4)) and the major fatty acid was ai-C(15 : 0). The G+C content of the genomic DNA was 72.9 mol%. Strain YIM 004(T) exhibited a 16S rRNA gene sequence similarity of 97.3 % and a DNA-DNA relatedness value of 18 % with respect to G. muralis DSM 14418(T). On the basis of the phenotypic and genotypic differences between the isolate and G. muralis, strain YIM 004(T) represents a novel species of the genus Georgenia, for which the name Georgenia ruanii sp. nov. is proposed. The type strain is YIM 004(T) (=CCTCC AB 204065(T)=DSM 17458(T)=KCTC 19029(T)). In addition, an emended description of the genus Georgenia is presented.

Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil.

Two bacterial strains, R2A1-13(T) and R2A45-3(T), were isolated from greenhouse soils in Korea. The cells of both strains were Gram-negative, aerobic and rod-shaped. 16S rRNA gene sequence analysis placed the isolates in the genus Flavobacterium within the family Flavobacteriaceae. Strain R2A1-13(T) was found to be related to Flavobacterium columnare IAM 14301(T), Flavobacterium saliperosum CGMCC1.3801(T) and Flavobacterium croceum EMB47(T), with sequence similarities of 96.8, 95.0 and 94.6 %, respectively. Strain R2A45-3(T) was found to be related to F. croceum EMB47(T) and Flavobacterium aquatile ATCC 11947(T), with sequence similarities of 94.7 and 94.6 %, respectively. Both strains contained iso-C(15 : 0) and iso-C(16 : 0) as the main fatty acids and contained a menaquinone with six isoprene units (MK-6) as the major isoprenoid quinone. The G+C contents of the DNA from strains R2A1-13(T) and R2A45-3(T) were 34 and 38 mol%, respectively. A polyphasic taxonomic study revealed that these strains belong to two novel species within the genus Flavobacterium, for which the names Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov. are proposed. The type strains of F. terrae sp. nov. and F. cucumis sp. nov. are R2A1-13(T) (=KACC 11731(T)=DSM 18829(T)) and R2A45-3(T) (=KACC 11732(T)=DSM 18830(T)), respectively.

Gene sequence phylogenies of the family microbacteriaceae.

The type strains of 32 species of 13 genera of the family Microbacteriaceae were analysed with respect to gene-coding phylogeny for DNA gyrase subunit B (gyrB), RNA-polymerase subunit B (rpoB), recombinase A (recA), and polyphosphate kinase (ppk). The resulting gene trees were compared with the 16S rRNA gene phylogeny of the same strains. The topology of neighbour-joining and maximum parsimony phylogenetic trees, based on nucleic-acid sequences and protein sequences of housekeeping genes, differed from one another, and no gene tree was identical to that of the 16S rRNA gene tree. Most genera analysed containing >1 strain formed phylogenetically coherent taxa. The three pathovars of Curtobacterium flaccumfaciens clustered together to the exclusion of the type strains of other Curtobacterium species in all DNA - and protein-based analyses. In no tree did the distribution of a major taxonomic marker, i.e., diaminobutyric acid versus lysine and/or ornithine in the peptidoglycan, or acyl type of peptidoglycan, correlate with the phylogenetic position of the organisms. The changing phylogenetic position of Agrococcus jenensis was unexpected: This strain defined individual lineages in the trees based on 16S rRNA and gyrB and showed identity with Microbacterium saperdae in the other three gene trees.

UV-radiation-induced formation of DNA bipyrimidine photoproducts in Bacillus subtilis endospores and their repair during germination.

The spore photoproduct (SP) is the main DNA lesion after UV-C irradiation, and its repair is crucial for the resistance of spores to UV. The aims of the present study were to assess the formation and repair of bipyrimidine photoproducts in spore DNA of various Bacillus subtilis strains using a sensitive HPLC tandem mass spectrometry assay. Strains deficient in nucleotide excision repair, spore photoproduct lyase, homologous recombination (recA), and with wild-type repair capability were investigated. Additionally, one strain deficient in the formation of major small, acid-soluble spore proteins (SASPs) was tested. In all SASP wild-type strains, UV-C irradiation generated almost exclusively SP (>95 %) but also a few by-photoproducts. In the major SASP-deficient strain, SP and by-photoproducts were generated in equal quantities. The status time of 60 min, >75% of the SP was repaired in wild-type strains and in the SASP-deficient strain, while half of the photoinduced SP was removed in the recA-deficient strain. SP-lyase-deficient spores repaired 20% of the SP produced. Thus, SP lyase, with respect to nucleotide excision repair, has a remarkable impact on the removal of SP upon spore germination.

Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea.

An orange-coloured bacterial strain, designated R2A15-11(T), was isolated from greenhouse soil. The strain was found to be strictly aerobic, Gram-negative, non-spore-forming and non-flagellated. The cells were short rods (0.7-0.9x1.0-1.5 mum) and produced flexirubin. Growth of the strain was observed at 10-35 degrees C, pH 5.0-8.0 and 0-3 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C(15 : 0), iso-C(15 : 1) G, iso-C(17 : 0) 3-OH and summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c). The genomic DNA G+C content was 45.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence of strain R2A15-11(T) revealed a clear affiliation with the phylum Bacteroidetes, and the highest levels of sequence similarity were found with respect to Terrimonas ferruginea ATCC 13524(T) (91.5 %), Terrimonas lutea DY(T) (90.2 %), Niastella yeongjuensis GR20-13(T) (89.9 %) and Niastella koreensis GR20-10(T) (89.7 %). On the basis of the polyphasic evidence from this study, strain R2A15-11(T) represents a novel genus and species, for which the name Niabella aurantiaca gen. nov., sp. nov. is proposed. The type strain of Niabella aurantiaca is R2A15-11(T) (=KACC 11698(T)=DSM 17617(T)).

Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea.

Two bacterial strains, designated GH34-4(T) and GH41-7(T), were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4(T) showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3(T) (97.5 %) and Lysobacter koreensis Dae16(T) (96.4 %), and strain GH41-7(T) showed highest sequence similarity to Lysobacter antibioticus DSM 2044(T) (97.5 %), Lysobacter enzymogenes DSM 2043(T) (97.5 %) and Lysobacter gummosus ATCC 29489(T) (97.4 %). Levels of DNA-DNA relatedness indicated that strains GH34-4(T) and GH41-7(T) represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4(T) and GH41-7(T) were iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 1)omega9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4(T) and GH41-7(T) were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4(T)=KACC 11587(T)=DSM 18244(T)) and Lysobacter niastensis sp. nov. (type strain GH41-7(T)=KACC 11588(T)=DSM 18481(T)) are proposed.

Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria.

Two strains, designated WB 3.4-79(T) and WB 3.3-25, were isolated from a hard-water sample collected from the Westerhöfer Bach, Lower Saxony, Germany. The strains shared 100 % DNA-DNA relatedness, indicating membership of the same genospecies. This close relationship was supported by identical 16S rRNA gene sequences and high similarities in fatty acid composition and biochemical characteristics. The G+C content of the genomic DNA of strain WB 3.4-79(T) was 48.5 mol% and the predominant ubiquinone was Q-8. Major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Major fatty acids (>10 %) were C(16 : 0) and C(16 : 1)omega7c. Polyhydroxybutyrate and polyphosphate granules as well as unidentified enterosomes and a polar organelle are visible by electron microscopy. Comparative 16S rRNA gene sequence analysis indicated that the isolates were placed within the class Betaproteobacteria, remotely related to Chitinibacter tainanensis DSM 15459(T), Silvimonas terrae KCTC 12358(T), Formivibrio citricus DSM 6150(T) and Iodobacter fluviatilis DSM 3764(T). On the basis of phylogenetic and phenotypic distinctness, we propose a novel genus, Deefgea gen. nov., with Deefgea rivuli sp. nov. as the type species. The type strain of Deefgea rivuli is strain WB 3.4-79(T) (=DSM 18356(T)=CIP 109326(T)).

Role of DNA repair by nonhomologous-end joining in Bacillus subtilis spore resistance to extreme dryness, mono- and polychromatic UV, and ionizing radiation.

The role of DNA repair by nonhomologous-end joining (NHEJ) in spore resistance to UV, ionizing radiation, and ultrahigh vacuum was studied in wild-type and DNA repair mutants (recA, splB, ykoU, ykoV, and ykoU ykoV mutants) of Bacillus subtilis. NHEJ-defective spores with mutations in ykoU, ykoV, and ykoU ykoV were significantly more sensitive to UV, ionizing radiation, and ultrahigh vacuum than wild-type spores, indicating that NHEJ provides an important pathway during spore germination for repair of DNA double-strand breaks.

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

A polyphasic study was carried out to clarify the taxonomic position of a Gram-negative bacterium isolated from soil cultivated with Korean ginseng in the Eumseong region of Korea. The novel strain, GP25-8(T), grew optimally at pH 6-7, 28 degrees C and 0-1 % NaCl (w/v). The major fatty acids were C(18 : 1)omega7c, summed feature 3 (C(16 : 1)omega7c/C(15 : 0) iso 2-OH) and C(16 : 0) (together representing 71.2 % of the total). The 16S rRNA gene sequence similarities between strain GP25-8(T) and members of the genus Burkholderia ranged from 94.7 to 97.4 %, indicating that this novel strain was phylogenetically related to members of that genus. The novel strain showed the highest sequence similarities to Burkholderia caryophylli ATCC 25418(T) (97.4 %) and Burkholderia phenazinium LMG 2247(T) (97.2 %); the levels of DNA-DNA hybridization with these strains were 28 and 12 %, respectively. These results support the conclusion that strain GP25-8(T) represents a novel species within the genus Burkholderia, for which the name Burkholderia soli sp. nov. is proposed. The type strain is GP25-8(T) (=KACC 11589(T)=DSM 18235(T)).

The phylogenetic significance of peptidoglycan types: Molecular analysis of the genera Microbacterium and Aureobacterium based upon sequence comparison of gyrB, rpoB, recA and ppk and 16SrRNA genes.

The type strains of 27 species of the genus Microbacterium, family Microbacteriaceae, were analyzed with respect to the phylogeny of the housekeeping genes coding for DNA gyrase subunit B (gyrB), RNA-polymerase subunit B (rpoB), recombinase A (recA) and polyphosphate kinase (ppk). The resulting gene trees were compared to the 16S rRNA gene phylogeny of the same species. The topology of neighbour-joining and maximum parsimony phylogenetic trees based upon nucleic acid sequences and protein sequences of housekeeping genes differed among each other and no gene tree was identical to that of the 16S rRNA gene tree. Only some species showed consistent clustering by all genes analyzed, but the majority of species branched with different neighbours in most gene trees. The failure to phylogenetically cluster type strains into two groups based upon differences in the amino acid composition of peptidoglycan on the basis of 16S rRNA gene sequence similarity, once leading to the union of the genera Microbacterium and Aureobacterium, was also seen in the analysis of recA, rpoB and gyrB gene and protein phylogenies. Analysis of the pkk gene and protein as well as of a concatenate tree, combining sequences of all five genes (total of 3.700 nucleotides), sees members of the former genus Aureobacterium and other type strains with lysine as diagnostic diamino acid to form a coherent cluster that branches within the radiation of Microbacterium species with ornithine in the peptidoglycan.

Taxonomic characterization of members of the genus Corallococcus: molecular divergence versus phenotypic coherency.

Corallococcus coralloides DSM 2259(T), Corallococcus exiguus DSM 14696(T), Corallococcus macrosporus DSM 14697(T) and more than 35 strains identified as members of Corallococcus on the basis of morphology were subjected to partial sequences analysis of three housekeeping genes (lepA, fusA and rpoB), complementing a recent phylogenetic analysis based on genes coding for 16S rRNA and gyrB. Phylogenetic analysis of each gene, generated by maximum likelihood and two different additive treeing algorithms, resulted in the separate position of C. macrosporus DSM 14697(T) and a few Corallococcus strains that were more closely related to Myxococcus xanthus than to the other members of Corallococcus. The latter strains formed three clearly separate clusters by 16S rRNA gene phylogeny. This relationship, however, was only partially recovered by the other gene trees. Group 1, embracing the type strains of C. coralloides and C. exiguus, only emerged as a coherent cluster in the 16S rRNA gene tree. In all other gene trees this cluster embraced organisms of cluster 3, which either formed coherent subclusters (gyrB, lepA) or which appeared polyphyletic (fusA, rpoB). Group 2 organisms consistently constituted a monophyletic cluster, though their branching within the gene trees differed. A concatenated tree, based on the analysis of about 5400 nucleotides of all five partial genes was most similar to the 16S rRNA gene tree. In order to determine whether the individual clusters that emerged by 16S rRNA gene analysis (>99.1% intracluster similarities) show phenetic properties that would allow their description as new species, a few strains of each group were subjected to the analysis of whole cell fatty acid and physiological properties. Riboprint patterns were generated for some members of group 1. While the DNA-DNA reassociation values and riboprint patterns confirmed the genomic heterogeneity of members of cluster 1, none of the other properties investigated were sufficiently discriminative to allow the formal description of strain clusters as new species.