Sung Taik Lee

Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes

Restriction digestion fragments of DNAs extracted from 14 representative strains of Saccharomonospora azurea, “Saccharomonospora caesia,” Saccharomonospora cyanea, Saccharomonospora glauca, and Saccharomonospora viridis and six “Saccharomonospora”-like isolates were separated by electrophoresis, Southern blotted onto nylon membranes, and hybridized by using two rRNA gene probes cloned from Streptomyces griseus subsp. griseus KCTC 9080. The following four restriction endonucleases were used: Bam HI, Sal I, Pvu II, and Xho I. The resultant five ribotype patterns were considered species specific. The genomic diversity revealed by ribotyping indicates that this method can be used to both characterize and identify saccharomonosporae. All of the test strains contained DNA with three rRNA gene clusters.

Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S Ribosomal DNA for Rapid Identification of Saccharomonospora Strains

Twenty-one strains of Saccharomonospora azurea, Saccharomonospora cyanea, Saccharomonospora glauca, Saccharomonospora viridis, and “Saccharomonospora caesia” were examined to evaluate the discriminatory value of 16S ribosomal DNA (rDNA) fingerprints. The 16S rDNAs were amplified by PCR by using oligonucleotide primers complementary to 16S rRNA genes. A restriction fragment length polymorphism (RFLP) analysis of the 16S rDNAs was performed with SmaI and MluI. The four validly described Saccharomonospora species could be differentiated on the basis of their characteristic 16S rDNA restriction patterns. The strains of “S. caesia” gave a restriction pattern identical to that of S. azurea K161T (T = type strain). This result was anticipated from the previous report that S. azurea K161T and the strains of “S. caesia” have identical 16S rRNA sequences. We found that purification of amplified 16S rDNA products following PCR was necessary for our RFLP analysis.

Nocardioides pyridinolyticus sp. nov., a Pyridine-Degrading Bacterium Isolated from the Oxic Zone of an Oil Shale Column

A bacterial strain which is able to degrade pyridine was previously isolated from the oxic zone of an oil shale column and described as Pimelobacter sp. strain OS4T. However, Pimelobacter species have been transferred to the genera Nocardioides and Terrabacter. Strain OS4T was identified as a member of the genus Nocardioides on the basis of chemotaxonomic analysis and phylogenetic inference based on 16S ribosomal DNA (rDNA) sequence analysis. The G+C content of strain OS4T is 72.5 mol%. The cell wall peptidoglycan contains LL-diaminopimelic acid as the diamino acid. The predominant menaquinone is MK-8(H4). The cellular fatty acid profile of strain OS4T is similar to that of the genus Nocardioides. The 16S rDNA similarity of strain OS4T with previously described Nocardioides species is 94.5% +/- 0.7%, and a phylogenetic tree based on 16S rDNA sequences revealed a distinct lineage for strain OS4T within the evolutionary radiation enclosed by the genus Nocardioides. Therefore, on the basis of our data, we propose that strain OS4T should be placed in the genus Nocardioides as a member of a new species, Nocardioides pyridinolyticus. The type strain of the new species is strain OS4 (= KCTC 0074BP).

Isolation and Characterization of Bacteria Capable of Degrading Phenol and Reducing Nitrate Under Low-Oxygen Conditions

Nitrate-reducing bacteria capable of degrading phenol were isolated from natural and contaminated environments under low-oxygen conditions with nitrate-containing media, using phenol as a sole carbon and energy source. A total of 27 bacteria able to degrade phenol and reduce nitrate under low-oxygen conditions were isolated from all of the inoculum samples, regardless of previous phenol contamination. For all of these bacteria, oxygen was an essential requirement for phenol degradation. Nitrate reduction by 19 of the strains was insensitive to 10 mM sodium azide, and these strains were placed into the α- and β-subclasses of Proteobacteria and two were Gram-positive bacteria. To date, the order of Rhizobiales has hardly been reported to have an ability to degrade aromatic compounds. Interestingly, our study showed that all isolates that were placed into the α-subclass of Proteobacteria are in the order of Rhizobiales. Furthermore, the genus Agrobacterium was isolated from most inoculum samples and one genus of Gram-positive bacteria, Staphylococcus, was also isolated. In the case of the remaining eight strains, nitrate reduction was inhibited by 10 mM sodium azide. Of these strains, seven were placed into the γ-subclass of Proteobacteria.

Classification of Nocardioides fulvus IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov.

By 16S rDNA sequence analysis, two strains identified previously as members of the genus Nocardioides, namely Nocardioides fulvus IFO 14399 and Nocardioides sp. ATCC 39419, were found to form lines of descent distinct from the genus Nocardioides. Therefore, the two strains were studied taxonomically in detail by phenotypic, particularly chemotaxonomic, characterization, and by phylogenetic analysis including other related taxa. The genomic DNA G + C contents of N. fulvus IFO 14399 and Nocardioides sp. ATCC 39419 are 70 and 68 mol%, respectively. The two strains contain LL-diaminopimelic acid as the diamino acid in their peptidoglycan, together with L-alanine at position 1 of the peptide subunit. The predominant menaquinone found in the two strains is MK-9(H4). The major cellular fatty acid found in the two strains is anteiso-C15:0 which is a minor component of members of the genus Nocardioides. The diagnostic polar lipid of the two strains is phosphatidylcholine. A phylogenetic tree was constructed which showed that the two strains from evolutionary lineages distinct from other LL-diaminopimelic-acid-containing taxa such as, for example, the genus Nocardioides. On the basis of our data, a new genus, Kribbella gen. nov., and two new species, Kribbella flavida gen. nov., sp. nov. and Kribbellla sandramycini gen. nov., sp. nov., are proposed. It is also proposed that the new genus be included in the family Nocardioidaceae.

Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium.

A p-nitrophenol-degrading bacterial strain was isolated from industrial wastewater. This strain (NSP41T) was identified as a member of the genus Nocardioides from chemotaxonomic characterizations and phylogenetic inference based on 16S rDNA sequence analysis. The G + C content is 71.4 mol%. The diamino acid in the cell-wall peptidoglycan is LL-diaminopimelic acid. The predominant menaquinone is MK-8(H4). The cellular fatty acid profile is similar to those of Nocardioides species. 16S rDNA sequence analysis show that strain NSP41T is the most related to Nocardioides simplex strains with a level of nucleotide similarity of 98.6%. The levels of 16S rDNA similarity between strain NSP41T and other Nocardioides species ranged from 93.8 to 95.1%. This organism is distinguishable from some other Nocardioides species as well as N. simplex strains by DNA-DNA relatedness data. This organism is different from N. simplex strains in some phenotypic characteristics. Therefore, on the basis of the data presented, a new species of the genus Nocardioides, Nocardioides nitrophenolicus, is proposed. The type strain of the new species is strain NSP41T (= KCTC 0457BPT).

Enhanced biodegradation of diesel oil by a newly identified Rhodococcus baikonurensis EN3 in the presence of mycolic acid

Aims:u2002 The aim of the present study was to isolate and characterize a bacterium, strain EN3, capable of using diesel oil as a major carbon and energy source, and to analyse the enhancement of diesel oil degradation by this organism using synthetic mycolic acid (2‐hexyl‐3‐hydroxyldecanoic acid).

Hymenobacter soli sp nov., isolated from grass soil

A taxonomic study using a polyphasic approach was performed on a Gram-stain-negative, aerobic, non-motile, non-spore-forming, rod-shaped bacterium, designated strain PB156(T), isolated from grass soil. Comparative 16S rRNA gene sequence studies showed that the isolate was clearly affiliated with the phylum Bacteroidetes, and most closely related to Hymenobacter soli PB17(T), Hymenobacter antarcticus VUG-A42aa(T) and Hymenobacter glaciei VUG-A130(T), showing 96.4, 96.2 and 95.9u200a% 16S rRNA gene sequence similarity, respectively, while all other species of the genus shared only 89.3-95.2u200a% similarity. The main polyamine present was sym-homospermidine. The predominant menaquinone was MK-7. The major fatty acids were C15u200a:u200a0 iso, summed feature 3 (C16u200a:u200a1ω6c and/or C16u200a:u200a1ω7c/t), C16u200a:u200a1ω5c and C15u200a:u200a0 anteiso. The G+C content of the genomic DNA of strain PB156(T) was 61.7 mol%. The combined genotypic and phenotypic data supported the conclusion that strain PB156(T) represents a novel species of the genus Hymenobacter, for which the name Hymenobacter ruber sp. nov. is proposed. The type strain is PB156(T) (u200a=u200aKCTC 32477(T)u200a=u200aJCM 19433(T)).

A phylogenetic analysis of the genus Saccharomonospora conducted with 16S rRNA gene sequences

Nearly complete sequences of 16S rRNA genes of representative strains of the genus Saccharomonospora were determined following the isolation and cloning of the amplified genes. The sequences were aligned with those of representatives of the family Pseudonocardiaceae, and a phylogenetic tree was inferred by the neighbor-joining method. The genus Saccharomonospora formed a distinct clade within the evolutionary radiation encompassed by the family Pseudonocardiaceae. The average nucleotide similarity value found between the type strains of the four validly described Saccharomonospora species was 97.5% +/- 1.0%. The most distant relationship was found between Saccharomonospora azurea and Saccharomonospora viridis K73 (96.3% similarity). In contrast, Saccharomonospora azurea K161 and Saccharomonospora caesia K163 had identical 16S rRNA gene sequences. The nucleotide sequence data suggest that the genus Saccharomonospora contains several new centers of variation.

Paenibacillus campinasensis sp. nov., a cyclodextrin-producing bacterium isolated in Brazil.

An alkaliphilic, endospore-forming bacterium isolated from Brazilian soil was taxonomically studied and is proposed as a new Paenibacillus species. This organism (strain 324T) was particularly distinguishable from other Paenibacillus species by its ability to grow optimally at pH 10 and 40 degrees C. The DNA G+C content was 5.0 mol%. The diamine acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. MK-7 was the predominant menaquinone and anteiso-C15:0 was the major fatty acid. Levels of 16S rDNA similarity between strain 324T and other Paenibacillus species were 90.6-95.9%. Phylogenetically, strain 324T formed an evolutionary lineage distinct from other species within the evolutionary radiation encompassing the genus Paenibacillus. Based on phenotyic and chemotaxonomic properties, and phylogenetic inference, it is proposed that strain 324T should be placed in the genus Paenibacillus as a new species is strain 324T should be placed in the genus Paenibacilus as a new species, Paenibacillus campinasensis. This type strain of the new species is strain 325T (= KCTC 0364BP).