Lysobacter dokdonensis sp. nov., isolated from soil.
ABSTRACT A Gram-negative, non-motile, rod-shaped bacterial strain, DS-58(T), was isolated from a soil sample from Dokdo, an island of Korea, and its taxonomic position was investigated. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-58(T) fell within the family Xanthomonadaceae. The isolate showed 96.9 % 16S rRNA gene sequence similarity with its closest phylogenetic neighbour, Lysobacter niastensis GH41-7(T), and 93.4-95.7 % 16S rRNA gene sequence similarity with other members of the genus Lysobacter. Strain DS-58(T) contained Q-8 as the predominant ubiquinone and iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 1)ω9c as the major fatty acids. The DNA G+C content was 68.1 mol%. Strain DS-58(T) could be distinguished phenotypically from type strains of closely related species of the genus Lysobacter and phylogenetically from all members of the genus Lysobacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-58(T) is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter dokdonensis sp. nov. is proposed. The type strain is DS-58(T) ( = KCTC 12822(T) = DSM 17958(T)).
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ABSTRACT: a b s t r a c t The microbial diversity of different kinds of stains present on the surface of 14 historical documents (nine parchments and five paper letters) was evaluated through a combination of cultural and molecular methods. The samples were recovered using adhesive tape and swabs and were afterwards treated in two different ways: (1) direct inoculation on agar plates; or (2) suspension in physiological solution and plating in specific plates for the growth of bacteria and fungi. The isolated microorganisms, before identification, were selected by two different PCR-based methods e f-ITS and f-CBH, for bacteria and fungi, respectively. The f-ITS method is based on the amplification of the internal transcribed sequence between the bacterial 16S and 23S rDNA. The f-CBH method is a new molecular selection tool oriented to the fungal cellobiohydrolase gene. Both PCR selection methods produced typical profiles, which clustered the isolates in order to reduce them for subsequent sequencing identification through the amplification of the fungal 28S rRNA and the bacterial 16S rRNA genes. The cellulolytic and proteolytic abilities were screened through the use of three plate assays, the Ostazin Brilliant Red H-3B (OBR-HEC), milk agar, and gelatin agar. Massilia timonae, Lysobacter dokdonensis, and strains belonging to the genus Bacillus sp., Microbacterium sp., and Curtobacterium sp. with different fungal members such as Aspergillus fumigatus, Penicillium commune, Mucor spinosus, and Phoma herbarum (all recovered from paper) displayed both biodegradative activities. The parchment isolates with a marked proteolytic activity were Bacillus cereus, Staphylococcus epidermidis, Pseudomonas oryzihabitans, Virgibacillus sp., Micromonospora sp., and again members of the fungal genera Penicillium, Mucor, and Phoma.International Biodeterioration & Biodegradation 05/2012; 70(70):117e125. DOI:10.1016/j.ibiod.2012.01.011 · 2.24 Impact Factor
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ABSTRACT: Dokdo, located east of the mainland of South Korea, is a volcanic island designated as a natural monument of South Korea due to its ecological value. Dokdo is divided into Dongdo and Seodo, islands with geological differences. The soil bacterial communities on Dokdo (Dongdo and Seodo) were analyzed using the pyrosequencing method. There were 1,693 and 1,408 operational taxonomic units (OTU) from Dongdo and Seodo, respectively. The statistical analyses (rarefaction curves as well as Chao1, Shannon, and Simpson indices) showed that bacterial diversity was slightly higher in Dongdo than Seodo. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. From the phylum level down to the species level, the number of classified reads considerably decreased due to the absence of information concerning unculturable or unidentified bacteria to date. Among the 36 phyla identified, three phyla (Proteobacteria, Actinobacteria and Acidobacteria) accounted for around 74.64%. The taxonomic composition was similar at the higher ranks (family and above) between Dongdo and Seodo, but a little different at the genus level. There were also various differences in the relative abundance of taxonomic ranks between Dongdo and Seodo. In particular, the proportion of the genus Acidobacterium (of the phylum Acidobacteria) was about six times higher in Seodo than Dongdo. In addition, the percentage of the genus Mycobacterium (of the phylum Actinobacteria) was nearly three times higher in Seodo than Dongdo, and the proportion of the genus Gaiella was about 3.7 times higher in Dongdo than Seodo. Overall, through the metagenomic analysis, the number of species identified in Dongdo and Seodo was 1,239 and 1,055, respectively. This information on the numerous culturable and unculturable bacteria is expected to help in the screening of new species in Dokdo.The Journal of General and Applied Microbiology 01/2014; 60(2):65-74. DOI:10.2323/jgam.60.65 · 0.60 Impact Factor
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ABSTRACT: A Gram-negative and aerobic bacterium, designated YIM 77875(T), was isolated from a geothermal soil sample collected at Rehai National Park, Tengchong, Yunnan Province, south-west China. Bacterial growth occurred from 37 to 65 °C (optimum 50 °C), pH 6.0-8.0 (optimum pH 7.0) and 0-1 % NaCl (w/v). Cells were rod-shaped and colonies were convex, circular, smooth, yellow and non-transparent. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 77875(T) belongs to the genus Lysobacter. The 16S rRNA gene sequence similarity values between strain YIM 77875(T) and other species of the genus Lysobacter were all below 94.7 %. The polar lipids of strain YIM 77875(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and five unknown phospholipids. The predominant respiratory quinone was Q-8 and the G+C content was 68.8 mol%. Major fatty acids were iso-C(16:0), iso-C(15:0) and iso-C(11:0). On the basis of the morphological and chemotaxonomic characteristics, as well as genotypic data, strain YIM 77875(T) represents a novel species, Lysobacter thermophilus sp. nov., in the genus Lysobacter. The type strain is YIM 77875(T) (CCTCC AB 2012064(T) = KCTC 32020(T)).Antonie van Leeuwenhoek 06/2012; 102(4):643-51. DOI:10.1007/s10482-012-9761-8 · 2.14 Impact Factor