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Nocardioides islandiensis sp. nov., isolated from soil in Bigeum Island Korea

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Abstract

A novel actinobacterium designated as MSL-26T was isolated from soil in Bigeum Island Korea. A polyphasic study was undertaken to establish the taxonomic position of isolate MSL-26T. Strain MSL-26T was found to have chemical and morphological characteristics similar to Nocardioides. The strain grew optimally at pH 7·5 and 28°C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MSL-26T forms a distinct line of descent within the radiation enclosed by the genus Nocardioides. The cell wall of strain MSL-26T contained LL-2, 6-diaminopimelic acid. The principal menaquinone was MK-8 (H4). The phospholipids detected were diphosphatidylglycerol, phosphatidylglycerol and some unidentified lipids. C18:1 w7c (50.38%) was the major fatty acid. The DNA G + C content of strain MSL-26T was 71.4 mol%. The 16S rRNA gene sequence of strain MSL-26T shares the highest sequence similarity with Nocardioides kribbensis KCTC 19038T (95.78%) and Nocardioides aquaticus DSM 11439T (95.52%). Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain MSL-26T should be classified as a novel species, for which the name Nocardioides islandiensis sp. nov. is proposed. The type strain is MSL-26T (=KCTC 19275T =DSM 19321T)

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References

  • Becker B, Lechevalier MP, Lechevalier HA (1965) Chemical composition of cell-wall preparation from strains of various form genera of aerobic actinomycetes. Appl Microbiol 13:236–243

    PubMed  CAS  Google Scholar 

  • Collins MD, Cockcroft S, Wallbanks S (1994) Phylogenetic analysis of a new LL-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov. Int J Syst Bacteriol 44:523–526

    PubMed  CAS  Google Scholar 

  • Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington, Seattle

    Google Scholar 

  • Felsenstein J (1985) Conference limits on phylogenies: an approach using the bootstrap. Evolution 39:783–789

    Article  Google Scholar 

  • Fitch WM, Margoliash E (1967) Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155:279–284

    Article  PubMed  CAS  Google Scholar 

  • Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005

    Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Google Scholar 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP 18) and a silver loaded ion exchanger as stationery phases. J Liq Chromatogr 5:2359–2367

    Article  CAS  Google Scholar 

  • Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245

    Article  PubMed  CAS  Google Scholar 

  • Lawson PA, Collins MD, Schumann P, Tindall BJ, Hirsch P, Labrenz M (2000) New LL-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmanniella lacustris sp. nov. Syst Appl Microbiol 23:219–229

    PubMed  CAS  Google Scholar 

  • Lechevalier MPA, Lechevalier HA (1980) The chemotaxonomy of Actinomycetes. In: Dietz T. (eds) Actinomycete Taxonomy, Society for Industrial Microbiology, Arlington, VA, p 22

  • Lee SD, Kang SO, Hah YC (2000) Hongia gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 50:191–199

    PubMed  CAS  Google Scholar 

  • Mesbah M, Premachandran U, Whitmann W (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Google Scholar 

  • Miller ES, Woese CR, Brenner S (1991) Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B- 3381 as Aeromicrobium erythreum gen. nov., sp. nov. Int J Syst Bacteriol 41:363–368

    PubMed  CAS  Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Moaledji K (1986) Comparison of gram-staining and alternate methods, KOH test and aminopeptidase activity in aquatic bacteria: their application to numerical taxonomy. J Microbiol Methods 5:303–310

    Article  Google Scholar 

  • Park YH, Yoon JH, Shin YK, Suzuki K, Kudo T, Seino A, Kim HJ, Lee JS, Lee S T (1999) 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. Int J Syst Bacteriol 49:743–752

    PubMed  CAS  Google Scholar 

  • Reasoner DJ, Geldreich EE (1985) A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49(1):1–7

    PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 20:1–6

    Google Scholar 

  • Schippers A, Schumann P, Spröer C (2005) Nocardioides oleivorans sp. nov., a novel crude oil-degrading bacterium. Int J Syst Evol Microbiol 55:1501–1504

    Article  PubMed  CAS  Google Scholar 

  • Sohn K, Hong SG, Bae SK, Chun J (2003) Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al.1999 as Kribbella koreensis comb.nov. Int J Syst Evol Microbiol 53:1505–1507

    Article  CAS  Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    CAS  Google Scholar 

  • Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491

    Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4888

    Article  Google Scholar 

  • Urzì C, Salamone P, Schumann P, Stackebrandt E (2000) Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50:529–536

    PubMed  Google Scholar 

  • Wang YM, Zhang ZS, Xu XL, Ruan JS, Wang Y (2001) Actinopolymorpha singaporensis gen. nov., sp. nov., a novel actinomycete from the tropical rainforest of Singapore. Int J Syst Evol Microbiol 51:467–473

    PubMed  CAS  Google Scholar 

  • Xu P, Li WJ, Xu LH, Jiang CL (2003) A microwave-based method for genomic DNA extraction from actinomycetes. Microbiology (in Chinese) 30:82–84

    CAS  Google Scholar 

  • Yi H, Chun J (2004a) Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54:1295–1299

    Article  PubMed  CAS  Google Scholar 

  • Yi H, Chun J (2004b) Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54:2151–2154

    Article  PubMed  CAS  Google Scholar 

  • Yoon JH, Rhee SK, Lee JS, Park YH, Lee ST (1997) Nocardioides pyridinolyticus sp.nov., a pyridine degrading bacterium isolated from the oxic zone of an oil shale column. Int J Syst Bacteriol 47:933–938

    PubMed  CAS  Google Scholar 

  • Yoon JH, Lee ST, Park YH (1998) Inter- and intra specific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rRNA gene sequences. Int J Syst Bacteriol 48:187–194

    Article  PubMed  CAS  Google Scholar 

  • Yoon JH, Kim IG, Kang KH, Oh TK, Park YH (2004) Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea. Int J Syst Evol Microbiol 54:71–75

    Article  PubMed  CAS  Google Scholar 

  • Yoon JH, Kim IG, Lee MH, Lee CH, Oh TK (2005a) Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. Int J Syst Evol Microbiol 55:809–814

    Article  PubMed  CAS  Google Scholar 

  • Yoon JH, Kim IG, Lee MH, Oh TK (2005b) Nocardioides kribbensis sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 55:1611–1614

    Article  PubMed  CAS  Google Scholar 

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Acknowledgement

This work was supported by the 21C Frontier Microbial Genomics and Application Centre program Korean Ministry of Science & Technology (MOST) and Korea Foundation for International Cooperation of Science & Technology (KICOS) through a grant provided by MOST in Global Partnership Program (No. M60602000001-06E0200-00100), Republic of Korea.

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  1. Functional Metabolomics Research Center, KRIBB, Daejeon, 305-806, Korea

    Syed G. Dastager, Jae-Chan Lee, Yoon-Jung Ju, Dong-Jin Park & Chang-Jin Kim

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  1. Syed G. Dastager
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  2. Jae-Chan Lee
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  3. Yoon-Jung Ju
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  4. Dong-Jin Park
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  5. Chang-Jin Kim
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Correspondence to Chang-Jin Kim.

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Dastager, S.G., Lee, JC., Ju, YJ. et al. Nocardioides islandiensis sp. nov., isolated from soil in Bigeum Island Korea. Antonie van Leeuwenhoek 93, 401–406 (2008). https://doi.org/10.1007/s10482-007-9217-8

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  • DOI: https://doi.org/10.1007/s10482-007-9217-8

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