1887

Abstract

A novel actinobacterium, designated strain UDF-1, was isolated from forest soil in Chungnam, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain UDF-1 formed a branched brownish-orange substrate mycelium with spherical or oval spores. No aerial mycelium was formed. Comparative 16S rRNA gene sequence analysis indicated that strain UDF-1 belongs to the genus , showing the highest sequence similarity to NEAU-CX1 (99.2 % 16S rRNA gene sequence similarity), ‘’ NEAU-MES19 (99.0 %), DSM 44398 (98.8 %) and IMSNU 22003 (98.8 %). The predominant menaquinones of strain UDF-1 were MK-10 (H) and MK-10 (H). The cell wall contained -diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C, anteiso-C and iso-C. The genomic DNA G+C content was 73.1 mol%. DNA–DNA relatedness between strain UDF-1 and closely related type strains in the genus was below 30 %. On the basis of the polyphasic analysis conducted in this study, strain UDF-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is UDF-1 (=KACC 18696=NBRC 111826).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001858
2017-06-01
2020-01-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/6/1746.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001858&mimeType=html&fmt=ahah

References

  1. Ørskov J. Investigations into the Morphology of the Ray Fungi Copenhagen: Levin and Munksgaard; 1923
    [Google Scholar]
  2. Li L, Hong K. Micromonospora ovatispora sp. nov. isolated from mangrove soil. Int J Syst Evol Microbiol 2016;66:889–893 [CrossRef]
    [Google Scholar]
  3. Thanaboripat D, Thawai C, Kittiwongwattana C, Laosinwattana C, Koohakan P et al. Micromonospora endophytica sp. nov., an endophytic actinobacteria of Thai upland rice (Oryza sativa). J Antibiot 2015;68:680–684 [CrossRef][PubMed]
    [Google Scholar]
  4. Phongsopitanun W, Kudo T, Mori M, Shiomi K, Pittayakhajonwut P et al. Micromonospora fluostatini sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2015;65:4417–4423 [CrossRef][PubMed]
    [Google Scholar]
  5. Zhang L, Li L, Deng Z, Hong K. Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil. Int J Syst Evol Microbiol 2015;65:4880–4885 [CrossRef][PubMed]
    [Google Scholar]
  6. Shen Y, Zhang Y, Liu C, Wang X, Zhao J et al. Micromonospora zeae sp. nov., a novel endophytic actinomycete isolated from corn root (Zea mays L.). J Antibiot 2014;67:739–743 [CrossRef][PubMed]
    [Google Scholar]
  7. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie van Leeuwenhoek 2014;105:307–315 [CrossRef][PubMed]
    [Google Scholar]
  8. Li C, Liu C, Zhao J, Zhang Y, Gao R et al. Micromonospora maoerensis sp. nov., isolated from a Chinese pine forest soil. Antonie Van Leeuwenhoek 2014;105:451–459 [CrossRef][PubMed]
    [Google Scholar]
  9. Supong K, Suriyachadkun C, Pittayakhajonwut P, Suwanborirux K, Thawai C. Micromonospora spongicola sp. nov., an actinomycete isolated from a marine sponge in the gulf of Thailand. J Antibiot 2013;66:505–509 [CrossRef][PubMed]
    [Google Scholar]
  10. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  11. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriologyvol.4 Baltimore, MD: Williams & Wilkins; 1989; pp.2452–2492
    [Google Scholar]
  12. Gerhardt P, Murray R. G. E, Wood W. A, Krieg N. R. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  13. Conn HJ, Breed RS. The use of the nitrate-reduction test in characterizing bacteria. J Bacteriol 1919;4:267–290[PubMed]
    [Google Scholar]
  14. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966;45:493–496[PubMed]
    [Google Scholar]
  15. Lee HJ, Han SI, Whang KS. Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil. Int J Syst Evol Microbiol 2012;62:856–859 [CrossRef][PubMed]
    [Google Scholar]
  16. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and clustal X version 2.0. Bioinformatics 2007;23:2947–2948 [CrossRef][PubMed]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  21. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  24. Garcia LC, Martínez-Molina E, Trujillo ME. Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum. Int J Syst Evol Microbiol 2010;60:331–337 [CrossRef][PubMed]
    [Google Scholar]
  25. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  26. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970;20:435–443 [CrossRef]
    [Google Scholar]
  27. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy Fairfax, VA: Society for Industrial Microbiology; 1980; pp.227–291
    [Google Scholar]
  28. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  29. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  30. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics Academic Press: London; 1985; pp.267–287
    [Google Scholar]
  31. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  32. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989;39:224–229 [CrossRef]
    [Google Scholar]
  33. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464[CrossRef]
    [Google Scholar]
  34. Fang B, Liu C, Guan X, Song J, Zhao J et al. Two new species of the genus Micromonospora: micromonospora palomenae sp. nov. and Micromonospora harpali sp. nov. isolated from the insects. Antonie van Leeuwenhoek 2015;108:141–150 [CrossRef][PubMed]
    [Google Scholar]
  35. Lee SD, Goodfellow M, Hah YC. A phylogenetic analysis of the genus Catellatospora based on 16S ribosomal DNA sequences, including transfer of Catellatospora matsumotoense to the genus Micromonospora as Micromonospora matsumotoense comb. nov. FEMS Microbiol Lett 1999;178:349–354 [CrossRef][PubMed]
    [Google Scholar]
  36. Hirsch P, Mevs U, Kroppenstedt RM, Schumann P, Stackebrandt E. Cryptoendolithic actinomycetes from antarctic sandstone rock samples: Micromonospora endolithica sp. nov. and two isolates related to Micromonospora coerulea Jensen 1932. Syst Appl Microbiol 2004;27:166–174 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001858
Loading
/content/journal/ijsem/10.1099/ijsem.0.001858
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error