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Abstract

A bacterial strain, PSGM2-16, was isolated from a pot of paddy soil grown with rice in Suwon region, Republic of Korea, and was characterized as having aerobic, Gram-stain-positive, short-rod-shaped cells with one polar flagellum. The 16S rRNA gene sequence of strain PSGM2-16 revealed the highest sequence similarities with DMZ1 (97.4 %), YIM C003 (97.2 %) and R-Ac013 (97.0 %), and the phylogenetic tree showed that strain PSGM2-16 formed a subgroup with HB09001 and YIM C003 within the family . The major fatty acids (>10 % of the total fatty acids) of strain PSGM2-16 were iso-C, Cω8 and iso-C. The predominant menaquinone was MK-8(H). The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three aminophospholipids and two phospholipids. The peptidoglycan was type A4γ with -diaminopimelic acid as the diagnostic diamino acid. DNA–DNA hybridization values between strain PSGM2-16 and closely related taxa were much less than 70 %. The genomic DNA G+C content of strain PSGM2-16 was 70.0 mol%. On the basis of the evidence presented, it is concluded that strain PSGM2-16 represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of the type species is PSGM2-16 ( = KACC 17299 = DSM 27137 = NBRC 109598).

Funding
This study was supported by the:
  • National Academy of Agricultural Science, Rural Development Administration (Award project no. PJ01095)
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2015-09-01
2024-12-03
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References

  1. Breznak J.A., Costilow R.N. ( 1994;). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137154. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  2. Collins M.D., Dorsch M., Stackebrandt E. ( 1989;). Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. Int J Syst Bacteriol 39 16 [View Article].
    [Google Scholar]
  3. Collins M.D., Routh J., Saraswathy A., Lawson P.A., Schumann P., Welinder-Olsson C., Falsen E. ( 2004;). Arsenicicoccus bolidensis gen. nov. sp. nov., a novel actinomycete isolated from contaminated lake sediment. Int J Syst Evol Microbiol 54 605608 [View Article] [PubMed].
    [Google Scholar]
  4. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [View Article] [PubMed].
    [Google Scholar]
  5. Fitch W.M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406416 [View Article].
    [Google Scholar]
  6. Gonzalez J.M., Saiz-Jimenez C. ( 2002;). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4 770773 [View Article] [PubMed].
    [Google Scholar]
  7. Groth I., Schumann P., Martin K., Schuetze B., Augsten K., Kramer I., Stackebrandt E. ( 1999;). Ornithinicoccus hortensis gen. nov. sp. nov., a soil actinomycete which contains l-ornithine. Int J Syst Bacteriol 49 17171724 [View Article] [PubMed].
    [Google Scholar]
  8. Groth I., Schumann P., Weiss N., Schuetze B., Augsten K., Stackebrandt E. ( 2001;). Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with l-ornithine in the peptidoglycan. Int J Syst Evol Microbiol 51 8187 [PubMed]. [CrossRef]
    [Google Scholar]
  9. Groth I., Schumann P., Schütze B., Augsten K., Stackebrandt E. ( 2002;). Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov., two novel actinobacteria isolated from a cave. Int J Syst Evol Microbiol 52 7784. [CrossRef]
    [Google Scholar]
  10. Hamada M., Tamura T., Yamamura H., Suzuki K., Hayakawa M. ( 2012;). Lysinimicrobium mangrovi gen. nov. sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove. Int J Syst Evol Microbiol 62 17311735 [View Article] [PubMed].
    [Google Scholar]
  11. Jung S.Y., Kim H.S., Song J.J., Lee S.G., Oh T.K., Yoon J.H. ( 2006;). Kribbia dieselivorans gen. nov. sp. nov., a novel member of the family Intrasporangiaceae . Int J Syst Evol Microbiol 56 24272432 [View Article] [PubMed].
    [Google Scholar]
  12. Kageyama A., Takahashi Y., Seki T., Tomoda H., O¯mura S. ( 2005;). Oryzihumus leptocrescens gen. Nov. sp. nov.. Int J Syst Evol Microbiol 55 25552559 [View Article] [PubMed].
    [Google Scholar]
  13. Kageyama A., Haga T., Kasai H., Shizuri Y., O¯mura S., Takahashi Y. ( 2008a;). Marihabitans asiaticum gen. nov. sp. nov., a meso-diaminopimelic acid-containing member of the family Intrasporangiaceae . Int J Syst Evol Microbiol 58 24292432 [View Article] [PubMed].
    [Google Scholar]
  14. Kageyama A., Matsumoto A., O¯mura S., Takahashi Y. ( 2008b;). Humibacillus xanthopallidus gen. nov., sp. nov.. Int J Syst Evol Microbiol 58 15471551. [CrossRef]
    [Google Scholar]
  15. Kalakoutskii L.V. ( 1989;). Genus Intrasporangium Kalakoutskii, Kirillova and Krassilnikov 1967, 79AL . . In Bergey's Manual of Systematic Bacteriology vol. 4, pp. 23952397. Edited by Williams S. T., Sharpe M. E., Holt J. G. Baltimore, MD: Williams & Wilkins;.
    [Google Scholar]
  16. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62 716721 [View Article] [PubMed].
    [Google Scholar]
  17. Lee S.D. ( 2006;). Phycicoccus jejuensis gen. nov. sp. nov., an actinomycete isolated from seaweed. Int J Syst Evol Microbiol 56 23692373 [View Article] [PubMed].
    [Google Scholar]
  18. Lee S.D., Lee D.W. ( 2007;). Lapillicoccus jejuensis gen. nov. sp. nov., a novel actinobacterium of the family Intrasporangiaceae, isolated from stone. Int J Syst Evol Microbiol 57 27942798 [View Article] [PubMed].
    [Google Scholar]
  19. Lim J.M., Kim S.J., Hamada M., Ahn J.H., Weon H.Y., Suzuki K., Ahn T.Y., Kwon S.W. ( 2014;). Oryzihumus terrae sp. nov. isolated from soil and emended description of the genus Oryzihumus . Int J Syst Evol Microbiol 64 23952399 [View Article] [PubMed].
    [Google Scholar]
  20. Martin K., Schumann P., Rainey F.A., Schuetze B., Groth I. ( 1997;). Janibacter limosus gen. nov. sp. nov., a new actinomycete with meso-diaminopimelic acid in the cell wall. Int J Syst Bacteriol 47 529534 [View Article] [PubMed].
    [Google Scholar]
  21. Maszenan A.M., Seviour R.J., Patel B.K.C., Schumann P., Burghardt J., Tokiwa Y., Stratton H.M. ( 2000;). Three isolates of novel polyphosphate-accumulating gram-positive cocci, obtained from activated sludge, belong to a new genus, Tetrasphaera gen. nov. and description of two new species, Tetrasphaera japonica sp. nov. and Tetrasphaera australiensis sp. nov.. Int J Syst Evol Microbiol 50 593603 [View Article] [PubMed].
    [Google Scholar]
  22. Minnikin D.E., O'Donnell A.G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J.H. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2 233241 [View Article].
    [Google Scholar]
  23. Prauser H., Schumann P., Rainey F.A., Kroppenstedt R.M., Stackebrandt E. ( 1997;). Terracoccus luteus gen. nov. sp. nov., an LL-diaminopimelic acid-containing coccoid actinomycete from soil. Int J Syst Bacteriol 47 12181224 [View Article] [PubMed].
    [Google Scholar]
  24. Pruesse E., Peplies J., Glöckner F.O. ( 2012;). sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28 18231829 [View Article] [PubMed].
    [Google Scholar]
  25. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425.
    [Google Scholar]
  26. Sasser M. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc;.
    [Google Scholar]
  27. Schumann P., Prauser H., Rainey F.A., Stackebrandt E., Hirsch P. ( 1997;). Friedmanniella antarctica gen. nov. sp. nov., an ll-diaminopimelic acid-containing actinomycete from Antarctic sandstone. Int J Syst Bacteriol 47 278283 [View Article] [PubMed].
    [Google Scholar]
  28. Seldin L., Dubnau D. ( 1985;). Deoxyribonucleic acid homology among Bacillus polymyxa, Bacillus macerans, Bacillus azotofixans, and other nitrogen-fixing Bacillus strains. Int J Syst Bacteriol 35 151154 [View Article].
    [Google Scholar]
  29. Stackebrandt E., Schumann P. ( 2000;). Description of Bogoriellaceae fam. nov. Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae . Int J Syst Evol Microbiol 50 12791285 [View Article] [PubMed].
    [Google Scholar]
  30. Stackebrandt E., Rainey F.A., Ward-Rainey N.L. ( 1997;). Proposal for a new hierarchic classification system, Actinobacteria classis nov.. Int J Syst Bacteriol 47 479491 [View Article].
    [Google Scholar]
  31. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28 27312739 [View Article] [PubMed].
    [Google Scholar]
  32. Tóth E.M., Kéki Z., Bohus V., Borsodi A.K., Márialigeti K., Schumann P. ( 2012;). Aquipuribacter hungaricus gen. nov. sp. nov., an actinobacterium isolated from the ultrapure water system of a power plant. Int J Syst Evol Microbiol 62 556562 [View Article] [PubMed].
    [Google Scholar]
  33. Wang Z.-G., Wang Y.-X., Liu J.-H., Chen Y.-G., Zhang X.-X., Wen M.-L., Xu L.-H., Peng Q., Cui X.-L. ( 2009;). Fodinibacter luteus gen. nov. sp. nov., an actinobacterium isolated from a salt mine. Int J Syst Evol Microbiol 59 21852190 [View Article] [PubMed].
    [Google Scholar]
  34. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 697703.
    [Google Scholar]
  35. Weon H.Y., Son J.A., Yoo S.H., Kim B.Y., Kwon S.W., Schumann P., Kroppenstedt R., Stackebrandt E. ( 2010;). Terrabacter aeriphilus sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 60 11301134 [View Article] [PubMed].
    [Google Scholar]
  36. Xiao C., Huang H., Ye J., Wu X., Zhu J., Zhan B., Bao S. ( 2011;). Ornithinibacter aureus gen. nov. sp. nov., a novel member of the family Intrasporangiaceae . Int J Syst Evol Microbiol 61 659664 [View Article] [PubMed].
    [Google Scholar]
  37. Yi H., Schumann P., Sohn K., Chun J. ( 2004;). Serinicoccus marinus gen. nov. sp. nov., a novel actinomycete with l-ornithine and l-serine in the peptidoglycan. Int J Syst Evol Microbiol 54 15851589 [View Article] [PubMed].
    [Google Scholar]
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