1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 2

sp. nov., isolated from rice paddy soil No Access

Abstract

Three pale-red-pigmented, Gram-stain-negative, coccobacilli-shaped, motile and strictly aerobic bacteria, strains MO17, MO41 and NPKOSM1, were isolated from rice paddy soil. Colonies were circular with entire edges, convex and pale red. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MO17, MO41 and NPKOSM1 belonged to the genus and were closely related to FW-3 (98.2 %), YC6724 (98.0 %), 5N26 (98.0 %), BUT-5 (97.8 %), YIM 78007 (97.7 %), TH-G33 (97.6 %) and DS-48 (96.8 %). The DNA–DNA hybridization values between strains MO17, MO41 and NPKOSM1 were 84–92 %, and the values between the three strains and their close phylogenetic relatives were also below 70 %. The major cellular fatty acids were C 7, C and summed feature 3 (C 7c and/or iso-C 2OH). The predominant respiratory quinone was identified as Q-10. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and two unknown phospholipids. Based on their distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus for which the name sp. nov. is proposed. The type strain is MO17 (=KACC 19933=NBRC 114495).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): rice paddy soil , Roseomonas and sp. nov.
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005251
2022-02-16
2024-04-24
Loading full text...

Full text loading...

References

  1. Kim S-J, Weon H-Y, Ahn J-H, Hong S-B, Seok S-J et al. Roseomonas aerophila sp. nov., isolated from air. Int J Syst Evol Microbiol 2013; 63:2334–2337 [View Article] [PubMed]
     [Google Scholar]
  2. Chaudhary DK, Kim J. Roseomonas nepalensis sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67:981–987 [View Article] [PubMed]
     [Google Scholar]
  3. Lee H-J, Whang K-S. Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field. Int J Syst Evol Microbiol 2020; 70:2132–2136 [View Article] [PubMed]
     [Google Scholar]
  4. Cho GY, Whang KY. Sandarakinorhabdus rubra sp. nov., and Sandarakinorhabdus oryzae sp. nov., isolated from oxidized rice paddy soil. Int J Syst Evol Microbiol 2021; 71:004722
     [Google Scholar]
  5. Lee H-J, Han S-I, Whang K-S. Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil. Int J Syst Evol Microbiol 2012; 62:856–859 [View Article] [PubMed]
     [Google Scholar]
  6. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  7. 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 [View Article] [PubMed]
     [Google Scholar]
  8. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  10. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  12. 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 [View Article] [PubMed]
     [Google Scholar]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  15. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  16. 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 [View Article]
     [Google Scholar]
  17. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  18. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  19. Jacobson E, Grauville WC, Fogs CE. Color Harmony Manual, 4th edn. Chicago: Container Corporation of America; 1958
     [Google Scholar]
  20. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  21. Zhang J, Gu T, Zhou Y, He J, Zheng L-Q et al. Terrimonas rubra sp. nov., isolated from a polluted farmland soil and emended description of the genus Terrimonas. Int J Syst Evol Microbiol 2012; 62:2593–2597 [View Article] [PubMed]
     [Google Scholar]
  22. Conn HJ, Breed RS. The use of the nitrate-reduction test in characterizing bacteria. J Bacteriol 1919; 4:267–290 [View Article] [PubMed]
     [Google Scholar]
  23. Smibert RM, Krieg NR. eds Manual of Method for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  24. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  25. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
     [Google Scholar]
  26. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromat 2006; 5:2359–2367 [View Article]
     [Google Scholar]
  27. 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
     [Google Scholar]
  28. He D, Kim J-K, Jiang X-Y, Park H-Y, Sun C et al. Roseomonas sediminicola sp. nov., isolated from fresh water. Antonie van Leeuwenhoek 2014; 105:191–197 [View Article]
     [Google Scholar]
  29. Kim DU, Ka JO. Roseomonas soli sp. nov., isolated from an agricultural soil cultivated with Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 2014; 64:1024–1029 [View Article] [PubMed]
     [Google Scholar]
  30. Chung EJ, Yoon HS, Kim KH, Jeon CO, Chung YR. Roseomonas oryzicola sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2015; 65:4839–4844 [View Article] [PubMed]
     [Google Scholar]
  31. Wang C, Deng S, Liu X, Yao L, Shi C et al. Roseomonas eburnea sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2016; 66:385–390 [View Article] [PubMed]
     [Google Scholar]
  32. Dong L, Ming H, Yin Y-R, Duan Y-Y, Zhou E-M et al. Roseomonas alkaliterrae sp. nov., isolated from an alkali geothermal soil sample in Tengchong, Yunnan, South-West China. Antonie van Leeuwenhoek 2014; 105:899–905 [View Article] [PubMed]
     [Google Scholar]
  33. Jiang C-Y, Dai X, Wang B-J, Zhou Y-G, Liu S-J. Roseomonas lacus sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2006; 56:25–28 [View Article] [PubMed]
     [Google Scholar]
  34. Yoon JH, Kang SJ, Oh HW, Oh TK. Roseomonas terrae sp. nov. Int J Syst Evol Microbiol 2007; 57:2485–2488 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005251
Loading
Roseomonas rubea sp. nov., isolated from rice paddy soil
Int J Syst Evol Microbiol 72, 005251 (2022); https://doi.org/10.1099/ijsem.0.005251
/content/journal/ijsem/10.1099/ijsem.0.005251
/content/journal/ijsem/10.1099/ijsem.0.005251
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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