1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 2

sp. nov., isolated from soil of a rice paddy, and emended description of the genus Anzai 2012 Free

Abstract

A Gram-staining-positive, strictly aerobic bacterium, designated R1, was isolated from a rice paddy in South Korea. Cells were non-motile cocci showing oxidase-negative and catalase-positive activities. Growth of strain R1 was observed at 10–37 °C (optimum, 30 °C) and pH 5.0–9.0 (optimum, pH 7.0). Strain R1 contained iso-C, summed feature 9 (comprising iso-Cω9/10-methyl C ), anteiso-C, iso-C and anteiso-Cω9 as the major fatty acids and MK-8 (H) and MK-8 (H) as the isoprenoid quinones. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, three unidentified phospholipids, four unidentified aminolipids, one unidentified glycolipid and four unidentified lipids. The peptidoglycan type was A4 with an -Lys−-Ser−-Glu interpeptide bridge containing a Gly residue. The G+C content of the genomic DNA was 64.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain R1 was most closely related to the members of the genus , YIM 7505 (97.7 %), TBS-100 (97.5 %) and ST13 (97.2 %). On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that strain R1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is R1 (=KACC 18597=JCM 31060). An emended description of the genus is also proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinobacteria , emended description , Flexivirga oryzae and new taxa, rice paddy
© 2017 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001657
2017-02-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/2/479.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001657&mimeType=html&fmt=ahah

References

  1. Anzai K, Sugiyama T, Sukisaki M, Sakiyama Y, Otoguro M et al. Flexivirga alba gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae. J Antibiot 2011; 64:613–616 [View Article][PubMed]
     [Google Scholar]
  2. Gao R, Liu BB, Yang W, Song PF, Chen W et al. Flexivirga endophytica sp. nov., an endophytic actinobacterium isolated from a leaf of Sweet Basil. Int J Syst Evol Microbiol 2016; 66:3388–3392 [View Article][PubMed]
     [Google Scholar]
  3. Kang W, Hyun DW, Kim PS, Shin NR, Kim HS et al. Flexivirga lutea sp. nov., isolated from the faeces of a crested ibis, Nipponia nippon, and emended description of the genus Flexivirga. Int J Syst Evol Microbiol 2016; 66:3594–3599 [View Article][PubMed]
     [Google Scholar]
  4. Kim JM, Le NT, Chung BS, Park JH, Bae JW et al. Influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl Environ Microbiol 2008; 74:7313–7320 [View Article][PubMed]
     [Google Scholar]
  5. 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 [View Article][PubMed]
     [Google Scholar]
  6. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007; 3:e56 [View Article][PubMed]
     [Google Scholar]
  7. 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]
     [Google Scholar]
  8. Felsenstein J. PHYLIP (Phylogeny Inference Package), Version 3.6a Seattle, WA: University of Washington; 2002
     [Google Scholar]
  9. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 9:1312–1313 [CrossRef]
     [Google Scholar]
  10. Jeon YS, Lee K, Park SC, Kim BS, Cho YJ et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article][PubMed]
     [Google Scholar]
  11. Chang HW, Nam YD, Jung MY, Kim KH, Roh SW et al. Statistical superiority of genome-probing microarrays as genomic DNA–DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. J Microbiol Methods 2008; 75:523–530 [View Article][PubMed]
     [Google Scholar]
  12. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 2006; 33:152–155
     [Google Scholar]
  13. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  14. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article][PubMed]
     [Google Scholar]
  15. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
     [Google Scholar]
  16. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article][PubMed]
     [Google Scholar]
  17. Gomori G. Preparation of buffers for use in enzyme studies. In Colowick SP, Kaplan NO. (editors) Methods in Enzymology New York: Academic Press; 1955 pp 138–146
     [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. (editor) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  19. Dabour N, Lapointe G. Identification and molecular characterization of the chromosomal exopolysaccharide biosynthesis gene cluster from Lactococcus lactis subsp. cremoris SMQ-461. Appl Environ Microbiol 2005; 71:7414–7425 [View Article][PubMed]
     [Google Scholar]
  20. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67 [CrossRef]
     [Google Scholar]
  21. Jeong SH, Park MS, Jin HM, Lee K, Park W et al. Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana. Int J Syst Evol Microbiol 2013; 63:332–338 [View Article][PubMed]
     [Google Scholar]
  22. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002; 4:770–773[PubMed] [CrossRef]
     [Google Scholar]
  23. 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]
  24. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–208 [CrossRef]
     [Google Scholar]
  25. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129 [CrossRef]
     [Google Scholar]
  26. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985; 18:123–156 [CrossRef]
     [Google Scholar]
  27. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  29. Minnikin DE, Patel P V, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001657
Loading
Flexivirga oryzae sp. nov., isolated from soil of a rice paddy, and emended description of the genus Flexivirga Anzai et al. 2012
Int J Syst Evol Microbiol 67, 479 (2017); https://doi.org/10.1099/ijsem.0.001657
/content/journal/ijsem/10.1099/ijsem.0.001657
/content/journal/ijsem/10.1099/ijsem.0.001657
Loading

Data & Media loading...

Supplements

Supplementary File 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