1887

Abstract

A bacterial strain, 17J42-9, was isolated from a soil sample collected on Jeju Island, Republic of Korea. Cells were observed to be Gram-stain negative and rod-shaped. Colonies were observed to be orange in colour on R2A agar. Analysis of 16S rRNA gene sequences showed that high levels of 16S rRNA sequence similarity were shared between 17J42-9 and IMCC1731 (98.2 %), Gsoil 085 (98.2 %) and ZZ-4 (97.8 %). Growth of strain 17J42-9 was observed at 10–37 °C, pH 6.0–8.5 and in the presence of 0–0.5 % NaCl. The genomic G+C content was calculated to be 38.6 mol%. The predominant respiratory quinone of the isolate was found to be MK-7; the major fatty acids were identified as summed feature 3 (C 7 and/or C 6) (34.1 %), Ciso (23.4 %) and Ciso 3-OH (10.8 %). The major polar lipids were found to be phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. The phenotypic and chemotaxonomic data support the affiliation of strain 17J42-9 with the genus . However, the DNA–DNA relatedness between the isolate and its closest phylogenetic neighbours was lower than 46 %. The results of 16S rRNA gene sequence similarity analysis, DNA–DNA hybridization analysis and the observed differentiating phenotypic properties from other closely related taxa clearly indicate that strain 17J42-9 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is 17J42-9 (=KCTC 62270=JCM 33056).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003651
2019-08-16
2019-10-18
Loading full text...

Full text loading...

References

  1. McBride MJ, Liu W, Lu X, Zhu Y, Zhang W et al. The family Cytophagaceae. In Rosenberg E, Stackebrandt E, Thompson FL, Lory S, DeLong EF et al. (editors) The Prokaryotes, 4th ed. Berlin, Heidelberg, Germany: Springer-Verlag; 2014; pp.577–593
    [Google Scholar]
  2. Saha P, Chakrabarti T. Emticicia oligotrophica gen. nov., sp. nov., a new member of the family 'Flexibacteraceae', phylum Bacteroidetes. Int J Syst Evol Microbiol 2006;56:991–995 [CrossRef][PubMed]
    [Google Scholar]
  3. Joung Y, Seo MA, Kang H, Kim H, Ahn TS et al. Emticicia aquatica sp. nov., a species of the family Cytophagaceae isolated from fresh water. Int J Syst Evol Microbiol 2015;65:4358–4362 [CrossRef][PubMed]
    [Google Scholar]
  4. Park SE, Lee S, Kim H, Ahn TY. Emticicia sediminis sp. nov. isolated from sediment of a shallow stream. Int J Syst Evol Microbiol 2015;65:2496–2499 [CrossRef][PubMed]
    [Google Scholar]
  5. Nam GG, Joung Y, Song J, Lim Y, Cho JC. Emticiciafontis sp. nov., isolated from a freshwater pond. Int J Syst Evol Microbiol 2016;66:5161–5166 [CrossRef][PubMed]
    [Google Scholar]
  6. Kang H, Kim H, Joung Y, Joh K. Emticicia paludis sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2016;66:3383–3387 [CrossRef][PubMed]
    [Google Scholar]
  7. Ngo HTT, Trinh H, Yang JE, Won KH, Chu DH et al. Emticicia aquatilis sp. nov., isolated from a freshwater sample. Int J Syst Evol Microbiol 2017;67:1703–1708 [CrossRef][PubMed]
    [Google Scholar]
  8. Liu QM, Ten LN, Yu HS, Jin FX, Im WT et al. Emticicia ginsengisoli sp. nov., a species of the family 'Flexibacteraceae' isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2008;58:1100–1105 [CrossRef][PubMed]
    [Google Scholar]
  9. Chen Q, Zang XX, Hang X, Wang HM, Jia WB et al. Emticicia soli sp. nov., a novel member of the family 'Flexibacteraceae', isolated from tetrabromobisphenol A-contaminated soil. Int J Syst Evol Microbiol 2017;67:2885–2890 [CrossRef][PubMed]
    [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  11. Yoon SH, Ha SM, 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 [CrossRef][PubMed]
    [Google Scholar]
  12. Stackebrandt E, Goebel BM. Taxonomic note: a place for dna-dna reassociation and 16s rrna sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
    [Google Scholar]
  13. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
  14. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  15. Wilson K. Preparation of Genomic DNA from Bacteria. In Ausubel FM. (editor) Current Protocols in Molecular Biology New York, NY: Jonh Wiley & Sons, Inc; 1997; pp.2.4.1–2.4.2
    [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 [CrossRef]
    [Google Scholar]
  17. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [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 [CrossRef][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. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  22. 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]
  23. 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]
  24. Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL et al. The MaSuRCA genome assembler. Bioinformatics 2013;29:2669–2677 [CrossRef][PubMed]
    [Google Scholar]
  25. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75 [CrossRef][PubMed]
    [Google Scholar]
  26. Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:6614–6624 [CrossRef][PubMed]
    [Google Scholar]
  27. Haft DH, Dicuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018;46:D851–D860 [CrossRef][PubMed]
    [Google Scholar]
  28. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  29. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016;44:W54–W57 [CrossRef][PubMed]
    [Google Scholar]
  30. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017;110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
  32. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  33. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014;64:352–356 [CrossRef][PubMed]
    [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  35. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049–1070 [CrossRef][PubMed]
    [Google Scholar]
  36. La HJ, Im WT, Ten LN, Kang MS, Shin DY et al. Paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 2005;55:1657–1660 [CrossRef][PubMed]
    [Google Scholar]
  37. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 9th ed. San Francisco, USA: Benjamin Cummings; 2010
    [Google Scholar]
  38. Lee M, Woo SG, Chae M, Shin MC, Jung HM et al. Stenotrophomonas daejeonensis sp. nov., isolated from sewage. Int J Syst Evol Microbiol 2011;61:598–604 [CrossRef][PubMed]
    [Google Scholar]
  39. Aslam Z, Im WT, Ten LN, Lee MJ, Kim KH et al. Lactobacillus siliginis sp. nov., isolated from wheat sourdough in South Korea. Int J Syst Evol Microbiol 2006;56:2209–2213 [CrossRef][PubMed]
    [Google Scholar]
  40. Lee JJ, Lee YH, Park SJ, Lee SY, Kim BO et al. Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 2017;67:1359–1365 [CrossRef][PubMed]
    [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Netwark, DE: MIDI Inc; 1990
    [Google Scholar]
  42. 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]
  43. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–205
    [Google Scholar]
  44. Ten LN, Jung HM, Im WT, Yoo SA, Lee ST et al. Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea. J Microbiol 2008;46:519–524 [CrossRef][PubMed]
    [Google Scholar]
  45. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996;42:457–469 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003651
Loading
/content/journal/ijsem/10.1099/ijsem.0.003651
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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