1887

Abstract

Two novel strains, J77-1 and J76-1, were isolated from farmland soil and were taxonomically characterized by a polyphasic approach. Both strains were yellow, Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacteria. These strains were non-sporulating, catalase-positive and oxidase-negative. J77-1 and J76-1 were able to grow at 15–40 °C, pH 5.0–10.0, and 0–1.0 % (w/v) NaCl concentration. Phylogenetic analyses revealed that both strains formed a distinct separate lineage within the family of the phylum . J77-1 and J76-1 showed low 16S rRNA gene sequence similarity to the most closely related type strain WPCB159 (85.09 %) and exhibited less than 85.0 % sequence similarity with other members of the family . The pairwise sequence similarity between strains J77-1 and J76-1 was observed to be 99.86 %. In both strains, the only respiratory quinone was menaquinone-7 (MK-7); the major polar lipid was phosphatidylethanolamine; and the major fatty acids were summed feature 3 (Cω7 and/or Cω6), C, iso-C, iso-C 3-OH Cω5, and C 3-OH. The genomic DNA G+C content values of J77-1 and J76-1 were 50.1 and 50.9 mol%, respectively. On the basis of the results of phenotypic, genotypic and phylogenetic analysis, J77-1 represents a novel species of a novel genus, for which the name gen. nov., sp. nov. is proposed, within the family . The type strain of is J77-1 (=KEMB 9005-548=KACC 19172=JCM 31920), and J76-1 is an additional strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002456
2017-12-01
2024-10-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/12/5252.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002456&mimeType=html&fmt=ahah

References

  1. Stanier RY. Studies on the cytophagas. J Bacteriol 1940; 40:619–635[PubMed]
    [Google Scholar]
  2. Mc Bride MJ, Liu W, Lu X, Zhu Y, Zhang W et al. The family Cytophagaceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. et al. (editors) The Prokaryotes– Other Major Lineages of Bacteria and the Archaea Berlin, Heidelberg: Springer-Verlag; 2014 pp. 577–593
    [Google Scholar]
  3. Nakagawa Y, Family I, Stainer C. Family I. Cytophagaceae Stainer 1940, 630AL . In Krieg NR, Staley JT, Brown DR, Hedlund BP, Ludwig W. et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 4 New York: Springer; 2011 pp. 371–423
    [Google Scholar]
  4. Baik KS, Kim MS, Kim EM, Kim HR, Seong CN. Dyadobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2007; 57:1227–1231 [View Article][PubMed]
    [Google Scholar]
  5. Liu QM, Im WT, Lee M, Yang DC, Lee ST. Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2006; 56:1939–1944 [View Article][PubMed]
    [Google Scholar]
  6. Dong Z, Guo X, Zhang X, Qiu F, Sun L et al. Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China. Int J Syst Evol Microbiol 2007; 57:862–865 [View Article][PubMed]
    [Google Scholar]
  7. Chaturvedi P, Reddy GS, Shivaji S. Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India. Int J Syst Evol Microbiol 2005; 55:2113–2117 [View Article][PubMed]
    [Google Scholar]
  8. Dahal RH, Kim J. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:308–314 [View Article][PubMed]
    [Google Scholar]
  9. Yoon J, Ishikawa S, Kasai H, Yokota A. Persicitalea jodogahamensis gen. nov., sp. nov., a marine bacterium of the family 'Flexibacteraceae', isolated from seawater in Japan. Int J Syst Evol Microbiol 2007; 57:1014–1017 [View Article][PubMed]
    [Google Scholar]
  10. Larkin JM, Williams PM. Runella slithyformis gen. nov., sp. nov., a curved, nonflexible, pink bacterium. Int J Syst Bacteriol 1978; 28:32–36 [View Article]
    [Google Scholar]
  11. Chelius MK, Henn JA, Triplett EW. Runella zeae sp. nov., a novel Gram-negative bacterium from the stems of surface-sterilized Zea mays . Int J Syst Evol Microbiol 2002; 52:2061–2063 [View Article][PubMed]
    [Google Scholar]
  12. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
    [Google Scholar]
  13. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  14. 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 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  17. 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]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  20. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  23. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article][PubMed]
    [Google Scholar]
  24. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp. 21–33
    [Google Scholar]
  25. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  26. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
    [Google Scholar]
  27. Hemraj V, Diksha S, Avneet G. A review on commonly used biochemical test for bacteria. Innovare J Life Sci 2013; 1:1–7
    [Google Scholar]
  28. Reichenbach H. The order Cytophagales . In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. et al. (editors) The Prokaryotes, 2nd ed. vol. 4 New York: Springer; 1992 pp. 3631–3675 [Crossref]
    [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 [View Article]
    [Google Scholar]
  30. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [Crossref]
    [Google Scholar]
  31. 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 [View Article]
    [Google Scholar]
  32. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed]
    [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  34. 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 [View Article]
    [Google Scholar]
  35. 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]
  36. 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 [View Article]
    [Google Scholar]
  37. Chelius MK, Triplett EW. Dyadobacter fermentans gen. nov., sp. nov., a novel Gram-negative bacterium isolated from surface-sterilized Zea mays stems. Int J Syst Evol Microbiol 2000; 50:751–758 [View Article][PubMed]
    [Google Scholar]
  38. Táncsics A, Kéki Z, Márialigeti K, Schumann P, Tóth EM. Siphonobacter aquaeclarae gen. nov., sp. nov., a novel member of the family 'Flexibacteraceae', phylum Bacteroidetes . Int J Syst Evol Microbiol 2010; 60:2567–2571 [View Article][PubMed]
    [Google Scholar]
  39. Finster KW, Herbert RA, Lomstein BA. Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2009; 59:839–844 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.002456
Loading
/content/journal/ijsem/10.1099/ijsem.0.002456
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