1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 61, Issue 7

sp. nov., isolated from leaf-and-branch compost Free

Abstract

A strictly aerobic, Gram-stain-negative, yellow-pigmented, non-spore-forming, motile (by gliding), rod-shaped bacterium, designated strain 15F3, was isolated from leaf-and-branch compost. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 15F3 was most closely related to WB 3.2-61 and formed a distinct phyletic lineage within the genus , the type genus of the family . Growth was observed at 10–34 °C (optimum, 30 °C) and pH 6.0–8.0 (optimum, pH 7.0). No growth occurred in the presence of ≥2 % (w/v) NaCl. Strain 15F3 reduced nitrate to nitrogen and showed catalase activity but no oxidase activity. The predominant cellular fatty acids were iso-C and summed feature 3 (comprising Cω7 and/or iso-C 2-OH). The major isoprenoid quinone was menaquinone-6. The G+C content of the genomic DNA was 31.1 mol%. On the basis of data from this polyphasic study, strain 15F3 may be classified as a representative of a novel species within the genus , for which the name sp. nov. is proposed; the type strain is 15F3 ( = KACC 14225  = JCM 16466).

  • Published Online:
© 2011 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.022467-0
2011-07-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/7/1595.html?itemId=/content/journal/ijsem/10.1099/ijs.0.022467-0&mimeType=html&fmt=ahah

References

  1. Ali Z., Cousin S., Frühling A., Brambilla E., Schumann P., Yang Y., Stackebrandt E. 2009; Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Int J Syst Evol Microbiol 59:2610–2617 [View Article][PubMed]
     [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [View Article][PubMed]
     [Google Scholar]
  3. Bernardet J.-F., Bowman J. P. 2006; The genus Flavobacterium . In The Prokaryotes: A Handbook on the Biology of Bacteria, 3rd edn. vol. 7 pp. 481–531 Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. New York: Springer;
     [Google Scholar]
  4. Bernardet J.-F., Segers P., Vancanneyt M., Berthe F., Kersters K., Vandamme P. 1996; Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46:128–148 [View Article]
     [Google Scholar]
  5. Bernardet J.-F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 2002; Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  6. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y. W. 2007; EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261 [View Article][PubMed]
     [Google Scholar]
  7. Cousin S., Päuker O., Stackebrandt E. 2007; Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek. Int J Syst Evol Microbiol 57:243–249 [View Article][PubMed]
     [Google Scholar]
  8. Han S. J., Yoo Y. J., Kang H. S. 1995; Characterization of a bifunctional cellulase and its structural gene. The cell gene of Bacillus sp. D04 has exo- and endoglucanase activity. J Biol Chem 270:26012–26019[PubMed] [CrossRef]
     [Google Scholar]
  9. Horn M. A., Ihssen J., Matthies C., Schramm A., Acker G., Drake H. L. 2005; Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa . Int J Syst Evol Microbiol 55:1255–1265 [View Article][PubMed]
     [Google Scholar]
  10. Humphry D. R., George A., Black G. W., Cummings S. P. 2001; Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. Int J Syst Evol Microbiol 51:1235–1243[PubMed]
     [Google Scholar]
  11. Janssen P. H., Yates P. S., Grinton B. E., Taylor P. M., Sait M. 2002; Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia . Appl Environ Microbiol 68:2391–2396 [View Article][PubMed]
     [Google Scholar]
  12. Kim J.-J., Kim H. N., Masui R., Kuramitsu S., Seo J. H., Kim K., Sung M. H. 2008; Isolation of uncultivable anaerobic thermophiles of the family Clostridiaceae requiring growth-supporting factors. J Microbiol Biotechnol 18:611–615[PubMed]
     [Google Scholar]
  13. Kim J.-H., Kim K.-Y., Cha C.-J. 2009; Flavobacterium chungangense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 59:1754–1758 [View Article][PubMed]
     [Google Scholar]
  14. Komagata K., Suzuki K. 1987; Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 19:161–207 [View Article]
     [Google Scholar]
  15. Lányí B. 1987; Classical and rapid identification methods for medically important bacteria. Method Microbiol 19:1–67 [View Article]
     [Google Scholar]
  16. Lee C. C., Smith M., Kibblewhite-Accinelli R. E., Williams T. G., Wagschal K., Robertson G. H., Wong D. W. S. 2006; Isolation and characterization of a cold-active xylanase enzyme from Flavobacterium sp.. Curr Microbiol 52:112–116 [View Article][PubMed]
     [Google Scholar]
  17. Lee J.-S., Lee K. C., Kim K. K., Hwang I. C., Jang C., Kim N. G., Yeo W. H., Kim B. S., Yu Y. M., Ahn J. S. 2009; Acinetobacter antiviralis sp. nov., from tobacco plant roots. J Microbiol Biotechnol 19:250–256 [View Article][PubMed]
     [Google Scholar]
  18. Li C., Hong Y., Shao Z., Lin L., Huang X., Liu P., Wu G., Meng X., Liu Z. 2009; Novel alkali-stable, cellulase-free xylanase from deep-sea Kocuria sp. Mn22. J Microbiol Biotechnol 19:873–880 [View Article][PubMed]
     [Google Scholar]
  19. Liu H., Liu R., Yang S.-Y., Gao W.-K., Zhang C.-X., Zhang K.-Y., Lai R. 2008; Flavobacterium anhuiense sp. nov., isolated from field soil. Int J Syst Evol Microbiol 58:756–760 [View Article][PubMed]
     [Google Scholar]
  20. Liu Y., Jin J.-H., Zhou Y.-G., Liu H.-C., Liu Z.-P. 2010; Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents. Int J Syst Evol Microbiol 60:417–421 [View Article][PubMed]
     [Google Scholar]
  21. McBride M. J., Braun T. F., Brust J. L. 2003; Flavobacterium johnsoniae GldH is a lipoprotein that is required for gliding motility and chitin utilization. J Bacteriol 185:6648–6657 [View Article][PubMed]
     [Google Scholar]
  22. McCammon S. A., Bowman J. P. 2000; Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov.. Int J Syst Evol Microbiol 50:1055–1063[PubMed] [CrossRef]
     [Google Scholar]
  23. Park M., Ryu S. H., Vu T. H., Ro H.-S., Yun P.-Y., Jeon C. O. 2007; Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 57:233–237 [View Article][PubMed]
     [Google Scholar]
  24. Powers E. M. 1995; Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758[PubMed]
     [Google Scholar]
  25. Rasmussen M. A., Madsen S. M., Stougaard P., Johnsen M. G. 2008; Flavobacterium sp. strain 4221 and Pedobacter sp. strain 4236 β-1,3-glucanases that are active at low temperatures. Appl Environ Microbiol 74:7070–7072 [View Article][PubMed]
     [Google Scholar]
  26. Reasoner D. J., Geldreich E. E. 1985; A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49:1–7[PubMed]
     [Google Scholar]
  27. Reichenbach H. 1989; Nonphotosynthetic, nonfruiting gliding bacteria. In Bergey's Manual of Systematic Bacteriology pp. 2011–2050 Edited by Staley J. T., Bryant M. P., Pfennig N., Holt J. G. Baltimore, MD: Williams and Wilkins;
     [Google Scholar]
  28. Riffel A., Brandelli A. 2002; Isolation and characterization of a feather-degrading bacterium from the poultry processing industry. J Ind Microbiol Biotechnol 29:255–258 [View Article][PubMed]
     [Google Scholar]
  29. Ryu S. H., Park J. H., Moon J. C., Sung Y., Lee S.-S., Jeon C. O. 2008; Flavobacterium resistens sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 58:2266–2270 [View Article][PubMed]
     [Google Scholar]
  30. Sambrook J., Russell D. W. 2001 Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  31. Singh B. K. 2009; Organophosphorus-degrading bacteria: ecology and industrial applications. Nat Rev Microbiol 7:156–164[PubMed] [CrossRef]
     [Google Scholar]
  32. Smibert R. M., Krieg N. R. 1981; General characterization. In Manual of Methods for General Microbiology pp. 409–443 Edited by Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. B. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  33. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp. 607–754 Edited by Gerhardt P. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  34. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [View Article]
     [Google Scholar]
  35. Stott M. B., Crowe M. A., Mountain B. W., Smirnova A. V., Hou S., Alam M., Dunfield P. F. 2008; Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 10:2030–2041 [View Article][PubMed]
     [Google Scholar]
  36. Tamaki H., Hanada S., Kamagata Y., Nakamura K., Nomura N., Nakano K., Matsumura M. 2003; Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments. Int J Syst Evol Microbiol 53:519–526 [View Article][PubMed]
     [Google Scholar]
  37. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [View Article][PubMed]
     [Google Scholar]
  38. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  39. Yoon J.-H., Lee S. T., Park Y.-H. 1998; Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 48:187–194 [View Article][PubMed]
     [Google Scholar]
  40. Yoon H. S., Aslam Z., Song G. C., Kim S. W., Jeon C. O., Chon T. S., Chung Y. R. 2009; Flavobacterium sasangense sp. nov., isolated from a wastewater stream polluted with heavy metals. Int J Syst Evol Microbiol 59:1162–1166 [View Article][PubMed]
     [Google Scholar]
  41. Zhang Z., Schwartz S., Wagner L., Miller W. 2000; A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214 [View Article][PubMed]
     [Google Scholar]
  42. Zhang D.-C., Wang H.-X., Liu H.-C., Dong X.-Z., Zhou P.-J. 2006; Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier. Int J Syst Evol Microbiol 56:2921–2925 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.022467-0
Loading
Flavobacterium banpakuense sp. nov., isolated from leaf-and-branch compost
Int J Syst Evol Microbiol 61, 1595 (2011); https://doi.org/10.1099/ijs.0.022467-0
/content/journal/ijsem/10.1099/ijs.0.022467-0
/content/journal/ijsem/10.1099/ijs.0.022467-0
Loading

Data & Media loading...

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