1887

Abstract

A yellow, nitrogen-fixing bacterial strain, NXU-44, isolated from the rhizosphere of switchgrass () in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus with highest sequence similarities to the type strains of (97.9 %), (97.6 %) and (97.5 %). The 16S rRNA gene sequence similarities to all other species of the genus were below 97.5 %. The fatty acid profile of strain NXU-44 consisted of the major fatty acids iso-C, iso-C 2-OH/Cω7 and iso-C 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound -homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was -diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is NXU-44 ( = LMG 28694 = CIP 110894).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000330
2015-09-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/9/2803.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000330&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 26102617 [View Article] [PubMed] .
    [Google Scholar]
  2. Altenburger P., Kämpfer P., Makristathis A., Lubitz W., Busse H.J. ( 1996;). Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47 3952 [View Article].
    [Google Scholar]
  3. Bashan Y., Holguin G., Lifshitz R. ( 1993;). Isolation and characterization of plant growth-promoting rhizobacteria. . In Methods in Plant Molecular Biology and Biotechnology, pp. 331345. Edited by Glick B. R., Thompson J. E. Boca Raton, FL: CRC Press;.
    [Google Scholar]
  4. Bergey D.H., Harrison F.C., Breed R.S., Hammer B.W., Huntoon F.M. ( 1923;). Genus II. Flavobacterium gen. nov.. Bergey's Manual of Determinative Bacteriology, pp. 97117 Baltimore: Williams & Wilkins;.
    [Google Scholar]
  5. Bernardet J.-F., Bowman J.P. ( 2006;). The genus Flavobacterium . . In The Prokaryotes. A Handbook on the Biology of Bacteria, pp. 487531. Edited by Dworkin M., Faldow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. vol. 7 , 3rd edn. New York: Springer;.
    [Google Scholar]
  6. 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, Cytrophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46 128148 [View Article].
    [Google Scholar]
  7. Brosius J., Palmer M.L., Kennedy P.J., Noller H.F. ( 1978;). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 75 48014805 [View Article] [PubMed] .
    [Google Scholar]
  8. Busse H.-J., Auling G. ( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11 18 [View Article].
    [Google Scholar]
  9. Busse H.J., Bunka S., Hensel A., Lubitz W. ( 1997;). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47 698708 [View Article].
    [Google Scholar]
  10. 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 243249 [View Article] [PubMed] .
    [Google Scholar]
  11. Felsenstein J. ( 1985;). Confidence limits of phylogenies: an approach using the bootstrap. Evolution 39 783791 [View Article].
    [Google Scholar]
  12. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. ( 1994). Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  13. Glaeser S.P., Galatis H., Martin K., Kämpfer P. ( 2013;). Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana . Int J Syst Evol Microbiol 63 28412847 [View Article] [PubMed] .
    [Google Scholar]
  14. Holguin G., Guzman M.A., Bashan Y. ( 1992;). Two new nitrogen-fixing bacteria from the rhizosphere of mangrove trees: Their isolation, identification and in vitro interaction with rhizosphere Staphylococcus sp. FEMS Microbiol Lett 101 207216 [View Article].
    [Google Scholar]
  15. Kämpfer P. ( 1990;). Evaluation of the Titertek-Enterobac-Automated System (TTE-AS) for identification of members of the family Enterobacteriaceae . Zentralbl Bakteriol 273 164172 [View Article] [PubMed] .
    [Google Scholar]
  16. Kämpfer P., Kroppenstedt R.M. ( 1996;). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42 9891005 [View Article].
    [Google Scholar]
  17. Kämpfer P., Steiof M., Dott W. ( 1991;). Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21 227251 [View Article] [PubMed] .
    [Google Scholar]
  18. 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 17541758 [View Article] [PubMed] .
    [Google Scholar]
  19. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62 716721 [View Article] [PubMed] .
    [Google Scholar]
  20. Kim M., Oh H.S., Park S.C., Chun J. ( 2014;). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64 346351. [CrossRef]
    [Google Scholar]
  21. Lane D.J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 125175. Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;.
    [Google Scholar]
  22. 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 417421 [View Article] [PubMed] .
    [Google Scholar]
  23. Liu M., Li Y.H., Liu Y., Zhu J.N., Liu Q.F., Liu Y., Gu J.G., Zhang X.X., Li C.L. ( 2011;). Flavobacterium phragmitis sp. nov., an endophyte of reed (Phragmites australis). Int J Syst Evol Microbiol 61 27172721 [View Article] [PubMed] .
    [Google Scholar]
  24. 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 756760 [View Article] [PubMed] .
    [Google Scholar]
  25. Lopez B.R., Bashan Y., Bacilio M. ( 2011;). Endophytic bacteria of Mammillaria fraileana, an endemic rock-colonizing cactus of the southern Sonoran Desert. Arch Microbiol 193 527541 [View Article] [PubMed] .
    [Google Scholar]
  26. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., other authors. ( 2004;). ARB: a software environment for sequence data. Nucl Acids Res 32 13631371. [CrossRef]
    [Google Scholar]
  27. Meier-Kolthoff J.P., Göker M., Spröer C., Klenk H.-P. ( 2013;). When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 195 413418 [View Article] [PubMed] .
    [Google Scholar]
  28. Montero-Calasanz M.C., Göker M., Rohde M., Spröer C., Schumann P., Busse H.-J., Schmid M., Tindall B.J., Klenk H.-P., Camacho M. ( 2013;). Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . Int J Syst Evol Microbiol 63 43864395 [View Article] [PubMed] .
    [Google Scholar]
  29. Pruesse E., Peplies J., Glöckner F.O. ( 2012;). SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28 18231829 [View Article] [PubMed] .
    [Google Scholar]
  30. Qu J.H., Li H.F., Yang J.S., Yuan H.L. ( 2008;). Flavobacterium cheniae sp. nov., isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 58 21862190 [View Article] [PubMed] .
    [Google Scholar]
  31. Reichenbach H. ( 1992;). The order Cytophagales Leadbetter 1974, 99AL . . In Bergey's Manual of Systematic Bacteriology vol. 3, pp. 20112073. Edited by Staley J. T., Bryant M. P., Pfennig N., Holt J. C. Baltimore: Williams & Wilkins;.
    [Google Scholar]
  32. Schumann P. ( 2011;). Peptidoglycan structure. . In Taxnonomy of Prokaryotes, Methods in Microbiology vol. 38, pp. 101129. Edited by Rainey F., Oren A. London: Academic Press; [View Article].
    [Google Scholar]
  33. Smibert R.M., Krieg N.R. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  34. Stamatakis A. ( 2006;). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22 26882690 [View Article] [PubMed] .
    [Google Scholar]
  35. Stolz A., Busse H.-J., Kämpfer P. ( 2007;). Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57 572576 [View Article] [PubMed] .
    [Google Scholar]
  36. Tindall B.J. ( 1990a;). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13 128130 [View Article].
    [Google Scholar]
  37. Tindall B.J. ( 1990b;). Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66 199202 [View Article].
    [Google Scholar]
  38. Vandamme P., Bernardet J.-F., Segers P., Kersters K., Holmes B. ( 1994;). New perspectives in the classification of the flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev.. Int J Syst Bacteriol 44 827831 [View Article].
    [Google Scholar]
  39. Yang J.-E., Kim S.-Y., Im W.-T., Yi T.-H. ( 2011;). Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 61 14081412 [View Article] [PubMed] .
    [Google Scholar]
  40. Yarza P., Richter M., Peplies J., Euzéby J., Amann R., Schleifer K.H., Ludwig W., Glöckner F.O., Rosselló-Móra R. ( 2008;). The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31 241250 [View Article] .
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000330
Loading
/content/journal/ijsem/10.1099/ijs.0.000330
Loading

Data & Media loading...

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