1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_12

sp. nov., isolated from root nodules of in New Zealand and Western Australia Free

Abstract

Seven strains, ICMP 19430, ICMP 19429, ICMP 19431, WSM4637, WSM4638, WSM4639 and WSM4640, were isolated from nitrogen-fixing nodules on roots of the invasive South African legume (subfamily Papilionoideae, tribe Phaseoleae) in New Zealand and Western Australia, and their taxonomic positions were investigated by using a polyphasic approach. All seven strains grew at 10–37 °C (optimum, 25–30 °C), at pH 4.0–9.0 (optimum, pH 6.0–7.0) and with 0–2 % (w/v) NaCl (optimum growth in the absence of NaCl). On the basis of 16S rRNA gene sequence analysis, the strains showed 99.0–99.5 % sequence similarity to the closest type strain, PsJN, and 98.4–99.7 % sequence similarity to LMG 19076. The predominant fatty acids were Cω7 (21.0 % of the total fatty acids in strain ICMP 19430), C (19.1 %), C cyclo (18.9 %), summed feature 3 (Cω7 and/or Cω6; 10.7 %) and C cyclo ω8 (7.5 %). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The major isoprenoid quinone was Q-8 and the DNA G+C content of strain ICMP 19430 was 63.2 mol%. The DNA–DNA relatedness of the novel strains with respect to the closest neighbouring members of the genus was 55 % or less. On the basis of 16S rRNA and gene sequence similarities and chemotaxonomic and phenotypic data, these strains represent a novel symbiotic species in the genus , for which the name sp. nov. is proposed, with the type strain ICMP 19430 ( = LMG 28415 = HAMBI 3637).

  • Published Online:
© 2015 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000639
2015-12-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/12/4716.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000639&mimeType=html&fmt=ahah

References

  1. Ardley J. K., Parker M. A., De Meyer S. E., Trengove R. D., O'Hara G. W., Reeve W. G., Yates R. J., Dilworth M. J., Willems A., Howieson J. G. ( 2012;). Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts. Int J Syst Evol Microbiol 62 2579–2588 [View Article] [PubMed].
     [Google Scholar]
  2. Beveridge T. J., Lawrence J. R., Murray R. G. E. ( 2007;). Sampling and staining for light microscopy. . In Methods for General and Molecular Bacteriology , 3rd edn.., pp. 19–33. Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;.
     [Google Scholar]
  3. Bowman J. P. ( 2000;). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50 1861–1868 [View Article] [PubMed].
     [Google Scholar]
  4. Breznak J. A., Costilow R. N. ( 2007;). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology , 3rd edn.., pp. 309–329. Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M, Snyder L. R. Washington, DC: American Society for Microbiology;.
     [Google Scholar]
  5. Chen W. M., James E. K., Coenye T., Chou J. H., Barrios E., de Faria S. M., Elliott G. N., Sheu S. Y., Sprent J. I., Vandamme P. ( 2006;). Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 56 1847–1851 [View Article] [PubMed].
     [Google Scholar]
  6. Chen W. M., de Faria S. M., James E. K., Elliott G. N., Lin K. Y., Chou J. H., Sheu S. Y., Cnockaert M., Sprent J. I., Vandamme P. ( 2007;). Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella . Int J Syst Evol Microbiol 57 1055–1059 [View Article] [PubMed].
     [Google Scholar]
  7. Chen W. M., de Faria S. M., Chou J. H., James E. K., Elliott G. N., Sprent J. I., Bontemps C., Young J. P. W., Vandamme P. ( 2008;). Burkholderia sabiae, sp. nov., isolated from root nodules of Mimosa caesalpiniifolia . Int J Syst Evol Microbiol 58 2174–2179 [PubMed]. [CrossRef]
    [Google Scholar]
  8. Coenye T., Laevens S., Willems A., Ohlén M., Hannant W., Govan J. R. W., Gillis M., Falsen E., Vandamme P. ( 2001;). Burkholderia fungorum sp. nov. and Burkholderia caledonica sp. nov., two new species isolated from the environment, animals and human clinical samples. Int J Syst Evol Microbiol 51 1099–1107 [View Article] [PubMed].
     [Google Scholar]
  9. Coenye T., Henry D., Speert D. P., Vandamme P. ( 2004;). Burkholderia phenoliruptrix sp. nov., to accommodate the 2,4,5-trichlorophenoxyacetic acid and halophenol-degrading strain AC1100. Syst Appl Microbiol 27 623–627 [View Article] [PubMed].
     [Google Scholar]
  10. Cole J. R., Wang Q., Cardenas E., Fish J., Chai B., Farris R. J., Kulam-Syed-Mohideen A. S., McGarrell D. M., Marsh T., other authors. ( 2009;). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37 (Database), D141–D145 [View Article] [PubMed].
     [Google Scholar]
  11. Collins M. D. ( 1994;). Isoprenoid quinones. . In Chemical Methods in Prokaryotic Systematics, pp. 265–309. Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;.
     [Google Scholar]
  12. De Meyer S. E., Cnockaert M., Ardley J. K., Trengove R. D., Garau G., Howieson J. G., Vandamme P. ( 2013a;). Burkholderia rhynchosiae sp. nov., isolated from Rhynchosia ferulifolia root nodules. Int J Syst Evol Microbiol 63 3944–3949 [View Article] [PubMed].
     [Google Scholar]
  13. De Meyer S. E., Cnockaert M., Ardley J. K., Maker G., Yates R., Howieson J. G., Vandamme P. ( 2013b;). Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 63 3950–3957 [PubMed]. [CrossRef]
    [Google Scholar]
  14. De Meyer S. E., Cnockaert M., Ardley J. K., Van Wyk B.-E., Vandamme P. A., Howieson J. G. ( 2014;). Burkholderia dilworthii sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 64 1090–1095 [View Article] [PubMed].
     [Google Scholar]
  15. Elliott G. N., Chen W.-M., Bontemps C., Chou J.-H., Young J. P. W., Sprent J. I., James E. K. ( 2007;). Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum . Ann Bot (Lond) 100 1403–1411 [View Article] [PubMed].
     [Google Scholar]
  16. Embley T. M., Wait R. ( 1994;). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121–161. Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;.
     [Google Scholar]
  17. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989;). 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 39 224–229 [View Article].
     [Google Scholar]
  18. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368–376 [View Article] [PubMed].
     [Google Scholar]
  19. Felsenstein J. ( 1993). phylip (phylogeny inference package), version 3.5c. Distributed by the author Department of Genome Sciences, University of Washington; Seattle: USA;.
     [Google Scholar]
  20. Garau G., Yates R. J., Deiana P., Howieson J. G. ( 2009;). Novel strains of nodulating Burkholderia have a role in nitrogen fixation with papilionoid herbaceous legumes adapted to acid, infertile soils. Soil Biol Biochem 41 125–134 [View Article].
     [Google Scholar]
  21. Garrity G. M., Bell J. A., Lilburn T. ( 2001;). Family I. Burkholderiaceae fam. nov. . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 2C, p. 575. Edited by Boone D. R., Castenholz R. W., Garrity G. M., Brenner D. J., Krieg N. R., Staley J. T. New York: Springer;. [CrossRef]
    [Google Scholar]
  22. Gillis M., Van Van T., Bardin R., Goor M., Hebbar P., Willems A., Segers P., Kersters K., Heulin T., Fernandez M. P. ( 1995;). Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N2-fixing isolates from rice in Vietnam. Int J Syst Bacteriol 45 274–289 [View Article].
     [Google Scholar]
  23. Goris J., De Vos P., Caballero-Mellado J., Park J., Falsen E., Quensen J. F. III, Tiedje J. M., Vandamme P. ( 2004;). Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov. Int J Syst Evol Microbiol 54 1677–1681 [View Article] [PubMed].
     [Google Scholar]
  24. Gyaneshwar P., Hirsch A. M., Moulin L., Chen W. M., Elliott G. N., Bontemps C., Estrada-de Los Santos P., Gross E., Dos Reis F. B. Jr, other authors. ( 2011;). Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. Mol Plant Microbe Interact 24 1276–1288 [View Article] [PubMed].
     [Google Scholar]
  25. Hall T. A. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41 95–98.
     [Google Scholar]
  26. Howieson J. G., Loi A., Carr S. J. ( 1995;). Biserrula pelecinus L. – a legume pasture species with potential for acid, duplex soils which is nodulated by unique root-nodule bacteria. Aust J Agric Res 46 997–1009 [View Article].
     [Google Scholar]
  27. Kim H.-B., Park M.-J., Yang H.-C., An D.-S., Jin H.-Z., Yang D.-C. ( 2006;). Burkholderia ginsengisoli sp. nov., a β-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 56 2529–2533 [View Article] [PubMed].
     [Google Scholar]
  28. 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 62 716–721 [PubMed]. [CrossRef]
    [Google Scholar]
  29. Kimura M. ( 1983). Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press;. [CrossRef]
    [Google Scholar]
  30. Kluge A. G., Farris F. S. ( 1969;). Quantitative phyletics and the evolution of anurans. Syst Zool 18 1–32 [View Article].
     [Google Scholar]
  31. Lemaire B., Dlodlo O., Chimphango S., Stirton C., Schrire B., Boatwright J. S., Honnay O., Smets E., Sprent J., other authors. ( 2015;). Symbiotic diversity, specificity and distribution of rhizobia in native legumes of the Core Cape Subregion (South Africa). FEMS Microbiol Ecol 91 1–17 [View Article] [PubMed].
     [Google Scholar]
  32. Liu W. Y. Y., Ridgway H. J., James T. K., James E. K., Chen W.-M., Sprent J. I., Young J. P. W., Andrews M. ( 2014;). Burkholderia sp. induces functional nodules on the South African invasive legume Dipogon lignosus (Phaseoleae) in New Zealand soils. Microb Ecol 68 542–555 [View Article] [PubMed].
     [Google Scholar]
  33. Mesbah M., Premachandran U., Whitman W. B. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39 159–167 [View Article].
     [Google Scholar]
  34. Miller P. H., Wiggs L. S., Miller J. M. ( 1995;). Evaluation of AnaeroGen system for growth of anaerobic bacteria. J Clin Microbiol 33 2388–2391 [PubMed].
     [Google Scholar]
  35. Nokhal T. H., Schlegel H. G. ( 1983;). Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 33 26–37 [View Article].
     [Google Scholar]
  36. Palleroni N. J. ( 2001;). Genus I. Burkholderia . . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 2C, pp. 575–600. Edited by Boone D. R., Castenholz R. W., Garrity G. M., Brenner D. J., Krieg N. R., Staley J. T. New York: Springer;.
     [Google Scholar]
  37. Pot B., Vandamme P., Kersters K. ( 1994;). Analysis of electrophoretic whole-organism protein fingerprints. . In Chemical Methods in Prokaryotic Systematics, pp. 493–521. Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;.
     [Google Scholar]
  38. Powers E. M. ( 1995;). Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. . In Appl Environ Microbiol 61, 3756–3758.
     [Google Scholar]
  39. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406–425 [PubMed].
     [Google Scholar]
  40. Sasser M. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids, Technical Note 101. Newark, DE: MIDI Inc. . http://www.microbialid.com/PDF/TechNote_101.pdf.
  41. Schlegel H. G., Lafferty R., Krauss I. ( 1970;). The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71 283–294 [View Article] [PubMed].
     [Google Scholar]
  42. Sessitsch A., Coenye T., Sturz A. V., Vandamme P., Barka E. A., Salles J. F., Van Elsas J. D., Faure D., Reiter B., other authors. ( 2005;). Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties. Int J Syst Evol Microbiol 55 1187–1192 [View Article] [PubMed].
     [Google Scholar]
  43. Sheu S. Y., Chou J. H., Bontemps C., Elliott G. N., Gross E., James E. K., Sprent J. I., Young J. P. W., Chen W. M. ( 2012;). Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil. Int J Syst Evol Microbiol 62 2272–2278 [View Article] [PubMed].
     [Google Scholar]
  44. Sheu S. Y., Chou J. H., Bontemps C., Elliott G. N., Gross E., dos Reis Junior F. B., Melkonian R., Moulin L., James E. K., other authors. ( 2013;). Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp. Int J Syst Evol Microbiol 63 435–441 [View Article] [PubMed].
     [Google Scholar]
  45. Spiekermann P., Rehm B. H. A., Kalscheuer R., Baumeister D., Steinbüchel A. ( 1999;). A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 171 73–80 [View Article] [PubMed].
     [Google Scholar]
  46. Suárez-Moreno Z. R., Caballero-Mellado J., Coutinho B. G., Mendonça-Previato L., James E. K., Venturi V. ( 2012;). Common features of environmental and potentially beneficial plant-associated Burkholderia . Microb Ecol 63 249–266 [View Article] [PubMed].
     [Google Scholar]
  47. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011;). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28 2731–2739 [View Article] [PubMed].
     [Google Scholar]
  48. 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]
  49. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R. ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Bacteriology , 3rd edn.., pp. 330–393. Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder R. . [View Article] Washington, DC: American Society for Microbiology;.
     [Google Scholar]
  50. Vandamme P. A. R., Govan J. R. W., LiPuma J. J. ( 2007;). Diversity and role of Burkholderia spp. . In Burkholderia Molecular Microbiology and Genomics vol. 1, pp. 1–28. Edited by Coenye T., Vandamme P. Wymondham, UK: Horizon Bioscience;.
     [Google Scholar]
  51. Versalovic J., Koeuth T., Lupski J. R. ( 1991;). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19 6823–6831 [View Article] [PubMed].
     [Google Scholar]
  52. Vincent J. M. ( 1970). A Manual for the Practical Study of the Root-Nodule Bacteria Oxford: Blackwell Scientific;.
     [Google Scholar]
  53. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463–464 [View Article].
     [Google Scholar]
  54. Wen C. M., Tseng C. S., Cheng C. Y., Li Y. K. ( 2002;). Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35 213–219 [View Article] [PubMed].
     [Google Scholar]
  55. Yabuuchi E., Kosako Y., Oyaizu H., Yano I., Hotta H., Hashimoto Y., Ezaki T., Arakawa M. ( 1992;). Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 36 1251–1275 [View Article] [PubMed].
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000639
Loading
Burkholderia dipogonis sp. nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia
Int J Syst Evol Microbiol 65, 4716 (2015); https://doi.org/10.1099/ijsem.0.000639
/content/journal/ijsem/10.1099/ijsem.0.000639
/content/journal/ijsem/10.1099/ijsem.0.000639
Loading

Data & Media loading...

Supplements

Supplementary Data

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