1887

Abstract

Two strains of Gram-stain-negative, rod-shaped bacteria were isolated from root nodules of the South African legume and authenticated on this host. Based on phylogenetic analysis of the 16S rRNA gene, strains WSM3930 and WSM3937 belonged to the genus , with the highest degree of sequence similarity to (98.84 %). Additionally, the housekeeping genes and were analysed since 16S rRNA gene sequences are highly similar between closely related species of the genus . The results obtained for both housekeeping genes, and , showed the highest degree of sequence similarity of the novel strains towards LMG 19076 (94.2 % and 94.5 %, respectively). Chemotaxonomic data, including fatty acid profiles and respiratory quinone data supported the assignment of strains WSM3930 and WSM3937 to the genus . DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains WSM3930 and WSM3937 from the most closely related species of the genus with validly published names. We conclude, therefore, that these strains represent a novel species for which the name sp. nov. is proposed, with strain WSM3937 ( = LMG 27174 = HAMBI 3354) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.048751-0
2013-11-01
2019-12-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/11/3944.html?itemId=/content/journal/ijsem/10.1099/ijs.0.048751-0&mimeType=html&fmt=ahah

References

  1. Achouak W. , Christen R. , Barakat M. , Martel M.-H. , Heulin T. . ( 1999; ). Burkholderia caribensis sp. nov., an exopolysaccharide-producing bacterium isolated from vertisol microaggregates in Martinique. . Int J Syst Bacteriol 49:, 787–794. [CrossRef] [PubMed]
    [Google Scholar]
  2. Aizawa T. , Ve N. B. , Nakajima M. , Sunairi M. . ( 2010a; ). Burkholderia heleia sp. nov., a nitrogen-fixing bacterium isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps in actual acid sulfate soil areas of Vietnam. . Int J Syst Evol Microbiol 60:, 1152–1157. [CrossRef] [PubMed]
    [Google Scholar]
  3. Aizawa T. , Bao Ve N. , Vijarnsorn P. , Nakajima M. , Sunairi M. . ( 2010b; ). Burkholderia acidipaludis sp. nov., aluminium-tolerant bacteria isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps in South-East Asia. . Int J Syst Evol Microbiol 60:, 2036–2041. [CrossRef] [PubMed]
    [Google Scholar]
  4. Aizawa T. , Vijarnsorn P. , Nakajima M. , Sunairi M. . ( 2011; ). Burkholderia bannensis sp. nov., an acid-neutralizing bacterium isolated from torpedo grass (Panicum repens) growing in highly acidic swamps. . Int J Syst Evol Microbiol 61:, 1645–1650. [CrossRef] [PubMed]
    [Google Scholar]
  5. 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. [CrossRef] [PubMed]
    [Google Scholar]
  6. 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. [CrossRef] [PubMed]
    [Google Scholar]
  7. 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. [CrossRef] [PubMed]
    [Google Scholar]
  8. 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. [CrossRef] [PubMed]
    [Google Scholar]
  9. Coenye T. , Vandamme P. . ( 2003; ). Diversity and significance of Burkholderia species occupying diverse ecological niches. . Environ Microbiol 5:, 719–729. [CrossRef] [PubMed]
    [Google Scholar]
  10. 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. [CrossRef]
    [Google Scholar]
  11. 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. [CrossRef]
    [Google Scholar]
  12. Garrity G. M. , Bell J. A. , Liburn T. . ( 2005; ). Family I. Burkholderiaceae . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2, pp. 438–475. Edited by Brenner D. J. , Krieg N. R. , Staley J. T. , Garrity G. M. . . New York:: Springer;.
    [Google Scholar]
  13. 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. [CrossRef]
    [Google Scholar]
  14. Goris J. , Suzuki K. , De Vos P. , Nakase T. , Kersters K. . ( 1998; ). Evaluation of a microplate DNA - DNA hybridization method compared with the initial renaturation method. . Can J Microbiol 44:, 1148–1153. [CrossRef]
    [Google Scholar]
  15. Goris J. , Dejonghe W. , Falsen E. , De Clerck E. , Geeraerts B. , Willems A. , Top E. M. , Vandamme P. , De Vos P. . ( 2002; ). Diversity of transconjugants that acquired plasmid pJP4 or pEMT1 after inoculation of a donor strain in the A- and B-horizon of an agricultural soil and description of Burkholderia hospita sp. nov. and Burkholderia terricola sp. nov.. Syst Appl Microbiol 25:, 340–352. [CrossRef] [PubMed]
    [Google Scholar]
  16. Howieson J. G. , Yates R. J. , Foster K. , Real D. , Besier B. . ( 2008; ). Prospects for the future use of legumes. . In Leguminous Nitrogen-Fixing Symbioses, pp. 363–394. Edited by Dilworth M. J. , James E. K. , Sprent J. I. , Newton W. E. . . London:: Elsevier;.
    [Google Scholar]
  17. Howieson J. G. , De Meyer S. E. , Vivas-Marfisi A. , Ratnayake S. , Ardley J. K. , Yates R. J. . ( 2013; ). Novel Burkholderia bacteria isolated from Lebeckia ambigua – a perennial suffrutescent legume of the fynbos. . Soil Biol Biochem 60:, 55–64. [CrossRef]
    [Google Scholar]
  18. 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. [CrossRef] [PubMed]
    [Google Scholar]
  19. Ludwig W. , Strunk O. , Westram R. , Richter L. , Meier H. , Yadhukumar , Buchner A. , Lai T. , Steppi S. . & other authors ( 2004; ). arb: a software environment for sequence data. . Nucleic Acids Res 32:, 1363–1371. [CrossRef] [PubMed]
    [Google Scholar]
  20. Mesbah M. , Premachandran U. , Whitman W. B. . ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic-acid by high-preformance liquid-chromatography. . Int J Syst Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  21. Mishra R. P. N. , Tisseyre P. , Melkonian R. , Chaintreuil C. , Miché L. , Klonowska A. , Gonzalez S. , Bena G. , Laguerre G. , Moulin L. . ( 2012; ). Genetic diversity of Mimosa pudica rhizobial symbionts in soils of French Guiana: investigating the origin and diversity of Burkholderia phymatum and other beta-rhizobia. . FEMS Microbiol Ecol 79:, 487–503. [CrossRef] [PubMed]
    [Google Scholar]
  22. Moulin L. , Munive A. , Dreyfus B. , Boivin-Masson C. . ( 2001; ). Nodulation of legumes by members of the beta-subclass of Proteobacteria. . Nature 411:, 948–950. [CrossRef] [PubMed]
    [Google Scholar]
  23. Pitcher D. G. , Saunders N. A. , Owen R. J. . ( 1989; ). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. . Lett Appl Microbiol 8:, 151–156. [CrossRef]
    [Google Scholar]
  24. Pruesse E. , Quast C. , Knittel K. , Fuchs B. M. , Ludwig W. , Peplies J. , Glöckner F. O. . ( 2007; ). silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with arb . . Nucleic Acids Res 35:, 7188–7196. [CrossRef] [PubMed]
    [Google Scholar]
  25. 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. [CrossRef] [PubMed]
    [Google Scholar]
  26. 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. [CrossRef] [PubMed]
    [Google Scholar]
  27. Spilker T. , Baldwin A. , Bumford A. , Dowson C. G. , Mahenthiralingam E. , LiPuma J. J. . ( 2009; ). Expanded multilocus sequence typing for burkholderia species. . J Clin Microbiol 47:, 2607–2610. [CrossRef] [PubMed]
    [Google Scholar]
  28. 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. [CrossRef] [PubMed]
    [Google Scholar]
  29. Valverde A. , Delvasto P. , Peix A. , Velázquez E. , Santa-Regina I. , Ballester A. , Rodríguez-Barrueco C. , García-Balboa C. , Igual J. M. . ( 2006; ). Burkholderia ferrariae sp. nov., isolated from an iron ore in Brazil. . Int J Syst Evol Microbiol 56:, 2421–2425. [CrossRef] [PubMed]
    [Google Scholar]
  30. Vancanneyt M. , Mengaud J. , Cleenwerck I. , Vanhonacker K. , Hoste B. , Dawyndt P. , Degivry M. C. , Ringuet D. , Janssens D. , Swings J. . ( 2004; ). Reclassification of Lactobacillus kefirgranum Takizawa et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended description of L. kefiranofaciens Fujisawa et al. 1988. . Int J Syst Evol Microbiol 54:, 551–556. [CrossRef] [PubMed]
    [Google Scholar]
  31. Vandamme P. , Goris J. , Chen W. M. , de Vos P. , Willems A. . ( 2002; ). Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes. . Syst Appl Microbiol 25:, 507–512. [CrossRef] [PubMed]
    [Google Scholar]
  32. Vanlaere E. , Baldwin A. , Gevers D. , Henry D. , De Brandt E. , LiPuma J. J. , Mahenthiralingam E. , Speert D. P. , Dowson C. , Vandamme P. . ( 2009; ). Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov.. Int J Syst Evol Microbiol 59:, 102–111. [CrossRef] [PubMed]
    [Google Scholar]
  33. Vincent J. M. . ( 1970; ). A Manual for the Practical Study of the Root-nodule Bacteria. International Biological Programme Handbook, , 15 edn.. Oxford:: Blackwell Scientific;.
    [Google Scholar]
  34. 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.[PubMed] [CrossRef]
    [Google Scholar]
  35. Yates R. J. , Howieson J. G. , Nandasena K. G. , O'Hara G. W. . ( 2004; ). Root-nodule bacteria from indigenous legumes in the north-west of Western Australia and their interaction with exotic legumes. . Soil Biol Biochem 36:, 1319–1329. [CrossRef]
    [Google Scholar]
  36. Yates R. J. , Howleson J. G. , Reeve W. G. , Nandasena K. G. , Law I. J. , Bräu L. , Ardley J. K. , Nistelberger H. M. , Real D. , O’Hara G. W. . ( 2007; ). Lotononis angolensis forms nitrogen fixing, lupinoid nodules with phylogenetically unique, fast-growing, pink-pigmented bacteria, which do not nodulate L. bainesii or L. listii. . Soil Biol Biochem 39:, 1680–1688. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.048751-0
Loading
/content/journal/ijsem/10.1099/ijs.0.048751-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most Cited This Month

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