Burkholderia dilworthii sp. nov., isolated from Lebeckia ambigua root nodules

International Journal of Systematic and Evolutionary Microbiology

Volumn 64, Issue PART 4, 2014, Pages 1090-1095

  De Meyer, Sofie E ^a   Cnockaert, Margo ^b   Ardley, Julie K ^a   Van Wyk, Ben Erik ^c   Vandamme, Peter A ^b   Howieson, John G ^a  

^a MURDOCH UNIVERSITY   (Australia)

^b GHENT UNIVERSITY   (Belgium)

^c UNIVERSITY OF JOHANNESBURG   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

QUINONE DERIVATIVE; RNA 16S;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; BURKHOLDERIA; BURKHOLDERIA CALEDONICA; BURKHOLDERIA DILWORTHII; BURKHOLDERIA RHYNCHOSIAE; CHEMOTAXONOMY; DNA DNA HYBRIDIZATION; GENE SEQUENCE; GENOTYPE; GYRB HOUSEKEEPING GENE; HOUSEKEEPING GENE; LEBECKIA AMBIGUA; LIPID COMPOSITION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NODULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; RECA HOUSEKEEPING GENE; RESPIRATORY CHAIN; RHIZOBIACEAE;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; BURKHOLDERIA; DNA, BACTERIAL; FABACEAE; FATTY ACIDS; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; ROOT NODULES, PLANT; SEQUENCE ANALYSIS, DNA; SOUTH AFRICA; UBIQUINONE;

EID: 84897933741     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.058602-0     Document Type: Article

References (36)

1. Aizawa, T., Bao Ve, N., 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.
2. 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.
3. 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.
4. 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.
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.
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.
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.
8. 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.
9. 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.
10. Elliott, G. N., Chen, W. M., Bontemps, C., Chou, J. H., Young, J. P. W., Sprent, J. I. & James, E. K. (2007a). Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum. Ann Bot (Lond) 100, 1403-1411.
11. Elliott, G. N., Chen, W. M., Chou, J. H., Wang, H. C., Sheu, S. Y., Perin, L., Reis, V. M., Moulin, L., Simon, M. F. & other authors (2007b). Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta. New Phytol 173, 168-180.
12. 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.
13. 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.
14. Garrity, G. M., Bell, J. A. & Liburn, T. (2005). Family I. Burkholderiaceae. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2C, p. 575. Edited by D. J. Brenner, N. R. Krieg & J. T. Staley. New York: Springer.
15. Gevers, D., Huys, G. & Swings, J. (2001). Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205, 31-36.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. le Roux, M. M. & Van Wyk, B.-E. (2007). A revision of Lebeckia sect. Lebeckia: the L. sepiaria group. S Afr J Bot 73, 118-130.
22. 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.
23. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
24. 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.
25. 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.
26. 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.
27. Sheu, S.-Y., Chou, J.-H., Bontemps, C., Elliott, G. N., Gross, E., dos Reis, F. B., Jr, 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. Vincent, J. M. (1970). A Manual for the Practical Study of the Root-Nodule Bacteria. Oxford: Blackwell Scientific.
34. Wieme, A., Cleenwerck, I., Van Landschoot, A. & Vandamme, P. (2012). Pediococcus lolii DSM 19927T and JCM 15055T are strains of Pediococcus acidilactici. Int J Syst Evol Microbiol 62, 3105-3108.
35. 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.
36. Yates, R. J., Howieson, 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.