Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb

International Journal of Systematic and Evolutionary Microbiology

Volumn 64, Issue PART 6, 2014, Pages 1906-1912

  Mavengere, Natasha R ^a   Ellis, Allan G ^a   Le Roux, Johannes J ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; RNA 16S;

ARTICLE; ASPALATHUS; ASPALATHUS ABIETINA; BACTERIUM ISOLATION; BURKHOLDERIA; BURKHOLDERIA ASPALATHI; BURKHOLDERIA SEDIMINICOLA; CHEMOTAXONOMY; CONTROLLED STUDY; DNA BASE COMPOSITION; GENE SEQUENCE; GENETIC SIMILARITY; GENOTYPE; NODULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PLANT ROOT; PRIORITY JOURNAL; RECA GENE; SOUTH AFRICA;

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

EID: 84902689452     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.057067-0     Document Type: Article

References (47)

1. Andam, C. P., Mondo, S. J. & Parker, M. A. (2007). Monophyly of nodA and nifH genes across Texan and Costa Rican populations of Cupriavidus nodule symbionts. Appl Environ Microbiol 73, 4686-4690.
2. Barrett, C. F. & Parker, M. A. (2005). Prevalence of Burkholderia sp. nodule symbionts on four mimosoid legumes from Barro Colorado Island, Panama. Syst Appl Microbiol 28, 57-65.
3. Barrett, C. F. & Parker, M. A. (2006). Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp. nodule bacteria on two Mimosa spp. in Costa Rica. Appl Environ Microbiol 72, 1198-1206.
4. Beukes, C. W., Venter, S. N., Law, I. J., Phalane, F. L. & Steenkamp, E. T. (2013). South African papilionoid legumes are nodulated by diverse Burkholderia with unique nodulation and nitrogen-fixation loci. PLoS ONE 8, e68406.
5. Bontemps, C., Elliott, G. N., Simon, M. F., Dos Reis Júnior, F. B., Gross, E., Lawton, R. C., Neto, N. E., de Fátima Loureiro, M., De Faria, S. M. & other authors (2010). Burkholderia species are ancient symbionts of legumes. Mol Ecol 19, 44-52.
6. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M. (1977). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81, 461-466.
7. Chen, W. M., Moulin, L., Bontemps, C., Vandamme, P., Béna, G. & Boivin-Masson, C. (2003). Legume symbiotic nitrogen fixation by β-proteobacteria is widespread in nature. J Bacteriol 185, 7266-7272.
8. Chen, W. M., de Faria, S. M., Straliotto, R., Pitard, R. M., Simões-Araùjo, J. L., Chou, J. H., Chou, Y. J., Barrios, E., Prescott, A. R. & other authors (2005a). Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America. Appl Environ Microbiol 71, 7461-7471.
9. Chen, W. M., James, E. K., Chou, J. H., Sheu, S. Y., Yang, S. Z. & Sprent, J. I. (2005b). β-Rhizobia from Mimosa pigra, a newly discovered invasive plant in Taiwan. New Phytol 168, 661-675.
10. Dance, D. A. B. (2000). Ecology of Burkholderia pseudomallei and the interactions between environmental Burkholderia spp. and humananimal hosts. Acta Trop 74, 159-168.
11. De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133-142.
12. Eisen, J. A. (1995). The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41, 1105-1123.
13. Elliott, G. N., Chou, J. H., Chen, W. M., Bloemberg, G. V., Bontemps, C., Martínez-Romero, E., Velázquez, E., Young, J. P., Sprent, J. I. & James, E. K. (2009). Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions. Environ Microbiol 11, 762-778.
14. Farrelly, V., Rainey, F. A. & Stackebrandt, E. (1995). Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61, 2798-2801.
15. 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 D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
16. 2-fixing isolates from rice in Vietnam. Int J Syst Bacteriol 45, 274-289.
17. 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.
18. 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.
19. Holmes, D. E., Nevin, K. P. & Lovley, D. R. (2004). Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int J Syst Evol Microbiol 54, 1591-1599.
20. 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.
21. Huss, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184-192.
22. Jorgensen, J. H. & Ferraro, M. J. (2009). Antimicrobial susceptibility testing: a review of general principles and contemporary practices. Clin Infect Dis 49, 1749-1755.
23. Kanu, S. A. & Dakora, F. D. (2012). Symbiotic nitrogen contribution and biodiversity of root-nodule bacteria nodulating Psoralea species in the Cape Fynbos, South Africa. Soil Biol Biochem 54, 68-76.
24. 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.
25. 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.
26. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
27. Lane, D. J., Pace, B., Olsen, G. J., Stahl, D. A., Sogin, M. L. & Pace, N. R. (1985). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 82, 6955-6959.
28. Leitão, J. H., Sousa, S. A., Ferreira, A. S., Ramos, C. G., Silva, I. N. & Moreira, L. M. (2010). Pathogenicity, virulence factors, and strategies to fight against Burkholderia cepacia complex pathogens and related species. Appl Microbiol Biotechnol 87, 31-40.
29. Lim, J. H., Baek, S. H. & Lee, S. T. (2008). Burkholderia sediminicola sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 58, 565-569.
30. 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.
31. Mishra, R. P., 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.
32. Moulin, L., Munive, A., Dreyfus, B. & Boivin-Masson, C. (2001). Nodulation of legumes by members of the β-subclass of Proteobacteria. Nature 411, 948-950.
33. Muyzer, G., de Waal, E. C. & Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59, 695-700.
34. Payne, G. W., Vandamme, P., Morgan, S. H., LiPuma, J. J., Coenye, T., Weightman, A. J., Jones, T. H. & Mahenthiralingam, E. (2005). Development of a recA gene-based identification approach for the entire Burkholderia genus. Appl Environ Microbiol 71, 3917-3927.
35. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607-654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
36. Somasegaran, P. & Hoben, H. J. (1994). Handbook for Rhizobia: Methods in Legume-Rhizobium Technology. New York: Springer.
37. Stackebrandt, E., Lang, E., Cousin, S., Päuker, O., Brambilla, E., Kroppenstedt, R. & Lünsdorf, H. (2007). Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria. Int J Syst Evol Microbiol 57, 639-645.
38. Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125-128.
39. Tamura, K., Nei, M. & Kumar, S. (2004). Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101, 11030-11035.
40. 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.
41. 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.
42. van Waasbergen, L. G., Balkwill, D. L., Crocker, F. H., Bjornstad, B. N. & Miller, R. V. (2000). Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences. Appl Environ Microbiol 66, 3454-3463.
43. Vandamme, P., Opelt, K., Knöchel, N., Berg, C., Schönmann, S., De Brandt, E., Eberl, L., Falsen, E. & Berg, G. (2007). Burkholderia bryophila sp. nov. and Burkholderia megapolitana sp. nov., mossassociated species with antifungal and plant-growth-promoting properties. Int J Syst Evol Microbiol 57, 2228-2235.
44. Vincent, J. M. (1970). A Manual for the Practical Study of the Root-Nodule Bacteria (IBP Handbook no. 15). Oxford: Blackwell Scientific.
45. 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.
46. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697-703.
47. 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.