Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia

International Journal of Systematic and Evolutionary Microbiology

Volumn 66, Issue 8, 2016, Pages 2836-2846

  Dobritsa, Anatoly P ^a   Samadpour, Mansour ^a  

^a Institute for Environmental Health Inc   (United States)

Author keywords

Bacterial systematics; Burkholderia; Caballeronia; Conserved sequence indels; Paraburkholderia; Reclassification

Indexed keywords

ARTICLE; BURKHOLDERIA; CABALLERONIA; CABALLERONIA CHOICA; CABALLERONIA CORDOBENSIS; CABALLERONIA GLATHEI; CABALLERONIA GRIMMIAE; CABALLERONIA HUMI; CABALLERONIA JIANGSUENSIS; CABALLERONIA MEGALOCHROMOSOMATA; CABALLERONIA SORDIDICOLA; CABALLERONIA TELLURIS; CABALLERONIA TERRESTRIS; CABALLERONIA UDEIS; CABALLERONIA ZHEJIANGENSIS; NEW GENUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARABURKHOLDERIA; PARABURKHOLDERIA DIPOGONIS; PARABURKHOLDERIA GINSENGITERRAE; PARABURKHOLDERIA HUMISILVAE; PARABURKHOLDERIA INSULSA; PARABURKHOLDERIA KIRSTENBOSCHENSIS; PARABURKHOLDERIA METALLIRESISTENS; PARABURKHOLDERIA MONTICOLA; PARABURKHOLDERIA PANACITERRAE; PARABURKHOLDERIA RHIZOSPHAERAE; PARABURKHOLDERIA SOLISILVAE; PARABURKHOLDERIA SUSONGENSIS; PHYLOGENY; PRIORITY JOURNAL; BURKHOLDERIACEAE; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS;

RNA 16S;

BASE COMPOSITION; BURKHOLDERIA; BURKHOLDERIACEAE; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84988346547     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijsem.0.001065     Document Type: Article

References (46)

1. Angus, A. A., Agapakis, C. M., Fong, S., Yerrapragada, S., Estrada-delosSantos, P., Yang, P., Song, N., Kano, S., Caballero-Mellado, J. & other authors (2014). Plant-associated symbiotic Burkholderia species lack hallmark strategies required in mammalian pathogenesis. PLoS One 9, e83779.
2. Baek, I., Seo, B., Lee, I., Lee, K., Park, S. C., Yi, H. & Chun, J. (2015a). Burkholderia megalochromosomata sp. Nov., isolated from grassland soil. Int J Syst Evol Microbiol 65, 959-964.
3. Baek, I., Seo, B., Lee, I., Yi, H. & Chun, J. (2015b). Burkholderia monticola sp. Nov., isolated from mountain soil. Int J Syst Evol Microbiol 65, 504-509.
4. Coenye, T., Laevens, S., Willems, A., Ohlén, M., Hannant, W., Govan, J. R., 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.
5. De Smet, B., Mayo, M., Peeters, C., Zlosnik, J. E., Spilker, T., Hird, T. J., LiPuma, J. J., Kidd, T. J., Kaestli, M. & other authors (2015). Burkholderia stagnalis sp. Nov. And Burkholderia territorii sp. Nov., two novel Burkholderia cepacia complex species from environmental and human sources. Int J Syst Evol Microbiol 65, 2265-2271.
6. Draghi, W. O., Peeters, C., Cnockaert, M., Snauwaert, C., Wall, L. G., Zorreguieta, A. & Vandamme, P. (2014). Burkholderia cordobensis sp. Nov., from agricultural soils. Int J Syst Evol Microbiol 64, 2003-2008.
7. Estrada-delosSantos, P., Vinuesa, P., Martínez-Aguilar, L., Hirsch, A. M. & Caballero-Mellado, J. (2013). Phylogenetic analysis of Burkholderia species by multilocus sequence analysis. Curr Microbiol 67, 51-60.
8. Farh, M. E. A., Kim, Y. J., Van An, H., Sukweenadhi, J., Singh, P., Huq, M. A. & Yang, D. C. (2015a). Burkholderia ginsengiterrae sp. Nov. And Burkholderia panaciterrae sp. Nov., antagonistic bacteria against root rot pathogen Cylindrocarpon destructans, isolated from ginseng soil. Arch Microbiol 197, 439-447.
9. Farh, M. E. A., Kim, Y. J., Van An, H., Sukweenadhi, J., Singh, P., Huq, M. A. & Yang, D. C. (2015b). Burkholderia ginsengiterrae sp. Nov. And Burkholderia panaciterrae sp. Nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, List no. 166, p. 3764. Edited by A. Oren & G. M. Garrity. Int J Syst Evol Microbiol 65, 3763-3767.
10. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17, 368-376.
11. Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39, 783-791.
12. Gerrits, G. P., Klaassen, C., Coenye, T., Vandamme, P. & Meis, J. F. (2005). Burkholderia fungorum septicemia. Emerg Infect Dis 11, 1115-1117.
13. Gillis, M., Tran, V. V., 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.
14. Gu, J. Y., Zang, S. G., Sheng, X. F., He, L. Y., Huang, Z. & Wang, Q. (2015). Burkholderia susongensis sp. Nov., a mineral-weathering bacterium isolated from weathered rock surface. Int J Syst Evol Microbiol 65, 1031-1037.
15. Guo, J. K., Ding, Y. Z., Feng, R. W., Wang, R. G., Xu, Y. M., Chen, C., Wei, X. L. & Chen, W. M. (2015a). Burkholderia metalliresistens sp. Nov., a multiple metal-resistant and phosphate-solubilising species isolated from heavy metal-polluted soil in Southeast China. Antonie Van Leeuwenhoek 107, 1591-1598.
16. Guo, J. K., Ding, Y. Z., Feng, R. W., Wang, R. G., Xu, Y. M., Chen, C., Wei, X. L. & Chen, W. M. (2015b). Burkholderia metalliresistens sp. Nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, List no. 165, p.2777. Edited by A. Oren & G. M. Garrity. Int J Syst Evol Microbiol, 2777-2783.
17. Gyaneshwar, P., Hirsch, A. M., Moulin, L., Chen, W. M., Elliott, G. N., Bontemps, C., Estrada-deLosSantos, P., Gross, E., Dos Reis, F. B. & other authors (2011). Legume-nodulating betaproteobacteria: Diversity, host range, and future prospects. Mol Plant Microbe Interact 24, 1276-1288.
18. Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41, 95-98.
19. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
20. Lee, J. C. & Whang, K. S. (2015). Burkholderia humisilvae sp. Nov., Burkholderia solisilvae sp. Nov. And Burkholderia rhizosphaerae sp. Nov., isolated from forest soil and rhizosphere soil. Int J Syst Evol Microbiol 65, 2986-2992.
21. Lemaire, B., Van Oevelen, S., De Block, P., Verstraete, B., Smets, E., Prinsen, E. & Dessein, S. (2012). Identification of the bacterial endosymbionts in leaf nodules of Pavetta (Rubiaceae). Int J Syst Evol Microbiol 62, 202-209.
22. Lim, Y. W., Baik, K. S., Han, S. K., Kim, S. B. & Bae, K. S. (2003). Burkholderia sordidicola sp. Nov., isolated from the white-rot fungus Phanerochaete sordida. Int J Syst Evol Microbiol 53, 1631-1636.
23. Liu, X. Y., Li, C. X., Luo, X. J., Lai, Q. L. & Xu, J. H. (2014). Burkholderia jiangsuensis sp. Nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil. Int J Syst Evol Microbiol 64, 3247-3253.
24. Lopes-Santos, L., Castro, D. B., Ottoboni, L. M., Park, D., Weir, B. S. & Destéfano, S. A. (2015). Draft genome sequence of Burkholderia andropogonis type strain ICMP2807, isolated from Sorghum bicolor. Genome Announc 3, e00455-15.
25. Lu, P., Zheng, L. Q., Sun, J. J., Liu, H. M., Li, S. P., Hong, Q. & Li, W. J. (2012). Burkholderia zhejiangensis sp. Nov., a methyl-parathion-degrading bacterium isolated from a wastewater-treatment system. Int J Syst Evol Microbiol 62, 1337-1341.
26. Oren, A. & Garrity, G. M. (2015a). List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 65, 2017-2025.
27. Oren, A. & Garrity, G. M. (2015b). List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 65, 2777-2783.
28. Palleroni, N. J., Kunisawa, R., Contopoulou, R. & Doudoroff, M. (1973). Nucleic acid homologies in the genus Pseudomonas. Int J Syst Bacteriol 23, 333-339.
29. Rusch, A., Islam, S., Savalia, P. & Amend, J. P. (2015). Burkholderia insulsa sp. Nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system. Int J Syst Evol Microbiol 65, 189-194.
30. Saitou, N. & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
31. Sawana, A., Adeolu, M. & Gupta, R. S. (2014). Molecular signatures and phylogenomic analysis of the genus Burkholderia: Proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. Nov. Harboring environmental species. Front Genet 5, 429.
32. Sawana, A., Adeolu, M. & Gupta, R. S. (2015a). Paraburkholderia gen. Nov. And Paraburkholderia spp. Comb. Nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, List no. 164, pp. 2019-2021. Edited by A. Oren & G. M. Garrity. Int J Syst Evol Microbiol 65, 2017-2025.
33. Sawana, A., Adeolu, M. & Gupta, R. S. (2015b). Paraburkholderia spp. Comb. Nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, List no.165, p. 2779. Edited by A. Oren & G. M. Garrity. Int J Syst Evol Microbiol 65, 2777-2783.
34. Sheu, S. Y., Chen, M. H., Liu, W. Y., Andrews, M., James, E. K., Ardley, J. K., De Meyer, S. E., James, T. K., Howieson, J. G. & other authors (2015). Burkholderia dipogonis sp. Nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia. Int J Syst Evol Microbiol 65, 4716-4723.
35. Steenkamp, E. T., van Zyl, E., Beukes, C. W., Avontuur, J. R., Chan, W. Y., Palmer, M., Mthombeni, L. S., Phalane, F. L., Sereme, T. K. & Venter, S. N. (2015). Burkholderia kirstenboschensis sp. Nov. Nodulates papilionoid legumes indigenous to South Africa. Syst Appl Microbiol 38, 545-554.
36. Steenkamp, E. T., van Zyl, E., Beukes, C. W., Avontuur, J. R., Chan, W. Y., Palmer, M., Mthombeni, L. S., Phalane, F. L., Sereme, T. K. & Venter, S. N. (2016). Burkholderia kirstenboschensis sp. Nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, List no. 170, p. 2463. Edited by A. Oren & G. M. Garrity. Int J Syst Evol Microbiol 66, 2463-2466.
37. Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30, 2725-2729.
38. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
39. Tian, Y., Kong, B. H., Liu, S. L., Li, C. L., Yu, R., Liu, L. & Li, Y. H. (2013). Burkholderia grimmiae sp. Nov., isolated from a xerophilous moss (Grimmia montana). Int J Syst Evol Microbiol 63, 2108-2113.
40. Vandamme, P., Holmes, B., Vancanneyt, M., Coenye, T., Hoste, B., Coopman, R., Revets, H., Lauwers, S., Gillis, M. & other authors (1997). Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. Nov. Int J Syst Bacteriol 47, 1188-1200.
41. Vandamme, P., De Brandt, E., Houf, K., Salles, J. F., Van Elsas, J., Spilker, T. & Lipuma, J. J. (2013). Burkholderia humi sp. Nov., Burkholderia choica sp. Nov., Burkholderia telluris sp. Nov., Burkholderia terrestris sp. Nov. And Burkholderia udeis sp. Nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil. Int J Syst Evol Microbiol 63, 4707-4718.
42. Vandamme, P. & Peeters, C. (2014). Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 106, 57-65.
43. 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.
44. Yabuuchi, E., Kosako, Y., Yano, I., Hotta, H. & Nishiuchi, Y. (1995). Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. Nov.: Proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. Nov., Ralstonia solanacearum (Smith 1896) comb. Nov. And Ralstonia eutropha (Davis 1969) comb. Nov. Microbiol Immunol. 39, 897-904.
45. Zolg, W. & Ottow, J. C. G. (1975). Pseudomonas glathei sp. Nov., a new nitrogen-scavenging rod isolated from acid lateritic relicts in Germany. Z Allg Mikrobiol 15, 287-299.
46. Zolg, W. & Ottow, J. C. G. (1980). P. Glathei Zolg and Ottow 1975. In Approved Lists of Bacterial Names, p. 351. Edited by V. B. D. Skerman, V. McGowan & P. H. A. Sneath. Int J Syst Bacteriol 30, 225-420.