1887

Abstract

Two strains of acid-neutralizing bacteria, E25 and E21, were isolated from torpedo grass () growing in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Thailand. Cells of the strains were Gram-negative, aerobic, non-spore-forming rods, 0.6–0.8 µm wide and 1.6–2.1 µm long. The strains showed good growth at pH 4.0–8.0 and 17–37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C, C cyclo and Cω7 as the major fatty acids. Their fatty acid profiles were similar to those reported for other species. The DNA G+C content of the strains was 65 mol%. On the basis of 16S rRNA gene sequence similarity, the strains were shown to belong to the genus Although the calculated 16S rRNA gene sequence similarity of E25 to strain E21 and the type strains of , , , and was 100, 98.7, 98.6, 97.6, 97.4 and 97.3 %, respectively, strains E25 and E21 formed a group that was distinct in the phylogenetic tree; the DNA–DNA relatedness of E25 to E21 and CIP 107921, LMG 22274, LMG 19450, LMG 23741 and LMG 23256 was 90, 42, 42, 42, 45 and 35 %, respectively. The results of physiological and biochemical tests including whole-cell protein pattern analysis allowed phenotypic differentiation of these strains from previously described species. Therefore, strains E25 and E21 represent a novel species, for which the name sp. nov. is proposed. The type strain is E25 ( = NBRC 103871  = BCC 36998).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.026278-0
2011-07-01
2019-12-05
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/7/1645.html?itemId=/content/journal/ijsem/10.1099/ijs.0.026278-0&mimeType=html&fmt=ahah

References

  1. Aizawa T. , Nguyen B. V. , Kimoto K. , Iwabuchi N. , Sumida H. , Hasegawa I. , Sasaki S. , Tamura T. , Kudo T. et al. ( 2007; ). Curtobacterium ammoniigenes sp. nov., an ammonia-producing bacterium isolated from plants inhabiting acidic swamps in actual acid sulfate soil areas of Vietnam. . Int J Syst Evol Microbiol 57:, 1447–1452. [CrossRef].[PubMed].
    [Google Scholar]
  2. Aizawa T. , Nguyen B. V. , Vijarnsorn P. , Kimoto K. , Sasaki S. , Nakajima M. , Sunairi M. . ( 2008; ). Application of symbiotic bacteria isolated from plants adapted to actual acid sulfate soil. . In Development of New Bioremediation Systems of Acid Sulfate Soil for Agriculture and Forestry, pp. 57–62. Edited by Sasaki S. , Ishii R. , Hasegawa I. , Tokuyama T. , Hanzawa K. , Sumida H. , Ueda S. , Noguchi A. , Matsumoto R. et al. . Kyoto:: Shoukadoh;.
    [Google Scholar]
  3. Aizawa T. , Urai M. , Iwabuchi N. , Nakajima M. , Sunairi M. . ( 2010; a). Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis). . Int J Syst Evol Microbiol 60:, 61–66. [CrossRef].[PubMed].
    [Google Scholar]
  4. Aizawa T. , Nguyen B. V. , Nakajima M. , Sunairi M. . ( 2010; b). 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]
  5. Aizawa T. , Nguyen B. V. , Vijarnsorn P. , Nakajima M. , Sunairi M. . ( 2010; c). 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]
  6. Baldani V. L. D. , Oliveira E. , Balota E. , Baldani J. I. , Kirchhof G. , Döbereiner J. . ( 1997; ). Burkholderia brasilensis sp. nov., uma nova espécie de bactéria diazotrófica endofitica. . An Acad Bras Cienc 69:, 116 (in Portuguese).
    [Google Scholar]
  7. Brämer C. O. , Vandamme P. , da Silva L. F. , Gomez J. G. C. , Steinbüchel A. . ( 2001; ). Burkholderia sacchari sp. nov., a polyhydroxyalkanoate-accumulating bacterium isolated from soil of a sugar-cane plantation in Brazil. . Int J Syst Evol Microbiol 51:, 1709–1713.[PubMed].[CrossRef]
    [Google Scholar]
  8. Burris R. H. . ( 1972; ). Nitrogen fixation – assay methods and techniques. . Methods Enzymol 24:, 415–431. [CrossRef].[PubMed].
    [Google Scholar]
  9. Caballero-Mellado J. , Martínez-Aguilar L. , Paredes-Valdez G. , Santos P. E. . ( 2004; ). Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species. . Int J Syst Evol Microbiol 54:, 1165–1172. [CrossRef].[PubMed].
    [Google Scholar]
  10. Caballero-Mellado J. , Onofre-Lemus J. , Estrada-de Los Santos P. , Martínez-Aguilar L. . ( 2007; ). The tomato rhizosphere, an environment rich in nitrogen-fixing Burkholderia species with capabilities of interest for agriculture and bioremediation. . Appl Environ Microbiol 73:, 5308–5319. [CrossRef].[PubMed].
    [Google Scholar]
  11. 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]
  12. 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]
  13. Chun J. , Lee J.-H. , Jung Y. , Kim M. , Kim S. , Kim B. K. , Lim Y.-W. . ( 2007; ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57:, 2259–2261.[CrossRef]
    [Google Scholar]
  14. Coenye T. , Vandamme P. . ( 2003; ). Diversity and significance of Burkholderia species occupying diverse ecological niches. . Environ Microbiol 5:, 719–729. [CrossRef].[PubMed].
    [Google Scholar]
  15. Ezaki T. , Hashimoto Y. , Takeuchi N. , Yamamoto H. , Liu S. L. , Miura H. , Matsui K. , Yabuuchi E. . ( 1988; ). Simple genetic method to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells. . J Clin Microbiol 26:, 1708–1713.[PubMed].
    [Google Scholar]
  16. 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]
  17. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef].[PubMed].
    [Google Scholar]
  18. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  19. Felsenstein J. . ( 2005; ). phylip (Phylogeny Inference Package) version 3.65. . Distributed by the author. Department of Genome Sciences, University of Washington;, Seattle, USA:.
  20. Hashidoko Y. , Tada M. , Osaki M. , Tahara S. . ( 2002; ). Soft gel medium solidified with gellan gum for preliminary screening for root-associating, free-living nitrogen-fixing bacteria inhabiting the rhizoplane of plants. . Biosci Biotechnol Biochem 66:, 2259–2263. [CrossRef].[PubMed].
    [Google Scholar]
  21. Jukes T. H. , Cantor C. R. . ( 1969; ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 2, pp. 21–132. Edited by Munro H. N. . . New York:: Academic Press;.
    [Google Scholar]
  22. Kimoto K. , Aizawa T. , Urai M. , Nguyen B. V. , Suzuki K. , Nakajima M. , Sunairi M. . ( 2010; ). Acidocella aluminiidurans sp. nov., an aluminium-tolerant bacterium isolated from Panicum repens grown in a highly acidic swamp in actual acid sulfate soil area of Vietnam. . Int J Syst Evol Microbiol 60:, 764–768. [CrossRef].[PubMed].
    [Google Scholar]
  23. Kluge A. G. , Farris F. S. . ( 1969; ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18:, 1–32. [CrossRef]
    [Google Scholar]
  24. Martínez-Aguilar L. , Díaz R. , Peña-Cabriales J. J. , Estrada-de Los Santos P. , Dunn M. F. , Caballero-Mellado J. . ( 2008; ). Multichromosomal genome structure and confirmation of diazotrophy in novel plant-associated Burkholderia species. . Appl Environ Microbiol 74:, 4574–4579.[CrossRef]
    [Google Scholar]
  25. Perin L. , Martínez-Aguilar L. , Paredes-Valdez G. , Baldani J. I. , Estrada-de Los Santos P. , Reis V. M. , Caballero-Mellado J. . ( 2006; ). Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize. . Int J Syst Evol Microbiol 56:, 1931–1937. [CrossRef].[PubMed].
    [Google Scholar]
  26. Pot B. , Vandamme P. , Kersters K. . ( 1994; ). Analysis of electrophoretic whole-organism protein fingerprints. . In Modern Microbial Methods (Chemical Methods Prokaryotic Systematics Series), pp. 493–521. Edited by Goodfellow M. , O’Donnell A. G. . . Chichester:: Wiley;.
    [Google Scholar]
  27. Reis V. M. , Estrada-de los Santos P. , Tenorio-Salgado S. , Vogel J. , Stoffels M. , Guyon S. , Mavingui P. , Baldani V. L. , Schmid M. et al. ( 2004; ). Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. . Int J Syst Evol Microbiol 54:, 2155–2162. [CrossRef].[PubMed].
    [Google Scholar]
  28. Ryu E. . ( 1938; ). On the Gram-differentiation of bacteria by the simplest method. . J Jpn Soc Vet Sci 17:, 31.
    [Google Scholar]
  29. Rzhetsky A. , Nei M. . ( 1992; ). A simple method for estimating and testing minimum evolution trees. . Mol Biol Evol 9:, 945–967.
    [Google Scholar]
  30. 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]
  31. Sasaki S. , Ishii R. , Hasegawa I. , Tokuyama T. , Hanzawa K. , Sumida H. , Ueda S. , Noguchi A., , Matsumoto R. et al. ( 2008; ). Development of New Bioremediation Systems of Acid Sulfate Soil for Agriculture and Forestry. Kyoto:: Shoukadoh;.
    [Google Scholar]
  32. Smibert R. M. , Krieg N. R. . ( 1994; ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  33. Stackebrandt E. , Goebel B. . ( 1994; ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  34. Tamaoka J. , Komagata K. . ( 1984; ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25:, 125–128. [CrossRef]
    [Google Scholar]
  35. Tamura T. , Hatano K. . ( 2001; ). Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and ‘Actinoplanes aurantiacus’ to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov.. Int J Syst Evol Microbiol 51:, 2119–2125.[PubMed].[CrossRef]
    [Google Scholar]
  36. Tamura T. , Nakagaito Y. , Nishii T. , Hasegawa T. , Stackebrandt E. , Yokota A. . ( 1994; ). A new genus of the order Actinomycetales, Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. nov. and Couchioplanes caeruleus subsp. azureus subsp. nov.. Int J Syst Bacteriol 44:, 193–203. [CrossRef].[PubMed].
    [Google Scholar]
  37. Tamura T. , Hayakawa M. , Hatano K. . ( 1999; ). Sporichthya brevicatena sp. nov.. Int J Syst Bacteriol 49:, 1779–1784. [CrossRef].[PubMed].
    [Google Scholar]
  38. Tamura K. , Dudley J. , Nei M. , Kumar S. . ( 2007; ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24:, 1596–1599. [CrossRef].[PubMed].
    [Google Scholar]
  39. 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. [CrossRef].[PubMed].
    [Google Scholar]
  40. 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]
  41. Vandamme P. , Pot B. , Gillis M. , De Vos P. , Kersters K. , Swings J. . ( 1996; ). Polyphasic taxonomy, a consensus approach to bacterial systematics. . Microbiol Rev 60:, 407–438.[PubMed].
    [Google Scholar]
  42. 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]
  43. 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. et al. ( 1987; ). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  44. Weber O. B. , Baldani V. L. D. , Teixeira K. R. S. , Kirchhof G. , Baldani J. I. , Döbereiner J. . ( 1999; ). Isolation and characterization of diazotrophic bacteria from banana and pineapple plants. . Plant Soil 210:, 103–113. [CrossRef]
    [Google Scholar]
  45. 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]
  46. Yamada Y. , Takinami-Nakamura H. , Tahara Y. , Oyaizu H. , Komagata K. . ( 1982; ). The ubiquinone systems in the strains of Pseudomonas species. . J Gen Appl Microbiol 28:, 7–12. [CrossRef]
    [Google Scholar]
  47. Yang H. C. , Im W. T. , Kim K. K. , An D. S. , Lee S. T. . ( 2006; ). Burkholderia terrae sp. nov., isolated from a forest soil. . Int J Syst Evol Microbiol 56:, 453–457. [CrossRef].[PubMed].
    [Google Scholar]
  48. Zhang H. , Hanada S. , Shigematsu T. , Shibuya K. , Kamagata Y. , Kanagawa T. , Kurane R. . ( 2000; ). Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE. . Int J Syst Evol Microbiol 50:, 743–749.[PubMed].[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.026278-0
Loading
/content/journal/ijsem/10.1099/ijs.0.026278-0
Loading

Data & Media loading...

Supplements

Photographs of an actual acid sulfate soil (AASS) and growing in an acidic pond in an AASS area in Thailand. (a) Sampling site (pH 2.9); (b) ; (c) soil from the sampling site. The wet grey mud at the bottom of the water is the pyrite (iron–sulfide) layer. Pyrite exposed to air is oxidized to sulfuric acid and, consequently, both soil and water show a lower pH. The mottled yellow layer above the wet mud is jarosite (a by-product of the oxidation process).

IMAGE

Extended 16S rRNA gene sequence-based phylogenetic trees reconstructed by using the neighbour-joining, minimum-evolution, maximum-parsimony and maximum-likelihood methods. [PDF](89 KB)

PDF

SDS-PAGE profiles of whole-cell extracts of sp. nov. strains and type strains of related species. Lanes: 1, sp. nov. E25 ; 2, sp. nov. E21; 3, CIP 107921 ; 4, LMG 22274 ; 5, LMG 19450 ; 6, LMG 23741T; 7, LMG 23256 ; 8, LMG 23612 ; 9, LMG 23149 ; 10, SA41 .

IMAGE

[PDF file of Supplementary Tables S1–S3](60 KB)

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