1887

International Journal of Systematic and Evolutionary Microbiology

Volume 60, Issue 10

sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil Free

Abstract

A Gram-positive bacterium, designated strain CBMB205, was isolated from the rhizosphere soil of traditionally cultivated, field-grown rice. Cells were strictly aerobic, motile, rod-shaped and formed endospores. The best growth was achieved at 30 °C and pH 7.0 in ammonium mineral salts (AMS) medium containing 600 mM methanol. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed strain CBMB205 in a clade with the species , and and revealed pairwise similarities ranging from 98.2 to 99.2 %. DNA–DNA hybridization experiments revealed a low level (<36 %) of DNA–DNA relatedness between strain CBMB205 and its closest relatives. The major components of the fatty acid profile were C anteiso, C iso, C iso and C anteiso. The diagnostic diamino acid of the cell wall was -diaminopimelic acid. The G+C content of the genomic DNA was 45.0 mol%. The lipids present in strain CBMB205 were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. The predominant respiratory quinone was MK-7. Studies of DNA–DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing enabled strain CBMB205 to be described as representing a novel species of the genus for which the name sp. nov. is proposed. The type strain is CBMB205 (=KACC 13105=NCCB 100236).

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Keyword(s): ACC, 1-aminocyclopropane-1-carboxylate deaminase , AMS, ammonium mineral salts and SEM, scanning electron microscope
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2010-10-01
2020-09-27
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References

  1. Anthony C. 1982 The Biochemistry of Methylotrophs London: Academic Press;
     [Google Scholar]
  2. Arfman N., Dijkhuizen L., Kirchhof G., Ludwig W., Schleifer K.-H., Bulygina E. S., Chumakov K. M., Govorukhina N. I., Trotsenko Y. A. other authors 1992; Bacillus methanolicus sp. nov., a new species of thermotolerant, methanol utilizing, endospore-forming bacteria. Int J Syst Bacteriol 42:439–445 [CrossRef]
     [Google Scholar]
  3. Atlas R. M. 1993 Handbook of Microbiological Media Edited by Parks L. C. Boca Raton, FL: CRC Press;
     [Google Scholar]
  4. Belimov A. A., Safronova V. I., Sergeyeva T. A., Egorova T. N., Matveyeva V. A., Tsyganov V. E., Borisov A. Y., Tikhonovich I. A., Kluge C. other authors 2001; Characterization of plant growth promoting rhizobacteria isolated from polluted soils and containing 1-aminocyclopropane-1-carboxylate deaminase. Can J Microbiol 47:642–652 [CrossRef]
     [Google Scholar]
  5. Bergey D. H., Breed R. S., Murray E. G. D., Hitchens A. P. 1939; Bacterium methylicum (Loew) Migula. ( Bacillus methylicus Loew. In Bergey's Manual of Determinative Bacteriology, 5th edn.p–597 Edited by Bergey D. H., Breed R. S., Murray E. G. D., Hitchens A. P. London, UK: Baillière, Tindall & Cox;
     [Google Scholar]
  6. Blaha D., Prigent-Combaret C., Sajjad Mirza M., Moënne-Loccoz Y. 2006; Phylogeny of the 1-aminocyclopropane-1-carboxylic acid deaminase-encoding gene acdS in phytobeneficial and pathogenic Proteobacteria and relation with strain biogeography. FEMS Microbiol Ecol 56:455–470 [CrossRef]
     [Google Scholar]
  7. Boden R., Thomas E., Savani P., Kelly D. P., Wood A. P. 2008; Novel methylotrophic bacteria isolated from the River Thames (London, UK. Environ Microbiol 10:3225–3236 [CrossRef]
     [Google Scholar]
  8. Bozzola J. J., Russell L. D. 1998 Electron Microscopy, 2nd edn. Sudbury, MS: Jones & Bartlett;
     [Google Scholar]
  9. Brautaset T., Jakobsen O. M., Flickinger M. C., Valla S., Ellingsen T. E. 2004; Plasmid-dependent methylotrophy in thermotolerant Bacillus methanolicus . J Bacteriol 186:1229–1238 [CrossRef]
     [Google Scholar]
  10. Cohn F. 1872; Untersuchungen über Bakterien. Beitr Biol Pflanz 1:127–224 (in German)
    [Google Scholar]
  11. Dedysh S. N., Knief C., Dunfield P. F. 2005; Methylocella species are facultatively methanotrophic. J Bacteriol 187:4665–4670 [CrossRef]
     [Google Scholar]
  12. DeLong E. F. 1992; Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89:5685–5689 [CrossRef]
     [Google Scholar]
  13. Dijkhuizen L., Arfmann N., Attwood M. M., Brooke A. G., Harder W., Watling E. M. 1988; Isolation and initial characterization of thermotolerant methylotrophic Bacillus strains. FEMS Microbiol Lett 52:209–214 [CrossRef]
     [Google Scholar]
  14. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
     [Google Scholar]
  15. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
     [Google Scholar]
  16. Francis I., Holsters M., Vereecke D. 2010; The Gram-positive side of plant–microbe interactions. Environ Microbiol 12:1–12 [CrossRef]
     [Google Scholar]
  17. Gerhardt P. R., Murray R. G. E., Wood W. A., Krieg N. R. (editors) 1994 Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;
     [Google Scholar]
  18. Ghosh S., Penterman J. N., Little R. D., Chavez R., Glick B. R. 2003; Three newly isolated plant growth-promoting bacilli facilitate the seedling growth of canola, Brassica campestris . Plant Physiol Biochem 41:277–281 [CrossRef]
     [Google Scholar]
  19. Glick B. R., Jacobson C. B., Schwarze M. M. K., Pasternak J. J. 1994; 1-Aminocyclopropane-1-carboxylic acid deaminase mutants of the plant growth promoting rhizobacterium Pseudomonas putida GR12–2 do not stimulate root elongation. Can J Microbiol 40:911–915 [CrossRef]
     [Google Scholar]
  20. Green P. N., Bousfield I. J. 1982; A taxonomic study of some Gram-negative facultatively methylotrophic bacteria. J Gen Microbiol 128:623–638
     [Google Scholar]
  21. Kalyuzhnaya M. G., De Marco P., Bowerman S., Pacheco C. C., Lara J. C., Lidstrom M. E., Chistoserdova L. 2006; Methyloversatilis universalis gen. nov., sp. nov. a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates. Int J Syst Evol Microbiol 56:2517–2522 [CrossRef]
     [Google Scholar]
  22. Kouker G., Jaeger K.-E. 1987; Specific and sensitive plate assay for bacterial lipase. Appl Environ Microbiol 53:211–213
     [Google Scholar]
  23. Kroppenstedt R. M. 1982; Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367 [CrossRef]
     [Google Scholar]
  24. Li J., Ovakim D. H., Charles T. C., Glick B. R. 2000; An ACC deaminase minus mutant of Enterobacter cloacae UW4 no longer promotes root elongation. Curr Microbiol 41:101–105 [CrossRef]
     [Google Scholar]
  25. Lidstrom M. E. 2006; Aerobic methylotrophic prokaryotes. In The Prokaryotes vol 2 pp 618–634 Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. NY, USA: Springer-Verlag;
     [Google Scholar]
  26. Loew O. 1892; Ueber einen Bacillus , welcher Ameisensäure und Formaldehyd assimilieren kann. Centralbl Bakteriol 12:462–465 (in German)
    [Google Scholar]
  27. Madhaiyan M., Poonguzhali S., Ryu J.-H., Sa T.-M. 2006; Regulation of ethylene levels in canola ( Brassica campestris ) by 1-aminocyclopropane-1-carboxylate deaminase-containing Methylobacterium fujisawaense . Planta 224:268–278 [CrossRef]
     [Google Scholar]
  28. Madhaiyan M., Kim B.-Y., Poonguzhali S., Kwon S.-W., Song M.-H., Ryu J.-H., Go S.-J., Koo B.-S., Sa T.-M. 2007a; Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice. Int J Syst Evol Microbiol 57:326–331 [CrossRef]
     [Google Scholar]
  29. Madhaiyan M., Poonguzhali S., Sa T.-M. 2007b; Characterization of 1-aminocyclopropane-1-carboxylate (ACC) deaminase containing Methylobacterium spp. and interactions with auxins and ACC regulation of ethylene in canola. Planta 226:867–876 [CrossRef]
     [Google Scholar]
  30. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [CrossRef]
     [Google Scholar]
  31. Migula W. 1900; Bacterium methylicum (Loew) Migula. In System der Bakterien. Handbuch der Morphologie, Entwicklungsgeschichte und Systematik der Bakterien vol 2 pp 447–448 Jena: Verlag von Gustav Fischer;
     [Google Scholar]
  32. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241 [CrossRef]
     [Google Scholar]
  33. Penrose D. M., Glick B. R. 2001; Levels of ACC and related compounds in exudate and extracts of canola seeds treated with ACC deaminase containing plant growth-promoting bacteria. Can J Microbiol 47:368–372 [CrossRef]
     [Google Scholar]
  34. Penrose D. M., Glick B. R. 2003; Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol Plant 118:10–15 [CrossRef]
     [Google Scholar]
  35. Poonguzhali S., Madhaiyan M., Sa T. M. 2006; Cultivation-dependent characterization of rhizobacterial communities from field grown Chinese cabbage Brassica campestris ssp pekinensis and screening of traits for potential plant growth promotion. Plant Soil 286:167–180 [CrossRef]
     [Google Scholar]
  36. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  37. Sasser M. 1990; Identification of bacteria through fatty acid analysis. In Methods in Phytobacteriology pp 199–204 Edited by Klement S., Rudolf K., Sands D. Budapest: Akademiai Kiado;
     [Google Scholar]
  38. Schleifer K. H. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156
     [Google Scholar]
  39. Seldin L., Dubnau D. 1985; Deoxyribonucleic acid homology among Bacillus polymyxa , Bacillus macerans , Bacillus azotofixans , and other nitrogen-fixing Bacillus strains. Int J Syst Bacteriol 35:151–154 [CrossRef]
     [Google Scholar]
  40. Skerman V. B. D., McGowan V., Sneath P. H. A. (editors) 1980; Approved lists of bacterial names. Int J Syst Bacteriol 30225–420 [CrossRef]
     [Google Scholar]
  41. 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]
     [Google Scholar]
  42. Ten L. N., Im W.-T., Kim M.-K., Kang M.-S., Lee S.-T. 2004; Development of a plate technique for screening of polysaccharide degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56:375–382 [CrossRef]
     [Google Scholar]
  43. 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 [CrossRef]
     [Google Scholar]
  44. Ueda T., Suga Y., Yahiro N., Matsuguchi T. 1995; Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177:1414–1417
     [Google Scholar]
  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 [CrossRef]
     [Google Scholar]
  46. Whittenbury R., Davies S. L., Wilkinson J. F. 1970; Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61:205–218 [CrossRef]
     [Google Scholar]
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Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil
Int J Syst Evol Microbiol 60, 2490 (2010); https://doi.org/10.1099/ijs.0.015487-0
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