1887

International Journal of Systematic and Evolutionary Microbiology

Volume 59, Issue 1

sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice Free

Abstract

A pink-pigmented, aerobic, facultatively methylotrophic bacterial strain, CBMB27, isolated from leaf tissues of rice ( L. ‘Dong-Jin’), was analysed using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species , and ; strain CBMB27 showed sequence similarities of 98.3, 98.5 and 97.3 %, respectively, to the type strains of these three species. DNA–DNA hybridization experiments revealed low levels (<38 %) of DNA–DNA relatedness between strain CBMB27 and its closest relatives. The sequence of the 1-aminocyclopropane-1-carboxylate deaminase gene () in strain CBMB27 differed from those of close relatives. The major fatty acid of the isolate was C 7 and the G+C content of the genomic DNA was 66.8 mol%. Based on the results of 16S rRNA gene sequence analysis, DNA–DNA hybridization, and physiological and biochemical characterization, which enabled the isolate to be differentiated from all recognized species of the genus , it was concluded that strain CBMB27 represents a novel species in the genus for which the name sp. nov. is proposed (type strain CBMB27 =LMG 24361 =KACC 11716 =DSM 19779).

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Keyword(s): ACCD, 1-aminocyclopropane-1-carboxylate deaminase
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2009-01-01
2020-01-25
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References

  1. Araújo, W. L., Marcon, J. & Maccheroni, W., Jr, Van Elsas, J. D., Van Vuurde, J. W. & Azevedo, J. L. ( 2002; ). Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol 68, 4906–4914.[CrossRef]
    [Google Scholar]
  2. Austin, B. & Goodfellow, M. ( 1979; ). Pseudomonas mesophilica, a new species of pink bacteria isolated from leaf surfaces. Int J Syst Bacteriol 29, 373–378.[CrossRef]
    [Google Scholar]
  3. Basile, D. V., Basile, M. R., Li, Q.-Y. & Corpe, W. A. ( 1985; ). Vitamin B12-stimulated growth and development of Jungermannia leiantha Grolle and Gymnocolea inflata (Huds.) Dum. (Hepaticae). Bryologist 88, 77–81.[CrossRef]
    [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. 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]
  6. Bozzola, J. J. & Russell, L. D. ( 1998; ). Electron Microscopy, 2nd edn. Sudbury, MA: Jones & Bartlett.
  7. Chanprame, S., Todd, J. J. & Widholm, J. M. ( 1996; ). Prevention of pink-pigmented methylotrophic bacteria (Methylobacterium mesophilicum) contamination of plant tissue cultures. Plant Cell Rep 16, 222–225.[CrossRef]
    [Google Scholar]
  8. Corpe, W. A. & Rheem, S. ( 1989; ). Ecology of the methylotrophic bacteria on living leaf surfaces. FEMS Microbiol Ecol 62, 243–250.[CrossRef]
    [Google Scholar]
  9. Doronina, N. V., Trotsenko, Y. A., Kuznetsov, B. B., Tourova, T. P. & Salkinoja-Salonen, M. S. ( 2002; ). Methylobacterium suomiense sp. nov. and Methylobacterium lusitanum sp. nov., aerobic, pink-pigmented, facultatively methylotrophic bacteria. Int J Syst Evol Microbiol 52, 773–776.[CrossRef]
    [Google Scholar]
  10. Gallego, V., García, M. T. & Ventosa, A. ( 2005; ). Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment. Int J Syst Evol Microbiol 55, 1429–1433.[CrossRef]
    [Google Scholar]
  11. Gallego, V., García, M. T. & Ventosa, A. ( 2006; ). Methylobacterium adhaesivum sp. nov., a methylotrophic bacterium isolated from drinking water. Int J Syst Evol Microbiol 56, 339–342.[CrossRef]
    [Google Scholar]
  12. Gerhardt, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (editors) ( 1994; ). Methods for General and Molecular Bacteriology. Washington, DC: American Society for Microbiology.
  13. Green, P. N. ( 1992; ). The genus Methylobacterium. In The Prokaryotes, 2nd edn, pp. 2342–2349. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  14. 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]
  15. Heumann, W. ( 1962; ). Die Methodik der Kreuzung sternbildender Bakterien. Biol Zentralbl 81, 341–354 (in German).
     [Google Scholar]
  16. Holland, M. A. & Polacco, J. C. ( 1992; ). Urease-null and hydrogenase-null phenotypes of a phylloplane bacterium reveal altered nickel metabolism in two soybean mutants. Plant Physiol 98, 942–948.[CrossRef]
    [Google Scholar]
  17. Idris, R., Trifonova, R., Puschenreiter, M., Wenzel, W. W. & Sessitsch, A. ( 2004; ). Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspi goesingense. Appl Environ Microbiol 70, 2667–2677.[CrossRef]
    [Google Scholar]
  18. Ito, H. & Iizuka, H. ( 1971; ). Taxonomic studies on a radio-resistant Pseudomonas. XII. Studies on the microorganisms of cereal grain. Agric Biol Chem 35, 1566–1571.[CrossRef]
    [Google Scholar]
  19. Jackson, E. F., Echlin, H. L. & Jackson, C. R. ( 2006; ). Changes in the phyllosphere community of the resurrection fern, Polypodium polypodioides, associated with rainfall and wetting. FEMS Microbiol Ecol 58, 236–246.[CrossRef]
    [Google Scholar]
  20. Jourand, P., Giraud, E., Béna, G., Sy, A., Willems, A., Gillis, M., Dreyfus, B. & de Lajudie, P. ( 2004; ). Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int J Syst Evol Microbiol 54, 2269–2273.[CrossRef]
    [Google Scholar]
  21. Kang, Y. S., Kim, J., Shin, H. D., Nam, Y. D., Bae, J. W., Jeon, C. O. & Park, W. ( 2007; ). Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis. Int J Syst Evol Microbiol 57, 2849–2853.[CrossRef]
    [Google Scholar]
  22. Koenig, R. L., Morris, R. O. & Polacco, J. C. ( 2002; ). tRNA is the source of low-level trans-zeatin production in Methylobacterium spp. J Bacteriol 184, 1832–1842.[CrossRef]
    [Google Scholar]
  23. Kouno, K. & Ozaki, A. ( 1975; ). Distribution of methanol-utilizing bacteria. In Proceedings of the International Symposium on Microbial Growth on C1 Compounds, pp. 11–21. Osaka, Japan: Society of Fermentation Technology.
  24. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  25. Kutschera, U. ( 2007; ). Plant-associated methylobacteria as co-evolved phytosymbionts: a hypothesis. Plant Signal Behav 2, 74–78.[CrossRef]
    [Google Scholar]
  26. 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]
  27. Madhaiyan, M., Poonguzhali, S. & Sa, T. M. ( 2007a; ). Metal tolerating methylotrophic bacteria reduces nickel and cadmium toxicity and promotes plant growth of tomato (Lycopersicon esculentum L.). Chemosphere 69, 220–228.[CrossRef]
    [Google Scholar]
  28. Madhaiyan, M., Poonguzhali, S. & Sa, T. M. ( 2007b; ). Characterization of 1-aminocyclopropane-1-carboxylate (ACC) deaminase containing Methylobacterium oryzae and interactions with auxins and ACC regulation of ethylene in canola (Brassica campestris). Planta 226, 867–876.[CrossRef]
    [Google Scholar]
  29. 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. ( 2007c; ). 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]
  30. McDonald, I. R. & Murrell, J. C. ( 1997; ). The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl Environ Microbiol 63, 3218–3224.
     [Google Scholar]
  31. 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]
  32. Patt, T. E., Cole, G. C. & Hanson, R. S. ( 1976; ). Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 26, 226–229.[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. Pirttilä, A. M., Laukkanen, H., Pospiech, H., Myllylä, R. & Hohtola, A. ( 2000; ). Detection of intracellular bacteria in the buds of Scotch pine (Pinus sylvestris L.) by in situ hybridization. Appl Environ Microbiol 66, 3073–3077.[CrossRef]
    [Google Scholar]
  35. Poonguzhali, S., Madhaiyan, M., Yim, W.-J., Kim, K.-A. & Sa, T.-M. ( 2008; ). Colonization pattern of plant root and leaf surfaces visualized by use of green-fluorescent-marked strain of Methylobacterium suomiense and its persistence in rhizosphere. Appl Microbiol Biotechnol 78, 1033–1043.[CrossRef]
    [Google Scholar]
  36. Rock, J. S., Goldberg, I., Ben-Bassat, A. & Mateles, R. I. ( 1976; ). Isolation and characterization of two methanol-utilizing bacteria. Agric Biol Chem 40, 2129–2135.[CrossRef]
    [Google Scholar]
  37. Sasser, M. ( 1990; ). Identification of bacteria through fatty acid analysis. In Methods in Phytobacteriology, pp. 199–204. Edited by Z. Klement, K. Rudolph & D. C. Sands. Budapest: Akademiai Kiado.
  38. Schauer, S. & Kutschera, U. ( 2008; ). Methylotrophic bacteria on the surfaces of field-grown sunflower plants: a biogeographic perspective. Theory Biosci 127, 23–29.[CrossRef]
    [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. Sy, A., Giraud, E., Jourand, P., Garcia, N., Willems, A., de Lajudie, P., Prin, Y., Neyra, M., Gillis, M. & other authors ( 2001; ). Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183, 214–220.[CrossRef]
    [Google Scholar]
  41. Sy, A., Timmers, A. C. J., Knief, C. & Vorholt, J. A. ( 2005; ). Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl Environ Microbiol 71, 7245–7252.[CrossRef]
    [Google Scholar]
  42. 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]
  43. Trotsenko, Y. A., Ivanova, E. G. & Doronina, N. V. ( 2001; ). Aerobic methylotrophic bacteria as phytosymbionts. Mikrobiologiia 70, 725–736 (in Russian).
     [Google Scholar]
  44. Urakami, T. & Komagata, K. ( 1984; ). Protomonas, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 34, 188–201.[CrossRef]
    [Google Scholar]
  45. Van Aken, B., Peres, C. M., Lafferty Doty, S., Yoon, J. M. & Schnoor, J. L. ( 2004; ). Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides × nigra DN34). Int J Syst Evol Microbiol 54, 1191–1196.[CrossRef]
    [Google Scholar]
  46. 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]
  47. Weon, H.-Y., Kim, B.-Y., Joa, J.-H., Son, J.-A., Song, M.-H., Kwon, S.-W., Go, S.-J. & Yoon, S.-H. ( 2008; ). Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int J Syst Evol Microbiol 58, 93–96.[CrossRef]
    [Google Scholar]
  48. Whittenbury, R., Phillips, K. C. & 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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Methylobacterium phyllosphaerae sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice
Int J Syst Evol Microbiol 59, 22 (2009); https://doi.org/10.1099/ijs.0.001693-0
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vol. , part 1, pp. 22 - 27

Enzyme reactions of sp. nov. CBMB27 and its closest relatives. [PDF](96 KB)

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