1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 63, Issue Pt_7

sp. nov. and sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces Free

Abstract

Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of and . 16S rRNA gene sequence analysis support the affiliation of all strains to the genus . The closest relatives of strains C34 and T5 were 23e (98.0 and 98.5 % sequence similarity, respectively) and JCM 2833 (97.0 and 97.2 %, respectively). Strain TA73 showed the highest sequence similarities to JT1 and F3.2 (both 97.9 %), followed by CBMB27 and DSM 19569 (both 97.8 %), C15 and JCM 2831 (both 97.7 %). The major components in the fatty acid profiles were Cω7, C and one unknown fatty acid for strain TA73 and Cω7, Cω7/iso-C 2-OH, C and C for strains C34 and T5. Physiological and biochemical analysis, including DNA–DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA–DNA hybridization studies also showed high similarities between strains C34 and T5 (59.6–100 %). Therefore, the isolates represent two novel species within the genus , for which the names sp. nov. (type strain TA73 = LMG 25778 = CCM 7786) and sp. nov. (type strain C34 = LMG 25777 = CCM 7787) are proposed.

  • Published Online:
Funding
This study was supported by the:
  • DFG Priority Program 1374 ‘Infrastructure-Biodiversity-Exploratories’ (Award Ka 875/6-1 to P. K.)
© 2013 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.047787-0
2013-07-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/7/2690.html?itemId=/content/journal/ijsem/10.1099/ijs.0.047787-0&mimeType=html&fmt=ahah

References

  1. Anesti V., Vohra J., Goonetilleka S., McDonald I. R., Sträubler B., Stackebrandt E., Kelly D. P., Wood A. P. ( 2004 ). Molecular detection and isolation of facultatively methylotrophic bacteria, including Methylobacterium podarium sp. nov., from the human foot microflora. . Environ Microbiol 6, 820–830. [View Article] [PubMed]
    [Google Scholar]
  2. Anesti V., McDonald I. R., Ramaswamy M., Wade W. G., Kelly D. P., Wood A. P. ( 2005 ). Isolation and molecular detection of methylotrophic bacteria occurring in the human mouth. . Environ Microbiol 7, 1227–1238. [View Article] [PubMed]
    [Google Scholar]
  3. Balachandar D., Raja P., Sundaram S. P. ( 2007 ). Genetic and metabolic diversity of pink-pigmented facultative methylotrophs in phyllosphere of tropical plants. . Braz J Microbiol 39, 68–73. [View Article]
    [Google Scholar]
  4. Bousfield I. J., Green P. N. ( 1985 ). Reclassification of bacteria of the genus Protomonas Urakami and Komagata 1984 in the genus Methylobacterium (Patt, Cole, and Hanson) emend. Green and Bousfield 1983. . Int J Syst Bacteriol 35, 209. [View Article]
    [Google Scholar]
  5. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. ( 1978 ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. . Proc Natl Acad Sci U S A 75, 4801–4805. [View Article] [PubMed]
    [Google Scholar]
  6. Cao Y. R., Wang Q., Jin R. X., Tang S. K., Jiang Y., He W. X., Lai H. X., Xu L. H., Jiang C. L. ( 2011 ). Methylobacterium soli sp. nov. a methanol-utilizing bacterium isolated from the forest soil. . Antonie van Leeuwenhoek 99, 629–634. [View Article] [PubMed]
    [Google Scholar]
  7. Chistoserdova L., Chen S. W., Lapidus A., Lidstrom M. E. ( 2003 ). Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. . J Bacteriol 185, 2980–2987. [View Article] [PubMed]
    [Google Scholar]
  8. Corpe W. A., Rheem S. ( 1989 ). Ecology of the methylotrophic bacteria on living leaf surfaces. . FEMS Microbiol Ecol 62, 243–250. [View Article]
    [Google Scholar]
  9. Delmotte N., Knief C., Chaffron S., Innerebner G., Roschitzki B., Schlapbach R., von Mering C., Vorholt J. A. ( 2009 ). Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. . Proc Natl Acad Sci U S A 106, 16428–16433. [View Article] [PubMed]
    [Google Scholar]
  10. Doronina N. V., Trotsenko Y. A., Tourova T. P., Kuznetsov B. B., Leisinger T. ( 2000 ). Methylopila helvetica sp. nov. and Methylobacterium dichloromethanicum sp. nov., novel aerobic facultatively methylotrophic bacteria utilizing dichloromethane. . Syst Appl Microbiol 23, 210–218. [View Article] [PubMed]
    [Google Scholar]
  11. 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. [View Article] [PubMed]
    [Google Scholar]
  12. Doronina N. V., Ivanova E. G., Suzina N. F., Trotsenko Iu. A. ( 2004 ). [Methanotrophs and methylobacteria are found in woody plant tissues within a winter period]. . Mikrobiologiia 73, 817–824 (in Russian). [PubMed]
    [Google Scholar]
  13. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [Google Scholar]
  14. Felsenstein J. ( 1995 ). phylip (phylogeny inference package) version 3.6. . Distributed by the author. Department of Genome Sciences, University of Washington;, Seattle, USA:.
     [Google Scholar]
  15. Fischer M., Bossdorf O., Gockel S., Hänsel F., Hemp A., Hessenmöller D., Korte G., Nieschulze J., Pfeiffer S. & other authors ( 2010 ). Implementing large-scale and long-term functional biodiversity research: The Biodiversity Exploratories. . Basic Appl Ecol 11, 473–485. [View Article]
    [Google Scholar]
  16. 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;.
     [Google Scholar]
  17. Green P. N. ( 2006 ). Methylobacterium. . In The Prokaryotes. A Handbook on the Biology of Bacteria, , 3rd edn., vol. 5, pp. 257–265. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. . New York:: Springer;.
     [Google Scholar]
  18. Green P. N., Bousfield I. J. ( 1983 ). Emendation of Methylobacterium (Patt, Cole, and Hanson 1976); Methylobacterium rhodinum (Heumann 1962) comb. nov. corrig.; Methylobacterium radiotolerans (Ito & Iizuka 1971) comb. nov., corrig.; and Methylobacterium mesophilicum (Austin & Goodfellow 1979) comb. nov. . Int J Syst Bacteriol 33, 875–877. [View Article]
    [Google Scholar]
  19. Green P. N., Bousfield I. J., Hood D. ( 1988 ). Three new Methylobacterium species: M. rhodesianum sp. nov., M. zatmanii sp. nov., and M. fujisawaense sp. nov. . Int J Syst Bacteriol 38, 124–127. [View Article]
    [Google Scholar]
  20. Holland M. A., Polacco J. C. ( 1994 ). PPFMs and other covert contaminants: is there more to plant physiology than just plant?. Annu Rev Plant Physiol Plant Mol Biol 45, 197–209. [View Article]
    [Google Scholar]
  21. Hoppe T., Peters K., Schmidt F. ( 2011 ). Methylobacterium bullatum sp. nov., a methylotrophic bacterium isolated from Funaria hygrometrica . . Syst Appl Microbiol 34, 482–486. [View Article] [PubMed]
    [Google Scholar]
  22. Ivanova E. G., Doronina N. V., Shepeliakovskaia A. O., Laman A. G., Brovko F. A., Trotsenko IuA. ( 2000 ). [Facultative and obligate aerobic methylobacteria synthesize cytokinins]. . Mikrobiologiia 69, 764–769 (in Russian). [PubMed]
    [Google Scholar]
  23. Ivanova E. G., Doronina N. V., Trotsenko IuA. ( 2001 ). [Aerobic methylobacteria are capable of synthesizing auxins]. . Mikrobiologiia 70, 452–458 (in Russian). [PubMed]
    [Google Scholar]
  24. Ivanova E. G., Fedorov D. N., Doronina N. V., Trotsenko IuA. ( 2006 ). [Production of vitamin B12 in aerobic methylotrophic bacteria]. . Mikrobiologiia 75, 570–572 (in Russian). [PubMed]
    [Google Scholar]
  25. Jones D. T., Taylor W. R., Thornton J. M. ( 1992 ). The rapid generation of mutation data matrices from protein sequences. . Comput Appl Biosci 8, 275–282. [PubMed]
    [Google Scholar]
  26. 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. [View Article] [PubMed]
    [Google Scholar]
  27. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of the protein molecules. . In Mammalian protein metabolism, pp. 21–132. Edited by Munro H. N. . New York:: Academic Press;.
     [Google Scholar]
  28. Kämpfer P., Kroppenstedt R. M. ( 1996 ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42, 989–1005. [View Article]
    [Google Scholar]
  29. Kämpfer P., Steiof M., Dott W. ( 1991 ). Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. . Microb Ecol 21, 227–251. [View Article]
    [Google Scholar]
  30. 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. [View Article] [PubMed]
    [Google Scholar]
  31. Kato Y., Asahara M., Arai D., Goto K., Yokota A. ( 2005 ). Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum. . J Gen Appl Microbiol 51, 287–299. [View Article] [PubMed]
    [Google Scholar]
  32. Kato Y., Asahara M., Goto K., Kasai H., Yokota A. ( 2008 ). Methylobacterium persicinum sp. nov., Methylobacterium komagatae sp. nov., Methylobacterium brachiatum sp. nov., Methylobacterium tardum sp. nov. and Methylobacterium gregans sp. nov., isolated from freshwater. . Int J Syst Evol Microbiol 58, 1134–1141. [View Article] [PubMed]
    [Google Scholar]
  33. 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. [View Article] [PubMed]
    [Google Scholar]
  34. Knief C., Frances L., Cantet F., Vorholt J. A. ( 2008 ). Cultivation-independent characterization of Methylobacterium populations in the plant phyllosphere by automated ribosomal intergenic spacer analysis. . Appl Environ Microbiol 74, 2218–2228. [View Article] [PubMed]
    [Google Scholar]
  35. Knief C., Ramette A., Frances L., Alonso-Blanco C., Vorholt J. A. ( 2010 ). Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. . ISME J 4, 719–728. [View Article] [PubMed]
    [Google Scholar]
  36. Knief C., Dengler V., Bodelier P. L. E., Vorholt J. A. ( 2012 ). Characterization of Methylobacterium strains isolated from the phyllosphere and description of Methylobacterium longum sp. nov. . Antonie van Leeuwenhoek 101, 169–183. [View Article] [PubMed]
    [Google Scholar]
  37. 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. [View Article] [PubMed]
    [Google Scholar]
  38. Konovalova H. M., Shylin S. O., Rokytko P. V. ( 2007 ). [Characteristics of carotenoids of methylotrophic bacteria of Methylobacterium genus]. . Mikrobiol Z 69, 35–41 (in Ukrainian). [PubMed]
    [Google Scholar]
  39. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing nucleic acid techniques in bacterial systematics. . In Nucleic acid techniques in bacterial systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M. . New York:: Wiley;.
     [Google Scholar]
  40. Lee S. W., Oh H. W., Lee K. H., Ahn T. Y. ( 2009 ). Methylobacterium dankookense sp. nov., isolated from drinking water. . J Microbiol 47, 716–720. [View Article] [PubMed]
    [Google Scholar]
  41. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. & other authors ( 2004 ). arb: a software environment for sequence data. . Nucleic Acids Res 32, 1363–1371. [View Article] [PubMed]
    [Google Scholar]
  42. 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. ( 2007 ). 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. [View Article] [PubMed]
    [Google Scholar]
  43. Madhaiyan M., Poonguzhali S., Kwon S. W., Sa T. M. ( 2009 ). Methylobacterium phyllosphaerae sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice. . Int J Syst Evol Microbiol 59, 22–27. [View Article] [PubMed]
    [Google Scholar]
  44. McDonald I. R., Kenna E. M., Murrell J. C. ( 1995 ). Detection of methanotrophic bacteria in environmental samples with the PCR. . Appl Environ Microbiol 61, 116–121. [PubMed]
    [Google Scholar]
  45. McDonald I. R., Doronina N. V., Trotsenko Y. A., McAnulla C., Murrell J. C. ( 2001 ). Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment. . Int J Syst Evol Microbiol 51, 119–122. [PubMed]
    [Google Scholar]
  46. Omer Z. S., Tombolini R., Gerhardson B. ( 2004 ). Plant colonization by pink-pigmented facultative methylotrophic bacteria (PPFMs). . FEMS Microbiol Ecol 47, 319–326. [View Article] [PubMed]
    [Google Scholar]
  47. Patt T. E., Cole G. C., Bland J., Hanson R. S. ( 1974 ). Isolation and characterization of bacteria that grow on methane and organic compounds as sole sources of carbon and energy. . J Bacteriol 120, 955–964. [PubMed]
    [Google Scholar]
  48. 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. [View Article]
    [Google Scholar]
  49. Pitcher D. G., Saunders N. A., Owen R. J. ( 1989 ). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. . Lett Appl Microbiol 8, 151–156. [View Article]
    [Google Scholar]
  50. Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J., Glöckner F. O. ( 2007 ). silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with arb . . Nucleic Acids Res 35, 7188–7196. [View Article] [PubMed]
    [Google Scholar]
  51. Raja P., Balachandar D., Sundaram S. P. ( 2008 ). Genetic diversity and phylogeny of pink-pigmented facultative methylotrophic bacteria isolated from the phyllosphere of tropical crop plants. . Biol Fertil Soils 45, 45–53. [View Article]
    [Google Scholar]
  52. 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]
  53. Schauer S., Kämpfer P., Wellner S., Spröer C., Kutschera U. ( 2011 ). Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort. . Int J Syst Evol Microbiol 61, 870–876. [View Article] [PubMed]
    [Google Scholar]
  54. Stamatakis A. ( 2006 ). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. . Bioinformatics 22, 2688–2690. [View Article] [PubMed]
    [Google Scholar]
  55. 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. [View Article] [PubMed]
    [Google Scholar]
  56. Tani A., Sahin N., Kimbara K. ( 2012a ). Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata. . Int J Syst Evol Microbiol 62, 1647–1652. [View Article] [PubMed]
    [Google Scholar]
  57. Tani A., Sahin N., Kimbara K. ( 2012b ). Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum . . Int J Syst Evol Microbiol 62, 2602–2607. [CrossRef]
    [Google Scholar]
  58. Trotsenko Y. A., Ivanova E. G., Doronina N. V. ( 2001 ). Aerobic methylotrophic bacteria as phytosymbionts. . Microbiology 70, 623–632. [View Article]
    [Google Scholar]
  59. Urakami T., Araki H., Suzuki K., Komogata K. ( 1993 ). Further studies of the genus Methylobacterium and description of Methylobacterium aminovorans sp. nov. . Int J Syst Bacteriol 43, 504–513. [View Article]
    [Google Scholar]
  60. Van Aken B., Peres C. M., Doty S. L., 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. [View Article] [PubMed]
    [Google Scholar]
  61. Versalovic J., Schneider M., de Bruijn F. J., Lupski J. R. ( 1994 ). Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. . Methods Mol Cell Biol 5, 25–40.
     [Google Scholar]
  62. Wellner S., Lodders N., Kämpfer P. ( 2011 ). Diversity and biogeography of selected phyllosphere bacteria with special emphasis on Methylobacterium spp. . Syst Appl Microbiol 34, 621–630. [View Article] [PubMed]
    [Google Scholar]
  63. Wellner S., Lodders N., Kämpfer P. ( 2012 ). Methylobacterium cerastii sp. nov., isolated from the leaf surface of Cerastium holosteoides . . Int J Syst Evol Microbiol 62, 917–924. [View Article] [PubMed]
    [Google Scholar]
  64. Williams S. T., Goodfellow M., Alderson G. ( 1989 ). Genus Streptomyces . . In Bergey’s Manual of Systematic Bacteriology, vol. 4, pp. 2452–2492. Edited by Williams S. T., Sharpe M. E., Holt J. G. . Baltimore:: Williams & Wilkins;.
     [Google Scholar]
  65. Yarza P., Richter M., Peplies J., Euzéby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R. ( 2008 ). The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. . Syst Appl Microbiol 31, 241–250. [View Article] [PubMed]
    [Google Scholar]
  66. Ziemke F., Brettar I., Höfle M. G. ( 1997 ). Stability and diversity of the genetic structure of a Shewanella putrefaciens population in the water column of the central Baltic. . Aquat Microb Ecol 13, 63–74. [View Article]
    [Google Scholar]
  67. Ziemke F., Höfle M. G., Lalucat J., Rosselló-Mora R. ( 1998 ). Reclassification of Shewanella putrefaciens Owen’s genomic group II as Shewanella baltica sp. nov. . Int J Syst Bacteriol 48, 179–186. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.047787-0
Loading
Methylobacteriumtrifolii sp. nov. and Methylobacteriumthuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces
Int J Syst Evol Microbiol 63, 2690 (2013); https://doi.org/10.1099/ijs.0.047787-0
/content/journal/ijsem/10.1099/ijs.0.047787-0
/content/journal/ijsem/10.1099/ijs.0.047787-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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