1887

Abstract

A reddish-orange-pigmented, Gram-stain-negative, aerobic, facultatively methylotrophic strain, N4211, isolated from arid soil, collected from Abuja, Nigeria, was analysed by using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain N4211 belonged to the genus . Strain N4211 was most closely related to GR16 (98.56 %), PMB02 (97.95 %) and GR3 (97.2 %), and the phylogenetic similarities to all other species of the genus with validly published names were less than 97.0 %. The major ubiquinones detected were Q-10. The major fatty acids were summed feature 7 (C 11/t9/t6). The DNA G+C content was 67.3 mol%. DNA–DNA relatedness of strain N4211 and the most closely related strains DSM 16371 and KCTC 12901 were 60.0 and 48.2 %, respectively. On the basis of phenotypic, phylogenetic and DNA–DNA hybridization data, strain N4211 is assigned to a novel species of the genus for which the name sp. nov. is proposed. The type strain is N4211( = KCTC 23615 = DSM 25844).

Funding
This study was supported by the:
  • Ondokuz Mayis University (OMU) (Award PYO. FEN. 1901.09.003)
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2013-08-01
2021-10-24
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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, 820830. [View Article] [PubMed]
    [Google Scholar]
  2. Austin B., Goodfellow M., Dickinson C. H. ( 1978 ). Numerical taxonomy of phylloplane bacteria isolated from Lolium perenne . . J Gen Microbiol 104, 139155. [View Article]
    [Google Scholar]
  3. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. ( 1977 ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81, 461466. [View Article] [PubMed]
    [Google Scholar]
  4. Chun J., Goodfellow M. ( 1995 ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. . Int J Syst Bacteriol 45, 240245. [View Article] [PubMed]
    [Google Scholar]
  5. Corpe W. A., Rheem S. ( 1989 ). Ecology of the methylotrophic bacteria on living leaf surfaces. . FEMS Microbiol Ecol 62, 243249. [View Article]
    [Google Scholar]
  6. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  7. 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, 1642816433. [View Article] [PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  9. Felsenstein J. ( 1985 ). Confidence limits on phylogeny: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  10. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  11. Gonzalez J. M., Saiz-Jimenez C. ( 2005 ). A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. . Extremophiles 9, 7579. [View Article] [PubMed]
    [Google Scholar]
  12. Goodfellow M., Alderson G., Lacey J. ( 1979 ). Numerical taxonomy of Actinomadura and related actinomycetes. . J Gen Microbiol 112, 95111. [View Article] [PubMed]
    [Google Scholar]
  13. Gordon R. E., Mihm J. M. ( 1962 ). Identification of Nocardia caviae (Erikson) nov. comb.. Ann N Y Acad Sci 98, 628636. [View Article]
    [Google Scholar]
  14. Green P. N. ( 1992 ). The genus Methylobacterium . . In The Prokaryotes, , 2nd edn., pp. 23422349. Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. . New York:: Springer;.
    [Google Scholar]
  15. 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 Methylobacteriu mesophilicum (Austin & Goodfellow 1979) comb. nov.. Int J Syst Bacteriol 33, 875877. [View Article]
    [Google Scholar]
  16. Hiraishi A., Furuhata K., Matsumoto A., Koike K. A., Fukuyama M., Tabuchi K. ( 1995 ). Phenotypic and genetic diversity of chlorine-resistant Methylobacterium strains isolated from various environments. . Appl Environ Microbiol 61, 20992107.[PubMed]
    [Google Scholar]
  17. 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, 197209. [View Article]
    [Google Scholar]
  18. Hsu S. C., Lockwood J. L. ( 1975 ). Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. . Appl Microbiol 29, 422426.[PubMed]
    [Google Scholar]
  19. Huss V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184192. [View Article] [PubMed]
    [Google Scholar]
  20. Ivanova E. G., Doronina N. V., Trotsenko Iu. A. ( 2001 ). [Aerobic methylobacteria are capable of synthesizing auxins]. . Mikrobiologiia 70, 452458.[PubMed]
    [Google Scholar]
  21. Jones K. L. ( 1949 ). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. . J Bacteriol 57, 141145.[PubMed]
    [Google Scholar]
  22. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21132. Edited by Munro H. N. . New York:: Academic Press;.
    [Google Scholar]
  23. Kämpfer P., Kroppenstedt R. M. ( 1996 ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42, 9891005. [View Article]
    [Google Scholar]
  24. 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, 28492853. [View Article] [PubMed]
    [Google Scholar]
  25. 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, 11341141. [View Article] [PubMed]
    [Google Scholar]
  26. Kelly K. L. ( 1964 ). Inter-Society Color Council–National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors. Washington, DC:: US Government Printing Office;.
    [Google Scholar]
  27. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  28. Kluge A. G., Farris F. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18, 132. [View Article]
    [Google Scholar]
  29. 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, 18321842. [View Article] [PubMed]
    [Google Scholar]
  30. Küster E. ( 1959 ). Outline of a comparative study of criteria used in characterisation of the actinomycetes. . Int Bull Bacteriol Nomencl Taxon 9, 97104.
    [Google Scholar]
  31. Lidstrom M. E., Chistoserdova L. ( 2002 ). Plants in the pink: cytokinin production by methylobacterium . . J Bacteriol 184, 1818. [View Article] [PubMed]
    [Google Scholar]
  32. 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, 2227. [View Article] [PubMed]
    [Google Scholar]
  33. Madhaiyan M., Poonguzhali S., Senthilkumar M., Lee J. S., Lee K. C. ( 2012 ). Methylobacterium gossipiicola sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the cotton phyllosphere. . Int J Syst Evol Microbiol 62, 162167. [View Article] [PubMed]
    [Google Scholar]
  34. Nash P., Krent M. M. ( 1991 ). Culture media. . In Manual Of Clinical Microbiology, , 5th edn., pp. 12681270. Edited by Ballows A., Hauser W. J., Herrmann K. L., Isenberg H. D., Shadomy H. J. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  35. Patt T. E., Cole G. C., Hanson R. S. ( 1976 ). Methylobacterium, a new genus of facultatively methylotrophic bacteria. . Int J Syst Bacteriol 26, 226229. [View Article]
    [Google Scholar]
  36. 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, 4553. [View Article]
    [Google Scholar]
  37. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  38. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
    [Google Scholar]
  39. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [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, 214220. [View Article] [PubMed]
    [Google Scholar]
  41. 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, 27312739. [View Article] [PubMed]
    [Google Scholar]
  42. Tani A., Sahin N., Kimbara K. ( 2012 ). Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum . . Int J Syst Evol Microbiol 62, 26022607. [View Article] [PubMed]
    [Google Scholar]
  43. Tindall B. J. ( 1990a ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  44. Tindall B. J. ( 1990b ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [View Article]
    [Google Scholar]
  45. Trotsenko Y. A., Ivanova E. G., Doronina N. V. ( 2001 ). Aerobic methylotrophic bacteria as phytosymbionts. . Mikrobiologiia 70, 725736 (in Russian).
    [Google Scholar]
  46. 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, 11911196. [View Article] [PubMed]
    [Google Scholar]
  47. 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, 463464. [View Article]
    [Google Scholar]
  48. Williams S. T., Goodfellow M., Alderson G., Wellington E. M. H., Sneath P. H. A., Sackin M. J. ( 1983 ). Numerical classification of Streptomyces and related genera. . J Gen Microbiol 129, 17431813.[PubMed]
    [Google Scholar]
  49. Yoshimura F. ( 1982 ). Phylloplane bacteria in a pine forest. . Can J Microbiol 28, 580592. [View Article]
    [Google Scholar]
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