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).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.049551-0
2013-08-01
2020-01-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/8/2823.html?itemId=/content/journal/ijsem/10.1099/ijs.0.049551-0&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. [CrossRef][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:, 139–155. [CrossRef]
    [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:, 461–466. [CrossRef][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:, 240–245. [CrossRef][PubMed]
    [Google Scholar]
  5. Corpe W. A., Rheem S.. ( 1989;). Ecology of the methylotrophic bacteria on living leaf surfaces. . FEMS Microbiol Ecol 62:, 243–249. [CrossRef]
    [Google Scholar]
  6. De Ley J., Cattoir H., Reynaerts A.. ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef][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:, 16428–16433. [CrossRef][PubMed]
    [Google Scholar]
  8. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  9. Felsenstein J.. ( 1985;). Confidence limits on phylogeny: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  10. 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]
  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:, 75–79. [CrossRef][PubMed]
    [Google Scholar]
  12. Goodfellow M., Alderson G., Lacey J.. ( 1979;). Numerical taxonomy of Actinomadura and related actinomycetes. . J Gen Microbiol 112:, 95–111. [CrossRef][PubMed]
    [Google Scholar]
  13. Gordon R. E., Mihm J. M.. ( 1962;). Identification of Nocardia caviae (Erikson) nov. comb.. Ann N Y Acad Sci 98:, 628–636. [CrossRef]
    [Google Scholar]
  14. Green P. N.. ( 1992;). The genus Methylobacterium. . In The Prokaryotes, , 2nd edn., pp. 2342–2349. 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:, 875–877. [CrossRef]
    [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:, 2099–2107.[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:, 197–209. [CrossRef]
    [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:, 422–426.[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:, 184–192. [CrossRef][PubMed]
    [Google Scholar]
  20. Ivanova E. G., Doronina N. V., Trotsenko Iu. A.. ( 2001;). [Aerobic methylobacteria are capable of synthesizing auxins]. . Mikrobiologiia 70:, 452–458.[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:, 141–145.[PubMed]
    [Google Scholar]
  22. Jukes T. H., Cantor C. R.. ( 1969;). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21–132. 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:, 989–1005. [CrossRef]
    [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:, 2849–2853. [CrossRef][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:, 1134–1141. [CrossRef][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:, 716–721. [CrossRef][PubMed]
    [Google Scholar]
  28. Kluge A. G., Farris F. S.. ( 1969;). Quantitative phyletics and the evolution of anurans. . Syst Zool 18:, 1–32. [CrossRef]
    [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:, 1832–1842. [CrossRef][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:, 97–104.
    [Google Scholar]
  31. Lidstrom M. E., Chistoserdova L.. ( 2002;). Plants in the pink: cytokinin production by methylobacterium. . J Bacteriol 184:, 1818. [CrossRef][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:, 22–27. [CrossRef][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:, 162–167. [CrossRef][PubMed]
    [Google Scholar]
  34. Nash P., Krent M. M.. ( 1991;). Culture media. . In Manual Of Clinical Microbiology, , 5th edn., pp. 1268–1270. 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:, 226–229. [CrossRef]
    [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:, 45–53. [CrossRef]
    [Google Scholar]
  37. 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]
  38. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
  39. Shirling E. B., Gottlieb D.. ( 1966;). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16:, 313–340. [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][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:, 2731–2739. [CrossRef][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:, 2602–2607. [CrossRef][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:, 128–130. [CrossRef]
    [Google Scholar]
  44. Tindall B. J.. ( 1990b;). Lipid composition of Halobacterium lacusprofundi. . FEMS Microbiol Lett 66:, 199–202. [CrossRef]
    [Google Scholar]
  45. Trotsenko Y. A., Ivanova E. G., Doronina N. V.. ( 2001;). Aerobic methylotrophic bacteria as phytosymbionts. . Mikrobiologiia 70:, 725–736 (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:, 1191–1196. [CrossRef][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:, 463–464. [CrossRef]
    [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:, 1743–1813.[PubMed]
    [Google Scholar]
  49. Yoshimura F.. ( 1982;). Phylloplane bacteria in a pine forest. . Can J Microbiol 28:, 580–592. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.049551-0
Loading
/content/journal/ijsem/10.1099/ijs.0.049551-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most cited articles

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