1887

Abstract

An aerobic, yellow-pigmented, facultatively methylotrophic, Gram-staining-negative, non-spore-forming bacterium, designated strain Gm-149, was isolated from the rhizosphere of cultivated soybean in India. Cells were motile by gliding. The predominant cellular fatty acids were iso-C, summed feature 3 (comprising iso-C 2-OH and/or C 7), C 3-OH and anteiso-C, and the major isoprenoid quinone was MK-6. The G+C content of the genomic DNA of strain Gm-149 was 35.6 mol%. Comparative 16S rRNA gene sequence analysis showed that strain Gm-149 formed a distinct phyletic line within the genus . Based on levels of pairwise 16S rRNA gene sequence similarity, strain Gm-149 was related most closely to the type strain of (97.1 %), but the level of DNA–DNA relatedness between these two strains was about 11.2 %. On the basis of phenotypic and genotypic data, strain Gm-149 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Gm-149 (=ICMP 17618=NBRC 105008).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.014019-0
2010-09-01
2020-09-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/9/2187.html?itemId=/content/journal/ijsem/10.1099/ijs.0.014019-0&mimeType=html&fmt=ahah

References

  1. Asker D., Beppu T., Ueda K. 2007; Unique diversity of carotenoid-producing bacteria isolated from Misasa, a radioactive site in Japan. Appl Microbiol Biotechnol 77:383–392 [CrossRef]
    [Google Scholar]
  2. Bergey D. H., Harrison F. C., Breed R. S., Hammer B. W., Huntoon F. M. (editors) 1923 Bergey's Manual of Determinative Bacteriology Baltimore, MD: Williams & Wilkins;
    [Google Scholar]
  3. Bernardet J.-F., Bowman J. P. 2006; The genus Flavobacterium . In The Prokaryotes vol 7 pp 481–531 Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. New York: Springer;
    [Google Scholar]
  4. Bernardet J.-F., Segers P., Vancanneyt M., Berthe F., Kersters K., Vandamme P. 1996; Cutting a Gordian knot: emended classification and description of the genus Flavobacterium , emended description of the family Flavobacteriaceae , and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46:128–148 [CrossRef]
    [Google Scholar]
  5. Bernardet J.-F., Nakagawa Y., Holmes B. 2002; Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070 [CrossRef]
    [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. 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]
  10. Chun J., Lee J. H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y. W. 2007; EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261 [CrossRef]
    [Google Scholar]
  11. Dunfield P. F., Khmelenina V. N., Suzina N. E., Trotsenko Y. A., Dedysh S. N. 2003; Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. Int J Syst Evol Microbiol 53:1231–1239 [CrossRef]
    [Google Scholar]
  12. Fautz E., Reichenbach H. 1980; A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8:87–91 [CrossRef]
    [Google Scholar]
  13. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [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. 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]
  17. 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]
  18. Kim B. Y., Weon H. Y., Cousin S., Yoo S. H., Kwon S. W., Go S. J., Stackebrandt E. 2006 Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 56, 1645–1649 [CrossRef]
  19. Kirchman D. L. 2002; The ecology of Cytophaga–Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39:91–100
    [Google Scholar]
  20. 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]
  21. Lidstrom M. E. 2006; The aerobic methylotrophic prokaryotes. In The Prokaryotes vol 2 pp 618–634 Edited by Dworkin M., Schleifer K.-H., Stackebrandt E. New York: Springer;
    [Google Scholar]
  22. Ludwig W., Euzéby J., Whitman W. B. 2008; Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes , Fibrobacteres , Fusobacteria , Acidobacteria , Verrucomicrobia , Dictyoglomi , and Gemmatimonadetes . Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 4 http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf
    [Google Scholar]
  23. 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]
  24. Madhaiyan M., Poonguzhali S., Sa T. M. 2007b; 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]
  25. Madhaiyan M., Poonguzhali S., Kwon S. W., Sa T. M. 2009; Methylobacterium phyllosphaerae sp. nov., a pink-pigmented facultatively methylotrophic bacterium from rice. Int J Syst Evol Microbiol 59:22–27 [CrossRef]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Pearson W. R., Lipman D. J. 1988; Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85:2444–2448 [CrossRef]
    [Google Scholar]
  29. 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 potential plant growth promoting bacteria. Plant Soil 286:167–180 [CrossRef]
    [Google Scholar]
  30. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  31. Sasser M. 1990; Identification of bacteria through fatty acid analysis. In Methods in Phytobacteriology pp 199–204 Edited by Klement Z., Rudolph K., Sands D. C. Budapest: Akademiai Kiado;
    [Google Scholar]
  32. 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]
  33. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R, Swings J. other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 [CrossRef]
    [Google Scholar]
  34. 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]
  35. 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]
  36. Ueda T., Suga Y., Yahiro N., Matsuguchi T. 1995; Phylogeny of Sym plasmids of rhizobia by PCR-based sequencing of a nodC segment. J Bacteriol 177:468–472
    [Google Scholar]
  37. 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]
  38. Yoon J.-H., Kang S.-J., Oh T.-K. 2006; Flavobacterium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 56:997–1000 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.014019-0
Loading
/content/journal/ijsem/10.1099/ijs.0.014019-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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