1887

Abstract

Strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from nitrogen-fixing nodules of the native legumes (from Zambia) and (from Texas, USA). Phylogenetic analysis of the 16S rRNA gene showed that the novel strains belong to the genus , with ≥96.1 % sequence similarity with type strains of this genus. The closest relative of the representative strains Lut6 and WSM3557 was TFB, with 97.6–98.0 % similarity, while WSM3693 was most closely related to 5420S-16, with 98.8 % similarity. Analysis of the concatenated sequences of four housekeeping gene loci (, , and ) and cellular fatty acid profiles confirmed the placement of Lut6, WSM3557 and WSM3693 within the genus . DNA–DNA relatedness values, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of Lut6, WSM3557 and WSM3693 from each other and from other species with validly published names. The sequence of Lut6 was placed in a clade that contained strains of , and , while the 100 % identical sequences of WSM3557 and WSM3693 clustered with , and strains. Concatenated sequences for and show that the sequences of Lut6, WSM3557 and WSM3693 were most closely related to that of CFN42 . On the basis of genotypic, phenotypic and DNA relatedness data, three novel species of are proposed: sp. nov. (type strain Lut6  = LMG 26460  = HAMBI 3236), sp. nov. (type strain WSM3557  = LMG 26455  = HAMBI 3237) and sp. nov. (type strain WSM3693  = LMG 26454  = HAMBI 3238).

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2012-11-01
2024-12-09
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410[PubMed] [CrossRef]
    [Google Scholar]
  2. Amrani S., Noureddine N.-E., Bhatnagar T., Argandoña M., Nieto J. J., Vargas C. 2010; Phenotypic and genotypic characterization of rhizobia associated with Acacia saligna (Labill.) Wendl. in nurseries from Algeria. Syst Appl Microbiol 33:44–51 [View Article][PubMed]
    [Google Scholar]
  3. Andam C. P., Parker M. A. 2007; Novel alphaproteobacterial root nodule symbiont associated with Lupinus texensis . Appl Environ Microbiol 73:5687–5691 [View Article][PubMed]
    [Google Scholar]
  4. Andam C. P., Mondo S. J., Parker M. A. 2007; Monophyly of nodA and nifH genes across Texan and Costa Rican populations of Cupriavidus nodule symbionts. Appl Environ Microbiol 73:4686–4690 [View Article][PubMed]
    [Google Scholar]
  5. Auling G., Busse H.-J., Egli T., El-Banna T., Stackebrandt E. 1993; Description of the Gram-negative, obligately aerobic, nitrilotriacetate (NTA)-utilizing bacteria as Chelatobacter heintzii, gen. nov., sp. nov., and Chelatococcus asaccharovorans, gen.nov., sp.nov.. Syst Appl Microbiol 16:104–112 [View Article]
    [Google Scholar]
  6. Barcellos F. G., Menna P., da Silva Batista J. S., Hungria M. 2007; Evidence of horizontal transfer of symbiotic genes from a Bradyrhizobium japonicum inoculant strain to indigenous diazotrophs Sinorhizobium (Ensifer) fredii and Bradyrhizobium elkanii in a Brazilian Savannah soil. Appl Environ Microbiol 73:2635–2643 [View Article][PubMed]
    [Google Scholar]
  7. Beringer J. E. 1974; R factor transfer in Rhizobium leguminosarum . J Gen Microbiol 84:188–198[PubMed] [CrossRef]
    [Google Scholar]
  8. Beveridge T. J., Lawrence J. R., Murray R. G. E. 2007; Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology pp. 19–33 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf T. M., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  9. Bligh E. G., Dyer W. J. 1959; A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917 [View Article][PubMed]
    [Google Scholar]
  10. Boatwright J. S., Wink M., van Wyk B.-E. 2011; The generic concept of Lotononis (Crotalarieae, Fabaceae): reinstatement of the genera Euchlora, Leobordea and Listia and the new genus Ezoloba . Taxon 60:161–177
    [Google Scholar]
  11. Bowra B. J., Dilworth M. J. 1981; Motility and chemotaxis towards sugars in Rhizobium leguminosarum . J Gen Microbiol 126:231–235
    [Google Scholar]
  12. Broughton W. J., Jabbouri S., Perret X. 2000; Keys to symbiotic harmony. J Bacteriol 182:5641–5652 [View Article][PubMed]
    [Google Scholar]
  13. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. 2002; Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov.. Int J Syst Evol Microbiol 52:1551–1558 [View Article][PubMed]
    [Google Scholar]
  14. Cummings S. P., Gyaneshwar P., Vinuesa P., Farruggia F. T., Andrews M., Humphry D., Elliott G. N., Nelson A., Orr C. et al. 2009; Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. Environ Microbiol 11:2510–2525 [View Article][PubMed]
    [Google Scholar]
  15. Eagles D. A., Date R. A. 1999; The CB Rhizobium/Bradyrhizobium Strain Collection. Genetic Resources Communication no. 30 St Lucia, Queensland: CSIRO Tropical Agriculture;
    [Google Scholar]
  16. Egli T. W., Auling G. 2005; Genus II. Chelatococcus . In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 2C pp. 433–437 Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. New York: Springer; [View Article]
    [Google Scholar]
  17. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 [View Article]
    [Google Scholar]
  18. Garland J. L., Mills A. L. 1991; Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57:2351–2359[PubMed]
    [Google Scholar]
  19. Geyer R., Peacock A. D., White D. C., Lytle C., Van Berkel G. J. 2004; Atmospheric pressure chemical ionization and atmospheric pressure photoionization for simultaneous mass spectrometric analysis of microbial respiratory ubiquinones and menaquinones. J Mass Spectrom 39:922–929 [View Article][PubMed]
    [Google Scholar]
  20. Goris J., Suzuki K., De Vos P., Nakase T., Kersters K. 1998; Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44:1148–1153 [View Article]
    [Google Scholar]
  21. Haukka K., Lindström K., Young J. P. W. 1998; Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Appl Environ Microbiol 64:419–426[PubMed]
    [Google Scholar]
  22. Hugh R., Leifson E. 1953; The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66:24–26[PubMed]
    [Google Scholar]
  23. Kanso S., Patel B. K. C. 2003; Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 53:401–406 [View Article][PubMed]
    [Google Scholar]
  24. Kohlerschmidt D. J., Musser K. A., Dumas N. B. 2009; Identification of aerobic Gram-negative bacteria. In Practical Handbook of Microbiology, 2nd edn. pp. 67–79 Edited by Goldman E., Green L. H. Boca Raton, FL: CRC Press;
    [Google Scholar]
  25. Lin D. X., Wang E. T., Tang H., Han T. X., He Y. R., Guan S. H., Chen W. X. 2008; Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea . Int J Syst Evol Microbiol 58:1409–1413 [View Article][PubMed]
    [Google Scholar]
  26. Ludwig W., Strunk O., Klugbauer S., Klugbauer N., Weizenegger M., Neumaier J., Bachleitner M., Schleifer K. H. 1998; Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554–568 [View Article][PubMed]
    [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 [View Article]
    [Google Scholar]
  28. Nandasena K. G., O’Hara G. W., Tiwari R. P., Sezmiş E., Howieson J. G. 2007; In situ lateral transfer of symbiosis islands results in rapid evolution of diverse competitive strains of mesorhizobia suboptimal in symbiotic nitrogen fixation on the pasture legume Biserrula pelecinus L.. Environ Microbiol 9:2496–2511 [View Article][PubMed]
    [Google Scholar]
  29. Normand P., Cournoyer B., Simonet P., Nazaret S. 1992; Analysis of a ribosomal RNA operon in the actinomycete Frankia . Gene 111:119–124 [View Article][PubMed]
    [Google Scholar]
  30. O’Hara G. W., Goss T. J., Dilworth M. J., Glenn A. R. 1989; Maintenance of intracellular pH and acid-tolerance in Rhizobium meliloti . Appl Environ Microbiol 55:1870–1876[PubMed]
    [Google Scholar]
  31. Reasoner D. J., Geldreich E. E. 1985; A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49:1–7[PubMed]
    [Google Scholar]
  32. Rivas R., Velázquez E., Willems A., Vizcaíno N., Subba-Rao N. S., Mateos P. F., Gillis M., Dazzo F. B., Martínez-Molina E. 2002; A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) Druce. Appl Environ Microbiol 68:5217–5222 [View Article][PubMed]
    [Google Scholar]
  33. Ronquist F., Huelsenbeck J. P. 2003; MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574 [View Article][PubMed]
    [Google Scholar]
  34. 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]
  35. Sullivan J. T., Patrick H. N., Lowther W. L., Scott D. B., Ronson C. W. 1995; Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment. Proc Natl Acad Sci U S A 92:8985–8989 [View Article][PubMed]
    [Google Scholar]
  36. Sy A., Giraud E., Jourand P., Garcia N., Willems A., de Lajudie P., Prin Y., Neyra M., Gillis M. et al. 2001; Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183:214–220 [View Article][PubMed]
    [Google Scholar]
  37. Takeda M., Suzuki I., Koizumi J. I. 2004; Balneomonas flocculans gen. nov., sp. nov., a new cellulose-producing member of the α-2 subclass of Proteobacteria . Syst Appl Microbiol 27:139–145 [View Article][PubMed]
    [Google Scholar]
  38. 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 [View Article][PubMed]
    [Google Scholar]
  39. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [View Article]
    [Google Scholar]
  40. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  41. Tindall B. J., Rosselló-Móra R., Busse H.-J., Ludwig W., Kämpfer P. 2010; Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266 [View Article][PubMed]
    [Google Scholar]
  42. Trujillo M. E., Willems A., Abril A., Planchuelo A.-M., Rivas R., Ludeña D., Mateos P. F., Martínez-Molina E., Velázquez E. 2005; Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov.. Appl Environ Microbiol 71:1318–1327 [View Article][PubMed]
    [Google Scholar]
  43. Versalovic J., Koeuth T., Lupski J. R. 1991; Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831 [View Article][PubMed]
    [Google Scholar]
  44. Vincent J. M. 1970 A Manual for the Practical Study of the Root-Nodule Bacteria Oxford: Blackwell Science Publications;
    [Google Scholar]
  45. Weon H.-Y., Kwon S.-W., Son J.-A., Jo E.-H., Kim S.-J., Kim Y.-S., Kim B.-Y., Ka J.-O. 2010; Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga . Int J Syst Evol Microbiol 60:2596–2600 [View Article][PubMed]
    [Google Scholar]
  46. Wilson K. 1989; Preparation of genomic DNA from bacteria.. In Current Protocols in Molecular Biology, unit2.4.1–2.4.2 Edited by Brenner F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. New York: Wiley;
    [Google Scholar]
  47. Yates R. J., Howieson J. G., Reeve W. G., Nandasena K. G., Law I. J., Bräu L., Ardley J. K., Nistelberger H. M., Real D., O’Hara G. W. 2007; Lotononis angolensis forms nitrogen fixing, lupinoid nodules with phylogenetically unique, fast-growing, pink-pigmented bacteria, which do not nodulate L. bainesii or L. listii . Soil Biol Biochem 39:1680–1688 [View Article]
    [Google Scholar]
  48. Zhang J., Song F., Xin Y. H., Zhang J., Fang C. 2009; Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga . Int J Syst Evol Microbiol 59:1997–2001 [View Article][PubMed]
    [Google Scholar]
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