1887

Abstract

Seven strains of symbiotic bacteria from root nodules of local races of Bambara groundnut () and peanuts () grown on subsistence farmers' fields in the Kavango region, Namibia, were previously characterized and identified as a novel group within the genus . To corroborate their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences with CCBAU 10071 being the most closely related type strain in the 16S rRNA gene phylogenetic analysis, and CCBAU 15774 in the ITS sequence analysis. Phylogenetic analysis of concatenated placed the strains in a highly supported lineage distinct from named species of the genus , most closely related to CCBAU 10071. The species status was validated by results of DNA–DNA hybridization. Phylogenetic analysis of genes placed the novel strains in a group with of ‘’ CCBAU 051107 that also nodulates peanuts. The combination of phenotypic characteristics from several tests including carbon source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus . Novel strain 58 2-1 induced effective nodules on and , and some strains on Based on the data presented, we conclude that our strains represent a novel species for which the name sp. nov. is proposed, with 58 2-1 [ = DSM 100298 = LMG 28792 = NTCCM0016 (Windhoek)] as the type strain. The DNA G+C content of strain 58 2-1 was 64.7 mol% ( ).

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2015-10-01
2019-10-21
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References

  1. Burbano C.S. , Liu Y. , Rösner K.L. , Reis V.M. , Caballero-Mellado J. , Reinhold-Hurek B. , Hurek T. . ( 2011;). Predominant nifH transcript phylotypes related to Rhizobium rosettiformans in field-grown sugarcane plants and in Norway spruce. Environ Microbiol Rep 3: 383–389 [CrossRef] [PubMed].
    [Google Scholar]
  2. Edgar R.C. . ( 2004;). muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797 [CrossRef] [PubMed].
    [Google Scholar]
  3. Felsenstein F. . ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791 [CrossRef].
    [Google Scholar]
  4. Gao J.L. , Sun J.G. , Li Y. , Wang E.T. , Chen W.X. . ( 1994;). Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan province. China. Int J Syst Evol Microbiol 44: 151–158.
    [Google Scholar]
  5. Grönemeyer J.L. , Berkelmann D. , Mubyana-John T. , Haiyambo D. , Chimwamurombe P. , Kasaona B. , Hurek T. , Reinhold-Hurek B. . ( 2013;). A survey for plant-growth-promoting rhizobacteria and symbionts associated with crop plants in the Okavango region or Southern Africa. Biodiversity and Ecology 5: 287–294 [CrossRef].
    [Google Scholar]
  6. Grönemeyer J.L. , Burbano C.S. , Hurek T. , Reinhold-Hurek B. . ( 2012;). Isolation and characterization of root-associated bacteria from agricultural crops in the Kavango region of Namibia. Plant Soil 356: 67–82.[CrossRef]
    [Google Scholar]
  7. Grönemeyer J.L. , Kulkarni A. , Berkelmann D. , Hurek T. , Reinhold-Hurek B. . ( 2014;). Rhizobia indigenous to the Okavango region in Sub-Saharan Africa: diversity, adaptations, and host specificity. Appl Environ Microbiol 80: 7244–7257 [CrossRef] [PubMed].
    [Google Scholar]
  8. Laguerre G. , Mavingui P. , Allard M.R. , Charnay M.P. , Louvrier P. , Mazurier S.I. , Rigottier-Gois L. , Amarger N. . ( 1996;). Typing of rhizobia by PCR DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars. Appl Environ Microbiol 62: 2029–2036 [PubMed].
    [Google Scholar]
  9. Larkin M.A. , Blackshields G. , Brown N.P. , Chenna R. , McGettigan P.A. , McWilliam H. , Valentin F. , Wallace I.M. , Wilm A. , other authors . ( 2007;). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948 [CrossRef] [PubMed].
    [Google Scholar]
  10. Lu J.K. , Dou Y.J. , Zhu Y.J. , Wang S.K. , Sui X.H. , Kang L.H. . ( 2014;). Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules. Int J Syst Evol Microbiol 64: 1900–1905 [CrossRef] [PubMed].
    [Google Scholar]
  11. Posada D. , Crandall K.A. . ( 1998;). modeltest: testing the model of DNA substitution. Bioinformatics 14: 817–818 [CrossRef] [PubMed].
    [Google Scholar]
  12. Pröpper M. , Gröngröft A. , Falk T. , Eschenbach A. , Fox T. , Gessner U. , Hecht J. , Hinz M.O. , Hoettich C. , other authors . ( 2010;). Causes and perspectives of land-cover change through expanding cultivation in Kavango. . In Biodiversity in Southern Africa 3: Implications for Land Use and Management, pp. 2–31. Edited by Jürgens N. , Schmiedel U. , Hoffman T. . Göttingen: Klaus Hess;.
    [Google Scholar]
  13. Rivas R. , Martens M. , de Lajudie P. , Willems A. . ( 2009;). Multilocus sequence analysis of the genus Bradyrhizobium . Syst Appl Microbiol 32: 101–110 [CrossRef] [PubMed].
    [Google Scholar]
  14. Schwarz G. . ( 1978;). Estimating the dimension of a model. Ann Stat 6: 461–464 [CrossRef].
    [Google Scholar]
  15. Stackebrandt E. , Ebers J. . ( 2006;). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152–155.
    [Google Scholar]
  16. Stepkowski T. , Moulin L. , Krzyzańska A. , McInnes A. , Law I.J. , Howieson J. . ( 2005;). European origin of Bradyrhizobium populations infecting lupins and serradella in soils of Western Australia and South Africa. Appl Environ Microbiol 71: 7041–7052 [CrossRef] [PubMed].
    [Google Scholar]
  17. Stepkowski T. , Hughes C.E. , Law I.J. , Markiewicz Ł. , Gurda D. , Chlebicka A. , Moulin L. . ( 2007;). Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees. Appl Environ Microbiol 73: 3254–3264 [CrossRef] [PubMed].
    [Google Scholar]
  18. 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]
  19. van Berkum P. . ( 1990;). Evidence for a third uptake hydrogenase phenotype among the soybean bradyrhizobia. Appl Environ Microbiol 56: 3835–3841 [PubMed].
    [Google Scholar]
  20. Vincent J.M. . ( 1970;). A Manual for the Practical Study of the Root Nodule Bacteria., Oxford: Blackwell Scientific;.
    [Google Scholar]
  21. Vinuesa P. , Silva C. , Werner D. , Martínez-Romero E. . ( 2005;). Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34: 29–54 [CrossRef] [PubMed].
    [Google Scholar]
  22. Vinuesa P. , Rojas-Jiménez K. , Contreras-Moreira B. , Mahna S.K. , Prasad B.N. , Moe H. , Selvaraju S.B. , Thierfelder H. , Werner D. . ( 2008;). Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent. Appl Environ Microbiol 74: 6987–6996 [CrossRef] [PubMed].
    [Google Scholar]
  23. Wang R. , Chang Y.L. , Zheng W.T. , Zhang D. , Zhang X.X. , Sui X.H. , Wang E.T. , Hu J.Q. , Zhang L.Y. , Chen W.X. . ( 2013;). Bradyrhizobium arachidis sp. nov., isolated from effective nodules of Arachis hypogaea grown in China. Syst Appl Microbiol 36: 101–105 [CrossRef] [PubMed].
    [Google Scholar]
  24. Willems A. , Doignon-Bourcier F. , Goris J. , Coopman R. , de Lajudie P. , De Vos P. , Gillis M. . ( 2001;). DNA-DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51: 1315–1322 [PubMed].[CrossRef]
    [Google Scholar]
  25. Willems A. , Munive A. , de Lajudie P. , Gillis M. . ( 2003;). In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA-DNA hybridizations. Syst Appl Microbiol 26: 203–210 [CrossRef] [PubMed].
    [Google Scholar]
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