1887

Abstract

Gram-negative strains Tri-36, Tri-38, Tri-48 and Tri-53 were isolated from root nodules of the relict legume (Pall.) Pers. originating from Zunduk Cape (Baikal Lake region, Russia). 16S rRNA gene sequencing showed that the novel isolates were phylogenetically closest to the type strains LMG 27899, LMG 22836, LMG 26470 and LMG 2283 while similarity levels between the isolates and the most closely related strain LMG 26470 were 98.8–99.5 %. The A and II genes of the isolates showed highest sequence similarities with LMG 27899 (95.4 and 89.5 %, respectively) and LMG 22836 (91.4 and 85.1 %, respectively). Comparative analysis of phenotypic properties between the novel isolates and the closest reference strains LMG 27899, LMG 22836 and LMG 26470 was performed using a microassay system. Average nucleotide identities between the whole genome sequences of the isolates Tri-38 and Tri-48 and LMG 27899, LMG 22836 and LMG 26470 ranged from 79.23 % for LMG 26470 to 85.74 % for LMG 27899. The common ABC genes required for legume nodulation were absent from strains Tri-38 and Tri-48, although some other symbiotic and genes were detected. On the basis of genotypic and phenotypic analysis, a novel species, sp. nov. (type strain Tri-48=LMG 30371=RCAM 03910), is proposed.

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2018-05-01
2024-10-03
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References

  1. Turuta O, Ryabtsev V, Novitskaya N, Vakarenko L. Protected microhabitats as a part of Baikal regional ecological network. In Plant Microreserves the Site Based Plant Conservation And Monitoring Network 2015 pp. 1–5
    [Google Scholar]
  2. Safronova V, Belimov A, Sazanova A, Kuznetsova I, Popova J et al. Does the Miocene-Pliocene relict legume Oxytropis triphylla form nitrogen-fixing nodules with a combination of bacterial strains?. Int J Environ Stud 2017; 74:706–714 [View Article]
    [Google Scholar]
  3. Knösel D. Prüfung von bakterien auf fähigkeit zur sternbildung. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg II Abt 1962; 116:79–100
    [Google Scholar]
  4. Mantelin S, Saux MF, Zakhia F, Béna G, Bonneau S et al. Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int J Syst Evol Microbiol 2006; 56:827–839 [View Article][PubMed]
    [Google Scholar]
  5. Mergaert J, Cnockaert MC, Swings J. Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend. Int J Syst Evol Microbiol 2002; 52:1821–1823 [View Article][PubMed]
    [Google Scholar]
  6. Valverde A, Velázquez E, Fernández-Santos F, Vizcaíno N, Rivas R et al. Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. Int J Syst Evol Microbiol 2005; 55:1985–1989 [View Article][PubMed]
    [Google Scholar]
  7. Flores-Félix JD, Carro L, Velázquez E, Valverde Á, Cerda-Castillo E et al. Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris . Int J Syst Evol Microbiol 2013; 63:821–826 [View Article][PubMed]
    [Google Scholar]
  8. Jiao YS, Yan H, Ji ZJ, Liu YH, Sui XH et al. Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens . Int J Syst Evol Microbiol 2015; 65:399–406 [View Article][PubMed]
    [Google Scholar]
  9. León-Barrios M, Ramírez-Bahena MH, Igual JM, Peix Á, Velázquez E et al. Phyllobacterium salinisoli sp. nov., isolated from a Lotus lancerottensis root nodule in saline soil from Lanzarote. Int J Syst Evol Microbiol 2018 [View Article][PubMed]
    [Google Scholar]
  10. Sánchez M, Ramírez-Bahena MH, Peix A, Lorite MJ, Sanjuán J et al. Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus . Int J Syst Evol Microbiol 2014; 64:781–786 [View Article][PubMed]
    [Google Scholar]
  11. Zhao L, Deng Z, Yang W, Cao Y, Wang E et al. Diverse rhizobia associated with Sophora alopecuroides grown in different regions of Loess Plateau in China. Syst Appl Microbiol 2010; 33:468–477 [View Article][PubMed]
    [Google Scholar]
  12. Jurado V, Laiz L, Gonzalez JM, Hernandez-Marine M, Valens M et al. Phyllobacterium catacumbae sp. nov., a member of the order 'Rhizobiales' isolated from Roman catacombs. Int J Syst Evol Microbiol 2005; 55:1487–1490 [View Article][PubMed]
    [Google Scholar]
  13. Novikova N, Safronova V. Transconjugants of Agrobacterium radiobacter harbouring sym genes of Rhizobium galegae can form an effective symbiosis with Medicago sativa . FEMS Microbiol Lett 1992; 72:261–268 [View Article][PubMed]
    [Google Scholar]
  14. Vincent JM. A manual for the practical study of root nodule bacteria. In IBP Handbook Oxford and Edinburgh: Blackwell Scientific Publications; 1970 pp. 73–97
    [Google Scholar]
  15. Safronova VI, Kuznetsova IG, Sazanova AL, Kimeklis AK, Belimov AA et al. Bosea vaviloviae sp. nov., a new species of slow-growing rhizobia isolated from nodules of the relict species Vavilovia formosa (Stev.) Fed. Antonie van Leeuwenhoek 2015; 107:911–920 [View Article][PubMed]
    [Google Scholar]
  16. Safronova V, Tikhonovich I. Automated cryobank of microorganisms: Unique possibilities for long-term authorized depositing of commercial microbial strains. In Mendez-Vilas A. (editor) Microbes in Applied Research: Current Advances and Challenges Singapore: World Scientific Publishing Co; 2012 pp. 331–334 [Crossref]
    [Google Scholar]
  17. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  18. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  19. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  20. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
    [Google Scholar]
  21. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  22. Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  24. Amaral GR, Dias GM, Wellington-Oguri M, Chimetto L, Campeão ME et al. Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 2014; 64:357–365 [View Article][PubMed]
    [Google Scholar]
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