1887

Abstract

Gram-negative strains Tri-36, Tri-38, Tri-48 and Tri-53 were isolated from root nodules of the relict legume Oxytropis triphylla (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 Phyllobacterium sophorae LMG 27899, Phyllobacterium brassicacearum LMG 22836, Phyllobacterium endophyticum LMG 26470 and Phyllobacterium bourgognense LMG 22837 while similarity levels between the isolates and the most closely related strain P. endophyticum LMG 26470 were 98.8–99.5 %. The recA and glnII genes of the isolates showed highest sequence similarities with P. sophorae LMG 27899 (95.4 and 89.5 %, respectively) and P. brassicacearum LMG 22836 (91.4 and 85.1 %, respectively). Comparative analysis of phenotypic properties between the novel isolates and the closest reference strains P. sophorae LMG 27899, P. brassicacearum LMG 22836 and P. endophyticum 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 P. sophorae LMG 27899, P. brassicacearum LMG 22836 and P. endophyticum LMG 26470 ranged from 79.23 % for P. endophyticum LMG 26470 to 85.74 % for P. sophorae LMG 27899. The common nodABC genes required for legume nodulation were absent from strains Tri-38 and Tri-48, although some other symbiotic nod and fix genes were detected. On the basis of genotypic and phenotypic analysis, a novel species, Phyllobacterium zundukense sp. nov. (type strain Tri-48=LMG 30371=RCAM 03910), is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002722
2018-04-05
2019-12-11
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/5/1644.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002722&mimeType=html&fmt=ahah

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 [CrossRef]
    [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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; [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [PubMed]
    [Google Scholar]
  20. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29: 1072– 1075 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [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 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002722
Loading
/content/journal/ijsem/10.1099/ijsem.0.002722
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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