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Bosea vaviloviae sp. nov., a new species of slow-growing rhizobia isolated from nodules of the relict species Vavilovia formosa (Stev.) Fed.

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Abstract

The Gram–negative, rod-shaped slow-growing strains Vaf-17, Vaf-18T and Vaf-43 were isolated from the nodules of Vavilovia formosa plants growing in the hard-to-reach mountainous region of the North Ossetian State Natural Reserve (north Caucasus, Russian Federation). The sequencing of 16S rDNA (rrs), ITS region and five housekeeping genes (atpD, dnaK, recA, gyrB and rpoB) showed that the isolated strains were most closely related to the species Bosea lathyri (class Alphaproteobacteria, family Bradyrhizobiaceae) which was described for isolates from root nodules of Lathyrus latifolius. However the sequence similarity between the isolated strains and the type strain B. lathyri LMG 26379T for the ITS region was 90 % and for the housekeeping genes it was ranged from 92 to 95 %. All phylogenetic trees, except for the rrs-dendrogram showed that the isolates from V. formosa formed well-separated clusters within the Bosea group. Differences in phenotypic properties of the B. lathyri type strain and the isolates from V. formosa were studied using the microassay system GENIII MicroPlate BioLog. Whole-cell fatty acid analysis showed that the strains Vaf-17, Vaf-18T and Vaf-43 had notable amounts of C16:0 (4.8–6.0 %), C16:0 3-OH (6.4–6.6 %), C16:1 ω5c (8.8–9.0 %), C17:0 cyclo (13.5–13.9 %), C18:1 ω7c (43.4–45.4 %), C19:0 cyclo ω8c (10.5–12.6 %) and Summed Feature (SF) 3 (6.4–8.0 %). The DNA–DNA relatedness between the strains Vaf-18T and B. lathyri LMG 26379T was 24.0 %. On the basis of genotypic and phenotypic analysis a new species Bosea vaviloviae sp. nov. (type strain RCAM 02129T = LMG 28367T = Vaf-18T) is proposed.

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Acknowledgments

We thank Pia Clercx for performing DNA–DNA hybridizations and excellent technical assistance. This work was partially supported by the Ministry of Education and Sciences of the Russian Federation (Agreement No. 14.604.21.0024, RFMEFI60414X0024) and by the European Union’s Seventh Framework Programme (BRIO project, grant KBBE 2010-4-266106). ITS sequencing analysis was supported by the Russian Science Foundation (Agreement No. 14-26-00094).

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Authors and Affiliations

  1. All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Saint Petersburg, Russia

    Vera I. Safronova, Irina G. Kuznetsova, Anna L. Sazanova, Anastasiia K. Kimeklis, Andrey A. Belimov, Evgeny E. Andronov, Alexander G. Pinaev, Elena P. Chizhevskaya & Igor A. Tikhonovich

  2. Gorsky State Agrarian University, Vladikavkaz, Russia

    Andrey R. Pukhaev

  3. North-Ossetian Nature Reserve, Republic North-Ossetia-Alania, Alagir, Russia

    Konstantin P. Popov

  4. Department of Biochemistry & Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium

    Anne Willems

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  1. Vera I. Safronova
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  2. Irina G. Kuznetsova
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  3. Anna L. Sazanova
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  4. Anastasiia K. Kimeklis
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  6. Evgeny E. Andronov
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  7. Alexander G. Pinaev
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  8. Elena P. Chizhevskaya
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  9. Andrey R. Pukhaev
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  12. Igor A. Tikhonovich
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Corresponding author

Correspondence to Vera I. Safronova.

Electronic supplementary material

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10482_2015_383_MOESM1_ESM.docx

Fig. S1 Phylogenetic tree of the family Bradyrhizobiaceae generated by the Neighbour-Joining method using the atpD gene sequences. Bootstrap values more than 30 % are given. Strains Bosea vaviloviae sp. nov. in bold. Type species are indicated by the letter “T” (DOCX 31 kb)

10482_2015_383_MOESM2_ESM.docx

Fig. S2 Phylogenetic tree of the family Bradyrhizobiaceae generated by the Neighbour-Joining method using the dnaK gene sequences. Bootstrap values more than 30 % are given. Strains Bosea vaviloviae sp. nov. in bold. Type species are indicated by the letter “T” (DOCX 31 kb)

10482_2015_383_MOESM3_ESM.docx

Fig. S3 Phylogenetic tree of the family Bradyrhizobiaceae generated by the Neighbour-Joining method using the recA gene sequences. Bootstrap values more than 30 % are given. Strains Bosea vaviloviae sp. nov. in bold. Type species are indicated by the letter “T” (DOCX 32 kb)

10482_2015_383_MOESM4_ESM.docx

Fig. S4 Phylogenetic tree of the family Bradyrhizobiaceae generated by the Neighbour-Joining method using the gyrB gene sequences. Bootstrap values more than 30 % are given. Strains Bosea vaviloviae sp. nov. in bold. Type species are indicated by the letter “T” (DOCX 30 kb)

10482_2015_383_MOESM5_ESM.docx

Fig. S5 Phylogenetic tree of the family Bradyrhizobiaceae generated by the Neighbour-Joining method using the rpoB gene sequences. Bootstrap values more than 30 % are given. Strains Bosea vaviloviae sp. nov. in bold. Type species are indicated by the letter “T” (DOCX 31 kb)

10482_2015_383_MOESM6_ESM.docx

Fig. S6 The unweighted pair group average clustering dendrogram showing the difference in phenotypic characteristics between the isolates from V. formosa and the type strain Bosea lathyri LMG 26379T (DOCX 56 kb)

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Safronova, V.I., Kuznetsova, I.G., Sazanova, A.L. 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 107, 911–920 (2015). https://doi.org/10.1007/s10482-015-0383-9

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