Skip to main content
SpringerLink
Log in

Genetic diversity of rhizobia isolated from nodules of the relic species Vavilovia formosa (Stev.) Fed.

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

Sixteen bacterial strains were isolated from root nodules of Vavilovia formosa plants originated from the North Ossetian State Natural Reserve (Caucasus, Russia). Phylogenetic analysis of these strains was performed using partial 16S rRNA gene and internally transcribed spacer (ITS) sequences. The results showed that the isolates belong to three families of root nodule bacteria. Twelve of them were related to the genus Rhizobium (family Rhizobiaceae) but four strains can be most probably identified as Phyllobacterium-related (family Phyllobacteriaceae), Bosea- and Rhodopseudomonas-related (family Bradyrhizobiaceae). Amplified fragment length polymorphism clustering was congruent with ITS phylogeny but displayed more variability for Rhizobium isolates, which formed a single group at the level of 30 % similarity. We expect that the isolates obtained can belong to new taxa at genus, species or subspecies levels. The results of PCR amplification of the nodulation genes nodC and nodX showed their presence in all Rhizobium isolates and one Rhodopseudomonas-related isolate. The nodC gene sequences of V. formosa isolates were closely related to those of the species Rhizobium leguminosarum bv. viciae but formed separate clusters and did not intermingle with any reference strains. The presence of the nodX gene, which is necessary for nodulation of Afghan peas (Pisum sativum L.) originated from the Middle East, allows the speculation that these wild-type pea cultivars may be the closest existing relatives of V. formosa. Thus, the studies of genetic diversity and symbiotic genes of V. formosa microsymbionts provide the primary information about their phylogeny and contribute to the conservation of this relict leguminous species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Akopian J, Sarukhanyan N, Gabrielyan I et al (2010) Reports on establishing an ex situ site for “beautiful” vavilovia (Vavilovia formosa) in Armenia. Gen Res Crop Evol 57:1127–1134

    Article  Google Scholar 

  • Bladergroen M, Spaink HP (1998) Genes and signal molecules involved in the rhizobia–leguminoseae symbiosis. Curr Opin Plant Biol 1:353–359

    Article  CAS  PubMed  Google Scholar 

  • Carjagin IP (1954) Flora of Azerbaijan. Academy of Sciences of the Azerbaijan SSR, Baku, p 580 (in Russian)

    Google Scholar 

  • Davis EO, Evans IJ, Johnston AWB (1988) Identification of nodX, a gene that allows Rhizobium leguminosarum biovar viciae strain TOM to nodulate Afghanistan peas. Mol Gen Genet 212:531–535

    Article  CAS  PubMed  Google Scholar 

  • De Meyer SE, Willems A (2012) Multilocus sequence analysis of Bosea species and description of Bosea lupini sp. nov., Bosea lathyri sp. nov. and Bosea robiniae sp. nov., isolated from legumes. IJSEM. doi:10.1099/ijs.0.035477-0

  • Dzyubenko NI, Dzyubenko EA (2009) Interactive agricultural ecological atlas of Russia and neighboring countries. Economic Plants and their Diseases, Pests and Weeds. http://www.agroatlas.ru/en/content/related/Vavilovia_formosa/. Accessed 5 April 2010

  • Fedorov AA (1939) Wild high-mountain peas of Caucasus. Trans Biol Inst Arm SSR 1:39–79 (in Russian)

    Google Scholar 

  • Firmin JL, Wilson KE, Carlson RW, Davies AE, Downie JA (1993) Resistance to nodulation of cv Afghanistan peas is overcome by nodX which mediates an O-acetylation of the Rhizobium leguminosarum lipo-oligosaccharide nodulation factor. Mol Microbiol 10:351–360

    Article  CAS  PubMed  Google Scholar 

  • Gossmann JA, Markmann K, Brachmann A, Rose LE, Parniske M (2012) Polymorphic infection and organogenesis patterns induced by a Rhizobium leguminosarum isolate from Lotus root nodules are determined by the host genotype. New Phytol. doi:10.1111/j.1469-8137.2012.04281

    PubMed  Google Scholar 

  • Hogg B, Davies AE, Wilson KE, Bisseling T, Downie JA (2002) The American phytopathological society competitive nodulation blocking of cv. Afghanistan pea is related to high levels of nodulation factors made by some strains of Rhizobium leguminosarum bv. viciae. MPMI 15:60–68

    Article  CAS  PubMed  Google Scholar 

  • Imhoff JF, Truper HG, Pfennig N (1984) Rearrangement of the species and genera of the phototrophic “purple nonsulfur bacteria”. IJSB 34:340–343

    Google Scholar 

  • Kenicer G, Smýkal P, Vishyakova M, Mikić A (2009) Vavilovia formosa, an intriguing Pisum relative. Grain Legumes 51:8–12

    Google Scholar 

  • Laguerre G, Nour SM, Macheret V et al (2001) Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology 147:981–993

    CAS  PubMed  Google Scholar 

  • Lie TA, Göktan D, Engin M, Pijnenborg J, Anlarsal E (1987) Co-evolution of the legume–Rhizobium association. Plant Soil 100:171–181

    Article  Google Scholar 

  • Lie TA, Goktan D, Engin M (1988) Rhizobium strains from wild and primitive legumes: a nuisance or a valuable gene pool? In: Beck DP, Materon LA (eds) Nitrogen fixation by legumes in Mediterranean agriculture. Springer, Netherlands, pp 121–129

    Chapter  Google Scholar 

  • Ma SW, Iyer VN (1990) New field isolates of Rhizobium leguminosarum biovar viciae that nodulate the primitive pea cultivar Afghanistan in addition to modern cultivars. Appl Envion Microbiol 56:2206–2212

    CAS  Google Scholar 

  • Mantelin S, Fischer-Le Saux M, Zakhia F, Bena G, Bonneau S, Jeder H, de Lajudie P, Cleyet-Marel J-C (2006) 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. IJSEM 56:827–839

    CAS  PubMed  Google Scholar 

  • Maxted N, Ambrose M (2001) Peas (Pisum L.). In: Maxted N, Bennett SJ (eds) Plant genetic resources of legumes in the Mediterranean. Kluwer, Dordrecht, pp 181–190

    Chapter  Google Scholar 

  • Mikić A, Smýkal P, Kenicer G et al (2009) A revival of the research on beautiful vavilovia (Vavilovia formosa syn. Pisum formosum). Pisum Genet 41:34–39

    Google Scholar 

  • Normand P, Ponsonnet C, Nesme X et al (1996) ITS analysis of prokaryotes. Mol Microb Ecol Man 5:1–12

    Google Scholar 

  • Novikova N, Safronova V (1992) Transconjugants of Agrobacterium radiobacter harbouring sym genes of Rhizobium galegae can form an effective symbiosis with Medicago sativa. FEMS Microbiol Lett 93:261–268

    Article  CAS  Google Scholar 

  • Ovtsyna AO, Rademaker GJ, Esser E et al (1999) Comparison of characteristics of the nodX genes from various Rhizobium leguminosarum strains. MPMI 12:252–258

    Article  CAS  PubMed  Google Scholar 

  • Patyka TI, Patyka NV, Patyka VF (2009) Phylogenetic interrelations between serological variants of Bacillus thuringiensis. Biopolym Cell 25:240–244

    Article  Google Scholar 

  • Petersen K, Cannegieter SC, van der Reijden TJ et al (2011) Diversity and clinical impact of Acinetobacter baumannii colonization and infection at a Military Medical Center. J Clin Microbiol 49:159–166

    Article  PubMed Central  PubMed  Google Scholar 

  • Ponsonnet C, Nesme X (1994) Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch Microbiol 161:300–309

    CAS  PubMed  Google Scholar 

  • Provorov NA (1994) The interdependence between taxonomy of legumes and specificity of their interaction with rhizobia in relation to evolution of the symbiosis. Symbiosis 17:183–200

    Google Scholar 

  • Rincón A, Arenal F, González I, Manrique E, Lucas MM, Pueyo JJ (2008) Diversity of rhizobial bacteria isolated from nodules of the gypsophyte Ononis tridentata L. growing in Spanish soils. Microb Ecol 56(2):223–233

    Article  PubMed  Google Scholar 

  • Safronova V, Chizhevskaya E, Bullitta S, Andronov E, Belimov A, Charles TC, Lindström K (2007) Presence of a novel 16S-23S rRNA gene intergenic spacer insert in Bradyrhizobium canariense strains. FEMS Microbiol Lett 269:207–212

    Article  CAS  PubMed  Google Scholar 

  • Safronova V, Tikhonovich I (2012) Automated cryobank of microorganisms: Unique possibilities for long-term authorized depositing of commercial microbial strains. In: Mendez-Vilas A (ed) Microbes in applied research: current advances and challenges. World Scientific Publishing Co., pp 331–334. doi:10.1142/9789814405041_0066

  • Sarita S, Sharma PK, Priefer UB, Prell J (2005) Direct amplification of rhizobia nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. FEMS Microbiol Ecol 54:1–11

    Article  CAS  PubMed  Google Scholar 

  • Sinjushin AA, Demidenko NV, Gostimskii SA (2009) Preliminary report on taxonomical position of Vavilovia formosa (Stev.) Fed. evidenced from morphological and molecular data. Pisum Genet 41:15–20

    Google Scholar 

  • Steven C (1812) Orobus formosus Steven. Mem Soc Imp Nat Moscou 4:50 (In French)

    Google Scholar 

  • Tikhonovich IA, Provorov NA (2007) Beneficial plant-microbe interactions. In: Dzhavakhiya V, Korpela T, Dyakov YT (eds) Comprehensive and Molecular Phytopathology. Elsevier, Amsterdam, pp 365–420

    Chapter  Google Scholar 

  • Ueda T, Suga Y, Yahiro N, Matsuguchi T (1995) Phylogeny of Sym plasmids of rhizobia by PCR-based sequencing of a nodC segment. J Bacteriol 177:48–472

    Google Scholar 

  • Valverde A, Velazquez E, Fernandez-Santos F et al (2005) Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. IJSEM 55:1985–1989

    CAS  PubMed  Google Scholar 

  • Vavilov NI (1951) The origin, variation, immunity and breeding of cultivated plants (English translation). The Ronald Press Co., New York

    Google Scholar 

  • Vincent JM (1970) A manual for the practical study of root nodule bacteria. IBP Handbook. Blackwell Scientific Publications, Oxford, pp 73–97

    Google Scholar 

  • Wdowiak-Wróbel S, Małek W (2005) Genomic diversity of Astragalus cicer microsymbionts revealed by AFLP fingerprinting. J Gen Appl Microbiol 51:369–378

    Article  PubMed  Google Scholar 

  • Willems A, Doignon-Bourcier F, Coopman R, Hoste B, de Lajudie P, Gillis M (2000) AFLP fingerprint analysis of Bradyrhizobium strains isolated from Faidherbia albida and Aeschynomene species. Syst Appl Microbiol 23:137–147

    Article  CAS  PubMed  Google Scholar 

  • Winarno R, Lie TA (1979) Competition between Rhizobium strains in nodule formation: interaction between nodulating and non-nodulating strains. Plant Soil 51:135–142

    Article  Google Scholar 

  • Wong FYK, Stackebrandt E, Ladha JK, Fleischman DE, Date RA, Fuerst JA (1994) Phylogenetic analysis of Bradyrhizobium japonicum and photosynthetic stem-nodulating bacteria from Aeschynomene species grown in separated geographical regions. Appl Environ Microbiol 60:940–946

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zakhia F, Jeder H, Willems A, Gillis M, Dreyfus B, de Lajudie P (2006) Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya. Microb Ecol 51(3):375–393

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Dr. Vishnyakova Margarita from the N. I. Vavilov Research Institute of Plant Industry for an inspiration of this study and valuable discussions. This work was supported by the Russian Foundation of Basic Research (Project No. 13-04-90833).

Author information

Authors and Affiliations

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

    Vera I. Safronova, Anastasiia K. Kimeklis, Elena P. Chizhevskaya, Andrey A. Belimov, Evgeny E. Andronov, Alexander G. Pinaev & 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

Authors
  1. Vera I. Safronova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anastasiia K. Kimeklis
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Elena P. Chizhevskaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andrey A. Belimov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Evgeny E. Andronov
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Alexander G. Pinaev
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Andrey R. Pukhaev
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Konstantin P. Popov
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Igor A. Tikhonovich
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vera I. Safronova.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Safronova, V.I., Kimeklis, A.K., Chizhevskaya, E.P. et al. Genetic diversity of rhizobia isolated from nodules of the relic species Vavilovia formosa (Stev.) Fed.. Antonie van Leeuwenhoek 105, 389–399 (2014). https://doi.org/10.1007/s10482-013-0089-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-013-0089-9

Keywords

Search

Navigation