Russian Journal of Genetics

, Volume 54, Issue 5, pp 525–535 | Cite as

Structural Polymorphism of Sinorhizobium meliloti Genes Related to Virulence and Salt Tolerance

  • M. L. Roumiantseva
  • A. S. Saksaganskaia
  • V. S. Muntyan
  • M. E. Cherkasova
  • B. V. Simarov
Genetics of Microorganisms


Analysis of the structural polymorphism of eight genes in Sinorhizobium meliloti (nodA, nodB, nodC, and nodH, as well as betA, betB, betC, and betB2) involved in virulence control and salt tolerance, respectively, was carried out in native populations from two geographically distant areas of alfalfa diversity. These areas are located in the North Caucasian gene center of cultivated plants (NCG) and in the modern center of introgressive hybridization of alfalfa located next to the Aral Sea area (PAG) subjected to salinization. RFLP types (alleles) of the nod and bet genes, similar to those in the reference strain Rm1021 (A-type) and different from them (divergent, or D-type alleles) were revealed. The combinations for A- and D-type alleles of the aforementioned genes (analysis of the linkage disequilibrium, LD) were studied in both populations. It was shown that D-type alleles of the nod genes were two times more frequent in the NCG population, while D-type alleles of the bet genes were predominantly identified in the PAG population. At the same time, different combinations of D-type alleles of both the nod and bet genes prevailed in populations. For instance, in the case of the glycine betaine metabolism pathway, these were the betC and betB2 genes in NCG population and betB and betA genes in PAG population. The state of linkage disequilibrium was shown for 60.7% of combinations of alleles of the nod and bet genes in the S. meliloti strains from NCG and more than twice less in strains from the PAG population. It was concluded that clonal lines prevailed in NCG, while the PAG population of S. meliloti had a panmictic structure with revealed single clonal lines.


Sinorhizobium meliloti native isolates reference strain Rm1021 nod and bet genes structural polymorphism PCR-RFLP analysis linkage disequilibrium (LD) centers of legume diversity 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Tikhonovich, I.A., Andronov, E.E., Borisov, A.Y., et al., The principle of genome complementarity in the enhancement of plant adaptive capacities, Russ. J. Genet., 2015, vol. 51, no. 9, pp. 831–846. doi 10.1134/S1022795415090124CrossRefGoogle Scholar
  2. 2.
    Sanchez-Canizares, C., Jorrín, B., Poole, P.S., and Tkacz, A., Understanding the holobiont: the interdependence of plants and their microbiome, Curr. Opin. Microbiol., 2017, vol. 38, pp. 188–196. doi 10.1016/j.mib.2017.07.001CrossRefPubMedGoogle Scholar
  3. 3.
    Janczarek, M., Rachwał, K., Marzec, A., et al., Signal molecules and cell-surface components involved in early stages of the legume-rhizobium interactions, Appl. Soil Ecol., 2014, vol. 85, pp. 94–113. doi 10.1016/j.apsoil.2014.08.010CrossRefGoogle Scholar
  4. 4.
    Doran, J.W. and Zeiss, M.R., Soil health and sustainability: managing the biotic component of soil quality, Appl. Soil Ecol., 2000, vol. 15, no. 1, pp. 3–11. doi 10.1016/S0929-1393(00)00067-6CrossRefGoogle Scholar
  5. 5.
    Flowers, T.J., Improving crop salt tolerance, J. Exp. Bot., 2004, vol. 55, no. 396, pp. 307–319. doi 10.1093/jxb/erh003CrossRefPubMedGoogle Scholar
  6. 6.
    Roumiantseva, M.L., Stepanova, G.V., Kurchak, O.N., et al., Selection of salt tolerant alfalfa (Medicago L.) plants from different varieties and their morphobiological and symbiotic properties analysis, S.-kh. Biol., 2015, vol. 50, no. 5, pp. 673–684. doi 10.15389/agrobiology. 2015.5.673rusGoogle Scholar
  7. 7.
    Ibragimova, M.V., Roumiantseva, M.L., Onishchuk, O.P., et al., Symbiosis between the root-nodule bacterium Sinorhizobium meliloti and alfalfa (Medicago sativa) under salinization conditions, Microbiology (Moscow), 2006, vol. 75, no. 1, pp. 77–81.CrossRefGoogle Scholar
  8. 8.
    Wais, R.J., Keating, D.H., and Long, S.R., Structurefunction analysis of Nod factor-induced root hair calcium spiking in Rhizobium-legume symbiosis, Plant Physiol., 2002, vol. 129, no. 1, pp. 211–224. doi 10.1104/pp.010690CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Geurts, R. and Bisseling, T., Rhizobium Nod factor perception and signaling, Plant Cell, 2002, vol. 14, suppl., pp. S239–S249. doi 10.1105/tpc.002451CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Torres Tejerizo, G., Del Papa, M.F., Soria-Diaz, M.E., et al., The nodulation of alfalfa by the acid-tolerant Rhizobium sp. strain LPU83 does not require sulfated forms of lipochitooligosaccharide nodulation signals, J. Bacteriol., 2011, vol. 193, no. 1, pp. 30–39. doi 10.1128/JB.01009-10CrossRefPubMedGoogle Scholar
  11. 11.
    Mergaert, P., Van Montagu, M., and Holsters, M., Molecular mechanisms of Nod factor diversity, Mol. Microbiol., 1997, vol. 25, no. 5, pp. 811–817. doi 10.1111/j.1365-2958.1997.mmi526.xCrossRefPubMedGoogle Scholar
  12. 12.
    Fujishige, N.A., Lum, M.R., De Hoff, P.L., et al., Rhizobium common nod genes are required for biofilm formation, Mol. Microbiol., 2008, vol. 67, no. 3, pp. 504–515. doi 10.1111/j.1365-2958.2007.06064.xCrossRefPubMedGoogle Scholar
  13. 13.
    Wang, D., Yang, S., Tang, F., and Zhu, H., Symbiosis specificity in the legume-rhizobial mutualism, Cell. Microbiol., 2012, vol. 14, no. 3, pp. 334–342. doi 10.1111/j.1462-5822.2011.01736.xCrossRefPubMedGoogle Scholar
  14. 14.
    Cooper, J.E., Early interactions between legumes and rhizobia: disclosing complexity in a molecular dialogue, J. Appl. Microbiol., 2007, vol. 103, no. 5, pp. 1355–1365. doi 10.1111/j.1365-2672.2007.03366.xCrossRefPubMedGoogle Scholar
  15. 15.
    Roumiantseva, M.L. and Muntyan, V.S., Root nodule bacteria Sinorhizobium meliloti: tolerance to salinity and bacterial genetic determinants, Microbiology (Moscow), 2015, vol. 84, no. 3, pp. 303–318. doi 10.7868/S0026365615030179CrossRefGoogle Scholar
  16. 16.
    Mandon, K., Osteras, M., Boncompagni, E., et al., The Sinorhizobium meliloti glycine betaine biosynthetic genes (betlCBA) are induced by choline and highly expressed in bacteroids, Mol. Plant-Microbe Interact., 2003, vol. 16, no. 8, pp. 709–719. doi 10.1094/MPMI.2003.16.8.709CrossRefPubMedGoogle Scholar
  17. 17.
    Cregut, M., Durand, M.J., and Thouand, G., The diversity and functions of choline sulphatases in microorganisms, Microb. Ecol., 2014, vol. 67, no. 2, pp. 350–357. doi 10.1007/s00248-013-0328-7CrossRefPubMedGoogle Scholar
  18. 18.
    Yurgel, S.N., Rice, J., Mulder, M., et al., Truncated betB2-144 plays a critical role in Sinorhizobium meliloti Rm2011 osmoprotection and glycine-betaine catabolism, Eur. J. Soil Biol., 2013, vol. 54, pp. 48–55. doi 10.1016/j.ejsobi.2012.10.004CrossRefGoogle Scholar
  19. 19.
    Debelle, F., Moulin, L., Mangin, B., et al., Nod genes and Nod signals and the evolution of the Rhizobium legume symbiosis, Acta Biochim. Pol., 2001, vol. 48, no. 2, pp. 359–365.PubMedGoogle Scholar
  20. 20.
    Vavilov, N.I., Tsentry proiskhozhdeniya kul’turnykh rastenii (Centers of Origin of Cultivated Plants), vol. 16, no. 2 of Trudy po Prikladnoi Botanike, Genetike i Selektzii, Leningrad: Nauka, 1926.Google Scholar
  21. 21.
    Ivanov, A.I., Lyutserna (Alfalfa), Moscow: Kolos, 1980.Google Scholar
  22. 22.
    Roumiantseva, M.L., Muntian, V.S., Mengoni, A., and Simarov, B.V., ITS-polymorphism of salt-tolerant and salt-sensitive native isolates of Sinorhizoblum meliloti—symbionts of alfalfa, clover and fenugreek plants, Russ. J. Genet., 2014, vol. 50, no. 4, pp. 348–359. doi 10.7868/S0016675814040109CrossRefGoogle Scholar
  23. 23.
    Roumiantseva, M.L., Simarov, B.V., Onishchuk, O.P., et al., Biologicheskoe raznoobrazie kluben’kovykh bakterii v ekosistemakh i agrotsenozakh: teoreticheskie osnovy i metody (Biological Diversity of Nodule Bacteria in Ecosystems and Agrocenoses: Theoretical Bases and Methods), Roumiantseva, M.L. and Simarov, B.V., Eds., St.-Petersburg: Vserossiyskiy Nauchno-Issledovatelskii Institut Sel’skokhozyaystvennoy Mikrobiologii Rossiyskoy Akademii Sel’skokhozyaystvennykh Nauk, 2011.Google Scholar
  24. 24.
    Haukka, K., Lindstrom, K., and Young, J.P.W., Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America, Appl. Environ. Microbiol., 1998, vol. 64, no. 2, pp. 419–426.PubMedPubMedCentralGoogle Scholar
  25. 25.
    Laguerre, G., Nour, S.M., Macheret, V., et al., Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts, Microbiology, 2001, vol. 147, part 4, pp. 981–993. doi 10.1099/00221287-147-4-981CrossRefPubMedGoogle Scholar
  26. 26.
    Rannala, B., Qiu, W.-G., and Dykhuizen, D.E., Methods for estimating gene frequencies and detecting selection in bacterial populations, Genetics, 2000, vol. 155, no. 2, pp. 499–508.PubMedPubMedCentralGoogle Scholar
  27. 27.
    Hammer, O., Harper, D.A.T., and Ryan, P.D., PAST: paleontological statistics software package for education and data analysis, Palaeontol. Electron., 2001, vol. 4, pp. 1–9.Google Scholar
  28. 28.
    Nei, M., Estimation of average heterozygosity and genetic distance from a small number of individuals, Genetics, 1978, vol. 89, no. 3, pp. 583–590.PubMedPubMedCentralGoogle Scholar
  29. 29.
    Excoffier, L. and Lischer, H.E.L., Arlequin Suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour., 2010, vol. 10, pp. 564–567. doi 10.1111/j.1755-0998.2010.02847.xCrossRefPubMedGoogle Scholar
  30. 30.
    Subbotina, A.R., Cherkasova, M.E., Muntyan, V.S., and Roumiantseva, M.L., betA gene polymorphism among Sinorhizobium meliloti strains of different geographical origin, Aspirant, 2015, nos. 6-2 (11), pp. 41–43.Google Scholar
  31. 31.
    Provorov, N.A., Vorobyov, N.I., and Andronov, E.E., Macro-and microevolution of bacteria in symbiotic systems, Russ. J. Genet., 2008, vol. 44, no. 1, pp. 6–20. doi 10.1134/S102279540801002XCrossRefGoogle Scholar
  32. 32.
    Penttinen, P., Raassaanen, L.A., Lortet, G., and Lindstroem, K., Stable isotope labelling reveals that NaCl stress decreases the production of Ensifer (Sinorhizobium) arboris lipochitooligosaccharide signalling molecules, FEMS Microbiol. Lett., 2013, vol. 349, no. 2, pp. 117–126. doi 10.1111/1574-6968CrossRefPubMedGoogle Scholar
  33. 33.
    Boto, L. and Martínez, J.L., Ecological and temporal constraints in the evolution of bacterial genomes, Genes, 2011, vol. 2, no. 4, pp. 804–828. doi 10.3390/genes2040804CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  • M. L. Roumiantseva
    • 1
  • A. S. Saksaganskaia
    • 1
  • V. S. Muntyan
    • 1
  • M. E. Cherkasova
    • 1
  • B. V. Simarov
    • 1
  1. 1.All-Russian Research Institute for Agricultural MicrobiologySt. Petersburg, PushkinRussia

Personalised recommendations