doi: 10.15389/agrobiology.2017.1.105eng

UDC 633.49:632.3.01/.08:577.21:57.088

Acknowledgements:
We thank S.N. Dedysh for assistance in molecular genetic analysis and Yu.M. Serekbaeva for her help in 16S rRNA gene sequencing. We are also sincerely grateful to Prof. Dr Frank Oliver Glöckner for his valuable comments on the use of the resource https://www.arb-silva.de.
Immunofluorescence microscopy was performed at the Symbiosis Center for collective use of scientific equipment (Institute of Biochemistry and Physiology of Plants and Microorganisms RAS, Saratov). DNA preparation, sequencing and assembly of the fragments were made in the Laboratory of microbiology of wetland ecosystems (Institute of Microbiology RAS, Moscow) and ZAO «Evrogen» (Moscow).

 

A BACTERIAL ISOLATE FROM THE RHIZOSPHERE OF POTATO
(Solanum tuberosum L.) IDENTIFIED AS Ochrobactrum lupini IPA7.2

G.L. Burygin1, I.A. Popova1, K.Yu. Kargapolova2, O.V. Tkachenko2,
L.Yu. Matora1, 3, S.Yu. Shchyogolev1, 3

1Institute of Biochemistry and Physiology of Plants and Microorganisms RAS, Federal Agency of Scientific Organizations, 13, prosp. Entuziastov, Saratov, 410049 Russia,
e-mail burygingl@gmail.com, iridecol@yandex.ru, matora_l@ibppm.ru, shegolev_s@ibppm.ru;
2N.I. Vavilov Saratov State Agrarian University, 1, Teatral’naya pl., Saratov, 410012 Russia,
e-mail kinaschchri@gmail.com, oktkachenko@yandex.ru;
3N.G. Chernyshevsky National Research Saratov State University, 83, ul. Astrakhanskaya, Saratov, 410012 Russia

Received November 14, 2016

 

We present the results of molecular, genetic, physiological and biochemical investigations of a bacterial isolate from the rhizosphere of potato (Solanum tuberosum L.) as an object to study plant—microbial associativity, used in particular to improve the existing technologies for the production of high-quality planting material by the method of plant culture micropropagation in vitro. To correctly identify the isolate at the species level, we took into account the results of analysis of the current status of prokaryote identification and systematics, reflected in a number of recent reviews. Phylogenetic constructs with strains of the genera Ochrobactrum, Brucella, Ensifer, Mesorhizobium, Rhizobium, and more (closely related to the isolate under study), which were generated by using DNA sequences of 16S rRNA genes, revealed the isolate in the immediate surroundings of members of the genus Ochrobactrum. The isolate turned out to be part of the taxonomic group Ochrobactrum anthropi — one of the 1912 taxonomic groups recorded to date, which comprise 6193 prokaryotic species and each include species with coinciding (or almost coinciding) sequences of 16S rRNA genes (http://www.ezbiocloud.net/identify). In accordance with the conceptual propositions formulated in the above-mentioned publications, the species differences within these groups are determined at the level of other molecular genetic (and biochemical and physiological) properties and, with a high probability, by horizontal gene transfer. With account taken of the resulting set of elements of the polyphasic approach, the strain isolated by us was found to be closest to the known type strain O. lupini LUP21, which is capable of reinfecting leguminous plants of the genus Lupinus and which carries nodulation and nitrogen fixation genes (nodD and nifH), transferred horizontally into it from rhizobial species. This gave us grounds to identify the isolate being examined as Ochrobactrum lupini IPA7.2.

Keywords: plant-microbe associativeness, Solanum tuberosum L., bacterial isolate, taxonomic identification, 16S rRNA, polyphasic approach, horizontal gene transfer, Ochrobactrum lupini.

 

Full article (Rus)

Full text (Eng)

 

REFERENCES

  1. Tikhonovich I.A., Provorov N.A. Simbiozy rastenii i mikroorganizmov: molekulyarnaya genetika agrosistem budushchego [Symbioses plants and microorganisms: molecular genetics of the future agricultural systems]. St. Petersburg, 2009 (in Russ.).
  2. Bloemberg G.V., Lugtenberg B.J.J. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Cur. Opin. Plant Biol., 2001, 4(4): 343-350 CrossRef
  3. Vessey J.K. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil, 2003, 255(2): 571-586 CrossRef
  4. Bashan Y., de-Bashan L.E., Prabhu S.R., Hernandez J.-P. Advances in plant growth-promoting bacterial inoculant technology: Formulations and practical perspectives (1998-2013). Plant Soil, 2014, 378(1-2): 1-33 CrossRef
  5. Bensalim S., Nowak J., Asiedu S.K. A plant growth promoting rhizobacterium and temperature effects on performance of 18 clones of potato. Am. J. Potato Res., 1998, 75(3): 145-152 CrossRef
  6. Volkogon V.V., Dimova S.B., Mamchur A.E. Sl's'kogospodars'ka mkrobologya (mzhvdomchii tematichnii naukovii zbrnik, Cherngv, Ukrana), 2006, 3: 19-25.
  7. Tkachenko O.V., Evseeva N.V., Boikova N.V., Matora L.Yu., Burygin G.L., Lobachev Yu.V., Shchyogolev S.Yu. Improved potato microclonal reproduction with the plant growth-promoting rhizobacteria Azospirillum. Agron. Sustain. Dev., 2015, 35(3): 1167-1174 CrossRef
  8. Woese C.R. Bacterial evolution. Microbiol. Rev., 1987, 51(2): 221-271.
  9. Kunin E.V. Logika sluchaya. O prirode i proiskhozhdenii biologicheskoi evolyutsii [Case logic — on the nature and origin of biological evolution]. Moscow, 2014 (in Russ.).
  10. Oren A., Garrity G.M. Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie van Leeuwenhoek, 2014, 106: 43-56 CrossRef
  11. Chun J., Rainey F.A. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int. J. Syst. Evol. Micr., 2014, 64(2): 316-324 CrossRef
  12. Matora L.Yu., Shvartsburd B.I., Shchegolev S.Yu. Immunokhimicheskii analiz O-spetsificheskikh polisakharidov pochvennykh azotfiksiruyushchikh bakterii Azospirillum brasilense. Mikrobiologiya, 1998, 67(6): 815-820 (in Russ.).
  13. Dedysh S.N., Panikov N.S., Tiedje J.M. Acidophilic methanotrophic communities from sphagnum peat bogs. Appl. Environ. Microb., 1998, 64(3): 922-929.
  14. Pruesse E., Peplies J., Glöckner F.O. SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics, 2012, 28(14): 1823-1829 CrossRef
  15. Trujillo M.E., Willems A., Abril A., Planchuelo A.-M., Rivas R., Ludeña D., Mateos P.F., Martínez-Molina E., Velázquez E. Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl. Environ. Microb., 2005, 71(3): 1318-1327 CrossRef
  16. Zurdo-Pineiro J.L., Rivas R., Trujillo M.E., Vizcaíno N., Carrasco J.A., Chamber M., Palomares A., Mateos P.F., Martínez-Molina E., Velázquez E. Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int. J. Syst. Evol. Micr., 2007, 57(4): 784-788 CrossRef
  17. Holmes B., Popoff M., Kiredjan M., Kersters K. Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as group Vd. Int. J. Syst. Bacteriol., 1988, 38(4): 406-416 CrossRef
  18. Lebuhn M., Achouak W., Schloter M., Berge O., Meier H., Barakat M., Hartmann A., Heulin T. Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int. J. Syst. Evol. Micr., 2000, 50(6): 2207-2223 CrossRef
  19. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., Yi H., Won S., Chun J. Introducing EzTaxon: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Micr., 2012, 62(3): 716-721 CrossRef
  20. Fox G.E, Wisotzkey J.D., Jurtshyk P., jr. How close is close: 16s rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol., 1992, 42(1): 166-170 CrossRef
  21. Wisniewski-Dye F., Borziak K., Khalsa-Moyers G., Alexandre G., Sukharnikov L.O., Wuichet K., Hurst G.B., McDonald W. H., Robert-
    son J.S., Barbe V., Calteau A., Rouy Z., Mangenot S., Prigent-Combaret C., Normand P., Boyer M., Siguier P., Dessaux Y., Elmerich C., Condemine G., Krishnen G., Kennedy I., Paterson A.H., Gonzalez V., Mavingui P., Zhulin I.B. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genetics, 2011, 7(12): e1002430 CrossRef
  22. Kim M., Oh H.S., Park S.C., Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Micr., 2014, 64(2): 346-351 CrossRef
  23. Paliy O., Shankar V., Sagova-Mareckova M. Phylogenetic microarrays. In: Bioinformatics and data analysis in microbiology. O?.T. Bishop (ed.). Caister Academic Press, Norfolk, 2014: 207-230.
  24. Yarza P., Yilmaz P., Pruesse E., Glöckner F.O., Ludwig W., Schleif-
    er K.-H., Whitman W.B., Euzéby J., Amann R., Rosselló-Móra R. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol., 2014, 12(9): 635-645 CrossRef
  25. Hall B.G. Phylogenetic trees made easy: a how-to manual. Sunderland, USA, 2011.
  26. Tindall B.J., Rosselló-Móra R., Busse H.-J., Ludwig W., Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Micr., 2010, 60: 249-266 CrossRef

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