doi: 10.15389/agrobiology.2016.5.654eng

UDC 573.22:581.55

Supported by Russian Science Foundation (project 14-26-00094).



A.O. Zverev, E.V. Pershina, N.A. Provorov, E.E. Andronov, E.N. Serikova

All-Russian Research Institute for Agricultural Microbiology, Federal Agency of Scientific Organizations,3, sh. Podbel’skogo, St. Petersburg, 196608 Russia,

Received July 6, 2016


Сhanges in the composition of microbial communities under the influence of root exudation of plants (rhizosphere effect) is widely reported in the scientific literature. A number of studies clearly show the rhizosphere effect of external factors such as soil type, species and plant variety, etc. The aim of this work is to study the effect of soil type and plant species using modern high-throughput sequencing techniques. This effect has been studied well by foreign counterparts, but such work on Russian soils and crops used in the domestic agro-industry, is carried out for the first time. We used two soils contrasting by their agrochemical parameters, black earth (Voronezh region), and sod-podzolic soil (Pskov region). Rye (Secale cereale L., k-6469) and wheat (Triticum aestivum L., k-54609) seeds obtained from VIR collection (St. Petersburg) were grown in a greenhouse on both soils for 42 days. Using NGS-V4 variable region sequenced 16S rDNA gene, microbial community composition in bulk soils and the rhizospheres formed on them was analyzed. Despite the short period of the experiment, clear rhizosphere effect was revealed in both soils. The strongest factor was the type of soil. Communities of bulk soil as well as rhizosphere communities on these soils, were significantly different from each other. Both soils show the same effect in the formation of rhizosphere communities of rye and wheat. Type of plant is the second largest (after the type of soil) factor in determining taxonomic composition of the rhizosphere microbiome. Communities of rye rhizosphere in general are closer to the communities of bulk soils than wheat rhizosphere communities. Also, the rhizosphere communities of rye on sod-podzolic soil according to the cluster analysis are closer in structure to the original communities of the soil. The taxonomic analysis of the communities at the level of phyla revealed several groups. They are most responsible for the rhizosphere effect. Formation of rhizosphere communities was accompanied by an increase in the number of Betaproteobacteria class sequences, while reducing the part of the bacteria of Verrucomicrobia phylum. Significant changes in the community occurred in wheat-cultivated sod-podzolic soil. According to the results of all analyzes, these communities differ significantly from the original communities of soil and rhizosphere communities of rye on sod-podzolic soil. Perhaps this can be attributed to an increased proportion of the genus Flavobacterium (phylum Bacteroidetes) bacteria in these communities. Using the method of high-throughput sequencing it has been clearly demonstrated the presence of rhizosphere effect on rye- and wheat-cultivated soils, as well as the features of the interaction of individual factors responsible for rhizosphere effect. However, to confirm rhizosphere effect, as well as for more detailed studies of the mechanisms underlying it, it is necessary, in addition to the taxonomic analysis carried out, to elucidate how the rhizosphere microbiome is influenced by the plant exudate composition. To do this a series of model experiments with introduction into the soil of certain root exudate substances of rye and wheat are already scheduled.

Keywords: rhizosphere effect, rhizosphere microbiom, metagenomic analysis, rye rhizosphere, wheat rhizosphere.


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  1. Kostychev S.P. Fiziologiya rastenii. Chast'. 2 [Plant physiology. Part 2]. Moscow-Leningrad, 1933 (in Russ.).
  2. Genkel' P.A. Fiziologiya rastenii s osnovami mikrobiologii [Plant physiology and fundamentals of microbiology]. Moscow, 1962 (in Russ.).
  3. Philippot L., Raaijmakers J.M., Lemanceau P., van der Putten W.H. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol., 2013, 11(11): 789-799 CrossRef
  4. Rovira A.D. Plant root exudates. Bot. Rev., 1969, 35: 35-57.
  5. Hale M.G., Moore L.D., Griffin G.J. Root exudates and exudation. In: Interaction between non-pathogenic soil microorganisms and plants. Y.R. Dommergues, S.V. Krupa (eds.). Amsterdam, 1978: 163-203.
  6. Tikhonovich I.A., Provorov N.A. Simbiozy rastenii i mikroorganizmov: molekulyarnaya genetika agrosistem budushchego [Microbial-plant symbiosis: molecular genetics of prospective agrosystems]. St. Petersburg, 2009 (in Russ.).
  7. Kravchenko L.V., Shaposhnikov A.I., Makarova N.M., Azarova T.S., L'vova K.A., Kostyuk I.I., Tikhonovich I.A. Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2011, 3: 71-75. Available No date (in Russ.).
  8. Shaposhnikov A.I., Belimov A.A., Kravchenko L.V., Vivanko D.M. Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2011, 3: 16-22. Available No date (in Russ.).
  9. Bais H.P., Weir T.L., Perry L.G., Gilroy S., Vivanco J.M. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu. Rev. Plant Biol., 2006, 57: 233-266 CrossRef
  10. Wieland G., Neumann R., Backhaus H. Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl. Environ. Microbiol., 2001, 67(12): 5849-5854 CrossRef
  11. Schreiter S., Ding G.C., Heuer H., Neumann G., Sandmann M., Grosch R., Kropf S., Smalla K. Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce. Front. Microbiol., 2014, 5: 144 CrossRef
  12. Chaparro J.M., Badri D.V., Vivanco J.M. Rhizosphere microbiome assemblage is affected by plant development. ISME J., 2014, 8(4): 790-803 CrossRef
  13. Winston M.E., Hampton-Marcell J., Zarraonaindia I., Owens S.M., Moreau C.S., Gilbert J.A., Hartsel J.A., Kennedy S.J., Gibbons S.M. Understanding cultivar-specificity and soil determinants of the Sannabis microbiome. PLoS ONE, 2014, 9(6): e99641 CrossRef
  14. Bulgarelli D., Garrido-Oter R., Münch P.C., Weiman A., Dröge J., Pan Y., McHardy A.C., Schulze-Lefert P. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe, 2015, 17(3): 392-403 CrossRef
  15. Coleman-Derr D., Desgarennes D., Fonseca-Garcia C., Gross S., Clingenpeel S., Woyke T., North G., Visel A., Partida-Martinez L.P., Tringe S.G. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol., 2016, 209(2): 798-811 CrossRef
  16. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev., 2004, 68: 669-685 CrossRef
  17. Lundberg D.S., Lebeis S.L., Paredes S.H., Yourstone S., Gehring J., Malfatti S., Tremblay J., Engelbrektson A., Kunin V., delRio T.G., Edgar R.C., Eickhorst T., Ley R.E., Hugenholtz P., Tringe S.G., Dangl J.L. Defining the core Arabidopsis thaliana root microbiome. Nature, 2012, 488(7409): 86-90 CrossRef
  18. Micallef S.A., Shiaris M.P., Colón-Carmona A. Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J. Exp. Bot., 2009: 60(6): 1729-1742 CrossRef
  19. van der Heijden M.G., Schlaeppi K. Root surface as a frontier for plant microbiome research. PNAS USA, 2015, 112(8): 2299-2300 CrossRef
  20. Bonito G., Reynolds H., Robeson M.S. 2nd, Nelson J., Hodkinson B.P., Tuskan G., Schadt C.W., Vilgalys R. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol. Ecol., 2014, 23(13): 3356-3370 CrossRef
  21. Bodenhausen N., Horton M.W., Bergelson J. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS ONE, 2013, 8(2): e56329 CrossRef
  22. Neumann G., Bott S., Ohler M.A., Mock H.P., Lippmann R., Grosch R., Smalla K. Root exudation and root development of lettuce (Lactucasativa L. cv. Tizian) as affected by different soils. Front. Microbiol., 2014, 5: 2 CrossRef
  23. Donn S., Kirkegaard J.A., Perera G., Richardson A.E., Watt M. Evolution of bacterial communities in the wheat crop rhizosphere. Environ. Microbiol., 2015, 3: 610-621 CrossRef
  24. Edwards J., Johnson C., Santos-Medellín C., Lurie E., Podishetty N.K., Bhatnagar S., Eisen J.A., Sundaresan V. Structure, variation, and assembly of the root-associated microbiomes of rice. PNASUSA, 2015, 112(8): E911-E920 CrossRef
  25. Andronov E.E., Pinaev A.G., Pershina E.V., Chizhevskaya E.P. Nauchno-metodicheskie rekomendatsii po vydeleniyu vysokoochishchennykh preparatov DNK iz ob"ektov okruzhayushchei sredy [Isolation of highly purified DNA from environmental objects: guidelines]. St. Petersburg, 2011 (in Russ.).
  26. Bates S.T., Berg-Lyons D., Caporaso J.G., Walters W.A., Knight R., Fierer N. Examining the global distribution of dominant archaeal populations in soil. ISME J., 2011, 5: 908-917 CrossRef
  27. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J., Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 2010, 7(5): 335-336 CrossRef
  28. DeSantis T.Z., Hugenholtz P., Larsen N., Rojas M., Brodie E.L., Keller K., Huber T., Dalevi D., Hu P., Andersen G.L. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 2006, 72(7): 5069-5072 CrossRef
  29. Lozupone C.A., Knight R. Global patterns in bacterial diversity. PNAS USA, 2007, 104(27): 11436-11440 CrossRef
  30. Hammer O., Harper D., Ryan P. PAST: Paleontological Statistics software package for education and data analysis. Paleontologia Electronica, 2001, 4(1): art. 4 (9pp).