Mikrobiol. Z. 2016; 78(2):43-51. Russian.
doi: https://doi.org/10.15407/microbiolj78.02.043

The Evaluation of Metagenome and Detection of Functionally Significant Polymorphisms
of Prokaryotes of Soil by Method of Pyrosequencingl

Patyka N.V., Kolodyazhnyi A.Yu., Ibatullin I.I.

National University of Life and Environmental Sciences of Ukraine
13 Heroyiv Oborony Str., Kyiv, 03041, Ukraine

It was evaluated the metagenome and functionally significant phylogenetic and taxonomic polymorphisms of prokaryotes of typical chernozem in agrocenoses of winter wheat by the method of pyrosequencing. Have been received 1708 operational taxonomic units and identified 335 taxons of prokaryotes. It was established, that the structure of prokaryotes metagenome of typical chernozem includes the representatives of the 2 Archaea and 22 Bacteria phylums, and absolutely dominants among them were Proteobacteria - 79.6 % and Actinobacteria - 12.9 %. The polymorphism of representation of prokaryotic taxons was observed at the level of families, and the dominants were Alcaligenaceae, Pseudomonadaceae, Solirubrobacteraceae, Gaiellaceae, Nitrososphaeraceae. It is shown phylogenetic links between the main representatives of prokaryotes’ metagenome of typical chernozem in agrocenoses of winter wheat. Thus, the use of pyrosequencing, in addition to estimation of structure and diversity, opens new perspectives for the study of functional component of prokaryotes’ metagenome of soil.

Key words: metagenome, prokaryotes, pyrosequencing, taxonomic structure, functionally significant polymorphisms, typical chernozem.

Full text (PDF, in Russian)

  1. Gadzalo Ya.M., Patyka N.V., Zarishnyak A.S. Agrobiologiya rizosfery rasteniy: monografiya. Kyiv: Agrarna nauka, 2015.
  2. Kolodyazhnyi O.Yu., Andronov Ye.Ye., Patyka M.V. Molekulyarno-biolohichne otsi­nyuvannya prokariotnoho kompleksu chornozemu typovoho za vyroshchuvannya pshenytsi ozymoi. Zbirnyk naukovykh prats NNTs «Instytut zemlerobstva NAAN». 2014; 1-2:61-67.
  3. Kolodyazhnyi O.Yu., Patyka M.V. Formuvannya mikrobnoho kompleksu chornozemu typovoho v ahrotsenozi pshenytsi ozymoi za riznykh system zemlerobstva. Visnyk Poltavskoi derzhavnoi ahrarnoi akademii. 2014; 2(73):26-33.
  4. Patyka M.V., Patyka T.I., Hryhoryuk I.P., Kruhlov Yu.V. Molekulyarno-henetychnyi analiz polimorfizmu metahenomnykh nukleotydnykh poslidovnostey entomopatohennykh bakteriy Bacillus thuringiensis i prokariotnoho kompleksu hruntiv. Dop. NAN Ukrainy. 2012; 1:164-170.
  5. Patyka N.V., Boroday V.V., Zhitkevich N.V., Khomenko E.V., Gnatyuk T.T., Koltunov B.A., Patyka V.F. Vliyanie biopreparatov na dinamiku chislennosti bakteriy i fitopatogennykh gribov v agroekosisteme kartofelya. Mikrobiol. Z. 2012; 74(2):28-35.
  6. Patyka N.V., Kruglov Yu.V., Berdnikov A.M., Patyka V.F. Rol Linum usitatissimum l. v formirovanii mikrobnykh soobshchestv podzolistykh pochv. Mikrobiol. Z. 2008; 70(1):59-70.
  7. Patyka N.V., Kruglov Yu.V., Patyka V.F. Osobennosti filogeneticheskikh pro­filey prokarioticheskikh mikroorganizmov podzolistykh pochv. Filiologiya i biokhimiya kult. rasteniy. 2009; 41(3):248-254.
  8. Patyka T.I., Patyka N.V., Patyka V.F. Filogeneticheskie vzaimosvyazi serolo­gicheskikh variantov Bacillus thuringiensis. Biopolymers and Cell. 2009; 25(3):240-244. https://doi.org/10.7124/bc.0007E2
  9. Tanchyk S.P., Demidov O.A., Manko Yu.P. Ekolohichna systema zemlerobstva v Li­sostepu Ukrainy. Metodychni rekomendatsii dlya vprovadzhennya u vyrobnytstvo. Kyiv: NUBiP Ukrainy, 2011.
  10. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009; 37:141-145. https://doi.org/10.1093/nar/gkn879
  11. Ganley A., Kobayashi T. Total rDNA repeat variation revealed by whole genome shotgun sequence data. Genome Research. 2007; 17:184-191. https://doi.org/10.1101/gr.5457707
  12. Kuczynski J., Stombaugh J., Walters W.A., Gonzalez A., Caporaso J.G., Knight R. Using QIIME to analyze 16S rRNA gene sequences from Microbial Communities. Curr. Protoc. In Bioinformatics. 2012.
  13. Kunin V., Copeland A., LapidusA., Mavromatis K., Hugenholtz P A Bioinformatician's Guide to Metagenomics. Microbiology and molecular biology reviews. 2008; 72(4):557-578. https://doi.org/10.1128/MMBR.00009-08
  14. Ronaghi M. Pyrosequencing: a tool for DNA sequencing analysis. Methods Mol. Biol. 2004; 255:211-219.
  15. Taran N.Y., Gonchar O.M., Lopatko K.G., Batsmanova L.M., Patyka M.V., Volkogon M.V. The effect of colloidal solution of molybdenum nanoparticles on the microbial composition in rhizosphere of Cicer arietinum L. Nanoscale Res. Lett. 2014; 9(1):289. https://doi.org/10.1186/1556-276X-9-289
  16. Tringe S.G., Rubin E.M. Metagenomics: DNA sequencing of environmental samples. Nature reviews: Genetics. Nature Publishing Group, 2005. Vol. 6. P. 805-814.
  17. Wooley J.C. Metagenomics: Facts and artifacts, and computational challenges. Journal of computer science and technology. 2010; 1(25):71-81. https://doi.org/10.1007/s11390-010-9306-4