Mikrobiol. Z. 2018; 80(6):109-122. Ukrainian.
doi: https://doi.org/10.15407/microbiolj80.06.109

Estimation of Prokaryotic Complex Methagenom of Chernozem Under Agricultural Use

Patyka N.V., Tonkha O.L., Patyka T.I., Kiroyants M.O., Veretyuk S.V.

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

Goal. Comprehensive studies of metagenomic resources and structure of prokaryotic diversity, which is formed in soils of different agricultural use (chernozem). Methods. Molecular-biological – extraction of total DNA, electrophoretic separation of products of 16s rRNA amplification, visual detection of DNA samples, analysis of restriction fragments length polymorphism, field – systems of agriculture. Results. It has been established that under soil protection systems (including without fertilizers), the species richness of prokaryotes of chernozem common in 2 - 3.8 times less than under plowing, which causes a permanent decrease in soil fertility. A diverse and trophically more complicated structure of the phylotypic structure of soil bacterial microbiocenosis has been revealed for a multi-depth fieldless cultivation (layer 0 - 5 cm). Basis of which are seven main clusters of dominant genotypes, which belong to representatives of 98 species, 31 % of which are non-cultivated. For plowing, the qualitative composition of soil microbiocenosis was characterized by seven clusters, with 57 species, 40 % of which were uncultivated. The application of plowing determines the differentiation in quantitative composition - in the upper (0 - 5 cm) layer 1.7 times the species richness of the bacterial complex, then in the lower (5 - 20 cm). The qualitative composition of the dominant prokaryotic genotypes is richer up to 73 % under using of a plow compared with the option of shallow, flat-cut cultivation. Conclusions. Agricultural systems, primarily due to soil cultivation, have a greater impact on the phylotypic diversity of soil microorganisms, and its most complex structure was for multidimensional fieldless cultivation. Plowing led to differentiation by the number of dominant genotypes in various soil lower.

Keywords: prokaryotic complex, tRFLP analysis, black soil, microbial diversity.

Full text (PDF, in Ukrainian)

  1. Patyka MV, Tanchik SP, Kolodjazhny OY, Ivanyk MF, Kryglov YV, Melnichyk MD, Patyka TI. [Formation of biodiversity and phylotypic structure of the eubacterial complex of chernozem typical in the cultivation of winter wheat.] Reports of the National Academy of Sciences of Ukraine. 2015; 11:163-171. Ukrainian.
  2. Moskalevska YP, Patyka MV. [Structural-functional formation of the genome of the prokaryote of the rhizosphere of sugar beet in a typical black soil.] Collection of scientific works of NSC "Institute of Agriculture of NAAS". 2014; 1(2):69-76. Ukrainian.
  3. Gadzalo YM, Patyka MV, Zarishnyak AS. [Agrobiology of the rhizosphere of plants.] In: monography Agricultural sciences. 2015. p. 368. Ukrainian.
  4. Patyka MV, Kolodjazhny OY, Ibatulin II. [Evaluation of the metagenome and detection of functionally significant polymorphisms of the prokaryotes of the soil using the pyrosequencing method]. Mikrobiol Z. 2016; 78(2):43-51. Ukrainian.
  5. The quality of the soil. Methods of determination of organic matter: DSTU 4289: 2004. State Committee of Ukraine. 2005. p. 9. National Standards of Ukraine.
  6. Zvyagincev DG, Babeva IP, Zenova GM. [Biology of the soil.] MSU publishing house; 2005. Russian.
  7. Ronaghi M. Pyrosequencing: a tool for DNA sequencing analysis. In: Methods Mol. Biol. 2004; 255:211–219.
  8. Tringe SG, Rubin EM. Metagenomics DNA sequencing of environmental samples. Nature reviews: Genetics. Nature Publishing Group; 2005; 6:805.
  9. Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus; 1987. p. 13-15.
  10. Felske A, Wolterink A, Van Lis R. Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Applied and Environmental Microbiology. 2000; 66:3998–4003. https://doi.org/10.1128/AEM.66.9.3998-4003.2000
  11. Moreira D. Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Nucleic Acids Research. 1998; 26(13):3309–3310. https://doi.org/10.1093/nar/26.13.3309
  12. Liu W, Marsh T, Cheng H, Forney L. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Environ. Microbiol. 1997; 63:4516–4522.
  13. Lu Guoqing, Moriyama, Etsuko. Vector NTI, a balanced all-in-one sequence analysis suite. Briefings in Bioinformatics. 2004; (4):378–388.