The estimation of metagenome and functionally polymorphisms of soil procaryote

Abstract

N.V. Patyka, V.M. Polozhenets, M.M. Dolya, R.M. Mamchur, N. V. Tsuman, T.M. Tymoshchuk, L.L. Dovbysh, I.A. Zhuravska, L.V. Nemerytska, T.O. Galagan, S.V. Stankevych, I.V. Zabrodina, L.V. Golovan, I.V. Klymenko

The paper estimates the metagenome as well as the functionally meaningful phylogenetic and taxonomic polymorphisms of orthic blacksoil procaryote in winter wheat agrocoenosis by using the pyrosequencing method. As many as 1708 taxonomic units and 335 procaryote taxons have been detected. The research has determined that the structure of metagenom of orthic black soil procaryote contained two archael and twenty two bacterial phyla, absolute dominants among which belonged to Proteobacteria –79,6 % and Actinobacteria – 12,9 %. The polymorphism of procaryotic taxons was observed on the level of families, herewith the dominating ones were: Alcaligenaceae, Pseudomonadaceae, Solirubrobacteraceae, Gaiellaceae, Nitrososphaeraceae. The paper shows some phylogenetic connections among the main representatives of procaryote metagenome which were formed in orthic black soil of winter wheat agrocoenosis. Thus, the use of pyrosequencing method, beside the estimation of structure and diversity, opens a prospect for studying the functional metagenome component of soil procaryote.

Keywords: Metagenome; Polymorphism; Procaryotic taxons; Soil; Agrocoenosis
 

References

Beljaev, V.I., Vol'nov, V.V., L. V. Sokolova, L.V., …Matsyura, A.V. (2017). Effect of sowing techniques on the agroecological parameters of cereal crops. Ukrainian Journal of Ecology, 7(2), 130-136, doi: 10.15421/2017_30Cole J. R., Wang Q., Cardenas E. & Fish J. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res., 37, 141–145.

Gadzalo Ya.M., Patyka N.V. & Zaryshniak A.S. (2015). Agrobiology of Plants Rhizosphere: monograph, Kyiv, Agrarian Science, 386.

Ganley A. & Kobayash T. (2007). Total rDNA repeat variation revealed by whole genome shotgun sequence data. Genome Research.17, 184–191.

Kolodiazhnyi O.Y., Andronov Ye.Ye. & Patyka M.V. (2014). Molecular and Biological Estimation of Procaryotic Complex of Orthic Blacksoil when Growing Winter Wheat. Collection of Scientific Articles of NSC “Institute for Farmig by NAAS”, 1–2, 61-67.

Kuczynski J., Stombaugh J., Walters W. A. & González A. (2012). Using QIIME to analyze 16S rRNA gene sequences from Microbial Communities. Curr. Protoc. In Bioinformatics. DOI: 10.1002/0471250953.bi1007s36.

Kunin V., Copeland A. & Lapidus A. (2008). A bioinformatician’s guide to metagenomics. Microbiology and molecular biology reviews. 72, 4, 557–578.

Patyka, M.V., Patyka, T.I. & Grygoriuk, I.P. (2012). Molecular and Genetic Polymorphism Analysis of Metagenomic Nucleotide Sequences of Entomopathogenic Bacteria Bacillus thuringiensis as well as of Soil Procaryotic Complex. Ad. NAS of Ukraine, 1, 164–170.

Patyka, N.V., Borodai, V.V. & Zhytkevych, N.V., et al. (2012). The Effect of Biopreparations on the Dynamic of Bacterial and Phytopathogenic Fungi Count in Potato Agroecosystem. Microbiol. Journal, 74, 2, 28–35.

Patyka, N.V., Kruglov, Y.V. & Patyka, V.F. (2009). Specifications of Phylogenetic Profiles of Procariotic Microorganisms of Podzol Soils. Physiology and Biochemistry of Cultivated Plants, 41, 3, 248–254.

Patyka, N.V., Kruglov, Y.V., Berdnikov, A.M. & Patyka V.F. (2008). The Role of Linumusitatissimuml in the formation of Microbial Communities of Podzol Soils. Microbiol. Journal, 1, 59–70.

Patyka, T.I., Patyka, N.V. & Patyka, V.F. (2009). Phylogenetic Interconnections of Serologic Variants of Bacillus thuringiensis. Biopolymersand Cell, 3, 240–244.

Ronaghi M. (2004). Pyrosequencing: a tool for DNA sequencing analysis. Methods Mol. Biol. 255, 211–219.

Tanchyk, S.P., Demydov, O.A. & Manko Y.P. (2011). Methodological Recommendations for Introducing into the Production: Ecological Farming System in Forest Steppe of Ukraine. Kyiv: NULES of Ukraine, 39.

Taran N., Gonchar O. & Lopatko K. (2014). The effect of colloidal solution of molybdenum nanoparticles on the microbial composition in rhizosphere of Cicerarietinum L. Nanoscale Res. Lett. 9 (1), 289. DOI: 10.1186/1556-276X-9-289.

Tringe S. & Rubin E. (2005). Metagenomics: DNA sequencing of environmental samples. Nature reviews: Genetics. Nature Publishing Group. 6, 805–814.

Wooley J. (2010). Metagenomics: Facts and artifacts, and computational challenges. Journal of computer science and technology. 1, 25, 71–81.

Yarovyi, S.O., Arabadzhi, L.I., Solonenko, A.M., Bren, O.G., Maltsev, E.I., Matsyura, A. V. (2017). Diversity of Cyanoprokaryota in sandy habitats in Pryazov National Natural Park (Ukraine). Ukrainian Journal of Ecology, 7(2), 91-95. Doi: 10.15421/2017_24

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