Abstract
The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
E. E. Andronov, S. N. Petrova, A. G. Pinaev, E. V. Pershina, S. Z. Rakhimgalieva, K. M. Akhmedenov, A. V. Gorobets, and N. K. Sergaliev, “Analysis of the structure of microbial community in soils with different degrees of salinization using T-RFLP and realtime PCR techniques,” Eurasian Soil Sci. 45 (2), 147–156 (2012).
V. A. Dumova, E. V. Pershina, Ya. V. Merzlyakova, Yu. V. Kruglov, and E. E. Andronov, “General trends in dynamics of soil microbial communities during a longterm field experiment according to the results of highperformance sequencing of 16S-rRNA gene libraries,” S-kh. Biol., No. 5, 85–92 (2013).
E. V. Pershina, E. E. Andronov, A. G. Pinaev, G. A. Akhmetova, V. A. Dumova, and N. A. Provorov, “T-RFLP analysis of dynamics of soil microbial communities affected by xenobiotics,” S-kh. Biol., No. 3, 81–87 (2011).
S. N. Petrova, E. E. Andronov, A. G. Pinaev, and E. V. Pershina, “Prospects of using molecular-genetic analysis in soil ecology,” Vestn. Orlovsk. Gos. Agrar. Univ. 26 (5), 45–48 (2010).
E. V. Pershina, G. S. Tamazyan, A. S. Dol’nik, A. G. Pinaev, N. Kh. Sergaliev, and E. E. Andronov, “T-RFLP analysis of the structure of microbial community of salt-affected soils,” Ekol. Genet. 10 (2), 32–40 (2012).
E. L. Chirak, E. V. Pershina, A. S. Dol’nik, O. V. Kutovaya, E. S. Vasilenko, B. M. Kogut, Ya. V. Merzlyakova, and E. E. Andronov, “Taxonomic structure of microbial communities in different soils according to the results of high-performance sequencing of 16S-rRNA gene libraries,” S-kh. Biol., No. 3, 100–109 (2013).
S. T. Bates, D. Berg-Lyons, J. G. Caporaso, W. A. Walters, R. Knight, and N. Fierer, “Examining the global distribution of dominant archaeal populations in soil,” ISME J., No. 4, 908–917 (2011).
E. Blochl, R. Rachel, S. Burggraf, D. Hafenbradl, H. W. Jannasch, and K. O. Stetter, “Pyrolobus fumarii gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113°C,” Extremophiles 1 (1), 14–21 (1997).
Brock Biology of Microorganisms, Ed. by M. Madigan and J. Martinko (Prentice Hall, Upper Side River, NJ, 2005).
J. G. Caporaso, J. Kuczynski, J. Stombaugh, et al., “QIIME allows analysis of high-throughput community sequencing data,” Nat. Methods 5 (7), 335–336 (2010).
R. Daniel, “The metagenomics of soil,” Nat. Rev. Microbiol. 3, 470–478 (2005).
J. M. DeBruyn, L. T. Nixon, M. N. Fawaz, A. M. Johnson, and M. Radosevich, “Global biogeography and quantitative seasonal dynamics of gemmatimonadetes in soil,” Appl. Environ. Microbiol. 17 (77), 6295–6300 (2011).
T. Z. DeSantis, P. Hugenholtz, N. Larsen, et al., “Green genes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB,” Appl. Environ. Microbiol. 72 (7), 5069–5072 (2006).
N. Fierer and R. B. Jackson, “The diversity and biogeography of soil bacterial communities,” Proc. Natl. Acad. Sci. U.S.A. 103, 626–631 (2006).
N. Fierer, J. W. Leff, B. J. Adams, U. N. Nielsen, S. T. Bates, C. L. Lauber, S. Owens, J. A. Gilbert, D. H. Wall, and J. G. Caporaso, “Cross-biome metagenomic analyses of soil microbial communities and their functional attributes,” Proc. Natl. Acad. Sci. U.S.A. 52 (109), 21390–21395 (2012).
J. Handelsman, “Metagenomics: application of genomics to uncultured microorganisms,” Microbiol. Mol. Biol. Rev. 68, 669–685 (2004).
A. Hartmann, P. Lemanceau, and J. I. Prosser, “Multitrophic interactions in the rhizosphere—rhizosphere microbiology: at the interface of many disciplines and expertises,” FEMS Microbiol. Ecol. 65, 179 (2008).
M. Hartmann, B. Frey, J. Mayer, P. Mäder, and F. Widmer, “Distinct soil microbial diversity under long-term organic and conventional farming,” ISME J., (2014). doi doi 10.1038/ismej.2014.210
C. L. Lauber, M. S. Strickland, M. A. Bradford, and N. Fierer, “The influence of soil properties on the structure of bacterial and fungal communities across land-use types,” Soil Biol. Biochem. 40 (9), 2407–2415 (2008).
R. Li, E. Khafipour, D. O. Krause, M. H. Entz, T. R. Kievit, and W. G. D. Fernando, “Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities,” PLoS One, (2012). doi 10.1371/journal.pone.0051897
C. A. Lozupone and R. Knight, “Global patterns in bacterial diversity,” Proc. Natl. Acad. Sci. U.S.A. 104 (27), 11436–11440 (2007).
M. Lupatini, A. K. A. Suleiman, R. J. S. Jacques, Z. I. Antoniolli, A. de Siqueira Ferreira, E. E. Kuramae, and L. F. W. Roesch, “Network topology reveals high connection levels and few key microbial genera within soils,” Front. Environ. Sci. 2 10 (2014). doi 10.3389/fenvs.2014.0001010.3389/fenvs.2014.00010
E. Martin, K. Klug, A. Frischmann, H. J. Busse, P. Kämpfer, and U. Jäckel, “Jeotgalicoccus coquinae sp. nov. and Jeotgalicoccus aerolatus sp. nov., isolated from poultry houses,” Int. J. Syst. Evol. Microbiol. 61, 237–241 (2011).
H. Nacke, A. Thurmer, A. Wollherr, C. Will, R. Daniel, et al., “Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils,” PLoS One 6, 1–12 (2011).
E. Pershina, E. Andronov, A. Pinaev, and N. Provorov, “Recent advances and perspectives in metagenomic studies of soil microbial communities,” in Management of the Microbial Resources in the Environment, Ed. by A. Malik, E. Grohmann, and M. Alves (Springer-Verlag, Berlin, 2013), pp. 141–166.
L. Ranjard, S. Dequiedt, M. Lelievre, P. A. Maron, C. Mougel, F. Morin, and P. Lemanceau, “Platform GenoSol: a new tool for conserving and exploring soil microbial diversity,” Environ. Microbiol. Rep. 1, 97–99 (2009).
L. F. W. Roesch, R. R. Fulthorpe, A. Riva, G. Casella, A. K. M. Hadwin, A. D. Ken, et al., “Pyrosequencing enumerates and contrasts soil microbial diversity,” ISME J. 1, 283–290 (2007).
M. R. Rondon, P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, M. R. Liles, K. A. Loiacono, B. A. Lynch, I. A. MacNeil, C. Minor, C. L. Tiong, M. Gilman, M. S. Osburne, J. Clardy, et al., “Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms,” Appl. Environ. Microbiol. 66, 2541–2547 (2000).
R. S. Shange, O. Ankumah, A. M. Ibekwe, R. Zabawa, and S. E. Dowd, “Distinct soil bacterial communities revealed under a diversely managed agroecosystem,” PLoS One 7 (7), e40338 (2012). doi 10.1371/journal. pone.0040338
M. A. Tanner, C. L. Everett, W. J. Coleman, M. M. Yang, and D. C. Youvan, “Complex microbial communities inhabiting sulfide-rich black mud from marine coastal environments,” Biotechnol. Alia 8, 1–16 (2000).
R. Upchurch, C.-Y. Chiu, K. Everetta, G. Dyszynskia, D. C. Colemanc, and W. B. Whitmana, “Differences in the composition and diversity of bacterial communities from agricultural and forest soils,” Soil Biol. Biochem. 40 (6), 1294–1305 (2008).
T. M. Vogel, P. Simonet, J. K. Jansson, P. R. Hirsh, J. M. Tiedje, J. D. van Elsas, M. J. Bailey, R. Nalin, and L. Philippot, “TerraGenome: a consortium for the sequencing of a soil metagenome,” Nat. Rev. Microbiol. 7, 252 (2009).
J. H. Yoon, K. C. Lee, N. Weiss, K. H. Kang, and Y. H. Park, “Jeotgalicoccus halotoleransgen nov., sp. nov. and Jeotgalicoccus psychrophilus sp. nov., isolated from the traditional Korean fermented seafood jeotgal,” Int. J. Syst. Evol. Microbiol. 53, 595–602 (2003).
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © E.V. Pershina, E.A. Ivanova, A.G. Nagieva, A.T. Zhiengaliev, E.L. Chirak, E.E. Andronov, N.Kh. Sergaliev, 2016, published in Pochvovedenie, 2016, No. 6, pp. 720–732.
Rights and permissions
About this article
Cite this article
Pershina, E.V., Ivanova, E.A., Nagieva, A.G. et al. A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan. Eurasian Soil Sc. 49, 673–684 (2016). https://doi.org/10.1134/S1064229316060090
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1064229316060090