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The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use

  • Soil Biology
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Abstract

The taxonomic structure of microbiomes in aggregates of different sizes from typical chernozems was investigated using sequencing of the 16S rRNA gene. The aggregate fractions of <0.25, 2–5, and >7 mm obtained by sieving of the soil samples at natural moisture were used for analysis. The highest prokaryote biomass (bacteria, archaea) was determined in the fractions <0.25 and aggregates 2–5 mm; the bacterial and archaeal biomass decreased in the following series: fallow > permanent black fallow > permanent winter wheat. The greatest number of fungi was recorded in the fraction <0.25 mm from the soils of the permanent black fallow and in all the studied aggregate fractions in the variant with permanent wheat. The system of agricultural use affected more significantly the structure of the prokaryote community in the chernozem than the size of aggregate fractions did. The most diverse microbial community was recorded in the soil samples of the fallow; the statistically significant maximums of the Shannon diversity indices and indices of phylogenetic diversity (PD) were recorded in the fractions <0.25 and 2–5 mm from the fallow soil. On the whole, the fine soil fractions (<0.25 mm) were characterized by higher diversity indices in comparison with those of the coarser aggregate fractions.

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References

  1. E. E. Andronov, A. G. Pinaev, E. V. Pershina, and E. P. Chizhevskaya, Methodological Recommendations for Isolation of Highly Purified DNA Preparations from Environmental Objects, Ed. by A. A. Belimov (St. Petersburg, 2011) [in Russian].

  2. E. S. Vasilenko, O. V. Kutovaya, A. K. Tkhakakhova, and A. S. Martynov, “Changes in the number of microorganisms depending on the size of aggregates of humus horizons of migrational-mycelial chernozem,” Byull. Pochv. Inst. im. V. V. Dokuchaeva 73, 150–173 (2014).

    Google Scholar 

  3. P. V. Vershinin, Soil Structure and Conditions for Its Formation (Moskovskii Rabochii, Moscow, 1981) [in Russian].

    Google Scholar 

  4. D. G. Zvyagintsev, I. P. Bab’eva, and G. M. Zenova, Biology of Soils (Moscow State University, Moscow, 2005) [in Russian].

    Google Scholar 

  5. B. M. Kogut, S. A. Sysuev, and V. A. Kholodov, “Water stability and labile humic substances of typical chernozems under different land uses,” Eurasian Soil Sci. 45 (5), 496–502 (2012).

    Article  Google Scholar 

  6. A. A. Romanycheva, O. M. Seliverstova, N. V. Verkhovtseva, and E. Yu. Milanovskii, “Comparative analysis of the structure of microbial communities and quantity of waterproof aggregates of leached chernozem,” Probl. Agrokhim. Ekol., No. 3, 30–34 (2013).

    Google Scholar 

  7. V. A. Kholodov, “The capacity of soil particles for spontaneous formation of macroaggregates after a wettingdrying cycle,” Eurasian Soil Sci. 46 (6), 660–667 (2013).

    Article  Google Scholar 

  8. G. Ya. Chesnyak and O. A. Chesnyak, “Influence of agricultural plants on acidity of soil solution of power chernozem of the Left-bank forest steppe UkrSSR,” Tr. Kharkov. S-kh. Inst. 181, 36–42 (1972).

    Google Scholar 

  9. E. V. Shein and E. Yu. Milanovskii, “The role of organic matter in the formation and stability of soil aggregates,” Eurasian Soil Sci. 36 (1), 51–58 (2003).

    Google Scholar 

  10. S. T. Bates, J. G. Berg-Lyons, W. A. Caporaso, et al., “Examining the global distribution of dominant archaeal populations in soil,” ISME J., No. 5, 908–917 (2010).

    Article  Google Scholar 

  11. Bergey’s Manual of Systematic Bacteriology, Vol. 5: The Actinobacteria, Ed. by M. Goodfellow, P. Kämpfer, H.-J. Busse, M. E. Trujillo, K.-I. Suzuki, W. Ludwig, and W. B. Whitman (Springer-Verlag, New York, 2012), pp. 1–2.

  12. 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).

    Article  Google Scholar 

  13. J. K. Carson, V. Gonzalez-Quiñones, D. V. Murphy, C. Hinz, J. A. Shaw, and D. B. Gleeson, “Low pore connectivity increases bacterial diversity in soil,” Appl. Environ. Microb., No. 76, 3936–3942 (2010).

    Article  Google Scholar 

  14. M. Davinic, L. M. Fultz, V. Acosta-Martinez, F. J. Calderón, S. B. Cox, S. E. Dowd, V. G. Allen, J. C. Zak, and J. Moore-Kucera, “Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition,” Soil Biol. Biochem., No. 46, 63–72 (2012).

    Article  Google Scholar 

  15. 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. 77 (17), 6295–6300 (2011).

    Article  Google Scholar 

  16. G.-C. Ding, Y. M. Piceno, H. Heuer, N. Weinert, A. Dohrmann, et al., “Changes of soil bacterial diversity as a consequence of agricultural land use in a semiarid ecosystem,” PLoS One. 8 (3), 1–14 (2013).

    Google Scholar 

  17. E. T. Elliott, “Aggregate structure and carbon, nitrogen, and phosphorus in native and cultivated soils,” Soil Sci. Soc. Am. J. 50, 627–633 (1986).

    Article  Google Scholar 

  18. N. Fierer, M. A. Bradford, and R. B. Jackson, “Toward an ecological classification of soil bacteria,” Ecology 6 (88), 1354–1364 (2007).

    Article  Google Scholar 

  19. N. Fierer and R. B. Jackson, “The diversity and biogeography of soil bacterial communities,” Proc. Natl. Acad. Sci. U.S.A. 103 (3), 626–631 (2006).

    Article  Google Scholar 

  20. A. Ganley and T. Kobayashi, “Total rDNA repeat variation revealed by whole-genome shotgun sequence data,” Genome Res., No. 17, 184–191 (2007).

    Article  Google Scholar 

  21. R. C. Garber, B. G. Turgeon, E. U. Selker, and O. C. Yoder, “Organization of ribosomal RNA genes in the fungus Cochliobolus heterostrophus,” Curr. Genet. 14 (6), 573–582 (1988).

    Article  Google Scholar 

  22. J. D. Jastrow, “Soil aggregate formation and the accrual of particulate and mineral-associated organic matter,” Soil Biol. Biochem. 28 (4-5), 665–676 (1996).

    Article  Google Scholar 

  23. G. Jurgens and A. Saano, “Diversity of soil archaea in boreal forest before and after clear-cutting and prescribed burning,” FEMS Microbiol. Ecol. 29. pp. 205–213 (1999).

    Google Scholar 

  24. D. J. Lane, “16S/23S rRNA sequencing,” in Nucleic Acid Techniques in Bacterial Systematics, Ed. by E. Stackebrandt and M. Goodfellow (Wiley, New York, NY, 1991), pp. 115–175.

    Google Scholar 

  25. S.-H. Lee, J.-O. Ka, and J.-C. Cho, “Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil,” FEMS Microbiol Lett. 285, 263–269 (2008.

  26. S. E. Moskalenko, S. V. Chabelskaya, S. G. Inge-Vechtomov, M. Philippe, and G. A. Zhouravleva, “Viable nonsense mutants for the essential gene SUP45 of Saccharomyces cerevisiae,” BMC Mol. Biol. 4 (2), 1–14 (2003).

    Google Scholar 

  27. D. Mummey, W. Holben, J. Six, and P. Stahl, “Spatial stratification of soil bacterial populations in aggregates of diverse soils,” Microb. Ecol., No. 51, 404–11 (2006).

    Article  Google Scholar 

  28. D. L. Mummey and P. D. Stahl, “Analysis of soil wholeand inner-microaggregate bacterial communities,” Microb. Ecol., No. 48, 41–50 (2004).

    Article  Google Scholar 

  29. P. Puget, C. Chenu, and J. Balesdent, “Total and young organic matter distributions in aggregates of silty cultivated soils,” Eur. J. Soil Sci. 46, 449–459 (1995).

    Article  Google Scholar 

  30. A. Sessitsch, A. Weilharter, M. H. Gerzabek, H. Kirchmann, and E. Kandeler, “Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment,” Appl. Environ. Microbiol. 67, 4215–4224 (2001).

    Article  Google Scholar 

  31. J. Six, H. Bossuyt, S. Degryze, and K. Denef, “A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics,” Soil Tillage Res. 79, 7–31 (2004).

    Article  Google Scholar 

  32. J. Six, K. Paustian, E. T. Elliott, and C. Combrink, “Soil structure and soil organic matter: I. Distribution of aggregate size classes and aggregate associated carbon,” Soil Sci. Soc. Am. J. 64, 681–689 (2000).

    Article  Google Scholar 

  33. A. K. Suleiman, L. Manoeli, J. T. Boldo, M. G. Pereira, and L. F. Roesch, “Shifts in soil bacterial community after eight years of land-use change,” Syst. Appl. Microbiol. 36 (2), 137–144 (2013).

    Article  Google Scholar 

  34. M. Takeuchi and K. Hatano, “Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov., and Agromyces brachium sp. nov., from the mangrove rhizosphere,” J. Int. J. Syst. Evol. Microbiol. 51, 1529–1537 (2001).

    Article  Google Scholar 

  35. J. A. van Veen and P. J. Kuikman, “Soil structural aspects of decomposition of organic matter by microorganisms,” Biogeochemistry 11 (3), 213–233 (1990).

    Article  Google Scholar 

  36. Y. Yu, Ch. Lee, J. Kim, and S. Hwang, “Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction,” Biotechnol. Bioeng. 89 (6), 670–679 (2005).

    Article  Google Scholar 

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Authors and Affiliations

  1. All-Russia Research Institute of Agricultural Microbiology, ul. Podbel’skogo, 3, Pushkin-8, St. Petersburg, 196608, Russia

    E. A. Ivanova, E. V. Pershina & E. E. Andronov

  2. Dokuchaev Soil Science Institute, Pyzhevskii per., 7, Moscow, 119017, Russia

    O. V. Kutovaya, A. K. Tkhakakhova, T. I. Chernov, L. G. Markina & B. M. Kogut

Authors
  1. E. A. Ivanova
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  2. O. V. Kutovaya
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  3. A. K. Tkhakakhova
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  4. T. I. Chernov
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  5. E. V. Pershina
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  6. L. G. Markina
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  7. E. E. Andronov
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  8. B. M. Kogut
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Correspondence to E. A. Ivanova.

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Original Russian Text © E.A. Ivanova, O.V. Kutovaya, A.K. Tkhakakhova, T.I. Chernov, E.V. Pershina, L.G. Markina, E.E. Andronov, B.M. Kogut, 2015, published in Pochvovedenie, 2015, No. 11, pp. 1367–1382.

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Ivanova, E.A., Kutovaya, O.V., Tkhakakhova, A.K. et al. The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use. Eurasian Soil Sc. 48, 1242–1256 (2015). https://doi.org/10.1134/S1064229315110083

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