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Effect of long-term application of agrotechnical techniques and crops on soil microbial communities

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Abstract

Effects of long-term application of various fertilizers and crops on soil microbiomes in a long-term field experiment were investigated using the library of the 16S rRNA gene sequences obtained by highthroughput sequencing of the total DNA. The communities exhibited high diversity, with 655 microbial genera belonging to 34 phyla detected (31 bacterial and 3 archaeal ones). For analysis of the effect of the studied factors on community structure, a linear model was developed in order to simplify interpretation of the data of high-throughput sequencing and to obtain biologically important information. Liming was shown to modulate the effect of mineral fertilizers on the structure of microbial populations. The differences in the structure and alpha-diversity of microbial communities were shown to depend more on the crops and liming than on the fertilizers applied. Interaction between the crop factor and liming expressed as an ambiguous effect of liming on the microbiome in the presence of different plants was reliably demonstrated. Thus, in the case of barley and clover, liming resulted in increased taxonomic diversity of the community, while in the case of potato and flax it had an opposite effect.

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References

  • Bates, S.T., Cropsey, G.W.G., Caporaso, J.G., Knight, R., and Fierer, N., Bacterial communities associated with the lichen symbiosis, Appl. Environ. Microbiol., 2011, vol. 77, pp. 1309–1314.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brockett, B.F.T., Prescott, C.E., and Grayston, S.J., Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in western Canada, Soil Biol. Biochem., 2012, vol. 44, pp. 9–20.

    Article  CAS  Google Scholar 

  • Buckley, D.H. and Schmidt T.M., The structure of microbial communities in soil and the lasting impact of cultivation, Microb. Ecol., 2001, vol. 42, pp. 11–21.

    CAS  PubMed  Google Scholar 

  • Caporaso, J.G., Bittinger, K., Bushman, F.D., DeSantis, T.Z., Andersen, G.L., and Knight, R., PyNAST: a flexible tool for aligning sequences to a template alignment, Bioinformatics, 2010, vol. 26, pp. 266–267.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pena, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R., QIIME allows analysis of high-throughput community sequencing data, Nature Methods, 2010, vol. 7, pp. 335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chaparro, J., Sheflin, A., Manter, D., and Vivanco, J., Manipulating the soil microbiome to increase soil health and plant fertility, Biol. Fert. Soils, 2012, vol. 48, pp. 489–499.

    Article  Google Scholar 

  • Dumova, V.A., Pershina, E.V., Merzlyakova, Ya.V., Kruglov, Yu.V., and Andronov, E.E., Main tendencies in formation of a soil microbial community under conditions of a stationary field experiment according to high-throughput sequencing of the 16S rRNA gene libraries, Sel’skokhozyaist. Biol., 2013, no. 5, pp. 85–92.

    Google Scholar 

  • Edgar, R.C., Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 2010, vol. 26, pp. 2460–2461.

    Article  CAS  PubMed  Google Scholar 

  • Faith, D.P., Conservation evaluation and phylogenetic diversity, Biol. Conserv., 1992, vol. 61, pp. 1–10.

    Article  Google Scholar 

  • Fierer, N. and Jackson, R.B., The diversity and biogeography of soil bacterial communities, Proc. Natl. Acad. Sci. U. S. A., 2006, vol. 103, pp. 626–631.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fierer, N., Lauber, C.L., Ramirez, K.S., Zaneveld, J., Bradford, M.A., and Knight, R., Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients, ISME J., 2012, vol. 6, pp. 1007–1017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geisseler, D. and Scow, K.M., Long-term effects of mineral fertilizers on soil microorganisms, Soil Biol. Biochem., 2014, vol. 75, pp. 54–63.

    Article  CAS  Google Scholar 

  • Hartmann, M., Frey, B., Mayer, J., Mäder, P., and Widmer, F., Distinct soil microbial diversity under long-term organic and conventional farming, ISME J., 2015, vol. 9, pp. 1177–1194.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hollister, E.B., Engledow, A.S., Hammett, A.J.M., Provin, T.L., Wilkinson, H.H., and Gentry, T.L., Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments, ISME J., 2010, vol. 4, pp. 829–838.

    Article  CAS  PubMed  Google Scholar 

  • Huber, T., Dalevi, D., Hu, P., and Andersen, G.L., Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Appl. Environ. Microbiol., 2006, vol. 72, pp. 5069–5072.

    Article  PubMed  PubMed Central  Google Scholar 

  • Janssen, P.H., Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes, Appl. Environ. Microbiol., 2006, vol. 72, pp. 1719–1728.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kowalchuk, G.A., Buma, D.S., de Boer, W., Klinkhamer, P.G.L., and van Veen, J.A., Effect of a aboveground plant species composition and diversity on the diversity of soil-borne microorganisms, Antonie van Leeuwenhoek, 2002, vol. 81, pp. 509–520.

    Article  PubMed  Google Scholar 

  • Lau, J.A. and Lennon, J.T., Rapid responses of soil microorganisms improve plant fitness in novel environments, Proc. Natl. Acad. Sci. U. S. A., 2012, vol. 109, pp. 14058–14062.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lauber, C.L., Hamady, M., Knight, R., and Fierer, N., Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale, Appl. Environ. Microbiol., 2009, vol. 75, pp. 5111–5120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McMurdie, P.J. and Holmes, S., phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 2013, vol. 8, no. 4, pp. 61217.

    Article  Google Scholar 

  • Omar, S.A. and Ismail, M., Microbial populations, ammonification and nitrification in soil treated with urea and inorganic salts, Folia Microbiol., 1999, vol. 44, pp. 205–212.

    Article  CAS  Google Scholar 

  • Pershina, E.V., Tamazyan, G.S., Dol’nik, A.S., Pinaev, A.G., Sergaliev, N.H., and Andronov, E.E., Investigation of the structure of a microbial community of saline soils by high-throughput sequencing, Ekol. Genet., 2012, vol. 10, no. 2, pp. 31–38.

    Google Scholar 

  • Ramirez, K.S., Lauber, C.L., Knight, R., Bradford, M.A., and Fierer, N., Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems, Ecology, 2010, vol. 91, no. 12, pp. 3463–3470.

    Article  PubMed  Google Scholar 

  • Shade, A., Caporaso, J.G., Handelsman, J., Knight, R., and Fierer, N., A meta-analysis of changes in bacterial and archaeal communities with time, ISME J., 2013, vol. 7, pp. 1493–1506.

    Article  PubMed  PubMed Central  Google Scholar 

  • van Bruggen, A.H.C. and Semenov, A.M., In search of biological indicators for soil health and disease suppression, Appl. Soil. Ecol., 2000, vol. 15, pp. 13–24.

    Article  Google Scholar 

  • Wessén, E., Hallin, S., and Philippot, L., Differential responses of bacterial and archaeal groups at high taxonomical ranks to soil management, Soil Biol. Biochem., 2010, vol. 42, pp. 1759–1765.

    Article  Google Scholar 

  • Zul, D., Denzel, S., Kotz, A., and Overmann, J., Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity, Appl. Environ. Microbiol., 2007, vol. 73, no. 21, pp. 6916–6929.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to I. O. Korvigo.

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Original Russian Text © I.O. Korvigo, E.V. Pershina, E.A. Ivanova, N.S. Matyuk, O.A. Savos’kina, E.L. Chirak, N.A. Provorov, E.E. Andronov, 2016, published in Mikrobiologiya, 2016, Vol. 85, No. 2, pp. 199–210.

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Korvigo, I.O., Pershina, E.V., Ivanova, E.A. et al. Effect of long-term application of agrotechnical techniques and crops on soil microbial communities. Microbiology 85, 231–242 (2016). https://doi.org/10.1134/S0026261716020107

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