Skip to main content
Log in

Microbiological Parameters of Soddy-Podzolic Soil and Its Rhizosphere in a Half-Century Field Experiment with Different Fertilizer Systems

  • SOIL BIOLOGY
  • Published:
Eurasian Soil Science Aims and scope Submit manuscript

Abstract

Regular application of mineral and organic fertilizers is one of the essential components of agricultural intensification. The application of fertilizers leads to the artificial enrichment of the soil with readily available substrates and biophilic elements, which can have a significant impact on the soil and rhizosphere microbiome. We studied the impact of different fertilizer systems on the quantitative parameters of various microbial groups in a soddy-podzolic soil (Umbric Albic Retisol) and the rhizosphere of potatoes and barley. The study was carried out on a long-term field experiment, in which mineral (NPK), organic (manure), and mixed (NPK + manure) fertilizer systems had been applied since 1968. The application of organic fertilizers increased the microbial biomass carbon (Cmic) in the bulk soil and the rhizosphere by 25–100% compared to the soil without fertilizers, while the use of mineral fertilizers, on the contrary, decreased the microbial biomass by 10–30%. Basal respiration and metabolic quotient (qСО2) increased in the following order: without fertilizers < NPK < NPK + manure < manure. The gene copy numbers of bacteria, archaea, and fungi significantly increased (by 1.5–2.5 times) under organic fertilizers and decreased (2–2.5 times) under NPK. The fungi/bacteria ratios varied from 32 to 100 and from 0.10 to 0.92 according to luminescent microscopy and quantitative PCR methods, respectively. The lowest ratios were revealed for variants with NPK, and the highest fungi/bacteria ratios were in variants with manure. Thus, the applied doses of mineral fertilizers should be compensated by the addition of fresh organic matter in order to maintain the stability of the soil—microorganisms—plant system.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.

Similar content being viewed by others

REFERENCES

  1. N. D. Ananyeva, E. A. Susyan, and E. G. Gavrilenko, “Determination of the soil microbial biomass carbon using the method of substrate-induced respiration,” Eurasian Soil Sci. 44 (11), 1215–1221 (2011).

    Article  Google Scholar 

  2. N. D. Ananyeva, L. M. Polyanskaya, E. V. Stolnikova, and D. G. Zvyagintzev, “Fungal to bacterial biomass ratio in the forests soil profile,” Biol. Bull. (Moscow) 37 (3), 254–262 (2010).

    Article  Google Scholar 

  3. E. V. Blagodatskaya, M. V. Semenov, and A. V. Yakushev, Activity and Biomass of Soil Microorganisms under Changing Environmental Conditions (Tov. Nauchn. Izd. KMK, Moscow, 2016) [in Russian].

    Google Scholar 

  4. I. V. Yevdokimov, “Dynamics of the rhizosphere effect in soils,” Eurasian Soil Sci. 46 (6), 676–684 (2013). https://doi.org/10.1134/S1064229313060021

    Article  Google Scholar 

  5. B. M. Kogut, M. A. Yashin, V. M. Semenov, T. N. Avdeeva, L. G. Markina, S. M. Lukin, and S. I. Tarasov, “Distribution of transformed organic matter in structural units of loamy sandy soddy-podzolic soil,” Eurasian Soil Sci. 49 (1), 45–55 (2016). https://doi.org/10.1134/S1064229316010075

    Article  Google Scholar 

  6. V. N. Kudeyarov and V. M. Semenov, “Problems of agrochemistry and the current state of chemicalization of agricultural production in the Russian Federation,” Agrokhimiya, No. 10, 3–17 (2014).

    Google Scholar 

  7. S. M. Lukin, E. I. Zolkina, and E. V. Marchuk, “The influence of long-term use of fertilizers on the productivity of crop rotation, the content and qualitative composition of soil organic matter,” Plodorodie 3 (120), 93–98 (2021). https://doi.org/10.25680/S19948603.2021.120.18

    Article  Google Scholar 

  8. L. M. Polyanskaya, S. M. Lukin, and D. G. Zvyagintsev, “The change in composition of microbial biomass in cultivated soils,” Eurasian Soil Sci. 30 (2), 172–177 (1997).

    Google Scholar 

  9. V. M. Semenov, T. N. Lebedeva, N. B. Zinyakova, D. A. Sokolov, and M. V. Semenov, “Eutrophication of arable soil: a comparative effect of mineral and organic fertilizer systems,” Eurasian Soil Sci. 56 (1), 49–62 (2023).

    Article  Google Scholar 

  10. M. V. Semenov, D. A. Nikitin, A. L. Stepanov, and V. M. Semenov, “The structure of bacterial and fungal communities in the rhizosphere and root-free loci of gray forest soil,” Eurasian Soil Sci. 52 (3), 319–332 (2019). https://doi.org/10.1134/S1064229319010137

    Article  Google Scholar 

  11. M. V. Semenov, “Metabarcoding and metagenomics in soil ecology research: achievements, challenges, and prospects,” Biol. Bull. Rev. 11 (1), 40–53 (2021). https://doi.org/10.1134/S2079086421010084

    Article  Google Scholar 

  12. C. Ai, G. Liang, J. Sun, X. Wang, P. He, W. Zhou, and X. He, “Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils,” Soil Biol. Biochem. 80, 70–78 (2015). https://doi.org/10.1016/j.soilbio.2014.09.028

    Article  Google Scholar 

  13. M. N. Ashraf, C. Hu, L. Wu, Y. Duan, W. Zhang, T. Aziz, A. Cai, M. M. Abrar, and M. Xu, “Soil and microbial biomass stoichiometry regulate soil organic carbon and nitrogen mineralization in rice-wheat rotation subjected to long-term fertilization,” J. Soils Sediments 20, 3103–3113 (2020). https://doi.org/10.1007/s11368-020-02642-y

    Article  Google Scholar 

  14. V. L. Bailey, J. L. Smith, and H. Bolton Jr., “Fungal-to-bacterial ratios in soils investigated for enhanced C sequestration,” Soil Biol. Biochem. 34, 997–1007 (2002). https://doi.org/10.1016/S0038-0717(02)00033-0

    Article  Google Scholar 

  15. D. P. Bebber and V. R. Richards, “A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity,” Appl. Soil Ecol. 175, 104450 (2022). https://doi.org/10.1016/j.apsoil.2022.104450

    Article  Google Scholar 

  16. R. L. Berendsen, C. M. Pieterse, and P. A. Bakker, “The rhizosphere microbiome and plant health,” Trends Plant Sci. 17, 478–486 (2012). https://doi.org/10.1016/j.tplants.2012.04.001

    Article  Google Scholar 

  17. B. S. Brar, J. Singh, G. Singh, and G. Kaur, “Effects of long-term application of inorganic and organic fertilizers on soil organic carbon and physical properties in maize–wheat rotation,” Agronomy 5, 220–238 (2015). https://doi.org/10.3390/agronomy5020220

    Article  Google Scholar 

  18. L. G. Carvalheiro, J. C. Biesmeijer, M. Franzén, J. Aguirre-Gutiérrez, L. A. Garibaldi, A. Helm, D. Michez, J. Pöyry, M. Reemer, O. Schweiger, L. van den Berg, M. Wallisdevries, and W. E. Kunin, “Soil eutrophication shaped the composition of pollinator assemblages during the past century,” Ecography 43, 209–221 (2020). https://doi.org/10.1111/ecog.04656

    Article  Google Scholar 

  19. C. Chenu, D. A. Angers, P. Barré, D. Derrien, D. Arrouays, and J. Balesdent, “Increasing organic stocks in agricultural soils: knowledge gaps and potential innovations,” Soil Tillage Res. 188, 41–52 (2019). https://doi.org/10.1016/j.still.2018.04.011

    Article  Google Scholar 

  20. P. Dang, C. Li, C. Lu, M. Zhang, T. Huang, C. Wan, H. Wang, Y. Chen, X. Qin, Y. Liao, and K. H. M. Siddique, “Effect of fertilizer management on the soil bacterial community in agroecosystems across the globe,” Agric., Ecosyst. Environ. 326, 107795 (2022). https://doi.org/10.1016/j.agee.2021.107795

    Article  Google Scholar 

  21. M. Diacono and F. Montemurro, “Long-term effects of organic amendments on soil fertility. a review,” Agron. Sustainable Dev. 30, 401–422 (2010). https://doi.org/10.1007/978-94-007-0394-0_34

    Article  Google Scholar 

  22. L. C. Dincă, P. Grenni, C. Onet, and A. Onet, “Fertilization and soil microbial community: a review,” Appl. Sci. 12, 1198 (2022). https://doi.org/10.3390/app12031198

    Article  Google Scholar 

  23. J. Ding, X. Jiang, D. Guan, B. Zhao, M. Ma, B. Zhou, F. Cao, X. Yang, L. Li, and J. Li, “Influence of inorganic fertilizer and organic manure application on fungal communities in a long-term field experiment of Chinese Mollisols,” Appl. Soil Ecol. 111, 114–122 (2017). https://doi.org/10.1016/j.apsoil.2016.12.003

    Article  Google Scholar 

  24. W. Y. Dong, X. Y. Zhang, X. Q. Dai, X. L. Fu, F. T. Yang, X. Y. Liu, and S. Schaeffer, “Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China,” Appl. Soil Ecol. 84, 140–147 (2014). https://doi.org/10.1016/j.apsoil.2014.06.007

    Article  Google Scholar 

  25. N. Fierer, “Embracing the unknown: disentangling the complexities of the soil microbiome,” Nat. Rev. Microbiol. 15, 579–590 (2017). https://doi.org/10.1038/nrmicro.2017.87

    Article  Google Scholar 

  26. G. Ge, Z. Li, F. Fan, G. Chu, Z. Hou, and Y. Liang, “Soil biological activity and their seasonal variations in response to long-term application of organic and inorganic fertilizers,” Plant Soil 326, 31–44 (2010). https://doi.org/10.1007/s11104-009-0186-8

    Article  Google Scholar 

  27. Y. Ge, J. B. Zhang, L. M. Zhang, M. Yang, and J. Z. He, “Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China,” J. Soils Sediments 8, 43–50 (2008). https://doi.org/10.1065/jss2008.01.270

    Article  Google Scholar 

  28. D. Geisseler and K. M. Scow, “Long-term effects of mineral fertilizers on soil microorganisms – a review,” Soil Biol. Biochem. 75, 54–63 (2014). https://doi.org/10.1016/j.soilbio.2014.03.023

    Article  Google Scholar 

  29. Z. Guo, “Fertilization regime has a greater effect on soil microbial community structure than crop rotation and growth stage in an agroecosystems,” Appl. Soil Ecol. 149, 103510 (2020). https://doi.org/10.1016/j.apsoil.2020.103510

    Article  Google Scholar 

  30. M. Hartmann, B. Frey, J. Mayer, P. Mäder, and F. Widmer, “Distinct soil microbial diversity under long-term organic and conventional farming,” ISME J. 9, 1177–1194 (2015). https://doi.org/10.1038/ismej.2014.210

    Article  Google Scholar 

  31. J. Hu, X. Lin, J. Wang, J. Dai, R. Chen, J. Zhang, and M. H. Wong, “Microbial functional diversity, metabolic quotient, and invertase activity of a sandy loam soil as affected by long-term application of organic amendment and mineral fertilizer,” J. Soils Sediments 11, 271–280 (2011). https://doi.org/10.1007/s11368-010-0308-1

    Article  Google Scholar 

  32. R. Huang, S. P. McGrath, P. R. Hirsch, I. M. Clark, J. Storkey, L. Wu, J. Zhou, and Y. Liang, “Plant–microbe networks in soil are weakened by century-long use of inorganic fertilizers,” Microb. Biotechnol. 12, 1464–1475 (2019). https://doi.org/10.1111/1751-7915.13487

    Article  Google Scholar 

  33. Y. Kuzyakov and E. Blagodatskaya, “Microbial hotspots and hot moments in soil: concept & review,” Soil Biol. Biochem. 83, 184–199 (2015). https://doi.org/10.1016/j.soilbio.2015.01.025

    Article  Google Scholar 

  34. C. L. Lauber, M. Hamady, R. Knight, and N. Fierer, “Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale,” Appl. Environ. Microbiol. 75 (15), 5111–5120 (2009). https://doi.org/10.1128/AEM.00335-09

    Article  Google Scholar 

  35. C. Lazcano, M. Gómez-Brandón, P. Revilla, and J. Domínguez, “Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function,” Biol. Fertil. Soils 49, 723–733 (2013). https://doi.org/10.1007/s00374-012-0761-7

    Article  Google Scholar 

  36. L. Liu, C. Li, S. Zhu, Y. Xu, H. Li, X. Zheng, and R. Shi, “Combined application of organic and inorganic nitrogen fertilizers affects soil prokaryotic communities compositions,” Agronomy 10, 132 (2020). https://doi.org/10.3390/agronomy10010132

    Article  Google Scholar 

  37. S. Liu, J. Wang, S. Pu, E. Blagodatskaya, Y. Kuzyakov, and B. Razavi, “Impact of manure on soil biochemical properties: a global synthesis,” Sci. Total Environ., 141003 (2020). https://doi.org/10.1016/j.scitotenv.2020.141003

  38. H. Luan, W. Gao, S. Huang, J. Tang, M. Li, H. Zhang, and D. Masiliūnas, “Substitution of manure for chemical fertilizer affects soil microbial community diversity structure and function in greenhouse vegetable production systems,” PLoS One 15, e0214041 (2020). https://doi.org/10.1371/journal.pone.0214041

    Article  Google Scholar 

  39. Q. Ma, Y. Wen, D. Wang, X. Sun, P. W. Hill, A. Macdonald, D. R. Chadwick, L. Wu, and D. L. Jones, “Farmyard manure applications stimulate soil carbon and nitrogen cycling by boosting microbial biomass rather than changing its community composition,” Soil Biol. Biochem. 144, 107760 (2020). https://doi.org/10.1016/j.soilbio.2020.107760

    Article  Google Scholar 

  40. A. A. Malik, S. Chowdhury, V. Schlager, A. Oliver, J. Puissant, P. G. Vazquez, N. Jehmlich, M. Bergen, R. I. Griffiths, G. Gleixner, and G. Gleixner, “Soil fungal: bacterial ratios are linked to altered carbon cycling,” Front. Microbiol. 7, 1247 (2016). https://doi.org/10.3389/fmicb.2016.01247

    Article  Google Scholar 

  41. R. Mendes, P. Garbeva, and J. M. Raaijmakers, “The rhizosphere microbiome: significance of plant beneficial plant pathogenic and human pathogenic microorganisms,” FEMS Microbiol. Rev. 37, 634–663 (2013). https://doi.org/10.1111/1574-6976.12028

    Article  Google Scholar 

  42. J. Pöyry, L. G. Carvalheiro, R. K. Heikkinen, I. Kühn, M. Kuussaari, O. Schweiger, P. M. van Bodegom, A. Valtonen, M. Franzén, “The effects of soil eutrophication propagate to higher trophic levels,” Global Ecol. Biogeogr. 26, 18–30 (2017). https://doi.org/10.1111/geb.12521

    Article  Google Scholar 

  43. K. S. Ramirez, C. L. Lauber, R. Knight, M. A. Bradford, and N. Fierer, “Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems,” Ecology 91, 3463–3470 (2010). https://doi.org/10.1890/10-0426.1

    Article  Google Scholar 

  44. J. Rousk, E. Bååth, P. C. Brookes, C. L. Lauber, C. Lozupone, J. G. Caporaso, et al., “Soil bacterial and fungal communities across a pH gradient in an arable soil,” ISME J. 4, 1340–1351 (2010). https://doi.org/10.1038/ismej.2010.58

    Article  Google Scholar 

  45. M. V. Semenov, G. S. Krasnov, V. M. Semenov, and A. H. van Bruggen, “Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems,” Appl. Soil Ecol. 154, 103641 (2020). https://doi.org/10.1016/j.apsoil.2020.103641

    Article  Google Scholar 

  46. M. V. Semenov, G. S. Krasnov, V. M. Semenov, N. Ksenofontova, N. B. Zinyakova, and A. H. van Bruggen, “Does fresh farmyard manure introduce surviving microbes into soil or activate soil-borne microbiota?,” J. Environ. Manage. 294, 113018 (2021). https://doi.org/10.1016/j.jenvman.2021.113018

    Article  Google Scholar 

  47. M. V. Semenov, G. S. Krasnov, V. M. Semenov, and A. van Bruggen, “Mineral and organic fertilizers distinctly affect fungal communities in the crop rhizosphere,” J. Fungi 8, 251 (2022). https://doi.org/10.3390/jof8030251

    Article  Google Scholar 

  48. J. Six, S. D. Frey, R. K. Thiet, and K. M. Batten, “Bacterial and fungal contributions to carbon sequestration in agroecosystems,” Soil Sci. Soc. Am. J. 70, 555–569 (2006). https://doi.org/10.2136/sssaj2004.0347

    Article  Google Scholar 

  49. M. Soares and J. Rousk, “Microbial growth and carbon use efficiency in soil: Links to fungal-bacterial dominance, SOC-quality and stoichiometry,” Soil Biol. Biochem. 131, 195–205 (2019). https://doi.org/10.1016/j.soilbio.2019.01.010

    Article  Google Scholar 

  50. J. F. Toljander, J. C. Santos-González, A. Tehler, and R. D. Finlay, “Community analysis of arbuscular mycorrhizal fungi and bacteria in the maize mycorrhizosphere in a long-term fertilization trial,” FEMS Microbiol. Ecol. 65, 323–338 (2008). https://doi.org// j.1574-6941.2008.00512.xhttps://doi.org/10.1111/j.1574-6941.2008.00512.x10.1111

  51. D. L. Valentine, “Adaptations to energy stress dictate the ecology and evolution of the Archaea,” Nat. Rev. Microbiol. 5, 316–323 (2007). https://doi.org/10.1038/nrmicro1619

    Article  Google Scholar 

  52. L. van Overbeek and J. D. Van Elsas, “Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.),” FEMS Microbiol. Ecol. 64, 283–296 (2008). https://doi.org/6941.2008.00469.xhttps://doi.org/10.1111/j.1574-6941.2008.00469.x10.1111/j.1574

  53. L. Wang, F. E. Y. Yang, J. Yuan, W. Raza, Q. Huang, and Q. Shen, “Long-term application of bioorganic fertilizers improved soil biochemical properties and microbial communities of an apple orchard soil,” Front. Microbiol. 7, 1893 (2016). https://doi.org/10.3389/fmicb.2016.01893

    Article  Google Scholar 

  54. J. Wu, C. Sha, M. Wang, C. Ye, P. Li, and S. Huang, “Effect of organic fertilizer on soil bacteria in maize fields,” Land 10, 328 (2021). https://doi.org/10.3390/land10030328

    Article  Google Scholar 

  55. X. Xiang, J. Liu, J. Zhang, D. Li, C. Xu, and Y. Kuzyakov, “Divergence in fungal abundance and community structure between soils under long-term mineral and organic fertilization,” Soil Tillage Res. 196, 104491 (2020). https://doi.org/10.1016/j.still.2019.104491

    Article  Google Scholar 

  56. X. Zhang, W. Dong, X. Dai, S. Schaeffer, F. Yang, M. Radosevich, L. Xu, X. Liu, and X. Sun, “Responses of absolute and specific soil enzyme activities to long term additions of organic and mineral fertilizer,” Sci. Total Environ. 536, 59–67 (2015). https://doi.org/10.1016/j.scitotenv.2015.07.043

    Article  Google Scholar 

  57. Z. Zhou, C. Wang, and Y. Luo, “Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality,” Nat. Commun. 11, 1–10 (2020). https://doi.org/10.1038/s41467-020-16881-7

    Article  Google Scholar 

Download references

Funding

This study was supported by the Russian Science Foundation, project no. 21-76-10025 (https://rscf.ru/en/project/ 21-76-10025/).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to M. V. Semenov.

Ethics declarations

The authors declare that they have no conflicts of interest.

Additional information

Translated by V. Klyueva

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Semenov, M.V., Ksenofontova, N.A., Nikitin, D.A. et al. Microbiological Parameters of Soddy-Podzolic Soil and Its Rhizosphere in a Half-Century Field Experiment with Different Fertilizer Systems. Eurasian Soil Sc. 56, 756–768 (2023). https://doi.org/10.1134/S1064229323600070

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1064229323600070

Keywords:

Navigation