Changes in the microbial community of sod-podzolic heavy loamy soil during cultivation of various agricultural crops

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Abstract

Field and laboratory studies were conducted in 2023 to assess changes in the composition of microbial communities of sod-podzolic heavy loamy soil when growing various crops in the crop rotation: mustard-winter wheat-barley. This sequential rotation of crops was chosen for the basic assessment of dynamic changes in the structure of soil microbiological communities caused by the cultivation of various agricultural crops. The microbial community in soil samples taken 1, 2, and 3 years after green manure plowing was analyzed by amplicon sequencing of the 16S rRNA gene of bacteria and archaea. The largest number of taxonomically significant groups of microorganisms (55) was found when comparing the soil used for growing winter wheat and after planting mustard. The number of specific taxa is halved (up to 24) when analyzing barley and mustard soils. The soils occupied under wheat and barley are almost identical in the composition of the dominant bacterial taxa. The most pronounced changes were observed among representatives of the Crenarchaeota archaea belonging to the Nitrososphaeria class. Individual taxa of this class have demonstrated high specificity in relation to the agroecological conditions of grain and mustard cultivation. It is shown that sideration has a minor effect on the composition of the microbial community, apparently primarily at the level of changes in the number of individual bacterial taxa.

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About the authors

А. A. Zavalin

Pryanishnikov All-Russian Research Institute of Agrochemistry

Author for correspondence.
Email: zavalin.52@mail.ru

академик РАН, доктор сельскохозяйственных наук

Russian Federation, Moskva

A. S. Karashaeva

Pryanishnikov All-Russian Research Institute of Agrochemistry

Email: zavalin.52@mail.ru

кандидат сельскохозяйственных наук

Russian Federation, Moskva

E. N. Starostina

Pryanishnikov All-Russian Research Institute of Agrochemistry

Email: zavalin.52@mail.ru
Russian Federation, Moskva

A. O. Zverev

All-Russian Research Institute of Agricultural Microbiology

Email: zavalin.52@mail.ru
Russian Federation, Sankt-Peterburg

References

  1. Методология биологических исследований почвы в рамках проекта «Микробиом России» / Т. И. Чернов, В. А. Холодов, Б. М. Когут и др. // Бюллетень Почвенного института им. В. В. Докучаева. 2017. Вып. 87.C. 100–112. doi: 10.19047/0136-1694-2017-87-100-113.
  2. Respones of soil physico-chemical properties, structure of the microbial community and crop yields to different fertilization practices in Russias’S conventional farming system. / A. N. Naliukhin, A. V. Kozlov, A. V. Eregin, et al. // Brazilian Journal of Biology: 2024. Vol. 84. e282493. URL: https://www.scielo.br/j/bjb/a/6cLdJhvfSzCvMyTD8mnbkrw/?format=pdf&lang=en (дата обращения: 14.05.2025). doi: 10.1590/1519-6984.282493.
  3. Чернов Т. И., Семенов М. В. Управление почвенными микробными сообществами: возможности и перспективы (обзор) // Почвоведение. 2021. № 12.C. 1506–1522. doi: 10.31857/S0032180X21120029.
  4. Unveiling the roles, mechanisms and prospects of soil microbial communities in sustainable agriculture / K. Kiprotich, E. Muema, C. Wekesa, et al. // Discover Soil: 2025. Vol. 2:10. URL: https://link.springer.com/article/10.1007/s44378-025-00037-4 (дата обращения: 14.05.2025). doi: 10.1007/s44378-025-00037-4.
  5. Biodiversity, and biotechnological contribution of beneficial soil microbiomes for nutrient cycling, plant growth improvement and nutrient uptake / N. Yadav, D. Kour, T. Kaur, et al. // Biocatalysis and Agricultural Biotechnology. 2021. Vol. 33. 102009. URL: https://www.sciencedirect.com/science/article/abs/pii/S1878818121001055 (дата обращения: 14.05.2025). doi: 10.1016/j.bcab.2021.102009.
  6. Изменение метагенома прокариотного сообщества как показатель плодородия пахотных дерново-подзолистых почв при применении удобрений / А. Н. Налиухин,C. М. Хамитова, А. П. Глинушкин и др. // Почвоведение. 2018. № 3.C. 331–337. doi: 10.7868/S0032180X18030073.
  7. Microbial community succession in soil is mainly driven by carbon and nitrogen contents rather than phosphorus and sulphur contents. / Sh. Tang, Q. Ma, K. A. Marsden, et al. // Soil Biology and Biochemistry. 2023. Vol. 180. 109019. URL: https://www.sciencedirect.com/science/article/abs/pii/S0038071723000810 (дата обращения: 14.05.2025). doi: 10.1016/j.soilbio.2023.109019.
  8. Влияние удобрений и средств химизации на плодородие почвы и питание растений / А. С. Карашаева, А. А. Завалин, Г. А Ивашенков и др. // АгроЭкоИнженерия. 2023. № 4(117).C. 4–14. doi: 10.24412/2713-2641-2023-4117-4-14.
  9. DADA2: High-resolution sample inference from Illumina amplicon data // B. J. Callahan, P. J. McMurdie, M. J. Rosen, et al. Nature Methods. 2016. Vol. 13. No. 7. P. 581–583. doi: 10.1038/nmeth.3869.
  10. P. J. McMurdie, S. Holmes. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data // PLoS ONE. 2013. Vol. 8. No. 4. P. e61217. URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0061217&type=printable (дата обращения: 14.05.2025). doi: 10.1371/journal.pone.0061217.
  11. Welcome to the tidyverse / H. Wickham, M. Averick, J. Bryan, et al. // Journal of Open Source Software. 2019. Vol. 4. No. 43. P. 1686. URL: https://www.theoj.org/joss-papers/joss.01686/10.21105.joss.01686.pdf (дата обращения: 14.05.2025). doi: 10.21105/joss.01686.
  12. Amplicon Sequencing of Fusarium Translation Elongation Factor 1α Reveals that Soil Communities of Fusarium Species Are Resilient to Disturbances Caused by Crop and Tillage Practices / P. M. Henry, S. I. Koehler, S. Kaur, et al. // Journal Phytobiomes, 2022. Vol. 6(3). P. 261–274. doi: 10.1094/PBIOMES-09-21-0053-R.
  13. Zhu A., Ibrahim J. G., Love M. I. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences // Bioinformatics. 2019. Vol. 35. No. 12. P. 2084–2092. doi: 10.1093/bioinformatics/bty895.

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2. Fig. 1. Alpha diversity of different soils using green manure.

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3. Fig. 2. Principal coordinates analysis for beta diversity distances (weighted Unifrac) of microbial communities using different types of green manure (the values of explained variability of the principal coordinates analysis axes are given in brackets).

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4. Fig. 3. Taxa that significantly change in abundance in comparison of soils from different agricultural crops.

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