UNLABELLED: Growing catch crops can improve soil health by enhancing microbial diversity, but their impact may be constrained by how they are managed. This study examined the effects of different catch crop species and soil cultivation methods on bacterial and fungal diversity, and total soil microbial biomass. A 3-year field experiment on Luvi-haplic Chernozem included two catch crop species and five mixtures (further catch crop species) and three cultivation methods (ploughing, reduced tillage and no tillage), resulting in 21 treatments (7 catch crop species x 3 soil cultivations). Soil samples (0–15 cm depth) were collected annually in autumn and spring since 2021 to 2024. Microbial biomass was assessed using the chloroform fumigation extraction method, while fungal and bacterial diversity was analysed by amplifying and sequencing the ITS2 region of rDNA and the V4 region of the 16 S rRNA gene for fungi and bacteria, respectively, via Illumina paired-end amplicon sequencing. Soil cultivation methods affected bacterial diversity, with reduced tillage showing higher diversity and evenness than ploughing, though neither differed from no-till. However, no effect was observed on fungal diversity, including AM fungi, or microbial biomass. Catch crop species did not significantly impact microbial diversity or biomass. Neither cultivation method nor catch crop species influenced the ratios of functional trophic groups, such as pathogens, saprotrophs or symbionts. This study underscores the critical role of soil management practices—especially reduced tillage—in promoting soil health, primarily through the enhancement of bacterial diversity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-15255-7.

Czech Agrifood Research Center Drnovská 507 Ruzyně Prague 6 161 06 Czech Republic

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Thorup-Kristensen, K., Magid, J. & Jensen, L. S. Catch crops and green manures as biological tools in nitrogen management in temperate zones.

Nevins, C. J., Nakatsu, C. & Armstrong, S. Characterization of microbial community response to cover crop residue decomposition.

King, A. E. & Hofmockel, K. S. Diversified cropping systems support greater microbial cycling and retention of carbon and nitrogen.

Tejada, M., Gonzalez, J. L., García-Martínez, A., Parrado, J. & M. & Effects of different green manures on soil biological properties and maize yield. PubMed

Piotrowska, A. & Wilczewski, E. Effects of catch crops cultivated for green manure and mineral nitrogen fertilization on soil enzyme activities and chemical properties.

Du, Z. et al. Effects of fertilization and clipping on carbon, nitrogen storage, and soil microbial activity in a natural grassland in Southern China. PubMed PMC

Kim, N., Zabaloy, M. C., Guan, K. & Villamil, M. B. Do cover crops benefit soil microbiome? A meta-analysis of current research.

Wanic, M., Żuk-Gołaszewska, K. & Orzech, K. Catch crops and the soil environment—a review of the literature.

Gabriel, J. L., Munoz-Carpena, R. & Quemada, M. The role of cover crops in irrigated systems: water balance, nitrate leaching and soil mineral nitrogen accumulation.

Sainju, U. M. et al. Cover crop effect on soil carbon fractions under conservation tillage cotton.

Kramer, S. et al. Carbon flow into microbial and fungal biomass as a basis for the belowground food web of agroecosystems.

Muhammad, I. et al. Cover cropping enhances soil microbial biomass and affects microbial community structure: a meta-analysis.

Che, T. et al. Mixed planting reduces the shaping ability of legume cover crop on soil microbial community structure.

Gentsch, N. et al. Catch crop diversity increases rhizosphere carbon input and soil microbial biomass.

Wayman, S. et al. The influence of cover crop variety, termination timing and termination method on mulch, weed cover and soil nitrate in reduced-tillage organic systems.

Romdhane, S. et al. Cover crop management practices rather than composition of cover crop mixtures affect bacterial communities in no-till agroecosystems. PubMed PMC

Adetunji, A. T., Ncube, B., Mulidzi, R. & Lewu, F. B. Management impact and benefit of cover crops on soil quality: a review.

Elfstrand, S., Båth, B. & Mårtensson, A. Influence of various forms of green manure amendment on soil microbial community composition, enzyme activity and nutrient levels in leek.

Storr, T., Simmons, R. W. & Hannam, J. A. Using frost-sensitive cover crops for timely nitrogen mineralization and soil moisture management.

Olofsson, F. & Ernfors, M. Frost killed cover crops induced high emissions of nitrous oxide. PubMed

Bielińska, E. & Mocek-Płóciniak, A. Impact of the tillage system on the soil enzymatic activity.

Harasim, E., Antonkiewitz, J. & Kwiatkowski, C. A. The effects of catch crops and tillage systems on selected physical properties and enzymatic activity of loess soil in a spring wheat monoculture.

Zuber, S. M. & Villamil, M. B. Meta-analysis approach to assess effect of tillage on microbial biomass and enzyme activities.

Bowles, T. M., Jackson, L. E., Loeher, M. & Cavagnaro, T. R. Ecological intensification and arbuscular mycorrhizas: a meta-analysis of tillage and cover crop effects.

FAO. Standard operating procedure for soil microbial biomass (carbon): chloroform fumigation-extraction method (Rome 2024). 10.4060/cc9423en

Řezáčová, V. et al. Organic fertilization improves soil aggregation through increases in abundance of eubacteria and products of arbuscular mycorrhizal fungi. PubMed PMC

Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PubMed PMC

Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the illumina HiSeq and miseq platforms. PubMed PMC

Řezáč, M., Řezáčová, V., Gloríková, N., Némethová, E. & Heneberg, P. Food provisioning to Pardosa spiders decreases the levels of tissue-resident endosymbiotic bacteria. PubMed PMC

Ihrmark, K. et al. New primers to amplify the fungal ITS2 region – evaluation by 454 - sequencing of artificial and natural communities. PubMed

White, T. J., Bruns, T. D., Lee, S. B. & Taylor, J. W. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics in PCR Protocols: a Guide To Methods and Applications (eds Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J.) 315–322 (Academic Press, Inc., New York, (1990).

Řezáčová, V., Némethová, E., Stehlíková, I., Czakó, A. & Gryndler, M. Arbuscular mycorrhizal fungus funneliformis mosseae improves soybean growth even in soils with good nutrition.

Mehlich, A. Mehlich 3 soil test extractant. A modification of the mehlich 2 extractant.

Řezáčová, V. et al. Geography and habitat predominate over climate influences on arbuscular mycorrhizal fungal communities of mid-European meadows. PubMed

Řezáč, M., Řezáčová, V. & Heneberg, P. Differences in the abundance and diversity of endosymbiotic bacteria drive host resistance of PubMed

Větrovský, T., Baldrian, P. & Morais, D. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. PubMed PMC

Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4.

Liebisch, F. et al. Seasonal dynamics and turnover of microbial Phosphorusin a permanent grassland.

Ramírez, M. et al. Seasonal and interannual fluctuation of the microbial soil community in a maize field under long-term conservation agriculture management.

Ter Braak, C. J. F. & Šmilauer, P.

Schmidt, R., Gravuer, K., Bossange, A. V., Mitchell, J. & Scow, K. Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. PubMed PMC

Wang, Z., Liu, L., Chen, Q., Wen, X. & Liao, Y. Conservation tillage increases soil bacterial diversity in the dryland of Northern China.

Schmidt, R., Mitchell, J. & Scow, K. Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities.

Li, Y. et al. Effect of no-tillage on soil bacterial and fungal community diversity: a meta-analysis.

Dong, W. Y., Liu, E., Yan, C. R., Zhang, H. H. & Zhang, Y. Q. Changes in the composition and diversity of topsoil bacterial, archaeal and fungal communities after 22 years conventional and no-tillage managements in Northern China.

De Vries, F. T. et al. Soil bacterial networks are less stable under drought than fungal networks. PubMed PMC

Ochoa-Hueso, R., Collins, S. L., Delgado-Baquerizo, M., Hamonts, K. & Power, S. A. Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents. PubMed

Smith, S. E. & Read, D. J.

Sommermann, L. et al. Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing. PubMed PMC

Jansa, J. et al. Diversity and structure of AMF communities as affected by tillage in a temperate soil. PubMed

Jongman, R. H., ter Braak, C. L. F. & van Tongeren, O. F. R. (eds)

Gao, H., Tian, G., Khashi, U., Rahman, M. & Wu, F. Cover crop species composition alters the soil bacterial community in a continuous pepper cropping system. PubMed PMC

Cazzaniga, S. G. et al. Pinpointing the distinctive impacts of ten cover crop species on the resident and active fractions of the soil Microbiome.

Muturi, E. J., Dunlap, C. A., Perry, W. L. & Rhykerd, R. L. Cover crop species influences soil fungal species richness and community structure. PubMed PMC

Aiyer, H. et al. Choice of cover crop influences soil fungal and bacterial communities in Prince Edward island, Canada. PubMed

Eisenhauer, N. et al. Plant diversity surpasses plant functional groups and plant productivity as driver of soil biota in the long term. PubMed PMC

Bockus, W. & Shroyer, J. The impact of reduced tillage on soilborne plant pathogens. PubMed

Schroeder, K. L. & Paulitz, T. C. Root diseases of wheat and barley during the transition from conventional tillage to direct seeding. PubMed

Engell, I. et al. The effects of conservation tillage on chemical and microbial soil parameters at four sites across Europe. PubMed PMC

Patkowska, E., Błażewicz-Woźniak, M., Konopiński, M. & Wach, D. The effect of cover crops on the fungal and bacterial communities in the soil under Carrot cultivation.

Janušauskaite, D., Arlauskiene, A. & Maikteniene, S. Soil mineral nitrogen and microbial parameters as influenced by catch crops and straw management.

Tedersoo, L. et al. Global diversity and geography of soil fungi. PubMed

Gafencu, A. M., Florea, A. M., Lipsa, F. D. & Ulea, E. Dynamics of soil bacterial communities under winter wheat in the north-east part of Romania.