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

Zobrazit více v PubMed

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

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. DOI

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

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 DOI PMC

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

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

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. DOI

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. DOI

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

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

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

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. DOI

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

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

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. DOI

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

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

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

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. DOI

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

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. DOI

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 DOI 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 DOI 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 DOI PMC

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

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 DOI

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

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

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

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

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

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 DOI PMC

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

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

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

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. DOI

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

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 DOI PMC

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

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 DOI 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. DOI

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

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

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

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

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

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

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

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

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.