Cropping practices have a great potential to improve soil quality through changes in soil biota. Yet the effects of these soil\uffe2\uff80\uff90improving cropping systems on soil fungal communities are not well known. Here, we analysed soil fungal communities using standardized measurements in 12 long\uffe2\uff80\uff90term experiments and 20 agricultural treatments across Europe. We were interested in whether the same practices (i.e., tillage, fertilization, organic amendments and cover crops) applied across different sites have predictable and repeatable effects on soil fungal communities and guilds. The fungal communities were very variable across sites located in different soil types and climatic regions. The arbuscular mycorrhizal fungi (AMF) were the fungal guild with most unique species in individual sites, whereas plant pathogenic fungi were most shared between the sites. The fungal communities responded to the cropping practices differently in different sites and only fertilization showed a consistent effect on AMF and plant pathogenic fungi, whereas the responses to tillage, cover crops and organic amendments were site, soil and crop\uffe2\uff80\uff90species specific. We further show that the crop yield is negatively affected by cropping practices aimed at improving soil health. Yet, we show that these practices have the potential to change the fungal communities and that change in plant pathogenic fungi and in AMF is linked to the yield. We further link the soil fungal community and guilds to soil abiotic characteristics and reveal that especially Mn, K, Mg and pH affect the composition of fungi across sites. In summary, we show that fungal communities vary considerably between sites and that there are no clear directional responses in fungi or fungal guilds across sites to soil\uffe2\uff80\uff90improving cropping systems, but that the responses vary based on soil abiotic conditions, crop type and climatic conditions.
Highlights
Soil fungi were analysed using standardized measurements in 12 long\uffe2\uff80\uff90term experiments and 20 agricultural treatments
Fungal communities responded to the cropping practices differently at different sites
Only reduced fertilization showed a consistent effect on AMF and plant pathogenic fungi, whereas the responses to tillage, cover crops and organic amendments were site specific.
Fungal community structure varied significantly between sites, crops and climate conditions; therefore, more cross\uffe2\uff80\uff90site studies are needed in order to manage beneficial soil fungi in agricultural systems.