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Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

The severity of drought is predicted to increase across Europe due to climate change. Droughts can substantially impact terrestrial nitrogen (N) cycling and the corresponding microbial communities. Here, we investigated how ammonia-oxidizing bacteria (AOB), archaea (AOA), and comammox (complete ammonia oxidizers) respond to simulated drought in a rain-out shelter experiment in the DOK long-term field trial comparing different organic and conventional agricultural practices since 1978. This study is part of the MICROSERVICES (BiodivERsA) project aiming to understand and predict the effects of climate change on crop-associated microbiomes and their ecosystem functions. We monitored the diversity, the composition, and the abundance of ammonia-oxidizers for five months by Illumina-based amplicon sequencing and quantitative real-time PCR using the amoA gene as molecular marker. We found that the effect of drought varied depending on the ammonia-oxidizing community and also on the agricultural practices. The community structures of AOA and comammox were more strongly affected by drought than the AOB community structure. Drought also had a stronger impact on the community structure in the biodynamic (organic) cropping system than in both the mixed and mineral-fertilized conventional systems. The abundance of ammonia oxidizers was also influenced by drought, with comammox clade B exhibiting the strongest sensitivity to drought. The drought effect on the community abundance was more prominent in the biodynamic and mixed-conventional systems than in the mineral-fertilized conventional system. We further found a significant interaction between drought and agricultural practices on the abundance of all groups of ammonia-oxidizers except AOB. Overall, our study showed that the impact of drought on ammonia oxidizers was modulated by agricultural practices and varied with time as well as among members of ammonia-oxidizers. These results underscore the significance of agricultural

Protists, a crucial part of the soil food web, are increasingly acknowledged as significant influencers of nutrient cycling and plant performance in farmlands. While topographical and climatic factors are often considered to drive microbial communities on a continental scale, higher trophic levels like heterotrophic protists also rely on their food sources. In this context, bacterivores have received more attention than fungivores. Our study explored the connection between the community composition of protists (specifically Rhizaria and Cercozoa) and fungi across 156 cereal fields in Europe, spanning a latitudinal gradient of 3000 km. We employed a machine-learning approach to measure the significance of fungal communities in comparison to bacterial communities, soil abiotic factors, and climate as determinants of the Cercozoa community composition. Our findings indicate that climatic variables and fungal communities are the primary drivers of cercozoan communities, accounting for 70% of their community composition. Structural equation modelling (SEM) unveiled indirect climatic effects on the cercozoan communities through a change in the composition of the fungal communities. Our data also imply that fungivory might be more prevalent among protists than generally believed. This study uncovers a hidden facet of the soil food web, suggesting that the benefits of microbial diversity could be more effectively integrated into sustainable agriculture practices.

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (−56%) and SOC stocks (−35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.

Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (−56%) and SOC stocks (−35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.

Agricultural management practices aimed at sequestering carbon (C) in soils can have synergies with many agroecosystem services, but may come at the cost of increased greenhouse gas (GHG) emissions and nutrient losses. We performed a systematic literature synthesis to review whether C sequestration practices show synergies with soil structure and soil biota, but generate trade-offs in terms of CO2 and N2O emissions or N and P losses worldwide. We also assessed whether the magnitude of trade-offs and synergies vary across climatic regions and over time. We performed systematic literature searches in the Web of Science for articles that: 1. experimentally assess the effect of minimising soil disturbance, diversifying agroecosystems, and/or increasing organic matter inputs versus standard practices, and 2. include measurements of C sequestration and at least another response variable related to synergies or trade-offs. We retrieved 771 publications, 537 of which were excluded based on i) the type of article (review, opinion papers), ii) a focus on non-soil habitats, forests or organic soils, or iii) experimental designs not matching our criteria. We included 234 studies that report 572 effects of sustainable practices on 228 sites located in 38 countries. Experiments averaged 10 years of monitoring and the majority reported effects of increasing organic matter inputs and minimising soil disturbance (88%) in temperate and continental climates (75%). Soil organic C increased without compromising crop yields considering all management practices together, i.e. positive effects of sustainable versus standard practices on C sequestration were more frequent than expected by chance. As expected, C sequestration promoted soil biota, but effects were more evident on biomass than on diversity. We also detected synergistic effects on soil aggregation, porosity, water retention and compaction. Negative effects of C retention practices were significant when considering GHG emissions

Agricultural management practices aimed at sequestering carbon (C) in soils show synergies with many agroecosystem services, but may come at the cost of increased greenhouse gas (GHG) emissions. We performed a systematic literature synthesis, followed by a meta-analysis and experimental measurements, to analyse whether C sequestration practices generate trade-offs in terms of CO2 and N2O emissions. We performed systematic literature searches in the Web of Science to look for articles published worldwide that experimentally assess the effect of: 1. minimising soil disturbance (reduced or no tillage), 2. diversifying agroecosystems (crop rotations, cover crops, intercropping), and/or 3. increasing organic matter inputs (crop residue retention, organic amendments) versus standard practices. We only included studies that quantified C sequestration and at least another response variable related to the synergies or trade-offs of C sequestration. We retrieved 771 publications, 537 of which were excluded based on the type of article, a focus on non-soil habitats, forests or organic soils, or experimental designs not matching our criteria. We included 234 studies that report 572 effects of sustainable practices on 228 sites located in 38 countries. Experiments averaged 10 years of monitoring and the majority reported effects of increasing organic matter inputs and minimising soil disturbance (88%) in temperate and continental climates (75%). Sustainable practices effectively sequestered more C than standard practices considering all studies together. In total, we detected 353 effects related to CO2 and N2O emissions, 51% of which were measured as field fluxes and 43% as laboratory fluxes. Taking both types of measurements, C sequestration increased GHG emissions, particularly CO2. However, the response of CO2 and N2O emissions (increase, neutral, decrease) of sustainable versus standard agricultural practices varied significantly depending on how emissions were measured (fie

Las prácticas de manejo agrícola que incrementan el secuestro de carbono (C) promueven otros servicios de los agroecosistemas, como el mantenimiento de la estructura y la fertilidad del suelo o de la biodiversidad edáfica. Sin embargo, pueden incrementar la emisión de gases de efecto invernadero (GEIs) y la pérdida de nutrientes. Con el objetivo de revisar si las prácticas de secuestro de C muestran sinergias con la estructura y la biota edáficas, pero generan trade-offs en términos de emisión de CO2 y N2O o pérdidas de N y P, realizamos una síntesis de literatura global. Realizamos búsquedas sistemáticas de literatura para detectar artículos que evaluaran experimentalmente el efecto de minimizar la perturbación del suelo, diversificar los agroecosistemas y/o incrementar los aportes de materia orgánica frente a la utilización de prácticas convencionales. Detectamos 771 publicaciones, de las cuales incluimos 234 que analizaban 572 efectos en 228 sitios de 38 países. Las prácticas de manejo sostenible incrementaron el C en el suelo sin comprometer el rendimiento de los cultivos. El secuestro de C tuvo efectos positivos sobre la biota del suelo, más evidentes en términos de biomasa que de biodiversidad, así como sobre la agregación, porosidad, retención de agua y reducción de la compactación. Los efectos negativos del secuestro de C fueron en términos de emisión de CO2 y pérdida potencial de N. Discutiremos cómo estos efectos variaron entre prácticas de manejo, en el tiempo y el espacio, y revisaremos los principales vacíos de conocimiento detectados en la literatura.

Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (−56%) and SOC stocks (−35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.

Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (-56%) and SOC stocks (-35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.