Soil organic carbon (SOC) sequestration in agricultural soils is an important tool for climate change mitigation within the EU soil strategy for 2030 and can be achieved via the adoption of soil management strategies (SMS). These strategies may induce synergistic effects by simultaneously reducing greenhouse gas (GHG) emissions and/or nitrogen (N) leaching. In contrast, other SMS may stimulate emissions of GHG such as nitrous oxide (N ₂ O) or methane (CH ₄ ), offsetting the climate change mitigation gained via SOC sequestration. Despite the importance of understanding trade‐offs and synergies for selecting sustainable SMS for European agriculture, knowledge on these effects remains limited. This review synthesizes existing knowledge, identifies knowledge gaps and provides research recommendations on trade‐offs and synergies between SOC sequestration or SOC accrual, non‐CO ₂ GHG emissions and N leaching related to selected SMS. We investigated 87 peer‐reviewed articles that address SMS and categorized them under tillage management, cropping systems, water management and fertilization and organic matter (OM) inputs. SMS, such as conservation tillage, adapted crop rotations, adapted water management, OM inputs by cover crops (CC), organic amendments (OA) and biochar, contribute to increase SOC stocks and reduce N leaching. Adoption of leguminous CC or specific cropping systems and adapted water management tend to create trade‐offs by stimulating N ₂ O emissions, while specific cropping systems or application of biochar can mitigate N ₂ O emissions. The effect of crop residues on N ₂ O emissions depends strongly on their C/N ratio. Organic agriculture and agroforestry clearly mitigate CH ₄ emissions but the impact of other SMS requires additional study. More experimental research is needed to study the impact of both the pedoclimatic conditions and the long‐term dynamics of trade‐offs and synergies. Researchers should simultaneously assess the impact of (multiple) agricultural SMS on SOC stocks, GHG emissions and N leaching. This review provides guidance to policymakers as well as a framework to design field experiments and model simulations, which can address knowledge gaps and non‐intentional effects of applying agricultural SMS meant to increase SOC sequestration.

Soil management strategies involving the application of organic matter (OM) inputs (crop residues, green and livestock manure, slurry, digestate, compost and biochar) can increase soil carbon storage but simultaneously lead to an increase in non‐CO ₂ greenhouse gas (GHG) emissions such as N ₂ O. Although multiple meta‐analyses have been conducted on the topic of OM input impacts on GHG, none has focused specifically on European arable soils. This study plugs this gap and can assist policymakers in steering European agriculture in a more sustainable direction. The objective of this meta‐analysis was to quantify how OM inputs of different nature and quality, but also the application strategy, can mitigate soil N ₂ O emissions in different pedoclimatic conditions in Europe. We quantitatively synthesised the results of over 50 field experiments conducted in 15 European countries. Diverse arable crops, mainly cereals, were cultivated in monoculture or in crop rotations on mineral soils. Cumulative N ₂ O emissions were monitored during periods of 30–1070 days in treatments, which received OM inputs, alone or in combination with mineral N fertiliser; and in controls fertilised with mineral N. The overall effect of OM inputs had a slight tendency to reduce N ₂ O emissions by 10% ( n = 53). With the increasing carbon‐to‐nitrogen ratio of the OM inputs, this mitigation effect became more pronounced. In particular, compost and biochar significantly reduced N ₂ O emissions by 25% ( n = 6) and 33% ( n = 8) respectively. However, their effect strongly depended on pedoclimatic characteristics. Regarding the other types of OM inputs studied, a slight N ₂ O emission reduction can be achieved by their application alone, without mineral N fertiliser (by 16%, n = 17). In contrast, their co‐application with mineral N fertiliser elevated emissions to some extent compared to the control (by 14%, n = 22). We conclude that amongst the seven OM inputs studied, the application of compost and biochar are the most promising soil management practices, clearly demonstrating N ₂ O emission reduction compared to mineral N fertiliser. In contrast, other OM inputs had a small tendency to mitigate N ₂ O emissions only when applied without mineral N fertiliser.

Mineral nitrogen (N) availability to heterotrophic micro-organisms is known to impact organic matter (OM) decomposition. Different pathways determining the N accessibility depend to a large extent on soil structure. Contact between soil mineral and OM substrate particles can facilitate N transport toward decomposition hot spots. However, the impact of soil structure on N availability to microbes and thus heterotrophic microbial activity and community structure is not yet fully understood. We hypothesized that carbon mineralization (Cmin) from low-N substrate would be stimulated by increased N availability caused by closer contact with soil particles or by a higher moisture level, enhancing potential for N-diffusion. Under opposite conditions retarded heterotrophic activity and a dominance of fungi were expected. A 128-days incubation experiment with CO₂ emission monitoring from artificially reconstructed miniature soil cores with contrasting soil structures, viz. high or low degree of contact between soil particles, was conducted to study impacts on heterotrophic activity. The soil cores were subjected to different water filled pore space percentages (25 or 50% WFPS) and amended with either easily degradable OM high in N (grass) or more resistant OM low in N (sawdust). X-ray μCT image processing allowed to quantify the pore space in 350 μm around OM substrates, i.e., the microbial habitat of involved decomposers. A lower local porosity surrounding sawdust particles in soils with stonger contact was confirmed, at least at 25% WFPS. Mineral N addition to sawdust amended soils with small particle contact at 25% WFPS resulted in a stimulated respiration. Cmin in the latter soils was lower than in case of high particle contact. This was not observed for grass substrate particles or at 50% WFPS. The interactive effect of substrate type and soil structure suggests that the latter controls Cmin through mediation of N diffusion and in turn N availability. Phospholipid fatty acid did not reveal promotion of fungal over bacterial biomarkers in treatments with N-limited substrate decomposition. Combining X-ray μCT with tailoring soil structure allows for more reliable investigation of effects on the soil microbial community, because as also found here, the established soil pore network structure can strongly deviate from the intended one.

Degradability of organic matter (OM) in soil depends on its spatial location in the soil matrix. A recent breakthrough in 3D-localization of OM combined dual-energy X-ray CT-scanning with OsO₄ staining of OM. The necessity for synchrotron-based µCT and the use of highly toxic OsO₄ severely limit applications in soil biological experiments. Here, we evaluated the potential of alternative staining agents (silver nitrate, phosphomolybdenic acid (PMA), lead nitrate, lead acetate) to selectively enhance X-ray attenuation and contrast of OM in CT volumes of soils containing specific mineral soil particle fractions, obtained via lab-based X-ray µCT. In comparison with OsO₄, administration of Ag⁺ and Pb²⁺ resulted in insufficient contrast enhancement of OM versus fine silt (< 20 µm) or clay (< 2 µm) mineral particles. The perfusion procedure used in this work induced changes in soil structure. In contrast, PMA staining resulted in a selective increase of OM’s attenuation contrast, which was comparable to OsO₄. However, OM discrimination from other soil phases remained a challenge. Further development of segmentation algorithms accounting for grey value patterns and shape of stained particulate OM may enable its automated identification. If successful in undisturbed soils, PMA staining may form an alternative to OsO₄ in non-synchrotron based POM detection.

The role of soil microbial communities in soil organic matter (OM) decomposition, transformation, and the global nitrogen (N) and carbon (C) cycles has been widely investigated. However, a comprehensive understanding of how specific agricultural practices and OM inputs shape microbial-driven processes across different European pedoclimatic conditions is still lacking, particularly regarding their effectiveness in mitigating greenhouse gas (GHG) emissions. This systematic review synthesizes current knowledge on the biotic mechanisms underlying soil C sequestration and GHG reduction, emphasizing key microbial processes influenced by land management practices. A rigorous selection was applied, resulting in 16 eligible articles that addressed the targeted outcomes: soil microorganism biodiversity, including microbiome composition and other common Biodiversity Indexes, C sequestration and non-CO₂ GHG emissions (namely N₂O and CH₄ emissions), and N leaching. The review highlights that, despite some variations across studies, the application of OM enhances soil microbial biomass (MB) and activity, boosts soil organic carbon (SOC), and potentially reduces emissions. Notably, plant richness and diversity emerged as critical factors in reducing N₂O emissions and promoting carbon storage. However, the lack of methodological standardization across studies hinders meaningful comparison of outcomes—a key challenge identified in this review. The analysis reveals that studies examining the simultaneous effects of agricultural management practices and OM inputs on soil microorganisms, non-CO₂ GHG emissions, and SOC are scarce. Standardized studies across Europe’s diverse pedoclimatic regions would be valuable for assessing the benefits of OM inputs in agricultural soils. This would enable the identification of region-specific solutions that enhance soil health, prevent degradation, and support sustainable and productive farming systems.