The global terrestrial carbon (C) cycle is intrinsically related to the management of agricultural ecosystems [1]. Although agricultural systems are significant sources of greenhouse gas emissions, they also possess substantial potential for soil organic carbon (SOC) sequestration, thereby contributing to regional food security and climate change mitigation [2]. Soil microorganisms, which are ubiquitous and highly diverse, play a pivotal role in maintaining ecosystem functioning, including soil organic matter decomposition, aggregate formation and stabilization, nutrient cycling, and plant–soil interactions [3]. Consequently, elucidating SOC dynamics and their underlying microbial regulatory mechanisms remains a critical frontier in terrestrial C cycle research.
Recent advances in state-of-the-art technologies, including high-frequency profile gas monitoring, physical and chemical fractionation of SOC, and high-throughput sequencing, have substantially improved our understanding of how conservation tillage, crop rotation, and targeted nutrient management modulate microbial C dynamics and promote soil C sequestration [4,5,6]. Despite these significant advances, major knowledge gaps continue to limit our ability to predict the stability and persistence of sequestered C across diverse agroecosystems. The primary challenge lies in the spatial decoupling between soil C fluxes and long-term C sequestration. A mechanistic understanding is still lacking regarding how microbially derived C intermediates traverse the heterogeneous soil matrix at the microscale, interact with mineral surfaces, and become physically protected within soil aggregates. Furthermore, although short-term organic or inorganic fertilization under intensive agronomic regimes can transiently stimulate microbial biomass and alter the molecular composition of SOC toward greater chemical recalcitrance [7], their long-term consequences, particularly soil acidification stress and deep-profile greenhouse gas emissions [8], remain insufficiently quantified. In addition, a pronounced scale mismatch persists between the functional potential inferred from multi-omics data and the actual metabolic activities expressed by microorganisms under dynamic field conditions. To address these pressing challenges, this Special Issue assembles integrative studies that harness cutting-edge technologies to unravel the microbial mechanisms governing C turnover, stabilization, and sequestration in agricultural ecosystems.
The Special Issue comprises six contributions that collectively advance our understanding of SOC dynamics and their interactions with microbial communities. The papers address a diverse array of topics, including land-use patterns, fertilization regimes, and crop straw management strategies. Broadly, the studies are organized into three main thematic areas: (i) soil microbial diversity across SOC gradients (Contribution 5); (ii) soil C emission and losses (Contributions 1 and 3); and (iii) SOC sequestration alongside its microbial drivers (Contributions 2, 4, and 6).
Shen et al. (Contribution 1) evaluated the effects of furrow corn straw mulch on soil erosion and SOC loss in sloping croplands. By field-monitoring of natural erosive rainfall events, the authors demonstrated that straw mulch significantly decreased runoff coefficients, sediment concentration, and the proportion of organic C loss in sediment relative to total C loss. The study further showed that common rainfall patterns exerted greater effects on soil erosion and SOC loss than special rainfall events, whereas furrow corn straw mulching effectively mitigated these adverse effects. These findings provide a practical field-scale management strategy for stabilizing the soil microenvironment, mitigating soil degradation and enhancing the long-term conservation of soil and water resources in cold-region agroecosystems.
Wang et al. (Contribution 2) investigated the effects of land use conversion from upland to paddy fields on SOC content and enzyme activity within soil aggregates. Their study revealed that microaggregates constituted the dominant aggregate fraction in typical black soils, and that agricultural reclamation significantly reduced both the mean weight diameter and geometric mean diameter of soil aggregates. Moreover, SOC content and enzyme activities within soil aggregates were found to be governed by both aggregate sizes and land-use transition, with the latter exerting a stronger influence. These findings suggest that the conversion from upland to paddy fields fundamentally alters the mechanisms governing SOC distribution and stabilization within aggregates, representing an important pathway for enhancing long-term SOC sequestration in agricultural ecosystems.
Shi et al. (Contribution 3) examined the impacts of nitrogen (N) fertilization on greenhouse gas emission dynamics and their vertical distributions within soil profiles. By integrating continuous field flux measurements with quantitative polymerase chain reaction (qPCR) analyses, the authors demonstrated that N application suppressed methane emissions while stimulating carbon dioxide (CO2) and nitrous oxide emissions at the surface. Across the soil profile, N addition increased CO2 concentrations throughout the 0–60 cm depth, with the top 30 cm layer emerging as the principal response hotspot. The study further identified soil pH and ammonium as the decisive microenvironmental drivers shaping the abundance and composition of functional microbial communities. These findings provide a critical mechanistic framework for understanding the coupled regulation of soil C and N cycling and offer valuable insights for managing biogeochemical processes in agricultural ecosystems.
Wang et al. (Contribution 4) evaluated the synergistic effects of co-applying organic amendments and synthetic fertilizers on microbially mediated C stabilization using an integrated metagenomic and advanced spectroscopic approach. By characterizing the structural composition of soil organic matter alongside the functional potential of soil microbial communities, the study demonstrated that combined organic–inorganic fertilization regimes significantly enhanced soil nutrient availability and enzyme activities while promoting the accumulation and stability of SOC fractions. Metagenomic analyses further underscored that this combined fertilization enriched the specific microbial functional genes associated with C fixation. These findings highlight the synergistic role of organic and inorganic fertilizers in improving soil C sequestration and provide a scientific basis for optimizing fertilization strategies in agricultural ecosystems.
Li et al. (Contribution 5) examined the microscale ecological boundaries and successional dynamics of soil microbial communities at the grassland–farmland interface. The study tracked how the steep environmental gradients across this structural ecotone reshape microbial alpha and beta diversity and alter the abundance of functional guilds involved in C and nutrient cycling. The findings demonstrated that edge effects at the agricultural interface induce substantial shifts in the composition of bacterial and fungal communities and weaken the stability and connectivity of microbial co-occurrence networks. These findings not only advance our understanding of soil–microorganism interactions across ecotonal boundaries but also provide a spatially explicit framework for predicting source–sink dynamics and biogeochemical processes at landscape interfaces.
Jiang et al. (Contribution 6) demonstrated that an optimal N application rate could promote the chemical stability of SOC in soybean–maize intercropping systems, whereas excessive N inputs suppress microbial biomass and C use efficiency through soil acidification. N-induced changes in soil pH further reshaped mineral surface properties and organo-mineral interactions, thereby exerting dual effects on SOC stabilization. Mechanistically, N addition shifted the functional group composition of SOC, promoting the accumulation of chemically recalcitrant C structures. This study provides a novel spectroscopic and mechanistic framework for elucidating C–N interactions and offers valuable insights for precision N management strategies aimed at simultaneously improving crop production and long-term soil C sequestration.
Soil organic C sequestration is fundamental to agricultural sustainability and global climate change mitigation [9]. Therefore, understanding the microbial mechanisms governing SOC turnover and stabilization is essential for optimizing agroecosystem functioning and sustaining crop productivity [10]. The studies assembled in this Special Issue present cutting-edge advances in agricultural soil management and bridge critical knowledge gaps by moving beyond bulk SOC stock measurements toward a mechanistic understanding of molecular-level C dynamics and microbe-mediated processes. In particular, these contributions reveal how diverse management practices and cropping configurations, including cereal–legume intercropping systems, reshape the molecular composition, chemical stability and persistence of SOC under varying anthropogenic inputs. By integrating advanced spectroscopic approaches with high-throughput sequencing technologies, these studies provide new insights into C-N coupling, microbial regulation of C transformation, and the organo-mineral interactions that underpin the stabilization of soil C pools.
Future studies should promote deeper interdisciplinary integration among soil biogeochemistry, microbial ecology, agronomy, and computational molecular modeling. Such integration will be crucial for decoding the evolution of soil C sequestration under increasingly complex climatic fluctuations and intensive management practices. Future efforts should leverage high-resolution multi-omics approaches, including metagenomics, metatranscriptomics, and metabolomics, alongside advanced isotope-tracing techniques to explore the real-time spatial arrangement of newly formed organo-mineral complexes. Additionally, long-term multi-site field experiments and predictive biogeochemical modeling can expand these localized molecular findings to a regional scale, quantifying how optimal agricultural management practices vary across different crop combinations and soil types. In conclusion, we hope that future interdisciplinary collaborations and innovative molecular technologies will further enhance the predictive capacity of agroecosystem C models, providing more practical, sustainable, and evidence-based solutions for global food security and environmental protection.
Author Contributions
Conceptualization, X.Y. and X.H.; funding acquisition, X.Y.; writing—original draft preparation, X.Y.; writing—review and editing, X.H. All authors have read and agreed to the published version of the manuscript.
Acknowledgments
X.Y. acknowledges support by the Natural Science Foundation of Xinjiang for Distinguished Young Scholars.
Conflicts of Interest
The authors declare no conflicts of interest.
List of Contributions
- Shen, H.; Li, H.; Liu, H.; Wu, J.; Li, C.; Liang, Y. Effects of Furrow Corn Straw Mulch on Soil Erosion and Organic Carbon Loss in Sloping Farmland in the Black Soil Region. Agronomy 2025, 15, 66.
- Wang, Y.; Shan, T.; Zhang, P.; Li, M. Changes in Soil Organic Carbon and Enzyme Activity After Land Use Change in Northeast China. Agronomy 2025, 15, 91.
- Shi, Y.; Wei, X.; Sheng, L.; Yang, X. Effects of Nitrogen Fertilization on Soil CH4, CO2, and N2O Emissions and Their Global Warming Potential in Agricultural Peatlands. Agronomy 2025, 15, 115.
- Wang, W.; Jiang, Y.; Cai, S.; Li, Y.; Qu, J.; Sun, L. Synergistic Effects of Organic and Chemical Fertilizers on Microbial-Mediated Carbon Stabilization: Insights from Metagenomics and Spectroscopy. Agronomy 2025, 15, 1555.
- Li, H.; Li, J.; Han, Z.; Zhu, W.; Liu, Z.; Sun, X.; Fu, C.; Xiao, H.; Qin, L.; Mei, L. Characteristics of Soil Nutrients and Microorganisms at the Grassland–Farmland Interface in the Songnen Agro-Pastoral Ecotone of Northeast China. Agronomy 2025, 15, 2032.
- Jiang, F.; Chen, X.; Chen, Y.; Peng, C.; Yuan, Z.; Che, P.; Cao, G.; Chen, G. Nitrogen Addition Reshapes Soil Carbon Molecular Composition via Nitrate–Enzyme Interactions in Soybean–Maize Intercropping. Agronomy 2026, 16, 1145.
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