Soil carbon (C) inputs from straw management is an essential strategy to address climate change. However, how different straw management strategies regulate the contributions of plant- and microbial-derived C to soil organic carbon (SOC) and the overall soil C budget remains unclear. To address this concern, we examined the effects of various straw return strategies on soil C dynamics in a rice-based system, with a particular focus on SOC formation and composition. Relative to straw return alone, it combined with organic fertilizer application increased total lignin phenols, whereas the addition of decomposing inoculants further enhanced this plantderived C contribution via an activated transformation pathway involving higher phospholipid fatty acid (PLFAs) and enzyme activities (BG: beta-1,4-glucosidase; CBH: cellobiohydrolase). Organic fertilization favored the accumulation of fungal necromass C, while addition of decomposing inoculants promoted bacterial necromass C formation under straw return. Fungal necromass C played a dominant role in SOC stabilization under straw return, while bacterial necromass C better reflected changes and turnover in the microbial community involved in SOC formation. Overall, the two soil C input strategies regulated SOC composition through distinct microbial pathways (fungal versus bacterial necromass formation), emphasizing the need to integrate microbial community traits and metabolites into the design of straw management strategies for SOC formation and climate mitigation.

Continuous cropping with excessive fertilization in tropical vegetable production incurs soil acidification, microbial imbalance, and low nitrogen (N) use efficiency, which has raised increasing concerns about soil health and N-oxide (N2O and NO) emissions. To address these environmental challenges, innovative solutions like integrated cultivation systems with diversified crop rotations have become imperative. Although previous studies have shown that diversified crop rotation systems can improve soil health, increase crop yields, and reduce Noxide emissions, evidence for intensive vegetable cropping systems in tropical climates remains limited. Here, we conducted a 2-year, four-season plot experiment in a tropical vegetable field to examine the effects of crop rotation system (bitter gourd-eggplant-bitter gourd-eggplant) relative to continuous cropping system (eggplant-eggplant-eggplant-eggplant) on soil health, microbial community, and associated N-cycling gene abundance and N-oxide emission fluxes. Relative to continuous cropping, crop rotation exhibited significantly lower average emission factors of fertilizer-induced N-oxide emissions (N2O: 1.88 % vs. 2.32 %; NO: 0.15 % vs. 0.23 %). This reduction was likely attributed to changes in the composition of the soil microbial community, an increase nosZ gene abundance, alongside a decrease trend in mineral N content. Crop rotation also boosted vegetable equivalent yield by 124.29 % and improved soil health by 11.52 %, along with elevating enzyme activities related to C and N cycles. Lower N-oxide emissions under the crop rotation regime were also shown to be associated with higher soil health. Enzyme activities mediated N-oxide emissions in continuous cropping through biochemical constraints, while soil properties regulated emissions in rotation systems via physicochemical pathways. Our findings underscore that crop rotation rather than continuous cropping would benefit crop production, soil health, and reduce N-oxide emissions in tropical agriculture.

Agricultural soils significantly contribute to global nitrous oxide (N2O) emissions. Different cropping regimes alter soil properties and microbial communities, influencing N2O emissions under nitrogen fertilization. However, the underlying mechanisms in black soil are unclear. We conducted a microcosm experiment using black soil subjected to 15 years of different cropping regimes: farmland fallow with no anthropogenic intervention (FALL), maize-soybean rotation (MSR), continuous soybean (CSC), and continuous maize (CMC). Our results showed that N2O emissions were significantly higher in the FALL soil than in the other three cropping regimes, irrespective of exogenous N addition. This was mainly caused by the higher availability of C and N substrates, as well as the greater abundances of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nirK genes. Furthermore, the elevated N2O emissions in FALL soils were also associated with shifts in microbial community composition and interaction. N2O emissions in FALL soils may also be linked to the enrichment of key bacterial taxa (e.g., Pseudonocardia) within co-occurrence networks associated with N2O production, and the decline in the relative abundance of key species (e.g., Gemmatimonas) involved in N2O reduction. These findings highlighted that the N2O emissions from farmland fallow without human management represent a non-negligible source of greenhouse gasses, particularly given the sustained microbial activity that persists even in the absence of crops and fertilizer inputs. Therefore, under scientific cropping systems and with proper nitrogen fertilizer application, the goal of reducing nitrous oxide emissions from black soil could be achieved.

Stabilized soil organic carbon is the most persistent fraction of soil carbon and plays a key role in long-term climate mitigation, yet its global distribution remains poorly constrained. Here we integrate georeferenced soil profiles with a machine learning model to map stabilized soil carbon in the upper one meter of soils worldwide. Global stabilized soil carbon is estimated at 1304 petagrams of carbon, representing about half of total soil carbon and concentrated in wetlands and cold-temperate regions. Soil properties explain most of the spatial variation, whereas climate and management effects show threshold responses. We further define soil negative carbon potential, the proportion of stabilized carbon in total soil carbon, as an indicator of stabilization efficiency and mitigation potential. Increasing this metric is associated with lower greenhouse gas emissions and improved economic outcomes with minimal yield trade-offs. These results provide benchmarks for Earth system models and inform soil-based climate mitigation strategies. Stabilized soil organic carbon totals 1304 pentagrams carbon globally about half of total soil carbon concentrated in wetlands and cold regions shown by mapping upper one-meter soils using georeferenced soil profiles and high precision machine learning models.

Soil microbial communities face intense competition in nutrient-limited environments under fertilizer imbalanced inputs in agriculture, yet how these dynamics drive ecological and evolutionary consequences remain poorly understood. A 35-year field-plot experiment was used to investigate the effects of long-term nutrient imbalance on soil community structure, antibiotic production, and antibiotic resistance gene (ARGs) proliferation under different fertilization regimes, namely, no added nutrients without straw, Ch; PK-only fertilization, PK; NK-only fertilization, NK; NP-only fertilization, NP; NPK fertilization, NPK; and NPK fertilization with straw, SNPK. Metagenomics, UPLC-MS/MS, and HT-qPCR methods revealed that nutrient-imbalanced soils (Ch, PK, NK, NP, NPK) exhibited 14-805 % higher antibiotic concentrations and 11-594 % greater ARGs abundance compared to balanced SNPK soils. Nutrient imbalance intensified microbial competition, evidenced by increased extracellular enzyme activities and negative species correlations in co-occurrence networks. Microbial abundance and alpha-diversity declined by 8-24 % in nutrient-imbalanced soils, alongside functional specialization (e.g., acetate fermentation and phosphorus storage). Balanced SNPK soils fostered stable microbial networks, efficient nutrient cycling, and lower antibiotic/ARG levels but paradoxically enriched mobile genetic elements, potentially accelerating ARGs spread. These findings underscore that long-term nutrient imbalance exacerbates microbial chemical warfare, elevating antibiotics and ARGs accumulation as adaptive responses to resource scarcity. This work provides actionable insights for policymakers and farmers to optimize fertilization strategies, addressing both agricultural productivity and emerging public health challenges posed by soil resistomes.

Plant litter constitutes a primary source of soil organic carbon (C) and nutrients in terrestrial ecosystems. Litter chemical composition critically regulates the formation and bioavailability of soil organic C fractions to microorganisms, thereby governing nitrogen (N) transformation processes and nitrous oxide (N2O) emissions. Nevertheless, the C-N coupling process driven by litter chemistry and its impacts on N2O emissions have received relatively little attention. Here, we collected litter samples from five >30-year-old tea tree varieties and examined the effects of their litter chemistry on soil organic C fractions, N transformations, and N2O emission pathways using 15N isotope tracing. Results revealed significant inter-varietal differences in the lignin and cellulose content of their leaf litter. Litter cellulose content positively regulated soil labile C contents, particularly dissolved organic carbon (DOC). Elevated DOC concentrations enhanced nirK + nirS gene abundance and gross NO3- consumption rates, amplifying co-denitrification contributions to enhanced N2O emissions. Soil C-acquiring enzymes involved in cellulose degradation (β-glucosidase and cellobiohydrolase) further stimulated co-denitrification-derived N2O emissions. Overall, soil DOC emerged as the central driver linking soil C dynamics and N2O emission pathways. These mechanistic insights significantly advance the predictive modeling of terrestrial N2O fluxes based on litter chemistry parameters. Furthermore, they enable optimization of N2O mitigation through precision management of pruning residues in tea plantations.

Rice paddies are a major source of methane (CH4), and effective mitigation strategies are urgently needed. Biochar has been proposed as a promising option; however, quantitative effects on CH4-cycling microbial processes and their underlying mechanisms remain unclear. Here, we conducted a meta-analysis and a random-effects model to evaluate the effects of biochar on CH4 emissions, crop yield, and key microbial functional genes and soil properties, drawing primarily on studies conducted in China. Overall, biochar application reduced CH4 emissions by 26.4% and increased rice yield by 6.2%. These responses were associated with enhanced plant biomass, which suppressed methanogen activity while stimulating methanotrophs, likely mediated by increased root oxygen release and rhizosphere carbon availability. Notably, the decreased mcrA/pmoA ratio highlighted a shift in microbial functional balance favoring CH4 mitigation. Our study provides a more comprehensive synthesis by linking biochar-induced changes in microbial functional genes to CH4 mitigation and crop productivity. These findings offer quantitative evidence and practical guidance for biochar application in climate-smart and sustainable rice cultivation.

The effect of ectomycorrhizal (ECM) fungi on the absorption and transport of heavy metals by host plants remains elusive. We experimentally assessed rapid cadmium (Cd) diffusion by two species of Suillus mycelium. Furthermore, we evaluated Cd absorption by ECM Pinus thunbergii Parl. and used transcriptomics to study the gene expression of P. thunbergii under Cd stress. In vitro experiments revealed that Cd2+ was transported through the apoplastic space more rapidly than through the mycelial symplast. The net Cd2+ influx rates in epitaxial hyphae were the highest, followed by those in the mantle of P. thunbergii inoculated with Suillus, whereas the lowest influx rate was found in the ECM-free fine root portions. Under Cd stress, the expression levels of PtZnTs, PtZIPs and PtHMA2 in ECM P. thunbergii roots were significantly higher than those in non-mycorrhized P. thunbergii. The assessment of Cd distribution in P. thunbergii revealed that Cd was transported to the needles of ECM P. thunbergii after 48 h; however, it was not detected in non-mycorrhized P. thunbergii. The essential element Cu exhibited similar results as the non-essential element Cd. Furthermore, two species ECM fungi Suillus accelerates the uptake and transport of Cd in the host plant P. thunbergii.

Paddy fields with excessive fertilizer application are potential N2O emission hotspots, which profoundly affect the greenhouse effect. Unlike prior regional models assuming uniform fertilization and static atmospheric N2O concentration, this study focuses on simulating the effects of fertilization heterogeneity and dynamic atmospheric N2O concentration on daily field-scale N2O emissions. Accordingly, this study presents a hybrid model (NAU-RSP-N2O) that combines multi-source remotely-sensed data, ML algorithms, and the water-air gas exchange model to predict daily field-scale N2O emissions in paddies. Firstly, we built Bayesian-optimized ML models using critical water quality parameters to predict dissolved N2O and incorporated SHAP analysis for interpretability. Secondly, the remotely-sensed data (fertilization information, LST) were used to drive models of water quality parameters, capturing their complex spatiotemporal changes. Finally, the water-air interface gas model considering the dynamic atmospheric N2O concentration simulated daily field-scale N2O emissions in paddy fields. The model demonstrated an average R2 of 0.72, with MAE of 1.56 mg center dot m-2 center dot d-1 and RMSE of 1.65 mg center dot m-2 center dot d-1. The NAU-RSP-N2O model effectively simulated daily field-scale N2O emissions and spatiotemporal patterns, highlighting the critical role of nitrogen management and atmospheric N2O levels in controlling emissions. Our findings present a novel approach for the large-scale prediction of N2O emissions from paddy fields, applicable across diverse rice-growing regions in China.

Bacillus velezensis SQR9 (SQR9) is known to not only promote plant growth and exert biocontrol but also to mitigate soil greenhouse gas (GHG) emissions. However, its effects on the soil organic carbon (SOC) pool, carbon footprint and net eco-economic benefits (NEEB) under field conditions remain poorly understood. We implemented a four-season field trial in tropical vegetable fields using two cropping patterns: continuous eggplant monoculture and a bitter gourd-eggplant rotation. Within each pattern, four fertilization treatments were established: conventional mineral N fertilizer (CF), partial mineral N substitution with organic fertilizer (OF), OF combined with SQR9 application (OFB) and no fertilization (Control). The results showed that OF and OFB treatments significantly reduced N2O emissions, global warming potential and GHG emission intensity, while increasing vegetable yield and SOC accumulation compared with CF, with OFB showing the best overall performance under both cropping systems. These beneficial effects were primarily attributed to improved soil properties, reduced abundances of denitrification-related nirS and nirK genes, and increased nosZ gene abundance, indicating limited N2O production and enhanced its reduction to N2. Furthermore, SQR9 inoculation promoted SOC accumulation, probably by enhancing microbial diversity, promoting activities of carbon-cycling enzymes, and increasing the relative abundances of key taxa such as Arthrobacter and Marmoricola. Together, these changes contributed to a lower carbon footprint and higher NEEB under OF and OFB treatments relative to CF. In conclusion, this study provides the first field-scale evidence that organic fertilizer substitution combined with SQR9 inoculation can simultaneously reduce N2O emissions, enhance SOC accumulation, reduce carbon footprint, and improve NEEB sustainability in tropical intensive vegetable systems.

The persistent accumulation of antibiotic resistance genes (ARGs) in agricultural soils, largely attributed to the widespread application of organic fertilizers, poses a substantial risk to human health. Investigating the occurrence patterns and key driving factors of ARGs in soil-vegetable systems under different fertilization regimes is essential for addressing this pervasive public health issue. Here, a pot experiment was conducted to characterize the ARG profiles in soil, root, and leaf compartments and to examine the ecological associations between bacterial-fungal interactions and ARG distributions. The results showed that ARGs were notably enriched in vegetable roots, and the extensive overlap of ARG subtypes between soil and vegetable tissues indicates a close linkage between soil and plant-associated resistomes. The application of animal manure-derived fertilizers markedly increased the total ARG abundance and the proportion of high-risk ARGs in roots, concurrently with enhanced bacterial-fungal co-occurrence patterns. Bio-organic fertilizers containing Bacillus and Trichoderma significantly increased ARG abundance in leaves, which was associated with strong correlations between potential ARG-hosting and highly abundant ARGs. Proteobacteria, Gemmatimonadota, and Planctomycetota were identified as putative ARG-hosting bacterial taxa. Bacterial community assembly in soil was more consistent with the neutral community model and exhibited higher network complexity in association with fungal communities than in vegetable tissues. Bacterial-fungal interactions, mobile genetic elements, and soil properties were jointly associated with variations in soil resistomes and plant-associated ARG patterns. This study advances our understanding of the ecological distribution and regulatory drivers of ARGs in soil-vegetable systems and provides valuable insights for evaluating resistome-related risks under organic fertilization practices.

Acidic soils are global hotspots of nitrous oxide (N2O) emissions, and biochar has been proposed as a promising mitigation strategy. However, most current evidence comes from short-term studies, and the legacy effects and underlying mechanisms remain poorly understood. Here, we collected acidic soil samples from three sites with and without biochar application, representing short-term (3 and 5 years) and long-term (9 years) legacy effects. Using microcosm incubations, isotope-based source partitioning, and microbial analyses, we evaluated N2O dynamics and their microbial drivers. The short-term legacy effects of biochar significantly reduced N2O emissions by inhibiting gross N2O production and enhancing N2O reduction. This was primarily attributed to reduced nitrification-derived N2O, increased nosZ gene abundance, and enrichment of taxa carrying the nosZ gene, such as Rhodanobacter and Gemmatimonas. In contrast, long-term legacy effects markedly increased N2O emissions because biochar suppressed N2O reduction more strongly than its production. This was linked to reduced nosZ abundance, increased fungal denitrification, and depletion of dissolved organic carbon and denitrifying bacteria. Together, these findings reveal that the legacy effects of biochar on N2O emissions diverge over time, driven by changes in microbial nitrogen cycling pathways. These results underscore the importance of incorporating temporal and microbial perspectives when evaluating the long-term climate impacts of biochar and developing sustainable soil management strategies.

Understanding the drivers and mechanisms underlying variations in autotrophic (Ra), heterotrophic (Rh), and total soil respiration (Rs) is essential for improving carbon management in croplands. In this four-year field study (2018–2021) conducted in a maize system, we compared practices without straw (NS) and with straw mulch (SM). Random Forest analysis identified bulk density, soil temperature, soil inorganic carbon, and urease activity as the primary determinants of Ra, Rh, and Rs. Straw mulch improved soil biodiversity, species richness, α-diversity, and evenness. Piecewise structural equation modeling further showed that soil microenvironmental changes regulate substrate availability by altering soil biological properties, which subsequently shape bacterial communities and microbial metabolism, ultimately controlling Rs. Compared with NS, on average over the four-year study period, SM substantially enhanced Ra and Rh by 96.9% and 82.2%, respectively, and increased maize grain yield and aboveground biomass by 9.7% and 6.2%. Notably, SM shifted the net ecosystem carbon budget from negative to positive, indicating a pronounced carbon sink effect. Overall, our findings highlight the pivotal role of straw amendments in regulating Rs and its components and elucidating the pathways through which these effects occur. These results provide mechanistic evidence supporting SM as a climate-smart agricultural practice that can simultaneously enhance crop productivity and contribute to agricultural carbon sequestration strategies and carbon neutrality targets.

Although organic fertilizer application may affect the prevalence of antibiotic resistance genes (ARGs) and nitrous oxide (N2O) emissions, the knowledge regarding the potential linkages between ARG profiles and N2O emissions in agricultural systems remains limited. Here, a pot experiment was conducted to investigate the soil resistome characteristics and N2O emission dynamics under organic fertilizer (OF) and bio-organic fertilizer (BOF) applications using a SmartChip PCR platform and a static opaque chamber method. The results revealed distinct soil resistome profiles under different fertilization regimes. BOF treatment significantly reduced the abundance of soil ARGs and mobile genetic elements, while increasing cumulative N2O emissions. Planctomycetota, Gemmatimonadota, and Bdellovibrionota, which are key taxa shaping ARG profiles, were markedly reduced under BOF treatment, and this reduction was associated with decreased ARG abundance. The increase in N2O emissions under BOF was primarily associated with the reduction of ARG-hosting bacteria, which may have indirectly contributed to an increase in the abundance of AOB-amoA and nirK genes. Key fungal species identified within the co-occurrence network had a limited impact on N2O emissions and related functional genes. Additionally, OF and BOF markedly increased vegetable yield, thereby reducing yield-scaled N2O emissions compared with the no fertilizer applied. Collectively, these findings highlight that the soil resistome and greenhouse gas emissions induced by organic fertilizers should be jointly considered in comprehensive ecological risk assessments to inform and optimize sustainable fertilization strategies.

Nitrogen (N) management is critical for ensuring food security and mitigating greenhouse gas (GHG) emissions. In rice paddies, the effectiveness of N management in maximizing yields and minimizing N losses is highly dependent on local environmental conditions and thus varies widely across regions. However, the influence of optimized, site-specific N management on methane (CH4) emissions remains poorly quantified and is not reflected in current IPCC Tier 1 methodologies. Here, we synthesize data from multiregional field experiments and conduct a meta-analysis to show that locally optimized N management practices-such as delayed fertilizer application, reduced N input, and deep placement-reduce CH4 emissions from rice paddies by 16%-21%. The experiments further show that these practices suppress CH4 emissions by lowering soil N availability and organic matter decomposition, thereby limiting substrates for methanogenesis. Combining survey data from 155 counties with machine learning models, we estimate that implementing optimized N strategies across China's rice-growing regions could reduce CH4 emissions by 16% while simultaneously increasing rice yields by 7%. These findings underscore the dual benefits of locally optimized N management for agricultural productivity and climate change mitigation, and provide a foundation for improving CH4 emission estimates under diverse management regimes.

Upland soils are a major anthropogenic source of nitrous oxide (N2O), and Jiangsu Province is one of the most intensive agricultural regions in China. However, a systematic understanding of regional N2O emission patterns and mitigation potentials at this provincial scale remains limited. Here we present a data-driven estimate of fertilizer-induced N2O emissions using regional and crop-specific emission factors (EFs) developed from 787 field observations across 122 studies. The mean N2O EF for upland croplands was 0.95 +/- 0.08% (95% CI), corresponding to total emissions of 34.89 +/- 6.19 Gg N yr-1. Southern Jiangsu contributed 57% of the total, while vegetables and cash crops were the dominant sources throughout the province. The estimated mitigation potential reached 11.60% (4.05 +/- 1.47 Gg N yr-1), with Wuxi showing the largest reduction capacity. Among optimized management practices, the combined application of inhibitors, reduced application of nitrogen fertilizer, and the use of controlled-release fertilizer were significant and effective in reducing N2O emissions by 31.13%, 26.78%, and 18.75%, respectively. Our findings reveal the spatially uneven distribution of N2O emissions and identify priority areas for implementing targeted mitigation strategies in Jiangsu's upland soils.

Abstract Rice paddies are among the largest anthropogenic sources of methane (CH4), yet substantial uncertainties persist in the long-term magnitude and spatiotemporal dynamics of the emissions. Here we show a spatially explicit global estimate of rice CH4 emissions from 1961 to 2020, leveraging a new high-resolution dataset and two Tier 3 modeling approaches (process-based and machine-learning-based). We find that global emissions have more than tripled over the past six decades, reaching a record high of 38.8 Tg CH4 yr−1 in 2020 based on the mean of the two Tier 3 estimates, both the rate and magnitude are substantially higher than conventional emission-factor-based inventories. Traditional rice-producing regions (e.g. Asia) dominated the increase due to expanded cultivation and intensified organic inputs, while Africa emerged as a rapidly growing source. Beyond trends in absolute emissions, the CH4 emission intensity (per unit of rice yield) declined across 70% of the global paddy area, mainly reflecting yield-driven efficiency gains. Notably, 44% of global rice production in the 2010 s occurs in countries with below-average emission intensity, with China being the largest contributor. By resolving long-term spatial heterogeneity with new data and models, this study provides a robust reassessment of the global rice methane budget and highlights pathways to reconcile food production with climate mitigation.

Antibiotic resistance genes (ARGs), recognized as emerging biological contaminants, pose a significant risk to human health due to the widespread and excessive antibiotic use. In this context, biochar has been identified as a promising and effective environmental remediation material for emerging contaminants. However, the effectiveness of biochar in mitigating antibiotics and ARGs remains highly uncertain across diverse environmental scenarios, thereby hindering a comprehensive understanding of its abatement performance. We conducted a meta-analysis to quantitatively assess the effects of biochar application on the presence of antibiotics and ARGs in soil-plant systems and manure. The results demonstrated that biochar application effectively reduced antibiotic concentrations in soil (-35.0%), plants (-59.1%), and manure (-47.9%), accompanied by substantial decreases in both absolute (-31.1% to -63.2%) and relative (-39.9% to -66.6%) ARG abundance. Notably, biochar exhibited a pronounced mitigation effect on high-risk ARGs in plants and mobile genetic elements (MGEs) in soil and manure. The abatement effect of biochar on antibiotics and ARGs varied with biochar properties, soil and manure properties, and experimental conditions, with the relative importance of these drivers differing markedly among environmental media. These mitigation effects were primarily attributed to biochar-induced alterations in soil and manure properties, bacterial communities, and MGEs. Importantly, this study also emphasizes that the potential ecological risks posed by biochar application can be simultaneously minimized. These findings advance our current understanding of the role of biochar amendments in addressing emerging contaminants across diverse environmental scenarios.

Understanding how agricultural management reshapes soil microbial organization to regulate ecosystem functions and greenhouse gas (GHG) dynamics is essential for developing climate-resilient farming systems. Here, we investigated how long-term (15 years) organic farming integrating rice–duck co-culture and hairy vetch rotation affects economic profit, soil health, and GHG emissions. This assessment combined 15N site preference analysis of nitrous oxide (N2O), 13C-labeled and DNA-based stable isotope probing, and microbial co-occurrence network modeling. Compared with the conventional rice–wheat rotation system, the organic farming system achieved a 2.5-fold increase in net economic profit. Long-term organic management enhanced soil health by restructuring cross-domain microbial networks and altering the abundance of keystone taxa. Microbial network complexity was negatively correlated with soil health, indicating that simplified microbial interaction structures may promote soil functioning. Organic farming reduced N2O emissions by 65%, which was associated with a lower nitrifier-to-denitrifier gene ratio and increased nosZ gene abundance. Methane emissions decreased by 12%, driven by a fivefold increase in active methanotrophs. Together, these results provide trait-based evidence linking microbial community organization to soil health improvement and GHG mitigation. Our findings advance fundamental understanding of the ecological mechanisms underlying organic management effects on soil biogeochemistry and offer a theoretical basis for designing low-emission, resilient agricultural systems.