Yonghong Wu

Microbiome‐mediated nitrate transformation is central to nitrogen cycling in agroecosystems, yet the governing principles linking microbial functional organization to ecosystem‐scale nitrogen outcomes remain poorly resolved. Here, combining ¹⁵ N tracing, high‐throughput quantitative PCR arrays and multi‐omics across a complete rice growth cycle with a tillering‐stage survey of 15 rice‐growing regions, we identify paddy‐field periphyton as a temporally dynamic dissimilatory nitrate reduction (DNR) system whose associated genes are geographically widespread. Under aerobic incubation (dissolved oxygen > 5 mg L ⁻¹ ), early‐stage communities are dominated by incomplete denitrifiers expressing norB/norC , producing transient N ₂ O, whereas later‐stage communities shift towards taxa active in dissimilatory nitrate reduction to ammonium (DNRA) and expressing nirB/nirD–nrfA/nrfH , promoting ammonium production. This transition suggests a phenology‐associated redistribution of nitrate/nitrite‐reduction pathways, redirecting nitrate‐derived nitrogen from gaseous intermediate production towards ammonium retention. Metatranscriptomics confirms coordinated suppression of denitrification and activation of DNRA, indicating a microbiome‐level transition from nitrogen loss to retention. Across the surveyed regions, both pathways were widespread but latitudinally structured, with the DNRA balance index showing a broadly unimodal pattern peaking at mid‐latitudes. Together, these results identify periphyton as an important dual‐functional DNR system linking microbiome organization to nitrogen cycling outcomes in rice paddies.

Sustainable residue management underpins agricultural productivity and climate resilience. Direct straw return (DSR) is widely adopted to enhance soil organic carbon (SOC) and fertility, yet its long‐term sustainability remains uncertain due to trade‐offs between C sequestration and greenhouse gas (GHG) emissions. By synthesizing 375 studies across China, we evaluate DSR's long‐term impacts on SOC, crop yield, and net carbon benefits (NCB) and propose an integrated strategy (DSR‐C) combining optimized tillage, nitrogen reduction, and microbial inoculation. Model‐simulated dynamics show that SOC accumulation and yield gains plateau over time, whereas the national‐scale NCB eventually turns negative due to persistent GHG emissions. Pareto optimization reveals an optimal trade‐off threshold (Knee point) at 1.4–5.5 years across regions. Significant regional heterogeneity governs these dynamics: upland wheat/maize systems sustain positive NCB for 6.4 to over 50 years, whereas rice‐dominated regions require temporal limits (1.6–3.5 years) to prevent transitioning from a net carbon sink to a net carbon source. Beyond these critical windows, yield increments stagnate while ecological trade‐offs intensify. By highlighting the dynamic, transient nature of agricultural carbon sinks, these findings provide a quantitative blueprint for region‐specific adaptive residue management, offering broad global relevance for scaling climate‐smart agriculture and accelerating decarbonization under future global change.

Microbial biofilms at soil–water interfaces mediate carbon exchange between soils and the atmosphere, yet whether substrate state alters their climate sensitivity remains poorly understood. Here, we analyzed 1080 rice-paddy sites across 26 regions of China to test whether soil organic carbon (SOC) regulates periphytic biofilm organic carbon (PB-TOC) responses to warming. SOC emerged as the dominant predictor of PB-TOC and showed a statistically supported threshold at ∼20 g kg–1. Below this threshold, PB-TOC increased with SOC and was positively associated with mean annual temperature and precipitation, consistent with a substrate-limited compensatory response. Above the threshold, PB-TOC approached saturation, and climate associations became negative, indicating greater vulnerability of carbon-rich interfaces. CMIP6-based projections suggest that under SSP5–8.5, China’s paddy-interface biofilm carbon pool could decline by about 0.70 Tg C by 2100, driven mainly by 4.5–6.8% losses in high-SOC regions that are only partly offset by modest gains in low-SOC regions (0.8–1.5%). These findings indicate that wetland climate responses are state-dependent and that substrate thresholds should be incorporated into carbon–climate assessments.

Persistent 4%–22% gaps in nitrogen (N) mass balances have hindered sustainable N management in paddy agriculture. Periphyton are known N sinks, yet their role in paddies remains unclear. We used 15N tracing in 840 paddies across China to quantify periphyton-associated N pools and their fate. Periphyton captured 6%–24% (mean: 12%) of the applied N fertilizer (i.e. ∼0.8 Tg N yr−1 nationwide), effectively accounting for the missing N in previous budgets. Most of the sequestered N was stored as bioavailable ammonium. Partitioning analysis revealed that periphyton-mediated N was subsequently released into residual soil N (512–640 kt), denitrification (56–128 kt) and ammonia volatilization (64–232 kt). Thus, periphyton act as transient N reservoirs, immobilizing N fertilizer early in the growing season and gradually releasing it through biomass decay. This overlooked pathway closes a critical gap in agroecosystem N cycling and supports more precise N management in rice systems.

The priming effect (PE) of soil organic matter (SOM) mineralization plays a crucial role in regulating soil carbon (C) dynamics. However, in flooded ecosystems like rice paddies, where the water‐soil interface is a critical hotspot for carbon turnover, the influence of periphytic biofilms (PB) on SOM mineralization and PE remains poorly understood. Here, we employed ¹³ C‐labeled PB and glucose to investigate PB‐mediated effects on SOM mineralization and PE in paddy soils. PB amendments significantly increased dissolved organic carbon (DOC), redox potential (Eh), and the microbial biomass carbon‐to‐nitrogen ratio (MBC:MBN), while reducing MBN and pH. These shifts stimulated CO ₂ emissions but suppressed CH ₄ emissions. In the early stage (day 7), CO ₂ PE was negative and inversely correlated with PB‐derived CO ₂ emissions, suggesting preferential utilization of labile PB‐C. As labile C was depleted, CO ₂ PE shifted to positive values under higher biomass inputs, with negative correlations to total nitrogen, implicating nitrogen mining. In contrast, CH ₄ PE remained consistently negative, indicating sustained suppression of SOM‐derived methanogenesis when PB served as an alternative substrate. Over 60 days, cumulative PE increased linearly with PB biomass ( R ² = 0.98, p < 0.05). In glucose‐amended soils, PB presence also lowered MBN and pH, reduced glucose‐induced PE, and enhanced net glucose‐C retention. These findings reveal PB's regulatory role by directly influencing SOM mineralization through stoichiometric constraints and indirectly modulating PE by restructuring soil biogeochemistry, offering mechanistic insights into C sequestration and greenhouse gas mitigation in paddy ecosystems.