Microbial versus plant carbon partitioning governs organic carbon formation pathways in paddy and upland soils under long-term fertilization.

Cadmium-containing straw return obstructs carbon storage and aggravates nitrogen deficiency in paddy soils.

Microbial diversity regulates mercury cycling in paddy soils.

The interaction between cadmium and water induces a nonlinear response in nitrogen cycling in paddy soils by restructuring microbial networks.

Multi-metal contamination is associated with microbial network simplification and functional adaptation in paddy soils: Insights from genome-resolved metagenomics.

Highly sensitive and portable digital microfluidics for on-site quantitative analysis of soil microbial counts.

Stage-dependent counteracting effects of biochar on arsenic mobilization and immobilization in paddy soil.

Phenological stage-specific DOM transformations sustain N2 fixation during rice growth in paddy soil

The vertical distribution and redox-dependent mobilization of arsenic in naturally contaminated karstic paddy soils from southwestern China

Differential effects of periphyton and rice straw decomposition on arsenic mobilization and methylation in flooded paddy soils.

Selenium (Se) application can reduce toxic element accumulation in rice, yet the mechanistic basis linking Se to rhizosphere oxygenation and Fe barrier formation remains unresolved. In a 103 day greenhouse pot experiment, sodium selenite was applied to multicontaminated paddy soil either as a soil amendment (1 mg kg-1) or foliar spray (40 mg L-1), with an untreated control. Soil Se application reduced grain concentrations of cadmium by 54%, arsenic by 34%, lead by 41%, chromium by 21%, nickel by 42%, and cobalt by 39%; foliar application achieved reductions of 12%-41%. To resolve the underlying mechanisms, we integrated planar optode and DGT-LA-ICP-MS imaging with physiological and molecular analyses. Selenium stimulated auxin accumulation by 2.74-fold and upregulated auxin biosynthesis and signaling genes (OsYUCCA1, OsTAA1, OsARF19), expanding constitutive aerenchyma from 34% to 65% of cortical area and sustaining radial oxygen loss. The resulting increase in rhizosphere oxygenation decreased labile Fe and Mn fluxes by 54%-89%, consistent with Fe/Mn oxide precipitation, and increased root surface Fe plaque by 5.64-fold, collectively restricting toxic element mobility through adsorption and coprecipitation. These findings establish an auxin-mediated aerenchyma-radial oxygen loss-iron barrier cascade as the mechanistic basis for Se-induced restriction of toxic element uptake by rice.

Atmospheric deposition is a pathway of trace metal contamination in agroecosystems, yet how divergent soils regulate the behavior and crop uptake of newly deposited trace metals remains incompletely understood. Here, we combined a field soil-transplantation experiment and a greenhouse pot experiment that separately imposed foliar and root exposure using six paddy soils from six major growing regions of China. Results showed that soil properties governed the speciation, mobility, and rice accumulation of deposited metals. Copper (Cu), lead (Pb), and zinc (Zn) exhibited greater solubility and grain accumulation in lower-pH, lower-sorption, and southern-provenance soils, whereas arsenic (As) was more mobile and accumulated preferentially in higher-pH, SOM-rich northern-provenance soils with finer texture. The pot experiment indicated that foliar exposure dominated trace metal enrichment in leaves and husks, whereas root exposure contributed more strongly to grain As in several soils. Elemental mapping of the flag leaf-node junction measured by LA-ICP-MS revealed distinct tissue-association patterns under the two pathways. Soil redox fluctuations further differentiated metal behavior: Cu increased after drainage, whereas As peaked under flooding. These findings show that element- and soil-property-specific responses shape food-safety risks posed by atmospheric deposition and support region-specific soil and emission management.

Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.

Fipronil, a phenylpyrazole insecticide, is widely used for the management of rice pests; however, its environmental fate and potential risks in tropical paddy ecosystems to food safety under varying soil conditions remain insufficiently understood. A field study was conducted in a tropical paddy ecosystem with sandy loam soil to evaluate the uptake, translocation, and dissipation dynamics of fipronil under different soil moisture regimes (flooded, saturated, and field capacity) with and without organic matter amendment. Fipronil and its metabolites in soil and plant samples were quantified using LC-MS/MS following the QuEChERS extraction method validated using standard method validation parameters. Fipronil applied at 75g a.i. ha⁻¹ (0.3G formulation) at 20 days after transplanting showed a progressive decline in soil residues from 0.70, 0.79, and 1.37µg g⁻¹ (day 1) to 0.01, 0.02, and 0.03µg g⁻¹ (30 DAA) under flooded, saturated, and field capacity conditions, respectively, indicating faster dissipation under flooded conditions. The dissipation of fipronil was 1.10% and 0.76% higher under flooded than saturated and field capacity conditions respectively. Organic matter-amended Fipronil soils showed higher persistence, with half-lives of 11.87 days (flooded without organic matter) to 13.75 days (field capacity with organic matter) in cropped soils and 20.82 days in non-cropped soil, indicating prolonged residue retention and potential environmental risks. Plant uptake was rapid, peaking at 2 days after application, followed by a gradual decline. Residue levels in plants were lower under organic amendment, indicating reduced bioavailability. Fipronil predominantly accumulated in roots, followed by stem and leaves, facilitating translocation to aerial parts. Among metabolites, Fipronil sulfone dominated, reaching 0.82µg g⁻¹ in field capacity, 0.63µg g⁻¹ in saturated, and 0.60µg g⁻¹ in flooded soils at 15 DAA, indicating oxidative persistence and higher toxicity. Sulfide (0.10µg g⁻¹ at 15 DAA), reflecting anaerobic degradation, while desulfinyl remained below 0.01µg g⁻¹. Harvest residues remained below MRL (< 0.01µg g⁻¹), indicating low health risk. These findings provide important scientific evidence for developing irrigation- and organic amendment-based pesticide management strategies to support safer fipronil use, residue regulation, and sustainable rice production in tropical paddy ecosystems.

The rice rhizosphere is a hot spot for nitrogen fixation using carbon sources from root exudates. We herein investigated the intensity of the nitrogen-fixing ability of each diazotroph interacting with other bacteria within the rhizosphere microbiota. We established the Test Tube Chemostat replicating Rice Rhizosphere (TCRR) based on four characteristics of the rice rhizosphere: root exudates, percolation, radial oxygen loss, and soil. The TCRR flora constructed by culturing paddy soil using TCRR showed the pH and high nitrogen-fixing ability of the rice rhizosphere. Twenty-five species of diazotrophs from the TCRR flora were categorized into two types: strains producing acetate and ethanol and strains utilizing them. A co-culture of both types resulted in high nitrogen fixation, mostly through the acetate interaction. High nitrogen fixation by the TCRR flora was further increased by an inoculation of both Klebsiella pasteurii NG13 and Azospirillum lipoferum FS. These results provide novel insights to develop biofertilizers.

Microbial arsenic (As) methylation is enhanced in flooded paddy soils, producing mainly dimethylarsenic (DMA), which can cause rice straighthead disease and large yield losses. Sulfate-reducing bacteria (SRB) have been implicated as primary As methylators, largely based on experiments employing molybdate as a selective inhibitor of SRB. However, the specificity of molybdate inhibition on SRB- and non-SRB-mediated As methylation remains inadequately evaluated. In this study, we showed that molybdate addition at 10 mmol kg-1 suppressed DMA production in flooded paddy soil by 41%, concomitant with decreased transcription of genes encoding dissimilatory sulfite reductase (by 78%) and arsenite S-adenosylmethionine methyltransferase (arsM, by 28%). Metatranscriptomic analysis showed that molybdate additions significantly suppressed the expression of 12 and 31 arsMs hosted by SRB and non-SRB, respectively. To decipher the effects of molybdate on As methylation, we performed pure culture experiments with representative SRB and non-SRB fermentative bacteria isolated from paddy soils. Molybdate specifically inhibited the growth of SRB and completely suppressed its As methylation. Molybdate also caused partial inhibition of As methylation by fermentative bacteria without affecting their growth. Integrated transcriptomic and targeted metabolomic analyses revealed that molybdate suppressed the As(III)-induced transcription of arsM and trx [encoding thioredoxin (Trx) required as a reductant for As methylation] and the biosynthesis of methyl donor S-adenosylmethionine (SAM), contributing to the partial inhibition of As methylation in non-SRB. These findings indicate that, although molybdate inhibits SRB growth specifically and the associated As methylation, it can also cause nontarget effects on As methylation mediated by fermentative bacteria, which should be taken into account when interpreting microbial contributions to As methylation in flooded paddy soils.

Novel nitric oxide dismutase drives effective NO degradation in oxygenic denitrification.

Deciphering the microbial and physicochemical pathways of biochar-based fertilizer in driving resource-use efficiency: A comparative study of two contrasting acidic soils.

Contamination by potentially toxic elements (PTEs) in soil-rice systems poses serious threats to food safety and human health. A total of 225 soil samples and 90 rice samples were collected from typical rice-growing areas in Chongqing, Southwestern China, to investigate PTE sources and transfer in the soil-rice system. The concentrations of 11 PTEs (As, Cd, Cr, Cu, Hg, Mn, Mo, Ni, Pb, Se, and Zn) were determined, and their sources and migration behaviors were investigated using a Positive Matrix Factorization (PMF) model combined with enrichment and transfer indices. Results showed that Zn and Mn dominated in soils, while As, Cd, and Hg exhibited pronounced spatial heterogeneity and signals of exogenous disturbance. PMF identified five pollution sources in soils: geological background (39.5%), agricultural sources (34.8%), light industrial activities & sewage irrigation (17.8%), arsenic-enriched urban disturbance mixed source (5.7%), and industrial emissions & atmospheric deposition (2.2%). Within rice plants, Cd, As, and Se were notably enriched in roots (BCF > 2.6), while grain translocation was limited, indicating a protective barrier. PMF source analysis for rice identified industrial activities & traffic (40.8%), agriculture & irrigation water (34.5%), and coal combustion & waste disposal (24.7%) as major contributors. Transfer coefficient patterns suggested element-specific translocation within rice plants, with Cd showing relatively stronger upward movement, Zn preferentially enriched in stems, and grain accumulation remaining low for most elements. This study provides insights into PTE source-associated patterns and transfer dynamics in soil-rice systems, providing a theoretical basis for paddy soil remediation and agricultural product safety management.

Synthetic herbicides pose environmental and health risks, driving the search for safer plant-derived alternatives. We isolated a novel aryltetralin lactone lignan from Taiwania flousiana, identified as 4-O-α-thevetopyranosyldiphyllin. The compound showed potent pre- and postemergence herbicidal activity against 13 monocot and dicot weeds, with IC50 values ranging from 0.18 to 4.72 μg/mL. Under greenhouse conditions, foliar application at 80 μg/mL for 7 days achieved over 85% inhibition in two test weeds, comparable to glyphosate. It exhibited systemic translocation and selectivity in crops such as rice. Soil degradation half-lives were 25.1 days in paddy soil and 63.0 days in vegetable soil. The compound disrupted microtubule organization by inhibiting tubulin polymerization, specifically binding to β-tubulin (TUB7) with a high affinity of -8.30 kcal/mol, as confirmed by molecular docking and dynamics simulations. These results indicated that 4-O-α-thevetopyranosyldiphyllin was a promising lead compound for the development of a new class of systemic herbicides targeting β-tubulin.