Soil microbial response to warming may potentially contribute to the positive priming effect, i.e., accelerating the decomposition of native soil organic carbon (SOC) under the outsourced carbon (C) input. Investigating microbiota that metabolize the outsourced C is essential to deciphering the mechanism of priming effect in response to warming and thus mitigating the SOC loss under warming climate. In this work, we monitored the priming effect at 25 degrees C, 35 degrees C and 45 degrees C over four weeks with weekly addition of 13C-glucose, and subsequently revealed microbial assemblage metabolizing glucose with the DNA stable-isotope probing (DNA-SIP) method. Warming initially inhibited the priming effect, and decreased bacterial alpha-diversity, K/r-strategists ratio (K/r) and recalcitrant C/labile C gene ratio (R/L) in week 1, suggesting that at the onset of the outsourced C input, the increased proportion of r-strategists preferentially utilize the added glucose over SOC to meet their C and energy demands. Yet, in week 4, positive priming effects were intensified by warming with up to 3.8-fold increase at 45 degrees C. Additionally, the primed C was positively correlated with K/r, R/L, and the abundances of chitin degradation genes in week 4. These functions concurred with an increase in the abundance of resource-acquisition strategists such as Streptomyces affiliated to Actinobacteria under warming conditions over time. From week 1 to 4, warming induced a distinctive change in glucose-assimilating bacterial community compositions with a particular decrease in the relative abundance of Actinobacteria while an enriched abundance of Chloroflexi. Taken together, warming-triggered change of priming effect depended on alternation of microbiota and metabolic function over time. These findings provide important insights of how warming mediates microbial metabolic use of fresh C and subsequent SOC mineralization, reflecting the positive feedback between soil C emission and climate warming.

Organic cultivation represents an environmentally friendly agricultural practice with the potential to enhance soil microbial diversities and functions. However, the mechanisms by which soil microbial communities regulate microbial metabolic efficiency under organic cultivation remain to be elucidated. Herein, the rice rhizosphere soil samples from three sites in Northeast China were compared for the differences in soil chemical properties, microbial biomass, enzyme activities, and microbial community diversities between organic and conventional rice cultivation at different growth stages. We also analyzed the contributions of these factors to the changes in microbial carbon use efficiency (CUE). Results showed that organic cultivation increased soil pH and available nutrient contents, alleviated microbial carbon and nitrogen limitations, and consequently improved microbial stoichiometric homeostasis and CUE. Conversely, microbial enzyme activities were significantly higher in conventional cultivation than in organic cultivation, especially during the later stages of rice growth. This resource allocation strategy of microorganisms led to a reduction in microbial diversity, biomass, and ultimately, a decrease in microbial CUE. Random forest analysis showed that the content of soil available nitrogen and the threshold element ratio for carbon: nitrogen (TERC:N) were most important predictors of microbial CUE. Additionally, we identified that Geobacteraceae-associated genus, Woesearchaeales-associated genus, Ferruginibacter and Propioniciclava had significant effects on microbial CUE at all three sites. Further, network analysis and partial least squares path model (PLS-PM) revealed that the specific microbial assemblies with high rrn copy number enhance microbial CUE by increasing biosynthesis. This study underscores the potential of organic farming in enhancing soil microbial CUE to mitigate ecosystem carbon losses, providing valuable insights for optimizing land management strategies to achieve soil carbon sequestration and advance sustainable agricultural practices.

Context: Soybean monoculture aggravates soil acidification and increases incidence of soybean root rot, thus seriously restricting soybean production. Although soil amendments are widely adopted to mitigate soil-borne diseases and enhance crop yields, the mechanisms for improving soil health remain unelucidated. Objective: This study employed microbial co-occurrence networks and ecological resistance indices to examine how soil amendments reshape microbial diversity, composition, and stability (bacteria, fungi and archaea), and to elucidate the mechanisms through which they alleviate continuous cropping obstacles in soybean. Methods: Based on a three-year field experiment combined with an in vitro co-culture experiment, no soil amendment (CON), lime (LM), lime with straw (LMSS), lime with cow manure (LMCM), crude chitin (CC), and commercial Si-Ca-K-Mg (CSC) amendments were applied to treat severe continuous cropping obstacles in soybean fields. This study evaluated the potential relationships among soil microbial communities, soybean root rot incidence, and soybean yield in response to different soil amendments. Results and conclusions: Soil amendments effectively decreased the soybean root rot incidence and increased soybean yields, with CC showing superior efficacy, achieving a 70 % reduction in disease incidence and over a 30 % increase in yield. Soil amendments noticeably enriched potentially beneficial species with diseasesuppressive and growth-promoting functions, such as Pantoea BASV4, Bacillus BASV6, Humicola FASV38, Tausonia FASV5, and Mortierella FASV6. Co-occurrence network analysis revealed that amendments enhanced microbial network stability and complexity. Notably, CC induced the most resistant microbial communities, whereas LMSS exhibited lower microbial resistance. Structural equation modeling and correlation analysis identified microbial resistance as a critical factor linking disease suppression and yield enhancement. In vitro coculture experiments confirmed that the rhizosphere bacterial suspensions from amended soils inhibited Fusarium oxysporum hyphal elongation, correlating strongly with the abundance of beneficial bacteria. These results demonstrated that targeted amendment application alleviates continuous cropping barriers by recruiting beneficial microbiota and enhancing community resistance. Implications: This study identifies the optimal amendment to ameliorate continuous cropping barriers, offering a theoretical framework and practical guidance for maintaining soil health and promoting crop production.

The conversion of crops to pastures has the potential to mitigate soil organic carbon (SOC) losses associated with long-term intensive cropping. Despite increasing evidence of pasture-induced SOC accumulation, microbial mechanisms governing the spatial sequestration of SOC within aggregate fractions throughout the soil profile of Mollisols under long-term monoculture remain largely unknown. Given the vigorous and deep rooting system of alfalfa, we investigated how the initial conversion of a > 50-year maize monoculture to alfalfa pasture influences SOC sequestration within aggregate fractions across the soil profile and associated microbial communities over the growing season. Alfalfa establishment significantly increased SOC in the mineral-associated aggregate fraction (P < 0.05), with the most pronounced accumulation at 40–50 cm depth (P < 0.01). Correspondingly, alfalfa cultivation markedly shifted microbial community composition. At the flowering stage, copiotrophic taxa such as Subgroup 10 and nitrogen-cycling groups including Nitrospira were enriched across aggregate fractions. At maturity, oligotrophic taxa including Pseudoxanthomonas, Massilia, and Moraxellaceae became more abundant. Notably, alfalfa-driven shifts in microbial community assembly were consistent across aggregate fractions. These findings demonstrate that conversion from maize to alfalfa promotes SOC accumulation in mineral-associated aggregates of deep soil layers. The enrichment of plant species-specific microbial taxa across aggregates suggests enhanced transformation and stabilization of fresh plant-derived carbon inputs.

Pod dehiscence, also known as pod shattering, is the process by which mature pods open and release their seeds at physiological maturity. In vegetable soybean (Glycine max L.), premature seed release from mature pods is a major cause of yield loss during seed production. As pod dehiscence occurs within the dehiscence zone, understanding the physiological mechanisms governing its formation and degradation is essential. To investigate these mechanisms, we compared the activities of pectinase, polygalacturonase (PG), cellulase, indole-3-acetic acid (IAA), gibberellin (GA), abscisic acid (ABA) and zeatin (ZA) in the pod ventral sutures of dehiscent vegetable soybean and indehiscent grain soybeans. The ventral sutures of dehiscent vegetable soybean exhibited significantly higher activities of pectinase, polygalacturonase, and cellulase, but lower concentrations of IAA and GA than those of indehiscent grain soybean. Reduced levels of IAA and GA in the dehiscence zone were associated with increased activities of cellulase, pectinase, and polygalacturonase activities, which may accelerate cell wall degradation and promote lignification, thereby promoting pod dehiscence.

Sustainable intensification of agriculture is dependent on higher fertiliser inputs and balanced nutrient management to increase crop productivity while simultaneously maintaining soil health. Since the long-term use of higher doses of inorganic fertilisers can negatively affect soil ecosystem stability, manure inputs may be a viable alternative that also alters microbial phosphorus (P) metabolism. Using metagenomics and genome binning, we evaluated the shifts in microbial communities and P-cycling genes in a Mollisol after substitution of mineral fertilisers with manure additions. Soil samples were collected at different depths (0-10, 10-20, 20-30, and 30-40 cm) from a field that had undergone 30 years of mineral fertiliser application before transitioning to the following four treatments, each of which was applied for 12 years: no fertilisers (CK), continued mineral fertilisers (CF), CF with 15 Mg ha-1 of cattle manure per year (FM1), and CF with 30 Mg ha-1 of cattle manure per year (FM2). In comparison with CF, CK decreased the concentrations of most P fractions, whereas manure addition had positive effects on P fractions. Different fertilisers yielded distinct P-related microbial communities and networks across various soil depths. At the functional gene level, manure application increased the relative abundance of inorganic P solubilisation genes, particularly in the 0-10 cm and 30-40 cm layers, while reducing the abundance of P-starvation-response genes across all layers. Both mineral fertilisers and manure enhanced the abundance of organic P mineralisation genes in the 10-20 cm and 30-40 cm layers. The abundance of the gcd gene showed a positive relationship with inorganic P solubilisation in the surface layer, whereas those of the ppk1, ppa, and ppx genes were positively correlated with inorganic P solubilisation in the subsoil layers. The construction of metagenome-assembled genomes (MAGs) showed that deeper soil layers offer greater potential for harbouring novel and undescribed microbial lineages and functional genes involved in the P cycle. Overall, supplementation of mineral fertilisers with manure additions significantly affected not only the P fractions but also the P metabolic capacities of the soil microbiome, influencing the soil P cycle in fertilised ecosystems.

Abstract Climate change, characterized by rising CO2 concentrations and warming, impacts soil microbial processes regulating nitrogen (N) availability for crops. This study aimed to elucidate the responses to elevated CO2 and warming of rhizosphere microbial communities involved in N mineralization under major cereal crops. A controlled pot experiment was conducted in open-top chambers with four treatments: ambient conditions (Control), elevated CO2 (700 ppm), warming (2°C above ambient), and their combination. Maize, wheat, and rice were grown in a Mollisol for 92 days. Functional microbial communities were characterized by sequencing of the chiA and pepA genes, which encode key enzymes involved in chitin and peptide degradation, respectively. Principal coordinate and network analyses revealed distinct, crop-specific microbial assemblages and responses to climate factors. Rice rhizosphere communities exhibited significantly greater functional resilience under elevated CO2 and warming compared with those of maize and wheat. This resilience may be attributed to anaerobic conditions of flooded rice paddies, which buffer temperature and moisture fluctuations and promote microbial functional redundancy, enabling species replacement as a primary adaptive response. In contrast, dryland systems (maize and wheat) showed higher sensitivity, with disrupted microbial networks, lower abundance of key taxa, and greater variability in predicted N mineralization potential. These findings highlight that crop-specific rhizosphere environments shape the resilience of N-cycling microbiomes under climate change. The study provides practical implications for N-fertilizer management and the design of climate-resilient cropping systems that maintain soil N supply in a warming and CO2-enriched climate.

Postharvest dehydration and senescence limit the shelf life of vegetable soybean. This study investigated the effects of pre-harvest potassium (K) fertilization and postharvest low-temperature storage on quality preservation, using physiological assays, widely targeted metabolomics, and transcriptomics in pods produced under K-deficient (K0) and K-sufficient (K120) conditions and stored at 4 °C or 25 °C. K120 seeds contained significantly higher K than K0 seeds (15.0 vs. 12.0 mg g−1 DW), confirming differential nutritional status. After 9 days of storage, low temperature combined with optimal K nutrition markedly reduced the fresh weight loss rate to 11.3%, compared to 66.5% under ambient temperature without K fertilization. This preservation was associated with suppressed lipoxygenase (LOX) activity, polyunsaturated fatty acid (PUFA) oxidation, and downregulation of α-linolenic acid metabolism and subsequent downregulation of JA biosynthesis. Metabolomic analysis further revealed co-enrichment of flavonoid and phenylpropanoid pathways, suggesting co-regulation of antioxidant defense with JA-driven senescence. Exogenous methyl jasmonate treatment increased endogenous JA levels and accelerated physiological maturation and senescence, confirming the promotive role of JA signaling; JA-mediated responses were closely linked with ethylene and abscisic acid (ABA) pathways. These results suggest that potassium nutrition and cold storage extend vegetable soybean shelf life by inhibiting LOX-mediated PUFA oxidation and JA-driven senescence signaling, within a broader metabolic network encompassing antioxidant defense and energy metabolism.

Soil acidification from long-term synthetic fertilizer use threatens agricultural sustainability. This study investigated the potential mechanisms by which long-term cattle manure application mitigates fertilizer-induced acidification in a high-organic-matter Mollisol. Soils were sampled from a decade-long field experiment with four treatments: no fertilizer (NoF), synthetic fertilizer alone (CF), and CF supplemented with 15 (CFM) or 30 Mg ha−1 (CFM2) of cattle manure. Samples collected in 2021 and 2022 from 0 to 40 cm depth were analyzed for soil pH, pH buffering capacity (pHBC), exchangeable H+ and Al3+, cation exchange capacity (CEC), exchangeable base cations, and responses to simulated acidification. Continuous synthetic fertilization decreased soil pH and pHBC, increased exchangeable Al3+, and depleted exchangeable base cations in the 0–20 cm plow layer. In the 0–10 cm layer, CFM2 raised soil pH to near-neutral conditions, 1.91 pH units higher than CF in 2022. Exchangeable Al3+ decreased from approximately 0.19 cmol kg−1 under CF to 0.09 and 0.04 cmol kg−1 under CFM and CFM2, respectively. NoF did not restore soil pH to its initial level. Cattle manure co-application increased soil pH, pHBC, CEC, and exchangeable K+, Ca2+, and Mg2+ in a dose-dependent manner. Under simulated acidification, soil resistance followed CFM2 > CFM > NoF > CF. The initial exchangeable base-cation pool under CFM2 was approximately 20% greater than CF, thereby providing a larger proton-neutralizing reservoir. These benefits were primarily confined to the 0–20 cm plow layer. Overall, cattle manure effectively mitigated synthetic fertilizer-induced acidification by rebuilding exchangeable base-cation pools and enhancing soil buffering capacity.

Different fertilization regimes strongly influence carbon cycling processes; however, the functional responses of microbial communities driving these processes remain poorly characterized. Here, metagenomic sequencing combined with binning approaches was applied to investigate the shifts in microbial composition and function related to soil carbon cycling in a 40-year fertilization experiment with six regimes in black soil. Fertilization altered the microbial assembly process, with chemical fertilization (CF) leading to a shift in community assembly toward deterministic processes through intensified heterogeneous selection compared to unfertilized control (NoF). Chemical fertilization plus straw application (CFS) significantly increased the abundance of genes related to recalcitrant carbon degradation (celF, chi, pel, and GE). Manure fertilization (M) increased the abundance of hcA associated with carbon fixation. While straw application (S) demonstrated no substantial impact on the functional gene profiles. The taxon-function co-occurrence network reveals that distinct key taxa exhibit convergent functional roles in carbon decomposition and transformation, whereas treatment-specialized taxa emerge as functional specialists, contrasting with these generalists. Both the carbon-cycling taxonomic groups and functional genes were governed by a shared suite of environmental factors (pH, Microbial biomass carbon, and Microbial biomass nitrogen), suggesting a consistent response of carbon-cycling functional genes and microbial taxa to environmental change. In addition, six metagenome-assembled genomes (MAGs) were found to harbor conserved carbon fixation genes (accA, icd, maeB), indicating their potential as biomarkers of soil carbon sequestration capacity. This study elucidates how long-term fertilization reshapes microbial carbon-cycling process, providing a genomic framework to guide sustainable soil management.

The synergistic mechanisms by which potassium high-efficiency (KHE) vegetable soybeans coordinate root exudation and microbial recruitment to enhance potasium absorption under low-K stress remain unclear. Integrating hydroponic and pot experiments, this study analyzed root organic acid exudation, soil potassium availability, microbiome structure, and isolated K-solubilizing bacteria using KHE and K low-efficiency (KLE) varieties. Results showed that under low-K stress, KHE plants exhibited a resilient exudation profile, notably surging malonic acid secretion. This trait mechanistically explains the effective soil K activation in pot experiments, indicated by significant rhizosphere acidification positively correlating with total K depletion. Concurrently, the KHE variety maintained a stable rhizosphere microbiome, characterized by the selective enrichment of specific bacterial (Paenibacillus, Rhodanobacter) and fungal (Penicillium, Aspergillus, Chaetomium) genera. To validate this, we isolated Paenibacillus strains BK1 and BK2 from the KHE rhizosphere. BK2 demonstrated potash feldspar activation (5.7

Atmospheric CO2 elevation promotes peanut biomass accumulation, yet the underlying molecular mechanisms remain unclear. This study investigated the physiological and molecular responses of two peanut cultivars (JH2 and JH54) to elevated CO2 (EC, 700 μmol·mol-1) versus ambient CO2 (CK, 400 μmol·mol-1) in open-top chambers, by analyzing photosynthetic traits, aboveground biomass, and leaf transcriptomic/metabolomic profiles. The results showed that EC significantly increased net photosynthetic rate, intercellular CO2 concentration, water use efficiency and biomass, but reduced stomatal conductance and pigment contents, with upregulated photosynthesis-related genes. Integrated multiomics revealed reprogrammed salicylic acid/abscisic acid signaling (lowering stomatal conductance and improving water use efficiency) and galactose metabolism (facilitating EC acclimation). Collectively, peanuts adapt to EC via coordinated transcriptomic-metabolomic adjustments in photosynthesis, hormone signaling and carbon metabolic reprogramming (especially galactose metabolism), providing a multilevel mechanistic insight into peanut's responses to rising atmospheric CO2.

Soil aggregates of different sizes provide distinct ecological niches for microbial communities, which perform specific functions in carbon (C) transformation. This highlights the importance of aggregate-scale microbial diversity in the sequestration of exogenous C sources, while relevant microbial mechanisms remain unclear. This study examined the effects of a decade-long organic amendment (cattle manure and crop residue) compared to chemical fertilizer application and a no-fertilizer control, on microbial community diversity and metabolic profiles across soil aggregate fractions in a Mollisol under a maize-soybean rotation system. 16S rRNA gene amplicon sequencing (Illumina MiSeq) and metagenomic sequencing (Illumina NovaSeq) were employed to characterize microbial taxonomic composition and functional gene profiles, respectively. Relative to the no-fertilizer control, manure amendment increased soil organic carbon (SOC) by 33–72% and nitrogen (N) accumulation by 33–95% across aggregates. Taxonomic analysis indicated that manure amendment led to a marked shift of microbial community composition, notably enriching copiotrophic Bacteroidota, which thrive in C-rich environments. Compared to the high C/N crop residue, the application of low C/N manure significantly reduced microbial community diversity and network complexity across aggregate fractions, but the changes were more pronounced in microaggregates. Metagenomic analysis further revealed significant upregulation of functional genes associated with hemicellulose and pectin degradation, while genes linked to chitin and lignin degradation were significantly downregulated across aggregate fractions. Moreover, a strong correlation was found between C and N mineralization genes. These findings suggest that long-term manure amendment, while enhancing SOC and specific microbial functions, may reduce microbial community structural complexity in C-rich environments. Thus, under manure amendment, the potential adverse effects of a less complex microbial community on the sequestration of quality SOC should be taken into account when developing fertilization strategies in Mollisol regions.

Pod dehiscence or pod shattering from mature soybean (Glycine max L.) is one of the most outstanding disadvantages in domesticated cultivars. Pod shattering in relation to 16 quantitative traits and 3 qualitative traits among 140 cultivars of vegetable soybeans, grain soybeans and small-grain soybeans was evaluated over two years. We found the pod shattering percentage is positively correlated with the number of productive branches, pod width, pod length, pod area, 100-seed weight, 1-seeded-pod percentage, 2-seeded-pod percentage and seed protein content, but negatively correlated with the plant height, pod height at the bottom, number of nodes on the main stem, 3-seeded-pod percentage, 4-seeded-pod percentage and seed oil content. The pod shattering percentage in vegetable soybeans is remarkably high, reaching up to 93%, 7.8 times higher than that of grain soybeans. A schematic model of the characteristics for shatter-susceptible and shatter-resistant soybean cultivars is proposed. The pod shattering in vegetable soybeans is related to the "umbrella-shaped" architecture and pod size. It is suggested to select lines with more 2-seeded and 3-seeded pods for vegetable soybeans, but a higher seed oil content and greater node number on the main stem for grain soybeans and small-grain soybeans, to avoid pod shattering in future breeding programmes.

Elucidating the intricate dynamics of microbial communities across soil profiles is essential for deciphering the mechanisms by which microorganisms regulate ecosystem functions. However, previous studies on soil microorganisms have predominantly centered on abundant taxa, neglecting the significant role of rare taxa in maintaining ecosystem functions. This study comprehensively analyzed the diversity and assembly processes of both rare and abundant microbial taxa in the profiles of Udic and Ustic Isohumosols in northeast China. We also explored the relative contribution of rare and abundant microbial taxa in maintaining ecosystem multifunctionality. Results showed that rare microbial taxa exhibited a higher diversity compared to abundant taxa, and rare microbial taxa occupied more central positions within networks. Furthermore, rare taxa displayed narrower ecological niche breadths and stronger phylogenetic signals, and their community assembly was predominantly governed by deterministic processes. In contrast, stochastic processes exert more pronounced influences on the assemblage of abundant taxa. Ecosystem multifunctionality was significantly reduced in deep soil horizons relative to the surface soil horizons. This is accompanied by close cooperation of microorganisms to cope with environmental stress in deep soils. This study highlights the pivotal role of rare microbial communities in shaping multifunctionality of ecosystems across the entire soil profiles.

Pod dehiscence or pod shattering refers to the opening and release of seeds from fully mature pods at ripening. The loss of seeds from mature vegetable soybean (Glycine max L.) pods is one of the most significant factors contributing to yield loss during seed production. To better understand the mechanisms of pod shattering in vegetable soybean, we conducted a comparative analysis of the moisture content, pod wall components, mineral elements, sucrose and soluble total sugars in pod valves during seeds filling. Five dehiscence vegetable soybeans and five indehiscence grain soybeans were examined in a field experiment. The pod valves of dehiscence vegetable soybeans exhibited significantly higher moisture, sucrose and soluble total sugar content at R5 (beginning seed) and R6 (full seed) stages, but lower at R8 (full maturity) stage than that of indehiscence grain soybeans. A faster dehydration rate and higher sugar transfer rate from R6 to R8 stage was observed in pod valves of vegetable soybeans than grain soybeans. The content of calcium, iron, and manganese in the pod valves was negatively correlated with the shattering percentage during the R5 and R6 stages. At the R8 stage, the content of carbon, total fiber and lignin is positively correlated with shattering percentage. The lower content of iron and manganese in the pod valves might be a signal affecting the transformation of photosynthetic products, and thus leading to fibrosis and lignification of pod valves. A diagram illustrating a possible mechanism of role of pod valve composition in pod dehiscence of soybean is developed.

The accumulation of heavy metals (HMs) and microplastics in soil has emerged as a major environmental challenge worldwide. In this study, a series of biochars were developed using hollyhock straw as the raw material to remediate soils co-contaminated with Pb, Cr, and Cd. Additional experiments were conducted to assess the impact of polyethylene microplastics (PE-MPs) on the efficacy of biochar in soil remediation. In this study, we utilized the inexpensive and readily available warm patches, which are composed of iron, vermiculite, and activated carbon, in combination with a green and economical deep eutectic solvent (MAG) as modifying agents for biochar. The warm patch and deep eutectic solvent-co-modified biochar (MAG-WIM/B) exhibited superior performance in immobilizing HMs, improving the soil physicochemical properties, enhancing the functional enzyme activity, and increasing the microbial community diversity of soil. Soil incubation experiments showed that the addition of MAG-WIM/B reduced DTPA-extractable Pb, Cr, and Cd contents by 50.8 %, 46.7 %, and 24.2 %, respectively, by day 82. Monte Carlo simulations further revealed a preferential adsorption of Pb in the ternary HM system. Moreover, the introduction of MAG-WIM/B led to a significant improvement in the urease activity and shifted the dominant microbial species from Proteobacteria to Actinobacteria. PE-MPs significantly limited the effectiveness of biochar in remediating HM-contaminated soil by altering its physicochemical properties and competing with HMs for the active sites present on biochar. This work provides a strategic framework for the remediation of soils co-contaminated with multiple HMs and PE-MPs.

Whether and how conventional (CP) and biodegradable microplastics (BP) affect viral communities and virus-carried antibiotic resistance genes (ARGs) in agricultural soils remains largely unknown. Here, we established a soil microcosm incubation with addition of 1 % (w/w) microplastics (MPs) in maize-cultivated soil that had been treated with different fertilizers for over 10 years, and the dynamic variations of viral communities and ARG profiles were investigated using a combination of metagenomic and metatranscriptomic methods. Our results revealed that BP, but not CP, significantly decreased viral α-diversity, changed viral community structure, community resistance and taxonomic turnover in all fertilized treatments. Caudoviricetes was the most dominate viral class and BP significantly increased the abundances of viral families (i.e. Phycodnaviridae) in all fertilized treatments, while CP altered the viral family abundance mainly observed in manure-amended soils. Also, BP was associated with increased ARG α-diversity, altered ARG community structure and community resistance, especially at the transcriptional level. Particularly, BP significantly enriched high-risk ARGs and mobile genetic elements (MGEs) in soils regardless of fertilization regimes. Correlation analysis revealed the important role of lytic viruses in shaping the abundance of high-risk ARGs and MGEs. Furthermore, BP induced more variations in reconstructed metagenome-assembled genome (MAGs), and significantly enriched high-risk ARGs carried by phage genomes. Co-occurrence patterns revealed three Actinobacteriota MAGs as primary viral hosts sharing high-risk ARGs with phages and containing multiple MGEs. Notably, we identified four viral genomes carrying ARG transcripts identical to their hosts. Both CP and BP differentially stimulated ARG expression in these virus-host systems, withmarkedlystronger effects observed in manure-amended soils. In conclusion, this study revealed a high risk of ARG dissemination induced by biodegradable MP residues regardless of fertilization regimes, while conventional MPs strengthen the ARG health risks mainly in manure-amended soils.

The mineralization of crop residue-nitrogen (N) is important for sustainable N supply to subsequent crops. However, the microbial mechanisms regarding residue-N mineralization over growth seasons are still unclear. We amended 15N-labelled maize and soybean residues to a Mollisol soil and found that, after three growth seasons, soybean plants utilized 43% and 37% of soybean and maize residue-N, respectively. Approximately 10.5% of soybean and 18.6% of maize residue-N were recovered in the labile N pools in soil. Over time, 82% of soybean residue-N was mineralized compared with 66% for maize residue-N. Greater increases in abundances of microbial functional genes involved in organic C decomposition, N mineralization, N2 fixation, and denitrification were observed in the soybean residue compared to the maize residue treatment. The study implies that soybean residue amendment may lower fertilizer N input more effectively than maize residue, considering the N balance between crop demand and soil supply in farming Mollisols.