Sulfur (S) is an essential nutrient for plant growth, influencing not only crop yields but also the composition and function of soil microbial communities. However, the differential effects of S fertilization on abundant and rare taxa in agricultural soils remain poorly understood. This study investigates the impact of different S fertilizer types on maize yield and the structure and stability of soil microbial communities, with a particular focus on abundant and rare taxa. S fertilization led to significant increases maize yield on two typical soils (black soil and sandy soil) (5.3–24.3%) and altered soil properties, including reducing pH (0.04–0.20) and increasing the available sulfur (AS) content (3.8–8.0 mg kg⁻¹), with ammonium sulfate having a more pronounced effect than elemental sulfur. Microbial analysis revealed distinct impacts on the diversity and community structure of both abundant and rare taxa. Elemental sulfur reduced the alpha diversity of abundant taxa more than ammonium sulfate, while NMDS indicated significant shifts in community structures, particularly among abundant taxa. Network analysis showed that S fertilization decreased the complexity of microbial interactions among rare taxa, with ammonium sulfate leading to simpler networks and elemental sulfur resulting in higher modularity. SEM highlighted that the diversity of rare taxa played a crucial role in influencing maize yield, alongside direct effects from soil properties such as AS and SAR (aryl sulfatase). Functional predictions demonstrated that amino acid metabolism and xenobiotic biodegradation and metabolism pathways were enriched in rare taxa, suggesting significant implications for soil health and crop productivity. This study provides new insights into the roles of abundant and rare bacterial taxa under S fertilization, emphasizing their importance in optimizing fertilization strategies for enhanced crop yield in specific soil types.

A well-developed rhizospheric system is crucial for maize to adapt to environmental stresses, thereby enhancing yield and quality. However, nitrogen (N) stress significantly impedes rhizospheric development and growth in maize. The genetic responses of maize’s rhizosphere to N stress under monocropping systems with exogenous inorganic N fertilization and intercropping systems reliant on biological N fixation are not well understood, especially regarding common and specific response genes. Therefore, through transcriptomic analysis, this study systematically investigated the gene expression and molecular responses of maize’s rhizosphere under two N supply regimes to N stress. The results showed that N stress generated 196 common and 3350 specific differentially expressed genes across the two systems, with the intercropping system exhibiting a stronger specific response. KEGG analysis revealed that the common genes, though few, are involved in key pathways essential for crop growth. Maize monocropping specific differentially expressed genes (MM) were enriched in pathways related to membrane lipids, cell wall formation, and intracellular signaling, while maize/alfalfa intercropping specific differentially expressed genes (MA) were linked to stress resistance through the glutathione metabolic pathway. WGCNA analysis identified five co-expression modules (CM). MA significantly increased the transcription factor families and structural domains directly targeting rhizospheric growth and development genes, including AP2, GRAS, Cys2His2 Zinc Finger, and LBD in CM blue. Conversely, MM significantly increased the transcription factor families and NAC structural domain targeting the promoters of N transporter protein genes in CM pink. This study emphasizes the importance of both common and specific genes in maintaining maize growth under suboptimal N supply in monocropping and intercropping systems.

Microbial inoculation represents an environmentally friendly biocontrol strategy that can enhance soil quality, improve crop growth efficiency, and promote sustainable agriculture. However, the long-term effects and ecological safety of non-native microbial inoculants in soil remain uncertain. Here, we explore and evaluate a safer and potentially more effective inoculation strategy—the reintroduction of native microbiota—to maintain agricultural ecosystem health. Native microbiota were extracted from black soil in northeastern China and reintroduced into the indigenous soil. Two treatments were established: original soil (control) and original soil with a mixture of native microbiota, each with nine replicates. Soil samples were collected at 0, 21, and 90 days post-inoculation. Using high-throughput sequencing and agronomic chemical analyses, we dynamically monitored soil nitrogen, phosphorus, and potassium contents, as well as microbial community composition. Crops were harvested at day 90 to measure dry weight, fresh weight, and SPAD values. The results revealed that the number of colonizing species was lower than the number of inoculated species, yet crop agronomic traits and chemical composition were significantly improved, particularly SPAD values and total phosphorus content. Soil abiotic factors exhibited limited resistance but retained partial recovery capacity, showing a notable increase in readily available potassium at days 0 and 21. Native microbiota inoculation promoted positive synergistic interactions within the microbial community. Furthermore, this study underscores the practical significance of cultivable microorganisms in agricultural applications. Collectively, our findings demonstrate the feasibility of native microbiota reintroduction, highlighting its potential to optimize soil microbial communities, enhance soil properties, and improve crop performance, thereby providing a scientific basis for soil remediation and sustainable agriculture.

Long-term intensive farming has degraded the structural stability of black soil in Northeast China. This study evaluated the effects of fermentation-derived materials and fungal-derived chitin on water-stable aggregates and microbial functional potential in this soil. Four treatments were established: sterile water control (CK), uninoculated fermentation broth substrate (W), live Trichoderma asperellum fermentation broth (P), and cell-free fermentation filtrate (F). Aggregate stability was monitored during a 60-day incubation, and metagenomic sequencing was performed on the most responsive 0.5–0.25 mm dry-sieved fraction. An exogenous chitin addition experiment was also conducted to evaluate the potential contribution of fungal cell-wall-derived chitin to aggregate stabilisation. The W, P, and F treatments increased the proportion of water-stable aggregates >0.25 mm, mean weight diameter, and geometric mean diameter, while decreasing fractal dimension. Among the treatments, the uninoculated fermentation broth substrate showed the strongest effect, particularly in the 0.5–0.25 mm dry-sieved fraction. Metagenomic analysis showed that the uninoculated fermentation broth substrate altered microbial community composition, changed the relative abundances of taxa such as Sphingomonas sediminicola, Priestia megaterium, and Trichoderma asperellum, and increased the relative abundance of carbohydrate-active enzyme-related genes, including those encoding glycosyltransferases, carbohydrate esterases, and glycoside hydrolases. Chitin addition also improved aggregate stability and altered microbial community structure. These findings suggest that the uninoculated fermentation broth substrate and fungal-derived chitin improved black soil aggregate stability, potentially through shifts in microbial community composition and carbohydrate-related functional potential. This study provides a scientific basis for using fermentation-derived materials to improve the structure of degraded black soil.