Background: The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown. Results: Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent. Conclusions: Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.

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.

Phosphorus (P) is an essential nutrient for maize growth, significantly affecting both yield and quality. Despite the typically high concentration of available P in black soils, the efficiency of crop uptake and utilization remains relatively low. This study aimed to evaluate the effects of different P fertilizers on maize yield, root growth parameters, and P use efficiency to identify strategies for optimizing P management in black soil regions. Field experiment results indicated that the combination of ammonium polyphosphate (APP) with other P fertilizers led to variations in yield and P fertilizer absorption efficiency. Various P fertilizers were tested, including diammonium phosphate (DAP), ammonium polyphosphate (APP), fused calcium magnesium phosphate (FCMP), a combination of DAP and FCMP (DAP+FCMP), and a control with no phosphate (CK). The results indicated that P application significantly increased maize yield, with APP (171.8 g/plant) outperforming other P application treatments. Different P fertilizer types significantly affect soil P content and the composition of P fractions. APP significantly increased both the total P (TP) and the proportion of inorganic P (Pi). Furthermore, APP application significantly improved root length (RL), surface area (SAR), and root activity (RA) compared to CK, leading to enhanced nutrient absorption. APP also significantly increased P uptake and utilization (REp, FPp, AEp, PHI, and PAC). In summary, by optimizing plant biomass and P uptake, APP can directly and indirectly influence maize yield. Improving rhizosphere properties through the selection of suitable fertilizer types can enhance fertilizer use efficiency and increase maize production.