Intercropping is a traditional and sustainable planting method that can make rational use of natural resources such as light, temperature, fertilizer, water, and CO₂. Due to its efficient resource utilization, intercropping, in particular, maize and legume intercropping, is widespread around the world. However, the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome, and proteome analyses were compared between maize monocropping and maize–peanut intercropping. The results show that an intercropping system enhanced the ability of carbon fixation and carboxylation of maize leaves. Apparent quantum yield (AQY), the light-saturated net photosynthetic rate (LSPn), the light saturation point (LSP), and the light compensation point (LCP) were increased by 11.6%, 9.4%, 8.9%, and 32.1% in the intercropping system, respectively; carboxylation efficiency (CE), the CO₂ saturation point (Cisat), the Rubisco maximum carboxylation rate (Vcmax), the maximum electron transfer rate (Jmax), and the triose phosphate utilization rate (TPU) were increased by 28.5%, 7.3%, 18.7%, 29.2%, and 17.0%, respectively; meanwhile, the CO₂ compensation point (Γ) decreased by 22.6%. Moreover, the transcriptome analysis confirmed the presence of 588 differentially expressed genes (DEGs), and the numbers of up-regulated and down-regulated genes were 383 and 205, respectively. The DEGs were primarily concerned with ribosomes, plant hormone signal transduction, and photosynthesis. Furthermore, 549 differentially expressed proteins (DEPs) were identified in the maize leaves in both the maize monocropping and maize–peanut intercropping systems. Bioinformatics analysis revealed that 186 DEPs were related to 37 specific KEGG pathways in each of the two treatment groups. Based on the physiological, transcriptome, and proteome analyses, it was demonstrated that the photosynthetic characteristics in maize leaves can be improved by maize–peanut intercropping. This may be related to PS I, PS II, cytochrome b6f complex, ATP synthase, and photosynthetic CO₂ fixation, which is caused by the improved CO₂ carboxylation efficiency. Our results provide a more in-depth understanding of the high yield and high-efficiency mechanism in maize and peanut intercropping.

Intercropping of maize (Zea mays L.) and peanuts (Arachis hypogaea L.) (M||P) significantly enhances crop yield. In a long-term M||P field experiment with two P fertilizer levels, we examined how long-term M||P affects topsoil aggregate fractions and stability, organic carbon (SOC), available phosphorus (AP), and total phosphorus (TP) in each aggregate fraction, along with crop yields. Compared to their respective monocultures, long-term M||P substantially increased the proportion of topsoil mechanical macroaggregates (7.6–16.3%) and water-stable macroaggregates (>1 mm) (13.8–36.1%), while reducing the unstable aggregate index (ELT) and the percentage of aggregation destruction (PAD). M||P significantly boosted the concentration (12.9–39.9%) and contribution rate (4.1–47.9%) of SOC in macroaggregates compared to single crops. Moreover, the concentration of TP in macroaggregates (>1 mm) and AP in each aggregate fraction of M||P exceeded that of the respective single crops (P<0.05). Furthermore, M||P significantly increased the Ca2-P, Ca8-P, Al-P, and Fe-P concentrations of intercropped maize (IM) and the Ca8-P, O-P, and Ca10-P concentrations of intercropped peanuts (IP). The land equivalent ratio (LER) of M||P was higher than one, and M||P stubble improved the yield of subsequent winter wheat (Triticum aestivum L.) compared with sole-crop maize stubble. P application augmented the concentration of SOC, TP, and AP in macroaggregates, resulting in improved crop yields. In conclusion, our findings suggest that long-term M||P combined with P application, sustains farmland productivity in the North China Plain by increasing SOC and macroaggregate fractions, improving aggregate stability, and enhancing soil P availability.