Soybean and maize have important industrial applications, as their yield and production distribution plays an important role in supporting the global agricultural industries. In maize and soybean intercropping system, yield optimization relies on a comprehensive understanding of the complex interactions between above-ground and below-ground processes. Therefore, to investigate the impacts of various planting and separation methods on the spatial distribution of roots, soil moisture, nutrient uptake, photosynthetic physiology of leaves at different positions as well as yield advantages in soybean and maize intercropping, a two-year field experiment was conducted. The results indicted that maize root length density (RLD) increased by 24.3 %-25.5 % in non-separated maize rows and by 25.5 %-30.2 % in 10 cm from the maize rows as compared to the below-ground separated. While soybean RLD was reduced by 13.2–16.5 % in soybean rows and by 34.5 %-36.5 % in 10 cm from soybean rows. The change of the above parameters resulted in a noteworthy decrease in soil water content within the rows of maize, which was effectively mitigated by the below-ground separation. The photosynthetic rate (Pn) in middle and lower leaves of maize increased by 51.1 % and 39.2 % in above and below-ground separation, while less in upper leaves. Above-ground separation can alleviate the decrease of Pn in the upper and middle leaves of soybean, which was only decreased by 2.7 % and 3.0 % as compared with monocropping. The main constraint on maize production is the Pn of the middle and lower leaves, the upper leaves being secondary factors. Intercropping enhanced chlorophyll fluorescence parameters, while below-ground separation decreased it in the middle and lower leaves of maize. However, above-ground separation increased fluorescence characteristics in soybeans across all leaves. Intercropped maize benefited more from the below-ground than above-ground advantages, while the opposite was true for soybeans. The above-ground separation improves the overall LER and contributes the most to the yield advantages.
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