Objectives Companion planting with potato onions can increase tomato yield. This study investigated the effect of co-cultivation on the rhizosphere soil functional microbial structure and the resulting nutrient absorption and distribution characteristics of tomatoes, aiming to reveal the microbiological mechanisms underlying interspecific interactions.

Methods A field experiment was carried out under shadding condition to examine the effect of co-cultivation on tomato yield and nutrient uptake.Three treatments were set up, including tomato monoculture, and co-cultivation of tomato with potato onion cultivar Wuchang, or Nong’an. The nutrient content of various parts of tomato plants was measured at 90 days after tomato transplanting (at tomato fruiting period). A pot experiment was also conducted, with the same three treatments as those in the field experiment, to measure root vitality, leaf chlorophyll content, and dry matter accumulation of tomato plants, and to calculate the competition coefficient (Ato) and relative yield (RYT) of tomato and potato onions under co-cultivation. Agar plating method was used to cultivate the microorganisms of the rhizosphere soil from the field experiment, PCR sequencing method was used to identify the species and relative abundances of functional bacteria and fungi, and to investigate the diversity of microbial structures.

Results 1) The co-cultivation promoted the absorption of N, P, K, Mn, Mo, Si, and B by tomato, and increased the allocation proportion of the nutrients in tomato roots and fruits, while decreasing the allocation in tomato leaves, resulting in an increase in nutrient utilization efficiency. 2) The co-cultivation significantly increased the shoot and root dry weight, as well as the root/shoot ratio of tomatoes, the RYT values of the two co-cultivation treatments were all greater than 1. The relative Ato of tomatoes under co-cultivation was far higher than 0, so tomato showed interspecific dominance and achieved significantly higher biomass accumulation under co-cultivation. 3) The leaf chlorophyll content of co-cultivated tomato was signifcantly higher than that of monocultured tomato at 23 days after transplanting, but the difference was not significant at the 90 days, while the root activity of co-cultivatated tomatos was significantly higher than that of monocultured plants throughout the entire intercropping period. 4) The relative abundance of unknown functional bacteria such as Pseudomonas, Bacillus, Rhizobium, and Microbacterium in the rhizosphere soil of co-cultivatated tomatos significantly increased, and new bacterial genera such as Sphingobium and Ochrobactrum were identified, while Arthrobacter and Acinetobacter disappeared. The changes in the structures of functional microbial communities were conducive to increasing the availability of nutrients in rhizosphere soil of co-cultivated tomatoes.

Conclusions The co-cultivation of tomatoes and potato onions could improve the functional structure of microoganisms in rhizosphere soil of tomato, which are conducive to the nutrient absorption of the co-cultivated plants. Tomato has competition advantages in the co-cultivation system, so co-cultivation enhances the nutrient absorption, allocation to reproductive organs, and the growth and yield formation of tomatoes.