Objectives The microbial community structures in rhizosphere soils of peas were determined under intercropping with mutual generation and constraining crops, to clarify the microbial mechanisms of the allelopathy phenomenon.

Methods Pea (Pisum sativum L.) was grown under three modes, intercropping mutual generation crop (pea/tomato, PT), mutual constraining crop (pea/chives, PA), and pea monoculture (PP), and the blank soil was also used as a control in the pot experiment. The test soil was red loam. At 50 days of transplanting, whole crops were dig out, and the rhizosphere soil of peas was collected by shaking the root slightly, based on high-throughput sequencing technology, analyzing the soil microbial community structures in rhizospheres of peas.

Results The microbial biomass P (MBP) of intercropping pea (PT) rhizosphere was significantly higher than that of intercropping (PA) and bowl pea (PP); the combination of phased pea plants increased the number of bacteria and fungi in each species, and the bacterial diversity and richness changed significantly; intercropping induced significant changes in the composition of bacterial and fungal communities in the rhizosphere of pea plants, Saccharomonospora and Thiobacillus, which can secrete the inhibitory substances for pea growth, and the pathogenic microorganisms, such as Fusarium enriched in rhizospheres of peas could be detected under the mutual constraining intercropping system (pea/chives, PA). In contrast, although soil bacterial and fungal diversities and richness in rhizospheres of peas could not be significantly improved, but their compositions were significantly altered by intercropping with mutual generation crops (pea/tomato, PT) which compared to those of intercropping with mutual constraining crops (pea/chives, PA). Additionally, the enrichment of Olpidiom, and the decline of Fusarium in rhizospheres of peas could be found in the mutual generation intercropping system (pea/tomato, PT).

Conclusions Intercropping with mutual generation crop help the enrichment of beneficial microorganisms, while intercropping with mutual constraining crop helps the enrichement of harmful and disease microorganisms in the rhizosphere soil of peas, which might be an important mechanism of the allelopathy phenomenon of peas intercropping with different crops.