The application of biochar stimulates the activities of microorganisms that affect soil quality and plant growth. However, studies on the impacts of biochar mainly focus on a monoculture, its effects on interspecific interactions are rarely reported. Here, we investigated the impacts of biochar on tomato/potato–onion intercropped (TO) in a pot experiment. Tomato monoculture (T) and TO were treated with no, 0.3, 0.6, and 1.2% biochar concentrations in a pot experiment. Microbial communities from tomato rhizosphere soil were analyzed by quantitative PCR and Illumina MiSeq. The results showed that compared with the tomato monoculture, 0.6%TO and 1.2%TO significantly increased tomato yield in 2018. TO and 1.2%TO significantly increased plant height and dry weight in 2018 and 2019. Biochar treatments increased soil pH, decreased NO3--N and bulk density, and increased the absorption of N, P, and K by tomato. Bacterial and fungal abundances increased with an increase in biochar concentration, while Bacillus spp. and Pseudomonas spp. abundances showed an “increase-decrease-increase” trend. Biochar had a little effect on bacterial diversities but significantly lowered fungal diversities. TO, 0.6%TO, and 1.2%TO increased the potentially beneficial organisms (e.g., Pseudeurotium and Solirubrobacter) and lowered the potentially pathogenic organisms (e.g., Kribbella and Ilyonectria). Different concentrations of biochar affected the bacterial and fungal community structures. Redundancy analysis indicated that the bacterial community was strongly correlated with soil pH, NO3--N, and EC, while the fungal community was closely related to soil NO3--N and moisture. The network analysis showed that biochar and intercropping affected the symbiosis pattern of the microorganisms and increased the proportion of positive interactions and nitrifying microorganisms (Nitrospirae) in the microbial community. Overall, our results indicated that monoculture and intercropping with biochar improved soil physicochemical states and plant nutrient absorption, and regulated soil microbial communities, these were the main factors to promote tomato growth and increase tomato productivity.

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Intercropping plays an essential role in agricultural production, impacting the soil’s physical and chemical properties and microbial communities. However, the responses of ammonia-oxidizing microorganisms in the continuous-cropping soil to different intercropping systems in different growing seasons are still insufficiently studied. Here, we investigated the effects of seven intercropping systems (alfalfa (Medicago sativa L.)/cucumber, trifolium (Trifolium repens L.)/cucumber, wheat (Triticum aestivum L.)/cucumber, rye (Secale cereale L.)/cucumber, chrysanthemum (Chrysanthemum coronrium L.)/cucumber, rape (Brassica campestris L.)/cucumber, mustard (Brassica juncea L.)/cucumber) on soil physical and chemical properties, potential nitrification rate (PNR), soil ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) communities in the greenhouse in spring and autumn. The results showed that, compared with cucumber monoculture, intercropping increased the soil NH4+-N and NO3−-N. The chrysanthemum–cucumber, rape–cucumber, and mustard–cucumber treatments increased soil PNR. Intercropping increased the AOA and AOB abundances in two seasons, especially in rape–cucumber, wheat–cucumber, chrysanthemum–cucumber, and trifolium–cucumber treatments. The ratio of AOA and AOB decreased with seasonal variation. The wheat–cucumber and rape–cucumber treatments increased soil AOA community diversity. Seasonal variation had a significant effect on the relative abundance of the AOB community. Nonmetric multidimensional scaling analysis showed that the AOA and AOB community structures were obviously different from spring to autumn. Redundancy analysis showed that the AOA community was significantly regulated by moisture, NO3−–N, and available potassium (AK), while the AOB community was significantly regulated by moisture, available phosphorus (AP), AK, NO3−-N, and pH. Network analysis showed that the co-occurrence relationship and complexity of AOA and AOB communities were different in two growing seasons. The AOB community may play a critical role in ammonia oxidation in autumn. Taken together, intercropping improved soil physicochemical state, increased soil PNR and significantly altered soil AOA and AOB communities. Seasonal variation significantly altered the AOA and AOB communities’ structure and interaction between them. The effect of seasonal variation on AOA and AOB communities was greater than intercropping.