Synergistic changes of rhizosphere bacterial community and soil properties in greenhouse soils under long-term tomato monoculture

Tomato is a dominant vegetable crop in China that is often continuously cultivated in greenhouses, which causes a series of soil quality issues such as nutrient imbalance or microbial degradation. The deterioration caused by long-term monoculture remain poorly understood. Here, we investigated the microbiological and edaphic parameters in a chronosequence of tomato monoculture greenhouse (0–20th years) in Northwest China via 16S rRNA sequencing and soil nutrient determination. We found that the rhizosphere bacteria shifted significantly throughout the 20-year cropping period, but was more closely related to the no monoculture soil bacteria in the last five-year period (15–20th years) than in the first five-years (1–6th year). Soil properties of nitrogen (N), phosphorus (P), and organic carbon (TOC) increased first, then decreased (9th year), and finally remained stable (15–20th year). In addition, monoculture influenced soil properties that subsequently drove the bacterial community change. N, P, and TOC directly affected bacterial composition and potential functions. Intriguingly, functional genes related to stress resistance increased, while others associated with microbial growth decreased, suggesting that monoculture increased the stress of bacterial community. This study revealed how bacteria and their functioning were impacted by 20 years of monoculture, which was strongly associated with the changes of soil properties. This further illustrates the cause of how soil health and quality deterioration in long-term monoculture systems. •Bacteria changed alongside soil properties under monoculture, in which N and P drive the variation in bacteria mainly.•Continuous cropping reduced the stability of bacterial co-occurrence networks and increased competition.•Continuous cropping caused the bacterial community deterioration while increased their resistance to stress.