The Changes in Rhizosphere Metabolome and Microbiota Are the Main Direct Obstacles to Continuous Cropping in Tobacco (Nicotiana tabacum L.)

Abstract

Continuous cropping obstacles (CC), typical of negative plant–soil feedback, have become a non-negligible constraint to the development of agriculture. In order to investigate the main direct drivers influencing the formation of CC soils from the rhizosphere of CC, tobacco fields were collected and their physicochemical properties, microbial community, and metabolomics were measured and analyzed. We also built a mixed linear model to evaluate the impact of these factors on CC. The results suggested that the pH, available potassium (AK), and zinc (Zn) were significantly higher in CC than in normal tobacco (NOR). However, the content of available nitrogen (AN) decreased significantly. Alpha diversity of the bacterial community was significantly reduced. Bacterial community structure also varied significantly in CC. The study identified an ecological cluster with a significant negative correlation with the above-ground biomass of plants. In this cluster, the pathogenic microbiome increased and the beneficial microbiome decreased. The orthogonal partial least squares discriminant analysis (OPLS-DA) indicated clear variations in the metabolomic profiles of the rhizosphere soil between the CC and the NOR. There was an accumulation of toxic compounds and a decrease of beneficial compounds in rhizosphere soils with CC. The mixed linear model showed that only microbiome and metabolites, rather than the soil’s physicochemical properties, significantly affected plant above-ground biomass. According to the model’s standardized coefficients, metabolites contributed more to the continuous crop obstacles than the microbial community. The soil’s physicochemical properties do not directly cause the emergence of CC. The allelochemicals and microbial community are the main direct obstacles to continuous cropping in tobacco, and allelochemicals contribute more than the microbial community.