Crop rotation-driven changes in rhizosphere metabolite profiles regulate soil microbial diversity and functional capacity

Plants are increasingly revealed to have the ability to shape microbiome composition and function by triggering rhizosphere metabolites. Rotation, a model of crop diversification, promotes crop production by influencing rhizosphere microbiome. However, the rhizosphere metabolites of different rice rotations are rarely reported and, in particular, the regulation of key metabolites on rhizosphere microbiome is unclear. To address this gap, we collected the bulk and rhizosphere soils of four crop rotations (rice-rice, tobacco-rice, rice-oilseed rape, and rice-rice-oilseed rape) to assess rhizosphere metabolites, soil bacterial and fungal diversity, as well as functional microbial populations from a long-term (more than 20 years) field experiment. Compared with the rice-rice system, rhizosphere metabolites, such as deazaflavin, 10-Deacetylbaccatin III, and paclobutrazol, significantly increased in the rice rotation systems with tobacco and oilseed rape. Metabolite components (e.g., azelaic acid, soyasapogenol B, and canrenone) and microbial taxa (Xanthobacteraceae, Bradyrhizobium, and Mortierella) were the keystones regulating the co-occurring correlations of rhizosphere metabolites and soil microorganisms. Compared with the rice-rice, the bulk and rhizosphere soil of rice rotations with oilseed rape or tobacco showed higher abundance of the microbial populations related to C degradation and fixation, N fixation, nitrification, nitrate reduction, inorganic P (Pi) solubilization, and organic P (Po) mineralization. Metabolites, such as 7-chloro-norlichexanthone, daidzein, and soyasapogenol B, were the keystones regulating the co-occurrence relationships of rhizosphere metabolites and functional microbial populations. Rhizosphere metabolite composition was positively related to the populations associated with C fixation and degradation, nitrification, and P solubilization, and negatively related to those associated with methane metabolism, nitrate reduction, denitrification, and anammox (P ≤ 0.05). Soyasapogenol B, daidzei, and [1,1'-biphenyl]− 2,2'-dicarboxylic acid enriched in rotation systems were negatively correlated with dominant microbial taxa such as phylum Bacteroidetes and Chytridiomycota, and positively correlated with phylum Zoopagomycota and the populations associated with key soil functions such as C degradation, nitrate reduction, and P solubilization (P ≤ 0.05). These results demonstrated the importance of rhizosphere metabolites in regulating soil microbiome composition and functional capacity, which deepens understanding of rotations improving rice production via rhizosphere effect.