Beyond genotype: the influence of developmental stage on rice rhizospheric microbiome-metabolome networks

Rhizosphere microbiomes and metabolomes are influenced by host genotype and developmental stage. However, there has been limited research that simultaneously profiles the rhizosphere microbiome and metabolism of rice across different genotypes and developmental stages. Furthermore, the interactions between rhizosphere microbiomes and metabolism in various plant genotypes and developmental stages are not well understood. Here, we investigated the diversity and composition of rhizosphere microbial community and metabolism across three hybrid rice varieties and their respective parent lines during three developmental stages (tillering, heading, and mature) using amplicon sequencing and untargeted metabolomics analyses. Plant developmental stages and genotypes significantly influence the rhizosphere microbiome and metabolome, with the impact of developmental stages being more pronounced. The composition of microbial communities and metabolites in the rhizosphere exhibited significant differences between the tillering stage and other developmental stages, with these differences becoming less distinct as the growth period continued. Hybrid rice displayed heterosis characteristics in their rhizosphere microorganisms compared to their parent varieties, as reflected by the significant enrichment of microbial species and the enhanced potential for microbial interactions within the co-occurrence network. Moreover, the differential microorganisms between the tillering and heading stages showed significant correlations with differential metabolites and soil chemical properties, including total phosphorus (TP), available phosphorus (AP), and nitrate nitrogen (NN). Taken together, this study contributes to our understanding of plant-microbiota-metabolome associations and provides a foundation for developing beneficial plant microbiomes and compounds to promote sustainable agricultural production.