Diterpenoid Phytoalexins Shape Rice Root Microbiomes and Their Associations With Root Parasitic Nematodes

Rice synthesises diterpenoid phytoalexins (DPs) which are known to operate in defence against foliar microbial pathogens and the root-knot nematode Meloidogyne graminicola. Here, we examined the role of DPs in shaping rice-associated root microbiomes in nematode-infested field soil. Further, we assessed how DPs affect interactions between the root microbiomes and M. graminicola. We used 16S and ITS2 rRNA gene amplicon analysis to characterise the root- and rhizosphere-associated microbiomes of DP knock-out rice mutants and their wild-type parental line, at an early (17 days) and late (28 days) stage of plant development in field soil. Disruption of DP synthesis resulted in distinct changes in the composition and structure of microbial communities both relative to the parental/wild-type line but also between individual mutants, indicating specificity in DP-microbe interactions. Moreover, the abundance of nematode-suppressive microbial taxa, including Streptomyces, Stenotrophomonas and Enterobacter was negatively correlated with that of Meloidogyne. Differential enrichment of microbial taxa in the roots of rice DP knock-out mutants versus wild-type suggests that DPs modulate specific taxa in the rice root microbiome. These findings indicate a role for DPs in plant-microbiome assembly and nematode interactions, further underscoring the potential of leveraging phytoalexins for sustainable management of crop diseases.