Diterpenoid phytoalexins shape rice root microbiomes and their associations with root parasitic nematodes

Rice synthesizes diterpenoid phytoalexins (DPs) are known to operate in defense against foliar microbial pathogens and root-knot nematode Meloidogyne graminicola. Here, we examined the role of DPs in shaping riceassociated root microbiomes in nematode-infested rice paddy soils. Further, we assessed how DPs affect interactions between the root microbiomes and nematode communities, particularly rice root-knot nematodes from the Meloidogyne genus. We used 16S and ITS2 rRNA gene amplicon analysis to characterize the rice root-and rhizosphere-associated microbiomes of DP knock-out 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 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, nematode-suppressive microbial taxa, including Streptomyces, Stenotrophomonas, Enterobacter, Massilia, and Acidibacter, negatively correlated with Meloidogyne. Comparative analysis revealed differential enrichment of microbial taxa in the roots of rice diterpenoid phytoalexin (DP) knock-out mutants versus wild-type, suggesting that DPs modulate specific taxa in the rice root microbiome. These findings indicate DPs role in plant-microbiome assembly and nematode interactions, further underscoring the potential of leveraging phytoalexins for sustainable management of crop diseases.