Differential Assembly of Rhizosphere Microbiome and Metabolome in Rice with Contrasting Resistance to Blast Disease

Abstract

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases threatening global rice production. Although host resistance represents a sustainable control strategy, the underlying mechanisms mediated by the rhizosphere microbiome remain poorly understood. In this study, we selected four rice varieties with varying resistance to blast and demonstrated, through an integrated approach of 16S rRNA/ITS amplicon sequencing, untargeted metabolomics, and soil physicochemical analysis, that the rice genotype reprograms the genotype-root exudate-rhizosphere microbiome system. Results showed that the resistant variety P104 significantly decreased the soil pH while increasing the contents of total nitrogen, ammonium nitrogen, and nitrate nitrogen. On the other hand, the susceptible variety P302 exhibited higher pH and available phosphorus content. Furthermore, the rhizosphere of P104 was enriched with specific beneficial microbes such as Desulfobacterota, Ascomycota, and Pseudeurotium, and activated defense-related metabolic pathways including cysteine and methionine metabolism and phenylpropanoid biosynthesis. In contrast, susceptible varieties showed reduced bacterial diversity and fostered a microecological environment more conducive to pathogen proliferation. Our findings indicate that blast-resistant rice genotypes are associated with a protective rhizosphere microbiome, potentially mediated by alterations in root metabolism, thereby suppressing pathogen establishment. These insights elucidate the underground mechanisms of blast resistance and highlight the potential of microbiome-assisted breeding for sustainable crop protection.

Keywords: microbial community; rhizosphere; rice blast; root exudates.

Figure 1

Abundance of the top ten bacteria (A,B), fungi (C,D), and nitrogen-fixing bacteria (E,F) in rice rhizosphere soil at the phylum and genus levels.

Figure 2

Box plots of α-diversity indices for bacteria (A) and fungi (B) in rhizosphere soil of rice.

Figure 3

PCoA plots of β-diversity for rhizosphere soil bacteria (A), fungi (B), and nitrogen-fixing bacteria (C) in rice. The circles are confidence ellipses drawn around the sample points of each processing group.

Figure 4

Changes in bacterial (A), fungal (B), and nitrogen-fixing bacterial (C) communities in rice rhizosphere soil based on weighted UniFrac distance.

Figure 5

Changes in the top 20 differentially expressed metabolites with the greatest continuous expression differences across rice varieties.

Figure 6

KEGG enrichment analysis bubble plots of differential metabolites in rice root systems under positive and negative ion conditions. (A) KEGG enrichment analysis bubble chart for the P104 and P206 groups under positive ion conditions; (B) KEGG enrichment analysis bubble chart for the P104 and P206 groups under negative ion conditions; (C) KEGG enrichment analysis bubble chart for the P104 and P302 groups under positive ion conditions; (D) KEGG enrichment analysis bubble plot for P104 and P302 groups under negative ion conditions; (E) KEGG enrichment analysis bubble plot for P104 and P309 groups under positive ion conditions; (F) KEGG enrichment analysis bubble plot for P104 and P309 groups under negative ion conditions.

Figure 7

Analysis of the correlation between soil physicochemical properties, rhizosphere soil microorganisms, and root metabolites in rice soil. (A) Correlation diagram between soil physicochemical properties and rhizosphere soil microorganisms. (B) Correlation diagram between soil physicochemical properties and root metabolites. (C) Correlation diagram between rhizosphere soil microorganisms and root metabolites. One asterisk (*) indicates p < 0.05, two asterisks (**) indicate p < 0.01.