Résumé
Meloidogyne graminicola, also known as the rice root-knot nematode, is the most damagingplant parasitic nematode, especially on rice in Asia. This obligate soilborne parasite creates galls that disturb the root morphology and physiology, making plants more susceptible to other diseases (e.g. blast) and / or abiotic stress (e.g. water stress). Since the root microbiome is important for plant health, we assessed the impact of M. graminicola on the root microbiome of rice plants. In this study, we present results obtained from a survey conducted in Northern Vietnam in 2017. We collected infected (with galls) and non-infected roots from three naturally infested rice fields. Using an amplicon barcoding approach, we observed different microbiome composition, diversity and network structures. Interestingly, we observed a higher species richness (24%) and diversity in infected roots but fewer enriched metabolic pathways based on the predicted functional profiling of these microbial communities. Some of these enriched pathways were related to pyruvate fermentation and TCA cycle. Differential abundance testing analyses highlighted that species such as Flavobacterium succinicans and Ensifer adhaerens were respectively enriched in non-infected and infected roots. Additionally, the infected community network was denser and more connected, and we identified specific hub taxa that could be keystones in these infected microbiomes. These findings show deep modifications of the rice root microbiome composition and functions when exposed to the parasitic pressure of M. graminicola. The identified indicator taxa and pathways could be used in future studies as markers of rice root infection.