Rice infection by the nematode Meloidogyne graminicola is associated with deep modifications of the root microbiome in terms of bacterial community composition, diversity and network structure with specific enriched bacterial taxa and predicted metabolic pathways.
Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant parasitic nematode, especially on rice. This obligate soilborne parasite induces gall formation that disturb the root morphology and physiology but its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern Vietnam where we collected infected (with galls) and non-infected root tips from the same plants in three naturally infested fields. Using a metabarcoding approach, we observe that M. graminicola infection caused deep modifications of the root bacterial community composition and network structure. Interestingly, we observed a higher species richness (+24%) and diversity in infected roots but only fewer enriched predicted metabolic pathways. We identified bacterial taxa enriched in infected roots that include several hub taxa, which could serve as potential indicators of the nematode infection. A more thorough analysis of the functional predictions highlighted a specialization of the bacterial metabolism towards anaerobic pathways which could be an important capacity to survive in the gall environment. In this study, we described the signature of the gall microbiome (the “gallobiome”) with shifting abundances and specificities that lead to a specialization of the functional capabilities of the microbiome.