Variations in plant’s cry for help evidenced by modifications of rice root microbiota induced by Blast or Brown spot diseases

Background: Plants can recruit specific microbes to help them defend themselves against phytopathogens, a process known as “cry for help”. In this study, we investigated whether a plant species modulates its root-associated microbiome differently - i.e. “cries out differently” - depending on the diversity of fungal pathogens attacking its leaves. To address this, we monitored changes in the root microbiome of Oryza sativa cv. Nipponbare following infection with two fungal pathogens: Pyricularia oryzae(leaf blast) and Bipolaris oryzae(brown spot), under controlled conditions and using the same soil. Results: Our results support the 'cry for help' hypothesis, suggesting that pathogen-induced stress drives the recruitment of beneficial microbes. While the composition of the root-associated microbiota remained globally stable after infection, subtle but significant taxonomic shifts were observed. Alpha diversity was unaffected, but changes in beta diversity occurred in micro-eukaryotic communities one week after brown spot infection and in bacterial communities two weeks after blast infection. Notably, beneficial taxa such as the bacterial genera Lentzea and Streptomyces, as well as the fungi Cladosporium halotolerans and Rhizophagus irregularis, were enriched in the bellow-ground microbiome of leaf-infected plants. The biocontrol potential of Rhizophagus irregularis was confirmed against blast but not brown spot infection. Conclusions: These results advance our understanding of the 'cry for help' hypothesis in rice and provide potential candidates for biocontrol. They highlight the complexity of plant-microbe interactions and suggest that rice plants specifically modulate their root microbiome in response to fungal infections, potentially shaping microbial communities to enhance defence strategies.