Barro M. auteur aut IRD Wonni I. auteur aut IRD Simonin Marie auteur aut IRD Kassankogno A. I. auteur aut IRD Klonowska Agnieszka auteur aut IRD Moulin Lionel auteur aut IRD Béna Gilles auteur aut IRD Somda I. auteur aut IRD Brunel Caroline auteur aut IRD Tollenaere Charlotte auteur aut IRD text journalArticle eng text/pdf born digital access Due to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant samples per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications. Irrigated rice and rainfed lowlands harbor contrasted root-associated microbiomes in small farmer's fields from Burkina Faso, with contrasted richness, and peculiar indicator taxa in each system. specialized irrigated rice rainfed lowlands root associated microorganisms metabarcoding Oryza sativa rice production system West Africa AFRIQUE DE L'OUEST BURKINA FASO 084 076 098 98 9 fiac085 [17 ] 2022 0168-6496 https://www.documentation.ird.fr/hor/fdi:010086001 10.1093/femsec/fiac085 0168-6496 [F B010086001] https://www.documentation.ird.fr/hor/fdi:010086001 https://www.documentation.ird.fr/intranet/publi/2022-10/010086001.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2022-10-07 2025-02-24 fdi:010086001 fre