The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

• DOI: 10.1093/femsec/fiac085
• Publication Date: 2022-07-22T18:51:22Z
• Authors: Mariam Barro; Issa Wonni; Marie Simonin; Abalo Itolou Kass...; Agnieszka Klonowska; Lionel Moulin; Gilles Béna; Irénée Somda; Caroline Brunel; Charlotte Tollenaere
• Keywords: Paddy field

Abstract 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 microbiota sampled 19 small farmer's fields from irrigated and rainfed lowlands Burkina Faso, using an amplicon metabarcoding approach 16S rRNA gene (prokaryotes, three plant samples per field) ITS (fungi, one sample field). In addition expected structure by root compartments (root vs rhizosphere) geographical zones, showed that production system major driver microbiome structure. systems, found higher diversity prokaryotic communities rhizosphere more complex co-occurrence networks, compared lowlands, while fungal exhibited opposite pattern (higher richness lowlands). Core taxa were different between two indicator species identified: mostly within Bacillaceae Burkholderiaceae Moraxellaceae areas. Finally, abundance was mycorrhizal fungi (both compartments) rhizobia (rhizosphere only). Our results highlight deep differences induced contrasted should consequently be considered engineering applications.