The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer’s fields in western Burkina Faso Article - Août 2022

Mariam Barro, Issa Wonni, Marie Simonin, Abalo Itolou Kassankogno, Agnieszka Klonowska, Lionel Moulin, Gilles Béna, Irénée Somda, Caroline Brunel, Charlotte Tollenaere

Mariam Barro, Issa Wonni, Marie Simonin, Abalo Itolou Kassankogno, Agnieszka Klonowska, Lionel Moulin, Gilles Béna, Irénée Somda, Caroline Brunel, Charlotte Tollenaere, « The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer’s fields in western Burkina Faso  », FEMS Microbiology Ecology, août 2022. ISSN 0168-6496

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 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.

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