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

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 sample 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.

Quantification of diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media using 16S amplicon barcoding

“…Oryza sativa ssp indica cv FKR64 plant roots were collected in a rice field near Bama village (western Burkina Faso, Kou Valley, 10.64384 N, -4.8302 E). This field was already assessed in a previous study and described by Barro et al [ 6 ]. Rice sampling was authorized by a national agreement between the Burkina Faso government and farmers within the framework of a rice productivity improvement program involving INERA.…”

“…in Arabidopsis [ 1 ] and wheat [ 2 ]). For rice, its microbiome has been widely described in different countries and rice culture practices [ 3 – 6 ]. This wealth of data has now provided a good overview of the main bacterial and fungal taxa inhabiting underground plant tissues (roots and rhizosphere), as well as those in their above-ground parts (phyllosphere and endosphere).…”

Old foe, new host: epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso

“…For that, an epidemiological survey focusing on two rice production systems (irrigated and rainfed lowland) was conducted in this West African country between 2016 and 2019 (Figure 1). In parallel, agricultural practices and the use or turnover of rice varieties were followed as well as the diversity of microbiome associated to rice roots and (known) rice pathogens (viral, bacterial and fungal) circulating in these fields (Barro et al 2022, 2021a, b; Billard et al 2023; Kaboré et al 2022; Tollenaere et al 2017). Based on these samples and metadata, we performed viral metagenomics analyses on rice and wild grass leaf samples collected in 2016-2017 (project MP1 in Moubset et al 2022).…”

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

“…Barro et al . [ 61 ] showed that the rice production system is a major driver of the microbiome structure in rice fields in Burkina Faso. Higher rhizosphere prokaryotic community diversity and more complex co-occurrence networks have been found in irrigated systems compared to rainfed lowlands, while the opposite pattern has been noted for fungal communities (higher richness in rainfed lowlands).…”

“…Over 3,800 rice root-associated bacteria were isolated from five bacterial culture media. A working collection of 1,013 isolates was characterized at the taxonomic (by 16S fragment sequencing) and phenotypic (in vitro PGP capacity) levels and cross-referenced with rice root microbiome barcode data (16S amplicons) obtained from the same rice fields [ 61 ] so as to identify core and hub taxa in the collection. A set of 45 representative strains of the culturable diversity was screened in controlled conditions for plant growth promotion capacities on two rice cultivars popular in Burkina Faso.…”