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

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.

Life Cycle Thinking for the environmental and financial assessment of rice management systems in the Senegal River Valley

Rice is a staple food in Senegal, which however imports more than 70% of the rice consumed annually to meet its domestic demand. Despite governmental efforts to increase rice self-sufficiency, both rice supply and yields remain low. Senegalese farmers face challenges related to irrigation infrastructure and fertiliser access, besides those derived from climate change. This study applies Life Cycle Assessment (LCA) combined with financial Life Cycle Costing (LCC) to evaluate alternative scenarios for rice management in the Senegal River Valley and identify sustainability hotspots and potential improvements. Specifically, rice cultivation in Ross Béthio (Saint Louis, Senegal) is assessed based on the observed agricultural practices during the dry seasons of 2016 and 2017. Two scenarios capturing conventional (CONV) and intensive (INT) practices are compared to two reference scenarios (SAED scenarios) according to the recommendations of the official agricultural advisory service. The INT scenario generates the lowest impacts per kg of paddy rice in seven out of thirteen impact categories, including climate change, freshwater and marine eutrophication, ozone depletion and water scarcity. This is due to the higher yields (7.4 t ha^-1) relative to CONV (4.8 t ha^-1) and the two reference SAED scenarios (6.0 t ha^-1). The two latter scenarios show the lowest values in the remaining categories, although they also generate slightly lower profits than INT (138 € t^-1 vs. 149 € t^-1) due to increased labour costs for additional fertilisation treatments. The results from both LCA and LCC underline the importance of increasing yields to decrease environmental impacts and production costs of rice when estimated per kg of product. Well-designed fertiliser application doses and timing and increased mechanisation can deliver further environmental benefits. Additional improvements (e.g. in irrigation, crop rotations, straw management) could be considered to promote the long-term sustainability and profitability of rice production in Senegal. LCA in combination with financial LCC is identified as a decision-support tool for evaluating the sustainability of alternative crop management practices. Life Cycle Thinking can still benefit from experiential learning based on information exchange between farmers, researchers and extension agents to contribute to a sustainable agriculture and ultimately to food security in Africa.

Environmental adaptation of the root microbiome in two rice ecotypes

The root microbiome plays a key role that can influence host plant growth and abiotic stress. While there has been extensive characterization of community structure, spatial compartmentalization, and the impact of drought stresses on the root microbiome in rice and other plants, there is relatively little known about the differences in root microbiome among rice ecotypes in natural upland and lowland fields. Herein, we used two rice ecotypes, upland and irrigated ecotype rice (two Indica and two Japonica genotypes), as a model to explore the responses of the root microbiome under different environmental conditions. We aimed to identify environment-induced adaptation in the root bacterial and fungal composition of rice ecotypes by high-throughput sequencing. Rice from lowland field or upland had significantly altered overall bacterial and fungal community compositions of the two ecotypes, with diversity of both ecotypes greatly decreased from lowland field to upland. The overall response of the root microbiome to upland conditions was taxonomically driven by the enrichment of family Enterobacteriaceae and genera Serratia, and phylum Ascomycota. Interestingly, rice ecotypes specifically enriched root microbes when they were transferred from their original environment, such as the enrichment of class Thermoleophilia and phylum Actinobacteria when the irrigated ecotype rice was moved from lowland to upland field. These results revealed that different environmental conditions and rice ecotypes resulted in a restructuring of root microbiome communities, and suggested the possibility that components responsible for the beneficial attributes in the altered root microbiome might contribute to the adaptation of different ecotypes in natural fields.

Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions

BACKGROUND

Stagnant flooding, where water of 25-50 cm remains until harvest time, is a major problem in rainfed lowland areas. Most of the Sub1 varieties, which can withstand around 2 weeks of complete submergence, perform poorly in these conditions. Hence, varieties tolerant of stagnant flooding are essential.

RESULTS

This paper presents the first study to map QTLs associated with tolerance to stagnant flooding, along with a parallel study under normal irrigation, using an F₇ mapping population consisting of 148 RILs derived from a cross of Ciherang-Sub1 and the stagnant-flooding tolerant line IR10F365. Phenotypic data was collected for 15 key traits under both environments. Additionally, survival rate was measured under stress conditions. Genotyping was performed using the Illumina Infinium genotyping platform with a 6 K SNP chip, resulting in 469 polymorphic SNPs. Under stress and irrigated conditions, 38 and 46 QTLs were identified, respectively. Clusters of QTLs were detected in both stress and normal conditions, especially on chromosomes 3 and 5.

CONCLUSIONS

Unique and common QTLs were identified and their physiological consequences are discussed. These beneficial QTLs can be used as targets for molecular breeding and can be further investigated to understand the underlying molecular mechanisms involved in stagnant flooding tolerance in rice.