Influence of plant genotype and soil on the wheat rhizosphere microbiome: identification of a core microbiome across eight African and European soils

An avenue to improve cereal yields is to harness and manipulate the plant microbiome to increase crop nutrition and resistance to pathogens and abiotic stressors. To develop microbiome engineering solutions, more research is needed to characterize plant microbiomes across contrasted geographical locations, agricultural practices and plant genotypes. Previous work on the wheat microbiome focused on bacterial diversity and more marginally on archaeal and fungal diversity. Hence, no integrative assessment of the wheat rhizospheric microbiome including protist diversity (i.e. amoeba, ciliates, stramenopiles) is currently available. Here, we characterized the rhizosphere microbiome of wheat by considering both prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal). The goals of this study were to determine the influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. An additional goal was to determine if a rhizosphere core microbiome existed across these different countries. We found a limited effect of the wheat genotype on the rhizosphere microbiome (explain 2% of variance) and observed that the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in microbiome structure were observed between the eight soils studied (57% of variance) and the two agricultural practices (10% of variance). However, despite these differences in microbiome composition across soils, we observed that 179 taxa (2 archaea, 104 bacteria, 41 fungi, 32 protists) were consistently associated to wheat roots, constituting a core microbiome. In addition to being prevalent, these few core taxa were highly abundant and collectively represented 50% of the relative abundance of our entire wheat microbiome dataset. We provide evidence of a wheat core microbiome and propose a “most wanted” taxa list, including 9 hubs (potential keystone taxa), that should be targets for future culturomics, metagenomics and for the creation of wheat synthetic microbiomes. Additionally, we confirm that protists are an integral part of the plant holobiont and we encourage more research to study their roles for plant nutrition and in controlling plant diseases.