LAUSR

Abstract Arbuscular mycorrhizal fungi (AMF) inoculation and preceding crop identity have been widely reported to affect crop performance and root-associated microbiomes. However, the underlying relationship between the resulting crop performance and the dynamics of root-associated microbiomes is still poorly explored. In this study, the interaction of AMF inoculant and preceding crop was tested in wheat (Triticum aestivum L.) and flax (Linum usitatissimum L.) based rotation systems under three fertilization levels. Effects on agronomic traits, root-associated microbiome, and the relationship between root-associated microbiome and crop productivity were investigated. Higher crop yields were produced following a pulse crop (i.e., Fabaceae harvested for dry seed) than a canola crop. Better yields were at least partially due to higher plant N and P uptake, possibly mediated by certain taxa of the root-associated microbiome, such as N2-fixing and H2-oxidizing bacteria. Some differential rhizosphere zOTUs between canola and pulse crops were significantly related to succeeding crop yield. The structure of the communities of AMF, fungi and bacteria responded differently to the influence of geographical location, plant identity and microecological zone (i.e. root and rhizosphere). Results showed that the microbial communities in belowground microecological zones have specific patterns of sensitivity to driving factors, and the dynamics of certain taxa belonging to some N2-fixing and H2-oxydizing bacterial groups may be involved in the effect of crop rotation on the productivity of wheat and flax.