Host plant selects bacterial rhizosphere microbiome function whereas community structure is determined by soil legacy

Abstract The drivers between host plant, associated rhizosphere microbiome functions, and related plant health implications are complex and a field of continuous development. Furthermore, understanding of the interplay between soil, plant, and microbiome across different plant species and contrasting geographical areas is scarce. The UK Crop Microbiome Cryobank project, the world's first open crop/soil microbiome resource can fill this research gap. It utilizes contrasting UK soil types, with comprehensive environmental and agronomic metadata and has generated associated rhizosphere and bulk soil microbiome information for six crops (wheat, barley, oats, fava beans, oilseed rape, and sugar-beet) including a bacterial culture collection and 16S rRNA gene datasets. Here, using functional and taxonomic data from 24,000 bacterial cultures and 315 16S rRNA gene metabarcoded soil libraries, we show that geographical location and soil environment primarily influence the phylogeny of rhizosphere bacterial communities, whereas crop genotype is key in determining the function of associated rhizosphere microbiota. Sugar-beet and oilseed rape predominantly select for drought tolerant microbes, barley for Zn-solubilizing microbes and fava bean has a reduced selection of N-mineralising microbes. These findings emphasise the need to consider the host plant’s developmental requirements and edaphic factors for successful deployment of microbiome facilitated agriculture.