Landscape scale analysis reveals multi-kingdom microbiome transitions linked to rotation and crop yield decline

Oilseed rape (Brassica napus, OSR), a globally important oilseed crop, suffers from significant yield decline when grown in short rotation. To elucidate the role of the environment on shaping the microbiome in relation to yield decline, we sampled OSR grown in 37 commercial farms spanning the UK and used 61 collected metadata. We examined bacterial, fungal and protist communities associated with the three below-ground compartments; roots, rhizosphere and bulk soil.