ERP120447 PRJEB37146 ena-STUDY-NIOO-KNAW-09-03-2020-12:16:58:603-961 Decomposing cover crops modify composition and functioning of root microbiomes of cash crop seedlings Root microbiome assembly during the seedling stage is of strong importance for subsequent performance of crops. Sowing of crops is increasingly done in soils that contain incorporated residues of cover crops. Here, we report the first extensive study of effects of decomposing cover crop residue on assembly of root microbiomes of cash crops seedlings. We studied bacterial (16S rDNA) and fungal (ITS2) community assembly in roots of four cash crop seedlings (asparagus, carrot, onion, and sugar beet) exposed to residues of seven cover crops species collected from field plots at two harvest times (autumn and winter). Within the context of cash crop species specific selection, we found significant effects of cover crop quality (measured with harvest time) and cover crop species identity on the composition of root-associated microbial communities. In addition, we show that there are significant correlations between cover crop induced shifts in root microbial taxa and disease tolerance of sugar beet seedlings against the pathogenic fungus Rhizoctonia solani. Our results show that incorporation of cover crops presents a possibility to steer composition and improve functioning of cash crop root microbiomes. Cover crops as Organic amendments Root microbiome assembly during the seedling stage is of strong importance for subsequent performance of crops. Sowing of crops is increasingly done in soils that contain incorporated residues of cover crops. Here, we report the first extensive study of effects of decomposing cover crop residue on assembly of root microbiomes of cash crops seedlings. We studied bacterial (16S rDNA) and fungal (ITS2) community assembly in roots of four cash crop seedlings (asparagus, carrot, onion, and sugar beet) exposed to residues of seven cover crops species collected from field plots at two harvest times (autumn and winter). Within the context of cash crop species specific selection, we found significant effects of cover crop quality (measured with harvest time) and cover crop species identity on the composition of root-associated microbial communities. In addition, we show that there are significant correlations between cover crop induced shifts in root microbial taxa and disease tolerance of sugar beet seedlings against the pathogenic fungus Rhizoctonia solani. Our results show that incorporation of cover crops presents a possibility to steer composition and improve functioning of cash crop root microbiomes. ENA-FIRST-PUBLIC 2021-07-25 ENA-LAST-UPDATE 2021-07-25