The assembly of root-associated microbes during the seedling stage has strong impact on subsequent performance of crops. Major factors influencing this assembly are crop species identity and composition of potential root-colonizing microbes in the bulk soil. The latter can be modified by soil management, such as organic amendments. The incorporation of residues of cover crops before the start of the growing season of cash crops presents an interesting option for steering of root-associated seedling microbiomes as there is a wide range of cover crops species with different properties available for farmers.

In a greenhouse study, we examined the effect of soil amendments with milled shoot and root materials of seven cover crop species (niger seed, phacelia, rapeseed, radish, vetch, black oat and buckwheat) on the soil nitrogen and biomass of seedlings of four cash crop species (asparagus, carrot, onion and sugar beet) and their root-associated bacteria and fungi. Field-grown cover crops material used for the study was collected at two time points (before and after winter) which had strong impact on plant elemental composition. Since the soil used for the study was a mixture of sandy arable soils with a history of soil-borne fungal diseases (Fusarium and Rhizoctonia), we also examined whether decomposing cover crop residues had an influence on the severity of damping-off diseases.

Within the context of a strong selection of root-associated microbes by cash crop species, we found significant modifying effects by cover crop materials. High-quality residues (with low C/N ratio) caused profound shifts within root-associated Proteobacteria and increases in relative abundance of certain microbial groups such as Bacillaceae and Mortierellomycetes. These changes coincided with differences in establishment and survival of cash crop seedlings. This indicates that fine-tuning of cover crops amendments for different cash crops is required to realize enhanced functioning of root microbiomes.

Sequencing data - ENA accession number PRJEB37146