Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings

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.