Potato yield and quality are linked to cover crop and soil microbiome, respectively

Crop-specific cultivation practices including crop rotation, cover cropping, and fertilisation are key measures for sustainable farming, for which soil microorganisms are important components. This study aims at identifying links between agronomic practices, potato yield and quality as well as soil microorganisms. We analysed the roles of cover crops and of the soil prokaryotic, fungal, and protistan communities in a long-term trial, differing in crop rotation, i.e. winter wheat or silage maize as pre-crop, presence and positioning of oil radish within the rotation, and fertilisation, i.e. mineral fertiliser, straw, manure, or slurry. Up to 16% higher yields were observed when oil radish grew directly before potatoes. Losses of potato quality due to infection with Rhizoctonia solani-induced diseases and common scab was 43–63% lower when wheat + oil radish was pre-crop under manure or straw + slurry fertilisation than for maize as pre-crop. This contrast was also reflected by 42% higher fungal abundance and differences in β-diversity of prokaryotes, fungi, and protists. Those amplicon sequence variants, which were found in the treatments with highest potato qualities and differed in their abundances from other treatments, belonged to Firmicutes (2.4% of the sequences) and Mortierellaceae (28%), which both comprise potential antagonists of phytopathogens. Among protists, Lobosa, especially Copromyxa, was 62% more abundant in the high potato quality plots compared to all others, suggesting that specific higher trophic organisms can improve crop performance. Our findings suggest that successful potato cultivation is related (1) to planting of oil radish before potatoes for increasing yield and (2) to fertilisation with manure or straw + slurry for enriching the microbiome with crop-beneficial taxa.