Cropping history shapes fungal, oomycete and nematode communities in arable soils and affects cavity spot in carrot

Fungal, nematode and oomycete communities in arable soil serve diverse ecological functions. However, little is known about the dynamics among these three taxonomic groups. In order to identify the driving factors and networks shaping these communities, and the influence of communities on the development of carrot cavity spot, we collected soil samples from more than sixty fields in which carrot was planned as the next crop, and analyzed the microbial communities using metabarcoding. Crop grown before sampling was best in explaining variation in community composition, but also soil type was shaping fungal and nematode communities, but not oomycete communities. Network analysis revealed that correlations between taxa within taxonomic groups were mostly positive whereas negative correlations dominated between taxa across the different taxonomic groups. Pythium intermedium and P. irregulare from soil samples were found to be associated with cavity spot disease in carrot, and were also found in the lesions of cavity spot. Our study demonstrate that previous crop and soil type significantly affect microbial communities and the development of symptoms of cavity spot in carrot. We also found that differences in co-occurrences within and between taxonomic groups exist.