Carrot storage diseases predominantly caused by mixed fungal infections

Fungal pathogens often cause severe post-harvest losses in stored carrot yields. In 2020 and 2021, carrot samples were collected in Finland from 26 fields with different soil types. The proportion of symptomatic carrots was assessed at two time points during the cold storage period. To analyse the occurrence of different fungal pathogens in the symptomatic carrots, DNA samples were prepared and tested for the presence of fungal pathogens by species-specific PCR. The most frequently detected pathogens were Cylindrocarpon spp. with 61% occurrence, followed by Fusarium avenaceum (44%), Mycocentrospora acerina (42%), Botrytis cinerea (12%), and Alternaria spp. (0.8%). B. cinerea and F. avenaceum were more common in carrots grown on organic soil, while M. acerina was more common in carrots grown on mineral soils. Mixed fungal infections were overrepresented in the symptomatic samples, in particular, Cylindrocarpon spp. often occurred together with F. avenaceum and M. acerina in the same samples. Amplicon sequencing of the fungal internal transcribed spacer region from the DNA of symptomatic tissues revealed that in addition to the pathogens—B. cinerea, M. acerina, Cylindrocarpon spp. and Sclerotinia sclerotiorum—the hyphomycete fungi Tetracladium spp. and the yeast Leucosporidium intermedium were abundant, and that Tetracladium spp. were more abundant in the carrots infected with M. acerina. A pathogenicity test confirmed that F. avenaceum is pathogenic to both the new season and old season carrots.