Post-harvest colonization of sugar beets accompanied by rot development is a serious problem due to sugar losses and
negative impact on processing quality. Studies on the microbial community associated with rot development and factors
shaping their structure are missing. Therefore, high-throughput sequencing was applied to describe the influence of
environment, plant genotype and storage temperature (8◦C and 20◦C) on three different communities in stored sugar beets,
namely fungi (internal transcribed spacers 1 and 2), Fusarium spp. (elongation factor-1α gene fragment) and oomycetes
(internal transcribed spacers 1). The composition of the fungal community changed during storage mostly influenced by
the storage temperature followed by a weak environmental effect. Botrytis cinerea was the prevalent species at 8◦C whereas
members of the fungal genera Fusarium and Penicillium became dominant at 20◦C. This shift was independent of the plant
genotype. Species richness within the genus Fusarium also increased during storage at both temperatures whereas the
oomycetes community did not change. Moreover, oomycetes species were absent after storage at 20◦C. The results of the
present study clearly show that rot development during sugar beet storage is associated with pathogens well known as
causal agents of post-harvest diseases in many other crops.