Detailed analysis of changes in epibacterial community composition caused by shell disease syndrome on the carapace of Cancer pagurus

Crustaceans suffer from the black spot shell disease syndrome, which is the result of bacterial degradation of the chitinous exoskeleton. The European brown crab, Cancer pagurus, is highly susceptible to this disease. We compared the bacterial communities of black spot affected and non-affected areas of the carapace by amplicon sequencing of 16S rRNA genes and 16S rRNA. We found that affected areas are less diverse within each spot compared to communities from non-affected areas. Communities of different affected spots are, however, more divergent from each other, compared to those of different non-affected areas. This indicates a reduced and shifted microbial community composition caused by the black spot disease. In affected areas Flavobacteriaceae rose up to one of the most abundant and active families, due to a massive increase of Aquimarina sp., suggesting a significant role in shell disease syndrome. Proteobacteria and Bacteroidetes were dominant phyla in communities detected by amplicon sequencing. Overall, we found a phylogenetical complex epibacterial community on the carapace of C. pagurus, harbouring opportunistic pathogens already in healthy areas.