Depuration of a solitary ascidian depletes transient bacteria without altering microbiome alpha-diversity

Depuration, or the process of clearing impurities from within the gut, is commonly applied to marine food products, such as oysters and mussels. This technique has proven effective at removing viruses and E. coli from shellfish and edible ascidians, with recent studies noting significant impacts on microbial alpha- and beta-diversity in the gut of depurated animals. Here, we examined the impact of a four-day depuration on bacteria in the branchial sac, gut, and hepatic gland of the solitary ascidian Pyura vannamei. Replicates were kept in filtered seawater for four days prior to dissection and compared to samples that were immediately processed following collection. The microbiome of additional replicates kept in unfiltered seawater for four days prior to processing, and the microbiome of one individual that died ~12 hours before processing were also characterized. 16S rRNA (V4) gene sequence analysis revealed no significant differences among all sources for microbial alpha-diversity but significant shifts in beta-diversity. The number of core bacteria (those shared among all individuals within sources) displayed a marked decrease across all body regions of depurated compared to wild individuals. Core bacteria shared across depurated and wild individuals consisted of genera associated with enhanced host health and resilience to pathogenic microbes and pollutants within other marine symbioses. Metagenomic studies are needed to confirm if similar functionality is present for the core bacteria of P. vannamei. Our results suggest that depuration is not necessary to obtain accurate microbial alpha-diversity profiles of ascidian microbiomes but can help differentiate transient from resident taxa in complex host-microbiome symbioses