Microbial Communities Associated with FarmedGenypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing

Simple Summary Aquaculture can supplement traditional fisheries to meet the demands of growing populations and may help reduce the overfishing of natural resources. The Chilean Aquaculture Diversification Program has encouraged technological developments for rearing native species such as the red conger eel (Genypterus chilensis), but intensive aquaculture practices have led to bacterial outbreaks ofVibriospp. andTenacibaculumspp. in farmed fish. This retrospective study analyzed the natural bacterial community associated with the recirculating seawater used in an experimentalG. chilensisaquaculture facility to determine if outbreak strains could be identified through regular monitoring. Water samples were analyzed by traditional culturing methods and culture-independent high-throughput amplicon sequencing of the 16S rRNA gene. The sequencing results showed a higher relative abundance ofVibrioandTenacibaculumspp. around the time of the outbreaks, but the most abundant genera of cultured isolates did not necessarily match those observed through sequencing. Cultured isolates were assayed for virulence factors and susceptibility to antibiotics to ascertain potential risks and treatments should future outbreaks occur. Although the predominant bacteria identified by the two approaches differed, valuable information was obtained from each method. We thus conclude that the dual monitoring approach is necessary to implement prophylactic measures to prevent future outbreaks. The red conger eel (Genypterus chilensis, Guichenot) is a native species included in the Chilean Aquaculture Diversification Program due to high commercial demand. In the context of intensified farming, prior reports link two disease outbreaks with emerging pathogens in theVibrioandTenacibaculumgenera. However, the roles remain unclear for the bacterial community and each specific bacterium is associated with the rearing environment for healthy specimens. The success of red conger eel farming therefore warrants research into the bacterial composition of aquaculture conditions and the antimicrobial susceptibilities thereof. This study used culturing methods and high-throughput sequencing to describe the bacterial community associated with water in whichG. chilensiswas farmed. With culturing methods, the predominant genera wereVibrio(21.6%),Pseudolteromonas(15.7%),Aliivibrio(13.7%), andShewanella(7.8%). Only a few bacterial isolates showed amylase, gelatinase, or lipase activity, and almost all showed inhibition zones to commonly-used antibiotics in aquaculture. By contrast, high-throughput sequencing establishedParaperlucidibaca,Colwellia,Polaribacter,Saprospiraceae, andTenacibaculumas the predominant genera, withVibrioranking twenty-seventh in abundance. High-throughput sequencing also established a link between previous outbreaks with increased relative abundances ofVibrioandTenacibaculum. Therefore, monitoring the presence and abundance of these potential pathogens could be useful in providing prophylactic measures to prevent future outbreaks.