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The increasing problem of antibiotic resistance in common pathogenic bacteria and the concern about the spreading of antibiotics in the environment bring the need to find new methods to control fish pathogens. Phage therapy represents a potential alternative to antibiotics, but its use in aquaculture requires a detailed understanding of bacterial communities, namely of fish pathogenic bacteria. Therefore, in this study the seasonal dynamics of the overall bacterial communities, microbiological water quality and disease-causing bacteria were followed in a marine aquaculture system of Ria de Aveiro (Portugal). Analysis of the bacterial diversity of the water samples by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments indicates that the bacterial community structure varied seasonally, showing a higher complexity during the warm season. The diversity of the main fish pathogenic bacteria, assessed by DGGE targeting the Vibrio genus, showed lower seasonal variation, with new dominating populations appearing mainly in the spring. Bacterial indicators, faecal coliforms and enterococci, enumerated by the filter-membrane method, also varied seasonally. The fluorescent in situ hybridization (FISH) results showed that the specific groups of bacteria varied during the study period and that the non-indigenous Enterobactereaceae family was the most abundant group followed by Vibrio and Aeromonas. The seasonal variation detected in terms of density and structure of total and pathogenic bacterial communities demonstrates the need for a careful monitoring of water through the year in order to select the suitable phages to inactivate fish pathogenic bacteria. The spring season seems to be the critical time period when phage therapy should be applied.

Evaluating seasonal dynamics of bacterial communities in marine fish aquaculture: a preliminary study before applying phage therapy