It is understood that there is an association between productivity and microbial diversity in aquaculture systems. For example, changes in bacterial microbiomes are implicated in animal performance, in disease development associated with both bacterial and viral origin, and in dysbiosis (disequilibrium in microbial communities) triggered by environmental stressors or diet choice. With the increasing utilization of novel DNA sequencing technologies, new concepts and cost-effective applications have emerged to better understand the role of microbial communities in the growth and health of farmed vertebrates and invertebrates. Evidence of any of the three main mechanisms that lead to dysbiosis -such as the decrease in diversity, the loss of beneficial bacteria and the expansion of pathogens or potentially harmful microorganisms- can be used as an indicator tool for productivity monitoring/forecasting purposes.
This work establishes a methodology and a pipeline for microbiome characterization in Recirculation Systems, emphasizing which parameters are essential for a fast turnaround of actionable information. In addition to core interpretations (such as alpha and beta diversity indexes, heatmaps, composition bar-plots at different taxa and other common indicators of microbial ecosystems) customized lists including cyanobacteria profiles; “watch lists” and “pathogen lists” and presence/absence of off-flavor compound producing species are included. Other in-depth analyses of the bacteria identified by full length 16s sequencing may include the description of general functional categories such as environmental, probiotic, nitrifying, iron-reducing, or predatory and parasitic species; and these analyses may be carried out as part of a routine monitoring program.
Considering that the list of detected bacterial species across several samples can reach the order of thousands, our intention in the report is to highlight the concerning points and the healthy balance, as well as a general overview of the system. In that way, decision makers can focus their attention on what matters and take the appropriate decisions on time for the wellness of the RAS system and the animals. Common applications of these studies include 1.- monitoring for correlation with water quality and animal performance and productivity; 2.- evaluation of disinfection treatments in RAS systems; 3.- forecasting of possible outbreaks or major issues; 4.- evaluation of probiotics, diets, or drug/vaccine treatments.