Monitoring microbial dynamics in a perch recirculating aquaculture system with fully automated online flow cytometry

Silva, Marisa (29 September 2022). Monitoring microbial dynamics in a perch recirculating aquaculture system with fully automated online flow cytometry In: Aquaculture Europe 2022 Rimini. Rimini. September 27 - 30. September 2022.

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Introduction Microorganisms are omnipresent and crucial players in all aquatic systems. They can have a large impact especially in recirculating aquaculture systems (RAS), where water is reused continuously. In these systems, tight control on water quality is essential for successful and safe fish production. Microorganisms affect fish health in a multitude of ways and control of a RAS is inextricably linked to microbial concentrations, be it in the fish tanks where pathogen growth must be avoided, or in the biofilter, where microbial populations must be maintained abundantly for nitrification. Online sensors are standard in the industry for multiple physicochemical parameters, however microbial concentrations are difficult to get by for fish farmers. Tracking of microbial dynamics requires sampling and analysis at very short intervals and ideally in real-time allowing for immediate interpretation/reaction. For decades this was impossible with conventional microbial cultivation-based methods but also with advanced molecular methods, which are still too labour-intensive, time-consuming, and costly for such applications. One promising approach is the use of flow cytometry, which allows fast, accurate and reproducible quantification and differentiation of total and intact cells. This detection method has specific advantages including: rapidness, sensitivity, reproducibility, accuracy in quantification, and differentiation of total and intact cells. Material and methods In a first step, grab samples across the RAS were analysed by our flow cytometry protocol for total and intact bacteria. A perch and a carp cultivation were compared in terms of microbial concentration. In a second step, we used a fully automated online flow cytometry system that overcomes the tedious and restricting practice of grab-sampling and subsequent cultivation on agar plates Besmer et al. (2014). This system was used to monitor a perch RAS cultivation system. In short, water samples were drawn directly from several points in the system, mixed with a fluorescent stain, incubated, and then measured by flow cytometry. Rinsing and extended cleaning were performed regularly and periodically respectively. The resulting large sets of flow cytometry data were batch processed with custom software. Results Flow cytometry could successfully be used for the measurements of the grab samples. Background could be separated well, and the measurements were technically highly reproducible. The measurements showed significant concentrations of total and intact bacteria across each of the RAS, on the order of 105 to 106 cells/ml. Strikingly, while clear differences were detected between the carp and the perch cultivation systems, the concentrations across different locations within each of these systems were very similar. The RAS is being monitored for an extended period, initiating one week prior to the fish entering the tanks, and continuing during the fish cultivation period. Changes in concentration of total and intact bacteria are being followed and compared with important process parameters like feeding and cleaning procedures. Discussion and conclusion Our results show the potential of advanced monitoring of microbial dynamics, which is critical for a better understanding of underlying causes of fluctuations as well as the ecological and operational consequences thereof. We expect that these findings will massively enhance process monitoring, water treatment design and improvement (e.g., disinfection in RAS). In addition, we expect a potential for optimisation of feed and other production processes, including conceptual approaches to smarter sampling schemes, but also new applied and fundamental research directions.

Item Type:

Conference or Workshop Item (Speech)


School of Agricultural, Forest and Food Sciences HAFL
School of Agricultural, Forest and Food Sciences HAFL > Agriculture
School of Agricultural, Forest and Food Sciences HAFL > Agriculture > Livestock and Horses


Silva, Marisa and
Janssens, Thomas


S Agriculture > SH Aquaculture. Fisheries. Angling




Thomas Janssens

Date Deposited:

18 Jan 2023 09:46

Last Modified:

18 Jan 2023 09:46

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