Aquaculture Europe 2023

September 18 - 21, 2023


Add To Calendar 21/09/2023 16:15:0021/09/2023 16:30:00Europe/ViennaAquaculture Europe 2023DOES THE FISH TANK HISTORY HAVE AN INFLUENCE ON THE MICROBIAL DIVERSITY IN RECIRCULATING AQUACULTURE SYSTEMS (RAS) AND HOW TO LIMIT THIS INFLUENCE?Strauss 3The European Aquaculture Societywebmaster@aquaeas.orgfalseDD/MM/YYYYaaVZHLXMfzTRLzDrHmAi181982


AL DAKDOUKI Salam*a ,  NIVELLE Renaud a , LEDORÉ Yannick a , CHANGEY Frédérique b, FONTAINE Pascal a


a University of Lorraine, INRAE, URAFPA, 54000, Nancy, France

b University of Lorraine, CNRS, LCPME, F-54000, Nancy, France

Corresponding author:




Aquaculture is undergoing rapid development worldwide (FAO, 2020), but the sustainability of aquaculture systems is more and more questioned in view of the many changes taking place (climate, animal welfare, antibiotic resistance, etc.) (Sudarshan et al., 2021) .  To reduce their dependence on  the surrounding unstable environment, the Recirculating Aquaculture Systems (RAS) have been developed. Those systems allow to reuse 90-99%  of water  but also to create an optimal growth environment for fish (temperature, nutrients, etc.). The functioning of RAS is highly dependent on the equilibrium between fish and microbial communities (e.g.: biofilter, associated biodiversity) (Kamali et al., 2022) .  This equilibrium could become more complex to achieve with the development of the polyculture in RAS (Thomas et al., 2020).

 The fish microbiota (tract, skin, and gills) is highly diverse, including bacteria, fungi, viruses  (Merrifield and Rodiles , 2015; Dulski et al., 2020; Dai et al., 2021) and is affected by intrinsic factors including trophic level, fish species (mainly linked with gastrointestinal tract morphology and diet) and environmental factor as season and captive-state (Egerton et al., 2018) . Fish have an intimate interaction with their surrounding environment resulting in a shaping effect on water microbial communities (Fourrier et al., 2022). This study suggest also that the RAS history (linked with biofilm memory) seems to influence water microbiome. A reliable protocol is required to stabilize and equilibrate initial microbial communities before studying the effects of fish communities on microbial communities. 

An experiment  was performed to select a  standardized  procedure to obtain  tanks with a microbial diversity as close as possible regardless of the history of the tanks.  The objective here is not to have a perfect disinfection of the tanks , but rather to have a starting situation (t0)  in the tanks  that is as similar as possible either by homogenizing the filtration substrates or either  by replacing them, limiting variability  due to fish rearing .

Materials and methods

 We compared 3 disinfection/homogenization modalities  (M) using 4 replicates  for each. That’s why 12 tanks were selected based on their rearing history of different fish species over the past 3 years .

  1.  M1: Emptying and filling of the tanks after cleaning (raw cleaning),
  2. M2: Raw cleaning, homogenization of  active  biofiltration substrates between fish tanks, standard protocol disinfection  which consists of chemical treatments (hydrogen peroxide and chloramine T) and physical treatments (high temperature and drying) (protocol currently used at the Aquaculture Experimental Platform PEA of the University of Lorraine).
  3.  M3:  Same as M2 but using new and inactive biofiltration substrates.

 The experiment lasted 30 days and water was sampled (days 0, 16, 23 and 30) to access physico-chemical parameters of water and microbial communities dynamic. The physicochemical parameters of water: temperature, dissolved oxygen, pH, NH4+, NO2-  and NO3- will be measured during the experiment. The microbial diversity  of tank water ( sampled on days 0, 16, 23 and 30) was assessed by metabarcoding approaches. Sequencing (Miseq 2x300 bp) was performed at the GIGA Institute (University of Liège) and bioinformatic analysis was performed using FROGS and R software.


 We observed  a significant effect of the treatment on the  dynamic of the  microbial communities. The most homogenous starting point in all replicates was obtained using the second modality M2. The results allowed us to select the most reliable  tested  protocol that can be used to study microbial communities regardless of the tank rearing history.


 Egerton S., Culloty S., Whooley J., Stanton C.,  and Ross R. P. 2018. The gut microbiota of marine fish. Frontiers in microbiology, 9, 873.

FAO. 2020. The state of world fisheries and aquaculture. Sustainability in action. Food and Agriculture Organization of the United Nations. 

Fourrier C. , Senff P. , Changey F., Mathieu L., Abed Al Rahim S. , Ledoré Y., Milla S., Charpentier N., and Fontaine P. 2022.  Is biculture with tench (Tinca tinca) a way to improve growth and physiological status of pikeperch ( Sander lucioperca) reared in RAS?  PERCIS-V.  

Dai L., Liu C., Peng L., Song C., Li X., Tao L., and Li G. 2021. Different distribution patterns of microorganisms between aquaculture pond sediment and water. Journal of Microbiology. Vol. 59, No. 4, pp. 376–388.

Dulski T., Kozlowski K., and Ciesielski  S. 2020. Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome .  Scientific reports. 10:4460.

Kamali S., Ward V . C.A., and Ricardez-Sandoval L. 2022. Dynamic modeling of recirculating aquaculture systems: Effect of management strategies and water quality parameters on fish performance. Aquacultural Engineering.

 Merrifield D. L. and Rodiles A. 2015. The fish microbiome and its interactions with mucosal tissues. In Mucosal health in aquaculture . pp. 273-295. Academic Press.

 Sudarshan S., Krishnaveni K., Alamelu V., and Aanand S. 2021. Antimicrobial resistance in aquaculture. AQUA INTERNATIONAL.

Thomas M. , Lecocq T. , Abregal C. , Nahon S., Aubin J., Jaeger C. , Wilfart A., Schaeffer L. , Ledoré Y. , Puillet L., and Pasquet A . 2020. The effects of polyculture on behavior and production of pikeperch in recirculation systems. Aquaculture Reports. Vol 17.