Aquaculture is an important source for food, nutrition, income and livelihoods for millions of people around the globe. But intensive fish farming is often associated with pathogen outbreaks as high amounts of veterinary drugs are used globally. As in many other environments, mostly the application of antimicrobials triggers the development of (multi)resistant microbiota. This process might be fostered by co-selection as a consequence of the additional use of antiparasitics.

Using antimicrobials in aquaculture not only affects the cultured fish species, but – to a so far unknown extent – also aquatic ecosystems connected to fish farms, including microbiota from water and sediment as well as its eukaryotes. Effects of this include an increase in the number of (multi)resistant microbes, as well as complete shifts in the microbial community structure and function. This “dysbiosis” might have consequences for the functioning of aquatic ecosystems.

In the frame of the project CONTACT (Consequences of antimicrobials and antiparasitics administration in fish farming for aquatic ecosystems), we study the consequences of antimicrobial and antiparasitic application in aquaculture for the cultured fish species as well as for the aquatic environments. To consider the variability of aquaculture practices, four showcases have been selected worldwide, covering freshwater and marine environments. They represent typical systems from the tropics, the Mediterranean and the temperate zone. For one showcase, a targeted mitigation approach to reduce the impact on aquatic ecosystems will be tested. We make use of molecular methods to study the structure and function of the microbiome of the administered fish. We also study non-target organisms and water bodies including metabarcoding approaches and metagenomics analysis which are based on directly extracted nucleic acids from the samples.

@CONTACT

In the first phase of the project, three showcase studies were successfully performed in model experiments under controlled conditions. They included experiments with Salmo trutta, Oreochromis sp. and Sparus aurata, representing the showcases from the temperate zone (fresh water), the tropics (fresh water) and the Mediterranean (marine) respectively. In addition, we were able to setup a robust analytical pipeline for the antibiotic compound (florfenicol), which is used as a model in our studies as it is used worldwide in aquaculture.

Our current analysis of the data clearly demonstrates that significant effects on the gut microbiome of the three fish species were visible, mainly during the phase of administration of the compounds under investigation. These manifested themselves in a clear reduction in diversity.

Effects became less significant when the application of the antibiotics was stopped, so much so that a regeneration of the microbiome was visible. But they still differed from the microbiome of the control group of fish, where no antibiotics had been applied, at the end of the experimental period. In addition, the application of compounds with antimicrobial/parasitic properties induced shifts in the microbiome of non-target organisms like mussels or seeweed. This may strongly affect the health and the fitness of these organisms and the subsequent food web structures in the affected ecosystems.

We also assessed functional consequences of these observed changes in the microbiomes of the administered fish as well as the non-target organisms. Here, we could identify a number of important genes which trigger host-microbe interactions which are affected by the administration of the antibiotic/parastic compounds tested both for target and non-target organisms.