Microbial Community Composition and Colonization in Compartmentalized Aquaculture Systems

Microbiomes influence nearly every aspect of health and disease across humans, animals, and ecosystems, yet we lack a functional understanding of their assembly and dynamics in complex settings. MiCo4Sys targets this gap by studying recirculating aquaculture systems (RAS) as semi-natural, compartmentalized systems with direct relevance for animal health and human protein consumption. Combining empirical and theoretical approaches, the project brings together a fish health group with microbiome and diagnostic expertise and a theoretical ecology group skilled in modeling and bioinformatics.

We aim to:

1. Characterize microbiome structure in time and space

  • Map spatial niches and reservoirs
  • Track long-term dynamics and environmental responses

2. Quantify biofilm colonization and repeatability

  • Develop models of stochastic colonization
  • Empirically monitor post-disturbance colonization
  • Estimate dispersal and interaction parameters

3. Analyze microbiome dynamics during disease and recovery

  • Identify early disease indicators
  • Link interventions to recovery patterns
  • Assess stability and system responses

The project is co-led between Irene Adrian-Kalchhauser at the Veterinary Faculty, and Claudia Bank at the Natural Sciences Faculty. It is funded by the Swiss National Reserch Foundation (Project # 204838).

Publications

Rieder, J., Berezenko, A., Meziti, A. and Adrian-Kalchhauser, I. (2025), The Future of Pathogen Detection in Aquaculture: Miniature Labs, Field-Compatible Assays, environmental DNA and RNA, CRISPR and Metatranscriptomics. Aqua. Fish & Fisheries, 5: e70062. https://doi.org/10.1002/aff2.70062

Rieder, J., Jemmi, E., Hunter, M. and Adrian-Kalchhauser, I. (2024), A Guide to Environmental DNA Extractions for Non-Molecular Trained Biologists, Ecologists, and Conservation Scientists. Environmental DNA, 6: e70002. https://doi.org/10.1002/edn3.70002

Rieder, J., Kapopoulou, A., Bank, C. et al. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. Environmental Microbiome 18, 8 (2023). https://doi.org/10.1186/s40793-023-00459-z

Rieder, J., Martin-Sanchez, PM., Osman, OA., et al. Detecting aquatic pathogens with field-compatible dried qPCR assays. Journal of Microbiological Methods 202 (2022). https://doi.org/10.1016/j.mimet.2022.106594.