The majority of studies in aquatic microbial ecology focus on the separate segments of aquatic ecosystem. Our project proposes comprehensive study of bacterial community within water column, sediment and fish as indicator of the aquatic environmental health status and its potential implications to human health. The project seeks to understand the genetic diversity of bacterial isolates in the aquatic environment, the relationships between environmental isolates, those from the healthy fish and from fish with clinical symptoms. These data are necessary to predict the origin and spreading pathways of bacterial indicators of water quality, as well as potentially pathogenic bacteria, both for fish and humans. Antibiotic resistance profiles will be explored to determine a potential link between selected model bacteria and their resistance, and the effects of different environmental stress factors. The overall strategy of the work plan is to implement a multidisciplinary approach for the examination of the complex bacterial ecosystem in the aquatic environment. Within the partnership, four tasks have been identified, equating to resolving of specific problem connected with aquatic microbial ecology: 1. Sampling network design and rationale, 2. Fish as model organisms, 3. Selected Model Bacteria and 4. Impact on human health. Research will be carried out using the infrastructures and expertise present within the consortium. The project will bring together state of the art research from currently fragmented research fields in the same area. This will create a basis for further actions in the prevention of diseases and disorders in fish caused by potential pathogens. Improved environmental sustainability will enhance the overall economical viability of the aquaculture sectors, concerned with lowering environmental impacts resulting from current practices. This will be of high interest to the general public, fish consumers, policy makers and policy administrators.