AquaATR is an interdisciplinary project to investigate the application of Fourier transform infrared spectroscopy using the attenuated total reflectance (ATR) method in aquaculture and biotechnology. The project aims to develop rapid and reliable diagnostic methods for the characterization of biological samples in aquatic systems, thereby contributing to the improvement of disease diagnostics, microbiological biodiversity research and biotechnological applications. The project will form a new research group with a focus on the following specific objectives: i) identification and subtyping of pathogens in aquaculture ii) taxonomic dereplication of the biodiversity of the cultivable fish microbiome iii) clinical diagnostics by analyzing fish body fluids iv) surface enhancement and optimization of spectral data and analysis. In a multidisciplinary approach that will encompass the scientific disciplines of molecular spectroscopy, biotechnology in biomedicine (especially veterinary medicine and food safety), general and applied microbiology, molecular biology, biochemistry, chemometrics and artificial intelligence. The application of ATR technology in this context opens up new possibilities in veterinary medicine, food safety, bioprospecting and biodiversity research. The methods developed within the project will have broad scientific and applied value, with the potential for implementation in various fields of science and industry.