Metabolic processes in the deep biosphere potentially have a profound influence on ocean biogeochemistry and – subsequently – ecology. Metagenomic and biogeochemical studies have laid the foundation for understanding these ecosystems, but we are sorely lacking information on the metabolic activity of these microbes, both as individual “species” and as communities. This project allowed the development of a comprehensive method to cover a wide range of metabolites in deep sea bacteria and has already proven very efficient at detecting the effect of pressure on Photobacterium profundum metabolism. There is a high number of metabolites responding strongly to the pressure regime, resulting in widely different pools of amino acids and sugars and membrane compositions. Those results shed a more detailed light on what it means for a bacterial cell to grow in deep sea conditions and will provide a solid base for interpreting future experiments.