The Ecophysiology Department, headed by Lotte Søgaard-Andersen, focuses on understanding how intracellular signalling networks are wired to allow bacteria to adapt and differentiate in response to changes in the environment or in response to self-generated signals. Specifically, the department has two aims. Firstly, they aim to understand how bacteria process information to generate appropriate output responses (e.g. changes in gene expression, changes in motility behavior). Secondly, they aim to understand how molecular machines involved in motility and secretion function and how their activity is regulated.  Ecophysiology currently has three research groups led by the following in parentheses:
* Bacterial secretion systems (Andreas Diepold)
* The intracellular organization and differentiation of bacteria (Simon Ringgaard)
* Bacterial development & differentiation (Lotte Søgaard-Andersen)