Microbial interactions in hydrogen-oxidizing communities

Microbial communities are primary drivers of element cycles on a planetary level and are essential for the functioning of all ecosystems on earth and in many industrial processes. A microbial community is a complex network, consisting of several sub-populations, which can interact with each other by antagonistic or cooperative processes. However, in contrast to individual microorganisms for which we know a lot about gene expression, stress response, etc., the knowledge about the complex network that is formed by collaborating microorganisms remains unsatisfactory. In the present project, we will further develop the 'collaboromes' concept that was developed at the Center for Microbial Ecology and Technology. These collaboromes are synthetic ecosystems built from isolated strains existing of a core population with a dedicated ecological functionality and (non-redundant) satellite populations supporting the core populations, however not contributing directly to the targeted functionality. Collaboromes, with their intermediate complexity and high controllability, allow for the study and elucidation of interactions contributing to or inhibiting functionality of the synthetic ecosystem. Here, hydrogen-oxidising communities will be studied, the reason for this is twofold. Firstly, since the whole community is depending on hydrogen-oxidation, the core function is well-defined, making it a good target to study collaboromes. Secondly, from an applied point of view, the analysis and understanding of these synthetic communities can lead to the development of highly productive collaboromes that can valorise common industrial and agricultural waste components such as carbon dioxide and ammonium as high-quality protein. In order to guide the production of collaboromes and to gain deeper insight in microbial interactions, predictive modelling approaches will be used. In short, the goal of this project is to gain insight into the interactions occurring in hydrogen-oxidising bacterial communities and to apply this knowledge to create highly productive and efficient collaboromes that grow on hydrogen, oxygen, carbon dioxide and ammonia and produce high quality protein. Initial prospective co-culturing with a core species and a satellite species will be done to collect growth rate data and to group species according to their positive or negative interaction influence. Predictive models will be made, validated and subsequently used to predict productive higher-order collaboromes. This process of collaborome construction, modelling, prediction and validation will yield insights in the interaction between core and satellite species of these communities and will lead to new understandings in the ecology of microbial communities. As such it can also bring forth highly productive collaboromes finding use in life support systems or industrial reactors validating waste products as high-quality protein.