Establishing a closed-loop, phototrophic microbial ecosystem

No microbe lives in isolation. Yet, our understanding of microbial interactions in nature is highly limited. Most of molecular and evolutionary microbiology research is conducted in the context of monocultures. This makes it hard to understand genotype-phenotype linkage fully, as microbes evolve under heterogenous conditions and in presence of other microbes, and limits molecular biology applications in synthetic biology to monoculture situations.

In Soyer group, we are interested in understanding and manipulating microbial interactions from a metabolic stance1. We aim to construct microbial communities of manageable complexity through de novo engineering or environmental selection. The resulting systems will become important model ecosystems to study microbial interactions and their evolution. At the same time, they will offer novel applications in synthetic biology and bioproduction. This latter direction of engineering so-called synthetic microbial communities is a promising emerging area of research within synthetic biology and can make use of both genetically engineered and wild type organisms1-4. While ecosystem engineering can exploit signaling molecules and spatial associations, it is believed that most common interactions arise through metabolic exchanges, which are both found naturally and exploited in synthetic engineering of microbial communities1,5-8.

In this project, you will work towards establishing a self-sustaining microbial ecosystem involving photo- and heterotrophs. In particular, we are interested in understanding metabolic interactions among these functional groups, both in terms of primary energy metabolites and secondary metabolites and minerals. To this end, we will focus on identifying, in detail, metabolic excretions of set of phototrophs under defined environmental conditions9, as well studying metabolic interactions in natural phototroph-heterotroph communities. For the latter approach, we will use existing fresh water communities in our group, while the former will focus on our established set of phototrophs and application of state-of-the art metabolite measurement. The resulting findings will feed into modeling of phototroph metabolism, as well as determining key interaction points with helper heterotrophs. The resulting understanding will be applied to establish closed ecosystems, where phototrophs and heterotrophs can sustain each other for extended periods of time, solely through provision of light energy.

Key experimental skills involved: Microbial skills in culturing, isolation. Microscopy skills in time laps microscopy. Data analysis skills. Mathematical modelling skills.