Investigating microbial interactions to drive complex conversion in bioprocesses

Microorganisms interact

In the ecosystems of environmental bioprocesses, substrate con-version are done by diverse microbial communities composed of microorganisms with different metabolic capabilities. Microorganisms affect each other and interact. We manipulate microbial interactions to optimize ecosystem function (e.g., change products, increase yield or kinetics, improve process stability).

Effects of pairwise interactions on microorganisms: positive (+), e.g., an increased activity, negative (­­–), e.g., a decreased activity, or neutral (0), e.g., unchanged behavior.

How to change interactions?

We modify microbial interactions (a) through bioaugmentation, i.e., by integrating desired bacteria into existing interaction networks and (b) by adding bioactive materials, e.g., activated carbon in anaerobic ecosystems to promote electron transfer.

Figure 1. Anaerobic digestion as an example of an interaction network. Hexagons represent substrates and intermediates, arrows show the flow of substrates; red lines illustrate substrate inhibitions.

Mutualism in photogranules

Making oxygenic photogranules (OPGs) convert a low-value and safe carbon source, e.g., CH4, into value-added products may enable promising applications in biotechnology [1]. We explore how functionally interesting, allochthonous bacteria, e.g., methanotrophs, can be best introduced and maintained in photogranules. We also investigate the stability and resistance of the engineered community against invasion.

Figure 2. Populations of bacteria with a desirable ecosystem function used as building block to engineer novel microbial communities.

Electronic parasitism in fermentation

Some electroactive bacteria can use a very wide range of electron acceptors, even other bacteria. The flow of discharged electrons can be useful to the receiving microorganism and lead to a mutualistic relationship, but it can also be detrimental, presenting a form of electronic parasitism [2]. We investigate the possible use of bacteria capable of interspecies electron transfer to drive fermentations.

Figure 3. An illustration of how an electroactive bacteria added in a mixed fermentation can inhibit the growth of unwanted bacteria, consume an unwanted product and favor the production of a desired molecule.

Modeling interactions

Dynamic systems models provide a powerful framework to explore interactions in microbial communities. We develop methods to evaluate interactions between populations using experimentally recorded time-series of microbial abundances and substrate or product concentrations (X and S, respectively, Figure 4). With mass balance models under thermodynamic constraints and control approaches [3], we evaluate the impact of interactions on growth rates.        

Figure 4. An interaction network (right panel) reconstructed from time series of microbial abundances (X vs. t) and of sub-strate or product concentrations (S vs. t)