Jan-Ulrich Kreft
Sketch of the branched catabolism of methylated phenolic plant compounds by Holophaga foetida. Four pathways are involved in the degradation of phenyl methyl ethers: (1) demethylation, (2) aromatic ring degradation by the phloroglucinol pathway, (3) sulphide methylation, and (4) methyl carbonylation by the acetyl-CoA pathway.
During my Diplom and PhD thesis with Bernhard Schink, I worked with a novel homoacetogenic bacterium because of its unusual features. We named it Holophaga foetida since it completely (holos) eats (phagein) its aromatic substrates (both the phenolic ring and the methyl groups of phenyl methyl ethers) and stinks (foetidus) due to the production of dimethyl sulfide from the methyl groups of the phenyl methyl ethers.
Holophaga foetida is a fascinating bacterium that among other things combines the two pathways of demethylation and ring degradation, that were known from its competitors, into one longer pathway, which yields more ATP, but the bacteria grow more slowly than the competitors that only demethylate or only degrade the aromatic ring. Nevertheless, Holophaga foetida is numerically more abundant than the faster growing competitors in all the sediments that we tested. I did not understand why this bacterium grows more slowly during my work in the Schink lab, but many years later while at Bonn, I came across kinetic theory that can in fact explain this observation.
See the papers for more information.
Individual-based modelling is a relatively new modelling approach that has gained a lot of popularity in the 1990's. This approach takes advantage of the modular self-organisation of populations and communities by describing such populations or communities in terms of their parts, the individual organisms. The population properties emerge as a result of the actions and interactions of these parts with each other and with the environment. The higher level of organisation therefore is not at all described in such a bottom-up model.
My aim is to establish IbM in Microbial Ecology.
As the first step, I wanted to prove that this approach is feasible for bacteria by writing a model of Escherichia coli colony development, dubbed "BacSim". The next step was the extension of BacSim to multi-species, multi-substrate biofilms. The latest completed step of model development was the inclusion of Extracellular Polymeric Substance (EPS) production as a further process. The task for the development of the model software is to include all major biological and mass transfer processes. This will allow the model to unify the theory in Microbial Ecology by encompassing all types of microbial communities.
Now that the necessary but rather technical phase of basic model development is over, I'm glad I can shift focus from technical issues to important biological questions. The first result of this new focus is the project on altruism in biofilms.
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ColoniesBiofilmsSlimy biofilmsSpoiled eggsBacSim: The program behind the IbM scenesQuantification of biofilm structureHow biofilms promote altruism |
Winogradsky discovered in 1890 that nitrification is carried out in two consecutive steps by two distinct groups of bacteria: ammonia-oxidizing bacteria and nitrite-oxidizing bacteria. An explanation for this division of labour is offered based on the kinetic theory of optimal design of metabolic pathways, which postulates the existence of an optimal length for a pathway that maximizes the rate of ATP production. Shortening long pathways could, therefore, increase growth rate. However, this would reduce growth yield if the shorter pathway has fewer ATP-generating steps. High yields would be advantageous when bacteria grow in clonal clusters, as is typical for biofilms. It is postulated that bacteria that completely oxidize ammonia to nitrate exist in such environments.
As an aside, I started the project NILS in close collaboration with Silke Heising. This project has had a tendency to demand increasing resources and several sub-projects have branched off, such as projects on sleeplessness and something else I can't remember right now.
Another, more recent, long-term project is IRIS, again in close collaboration with Silke Heising. The two systems studied in our projects NILS and IRIS are interacting closely, in reciprocal adaptation and evolving communication.
