Project properties
Title Experimental evolution of bacterial communities
Group Genetics, Laboratory of
Project type thesis
Credits 32
Supervisor(s) Sijmen Schoustra
Examiner(s) Bas Zwaan
Contact info Sijmen Schoustra
Begin date 2017/06/16
End date 2021/06/30
Description Experimental evolution aims to increase understanding of evolution and adaptions that lead to the world we live in at the moment. Bacteria are interesting model organisms as they have quick reproduction times and can be stored in the freezer to be revived at a later stage. Most evolution experiments are done with one single genotype. In that way the experiment can focus on the specific ways of adaption this genotype goes through.
In nature however, all organisms live in close relation with other organisms. To have a better idea on the influence of these close relationships evolution experiments can also be done with communities of bacteria. The best would be a community that represents all interactions and patterns that can be found in nature but simpler than most natural communities.
The model systems of the experiments described below are undefined starter cultures of a fermented product from Zambia. These starter cultures have a comparable community if you look at the most abundant species. The differences in the communities can be found in the bacteria that have a small abundance. In previous evolution experiments, the communities were transferred for over 100 generations. This allowed bacteria with a small abundance in some communities to increase in abundance while other communities stayed close to their original species distribution. At the end of the evolution experiment this divergent showed clear patterns.
The selection pressures put on the community are dependent of the way of transferring. This can be the volume of the transfer, the way of transferring (the liquid part or the biofilm), the time of transferring (in the exponential phase of bacterial growth or stationary phase) and many other variables.

Effect of bottleneck on community evolution
In order to find out how strong the drive to this divergence is, we can make it more difficult for bacteria of small abundance to grow out in the medium. We do this by making transfers with a higher dilution rate; only transferring the bacteria present in high abundance. This bottleneck can have an influence on final evolution outcomes. Experimental work will consists of several pilot experiments, in order to know which dilution rates can best be used. This pilot work will be followed by a short term evolution experiment of about 2 months. During these experiments the bacterial communities can be analysed using both culture and non-culture techniques.

Reaching evolutionary endpoints
Previously performed evolution experiment shows that in some lines L. crispatus became the main lactobacillus species. In the starting communities and in the other lines L. crispatus was present, but in lower amounts. It might be that the point at which this experiment was stopped was not the evolutionary endpoints of some of those lines. By sequencing the bacterial communities at other time points we can see in what way L. crispatus developed to be the main player. Also by transferring the lines for another 2 months the evolutionary endpoint could be reached.

Changing selection pressures
By transferring the bacteria to a new growth environment while they are in stationary phase we select for bacteria that are good at surviving at low pH. When transferring in an earlier phase of the fermentation cycle, like in exponential phase, we select for bacteria that have the highest growth rate at that stage. By playing with these fermentation times it can be seen if these selection pressures are stronger than others, like environment, as well as if they are the same for every community.
Used skills Microbiology, PCR, 16S amplicon sequencing, qPCR, GC-MS metabolomics
Requirements