Artificially selecting bacterial communities using propagule strategies

Artificial selection is a promising approach to manipulate microbial communities. Here, we report the outcome of two artificial selection experiments at the microbial community level. Both used “propagule” selection strategies, whereby the best-performing communities are used as the inocula to form a new generation of communities. Both experiments were contrasted to a random selection control. The first experiment used a defined set of strains as the starting inoculum, and the function under selection was the amylolytic activity of the consortia. The second experiment used multiple soil communities as the starting inocula, and the function under selection was the communities’ cross-feeding potential. In both experiments, the selected communities reached a higher mean function than the control. In the first experiment this was caused by a decline in function of the control, rather than an improvement of the selected line. In the second experiment, this response was fueled by the large initial variance in function across communities, and stopped when the top-performing community “fixed” in the metacommunity. Our results are in agreement with basic expectations from breeding theory, pointing to some of the limitations of community-level selection experiments which can inform the design of future studies.