Biology subjects

Osborne, M. L.

Publications and source records attributed to Osborne, M. L..

2 recordsLinked to original sources

bioRxiv2020

Artificially selecting microbial communities using propagule strategies

Artificial selection is a promising approach to manipulate the function of microbial communities. Here, we report the outcome of two artificial selection experiments at the microbial community level. Both experiments used "propagule" strategies, in which a set of the best-performing communities are used as the inocula to form a new generation of communities. In both cases, the selected communities are compared to a control treatment where communities are randomly selected. 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 a diverse set of natural communities as the inoculum, and the function under selection was the cross-feeding potential of the resulting communities towards a reference bacterial strain. In both experiments, the selected communities reached a higher mean and a higher maximum function than the control. In the first experiment this is caused by a decline in function of the control, rather than an improvement of the selected line. In the second experiment, the strong response of the mean is caused by the large initial variance in function across communities, and is the immediate consequence of the spread of the top-performing community in the starting group, whose function does not increase. Our results are in agreement with basic expectations of artificial selection theory, pointing out some of the limitations of community-level selection experiments which can inform the design of future studies.

evolutionary biology↗

bioRxiv2018

High-order interactions dominate the functional landscape of microbial consortia

Understanding the link between community composition and function is a major challenge in microbial ecology, with implications for the management of natural microbiomes and the design of synthetic consortia. For this purpose, it is critical to understand the extent to which community functions and properties can be predicted from species traits and what role is played by complex interactions. Inspired by the study of complex genetic interactions and fitness landscapes, here we have examined how the amylolytic function of combinatorial assemblages of seven starch-degrading soil bacteria depends on the functional contributions from each species and their interactions. Filtering our experimental results through the theory of enzyme kinetics, we show that high-order functional interactions dominate the amylolytic rate of our consortia, even though this function is biochemically simple, redundantly distributed in the community, and additive in the absence of inter-species interactions. As the community grows in size, the contribution of high-order functional interactions grows too, making the community function increasingly unpredictable. We can explain the prevalence of high order effects and their sign from the redundancy of ecological interactions in the network, in particular from redundant facilitation towards a high-performing community member. Our results suggest that even simple functions can be dominated by complex interactions, posing challenges for the predictability and bottom-up engineering of ecosystem function in complex multi-species communities.

ecology↗