Competition and cooperation: The plasticity of bacteria interactions across environments
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Abstract
Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is why some species engage in cooperative interactions, whereas others compete. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By scanning thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions to the availability of environmental resources.
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A key result from our analyses is the high degree of plasticity in bacteria interactions depending on the environmental context.
The plasticity of interactions is neatly demonstrated here. I wonder if the authors have any intuition about whether this plasticity could be controlled or reduced in more complex communities. In other words, would the presence of more species stabilize the interactions in the community regarding environmental changes?
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Exploring the constraints and cooperative potential as microbial communities grow presents a fascinating avenue for further investigation.
Thank you for this very interesting and clearly presented work! Looking forward to seeing what comes next for more complex communities.
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In addition to the essential compounds, we randomly added a fixed number of environmental compounds that could be utilized by at least one of the bacteria (50 additional compounds for smaller environments; or 100 for larger, see Methods: Algorithm for generating environments).
I am curious to know if some of these random environments are similar to known/relevant ecological niches, and which one? It could be informative to add this information somewhere if available.
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We found that the most common default interaction in both collections is neutral (see Fig. 1B), 49% in AGORA and 59% in CarveMe. Of the remaining interactions, we found that the CarveMe collection has more competitive interactions than AGORA and both collections have few cases of cooperation (2% AGORA and 0% CarveMe).
Have the authors investigated whether the distribution of competition and cooperation interactions shows any correlation with the phylogenetic distance of the species?
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The joint environment was created by combining the default environments of the two bacteria such that both were guaranteed to grow.
When both original environments shared similar compounds, did you add up the concentrations of these compounds, or did you keep the concentration from the original environment with the highest concentration?
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