Solowiej-Wedderburn Josephine, Pentz Jennifer T, Lizana Ludvig, Schroeder Bjoern O, Lind Peter A, Libby Eric
Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden.
Integrated Science Lab (IceLab), Umeå University, Umeå, Sweden.
PLoS Comput Biol. 2025 Jul 24;21(7):e1013213. doi: 10.1371/journal.pcbi.1013213. eCollection 2025 Jul.
Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. 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 computationally simulating 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 modeling 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 in response to the availability of environmental resources.
细菌生活在多样的群落中,形成相互作用物种的复杂网络。细菌生态学中的一个核心问题是物种间是进行合作还是竞争。但这个问题常常忽略了环境的作用。在这里,我们使用来自两个不同开放获取集合(AGORA和CarveMe)的基因组规模代谢网络,来评估不同微生物在不同环境条件下(提供不同环境化合物)的成对相互作用。通过对每个集合中的10000对细菌的数千种环境进行计算模拟,我们发现大多数对能够根据环境资源的可用性既进行竞争又进行合作。这种建模方法使我们能够确定环境之间的共性,这些共性可能促进一对物种之间合作或竞争的潜力。也就是说,合作相互作用,尤其是专性合作,在多样性较低的环境中最为常见。此外,随着化合物从环境中被去除,我们发现相互作用倾向于向专性方向退化。然而,我们还发现,平均而言,至少有一种化合物可以从环境中去除,从而将相互作用从竞争转变为兼性合作,反之亦然。我们的方法共同表明,微生物相互作用对环境资源可用性的响应具有高度可塑性。