Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.

微生物群落是由环境代谢物塑造的，但控制不同群落在任何给定条件下是否趋同或分歧的原理仍然未知，这对微生物组工程的可行性提出了基本问题。在这里，我们研究了在代谢复杂性不断增加的实验室条件下生长的一组天然微生物群落的纵向组装动力学。我们发现，不同的微生物群落在代谢简单的条件下生长时往往会变得相似，但随着环境代谢复杂性的增加，它们的组成会出现差异，我们将这种现象称为分歧复杂性效应。对这些群落的比较分析表明，这种差异是由群落多样性和能够降解复杂代谢物的专业分类单元的分类驱动的。群落动力学的生态模型表明，新陈代谢本身的层次结构（其中复杂的分子被酶促降解为逐渐简单的分子，然后参与群落成员之间的交叉喂养）对于概括我们的实验观察是必要且充分的。除了帮助理解环境在群落组装中的作用之外，分歧复杂性效应还可以深入了解哪些环境支持多种群落状态，从而能够为微生物组工程应用寻找所需的生态系统功能。