Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 3498838, Haifa, Israel.
Commun Biol. 2022 Mar 28;5(1):276. doi: 10.1038/s42003-022-03184-4.
Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
微生物相互作用塑造了微生物群落的结构和功能，对生物地球化学循环和生态系统健康有着深远的影响。然而，大多数相互作用机制仅在模型系统中进行研究，其普遍性尚不清楚。为了系统地探索海洋细菌的功能和相互作用潜力，我们开发了一种基于特征的方法，并将其应用于 473 个完整基因组（248 属），这些基因组代表了海洋微生物群落的很大一部分。我们确定了基因组功能群（GFC），这些功能群将具有共同生态和生活史的细菌分类群分组。大多数 GFC 揭示了独特的相互作用特征组合，包括铁载体（10%的基因组）、植物激素（3-8%）和不同的 B 族维生素（57-70%）的产生。由 Alpha-和 Gammaproteobacteria 组成的特定 GFC 表现出比预期更多的相互作用特征，因此预计它们将优先协同和/或拮抗地与细菌和浮游植物相互作用。关联特征群（LTC）识别可能一起进化的特征（例如，分泌系统、氮代谢调控和 B 族维生素转运蛋白），为微生物相互作用的复杂机制提供了可测试的假设。我们的方法将多维基因组信息转化为海洋细菌及其潜在功能的图谱，这对于理解控制群落组装和动态的基本规则是很重要的。
