CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.
College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
Nat Commun. 2024 Sep 17;15(1):8166. doi: 10.1038/s41467-024-52532-x.
Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.
微生物群落表现出复杂的相互作用，这些相互作用是由代谢依赖性支撑的。为了阐明这些依赖性，我们提出了一种利用随机矩阵理论对宏基因组组装基因组进行分析的工作流程，以构建共生和代谢互补网络。我们将这种方法应用于温度梯度温泉，揭示了热应激和代谢合作之间的相互作用。我们的分析表明，随着温度的升高，代谢相互作用的频率增加。氨基酸、辅酶 A 衍生物和碳水化合物作为关键的交换代谢物出现，为协同依赖关系奠定了基础，其中共生相互作用比互利相互作用更为普遍。这些代谢交换在亲缘关系较远的物种之间最为普遍，尤其是古菌与细菌的合作，这是对恶劣环境的重要适应。此外，我们发现基础代谢物交换与基因组大小差异之间存在显著的正相关关系，这可能表明精简基因组可以利用与代谢更丰富的伙伴合作的手段。这种现象在另一个具有相似温度波动范围的堆肥系统中也得到了证实。我们的工作流程为破译微生物相互作用的代谢互补机制提供了一种可行的方法，我们的研究结果表明，环境压力调节嗜热菌的合作策略，而这些依赖性在它们的共同进化过程中已经被潜在地固定在它们的基因组中。
