Inverse stable isotope probing-metabolomics (InverSIP) identifies an iron acquisition system in a methane- oxidizing bacterial community

• 成果类型: Article
• 署名作者: Robes, Jose Miguel D.; Liebergesell, Tashi C. E.; Beals, Delaney G.; Yu, Xinhui; Brazelton, William J.; Puri, Aaron W.
• 署名单位: United States Department of Energy (DOE); Oak Ridge National Laboratory; Utah System of Higher Education; University of Utah; Utah System of Higher Education; University of Utah; Utah System of Higher Education; University of Utah
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-14735
• DOI: 10.1073/pnas.2507323122
• 发表日期: 2025-09-09
• 关键词: siderophores; monooxygenase; enterobactin; receptor; assay; biosynthesis; PRODUCTS; tool

摘要

Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural ecosystems, methane is sequestered by microbial communities, yet little is known about how constituents of methane-oxidizing communities interact with each other and their environment. This lack of mechanistic understanding is a common issue for many important microbial communities, but it is difficult to draw links between available sequencing information and the metabolites that govern community interactions. Here, we develop and apply a technique called inverse stable isotope probing-metabolomics (InverSIP) to bridge the gap between metagenomic and metabolomic information and functionally characterize interactions in a complex methane-oxidizing community. Using InverSIP, we link a highly transcribed biosynthetic gene cluster in the community with its secondary metabolite product: methylocystabactin, a triscatecholate siderophore not previously observed in nature. We find that production of methylocystabactin is widespread among methanotrophic alphaproteobacteria and that it can be used by another methanotroph in the community that does not produce this siderophore itself. Functional assays reveal that methylocystabactin supports methanotroph growth and the activity of the methane-oxidizing enzyme soluble methane monooxygenase under conditions where bioavailable iron is limited, establishing an important molecular link between methane-oxidation and the insoluble iron found in many natural environments. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities and establish InverSIP as a broadly applicable genomics-guided strategy for characterizing metabolites in microbial ecosystems. Significance Methane-oxidizing bacterial communities perform a critical ecosystem function by consuming this potent greenhouse gas, but the molecular mechanisms governing their activity are not well understood. We developed a genomics-guided method for studying microbial communities and used it to identify an iron-chelating secondary metabolite used by many methane-oxidizing bacteria to access iron in the environment and support methane oxidation. This work provides mechanistic details about how these environmentally important bacteria interact with their environment, which will enable the prediction and optimization of their functions from sequencing data in the future. The approaches described can also be used to characterize other microbial communities of interest that play essential roles in environmental and human health.