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

Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural environments, methane is sequestered by microbial communities. However, little is known about how constituents of methane-oxidizing communities interact with each other and their environment despite growing amounts of DNA and RNA sequencing data for these consortia. Here we use a technique called inverse stable isotope probing-metabolomics (InverSIP) to link a highly transcribed biosynthetic gene cluster in a methane-oxidizing bacterial community with its secondary metabolite product. We discover that methane-oxidizing bacteria (methanotrophs) use a triscatecholate siderophore, termed methylocystabactin, that has not been previously observed in nature to sequester iron in this complex setting. We show that production of methylocystabactin is widespread amongst methanotrophic alphaproteobacteria and is important for activity of the enzyme soluble methane monooxygenase under metal limitation. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities, and this genomics-guided approach can also be used for the functional characterization of other microbial communities in the future.