Tracking Microbial Activity

Understanding a microbial community requires more than knowing which microorganisms are present: it requires identifying which organisms are active and how their activities shape the flow of carbon through the community. This is particularly challenging in groundwater, where microbes face strong nutrient limitations, leading to typically low cell numbers. Yet these communities can sustain substantial microbial activity and thus provide an important setting for understanding how microorganisms acquire and redistribute carbon under oligotrophic conditions.

 Our research combines metabolic labeling approaches with meta'omics and single-cell methods to resolve microbial activity and carbon fluxes in groundwater communities. Stable isotope labeling allows us to directly trace carbon uptake and identify active microorganisms, which we link to their genomic potential, gene expression and protein production using metagenomics, metatranscriptomics and metaproteomics. Raman microspectroscopy and nanoSIMS further resolve isotope incorporation at the single-cell level. Together, these approaches address questions such as: Who is actively fixing CO₂ in groundwater? What strategies do chemolithoautotrophs use to persist under oligotrophic conditions? How is newly produced organic carbon distributed through the community, and how is this influenced by host-dependent bacteria of the CPR group? By following carbon from its fixation into individual cells and across the community, we aim to uncover how activity and interactions shape groundwater microbiomes.