Stromatolites are laminated, presumably microbial, structures, consisting largely of an authigenic precipitate, and manifest the appearance of microbial life in the geological rock record at least 3.4 Ga ago. Thus, stromatolites provide unique geochemical archives of aqueous environments on Earth and their habitability. It is, however, still incompletely understood under which physico-chemical conditions stromatolites formed and how these environments changed with the co-evolution of the atmosphere-hydrosphere-lithosphere systems through deep time.
This contribution targets the potential and pitfalls of emerging and established isotope applications to stromatolites based on improved and newly developed analytical and technical facilities in the last decades. I will provide an overview of present data and the interpretation of novel applications of stable and radiogenic isotope systems in stromatolites. Although the behaviour and fractionation processes of different isotope systems in stromatolites and microbial mats are sometimes incompletely understood, the different isotope proxies have the unique potential to better understand and reconstruct microbial habitats through deep time. Primarily, radiogenic isotopes are used to directly date stromatolites and determine the source of elements in ancient stromatolite environments; stable isotopes are used to understand redox conditions, metal availability, and (biogenic) metal cycling processes in microbial habitats. I provide insights into different isotope applications and their future perspectives to bridge the gap between geochemistry and microbiology and better understand the evolution of microbial life in stromatolite-forming environments on Earth and beyond.