Probing the Ecological Functions of Thermophiles Using Cultivation-Dependent and Cultivation-Independent Techniques

High-temperature geothermal springs are ecosystems that resemble early Earth, offering insights into the origins and early evolution of life. In these unique ecosystems, thermophilic microorganisms thrive. However, our knowledge of thermophiles remains limited. A major challenge is that many thermophiles remain uncultivated. The primary goal of this dissertation was to explore the diversity, metabolism, and ecological functions of thermophiles using cultivation-dependent and cultivation-independent approaches. Chapter 1 provides a broad overview of geothermal spring ecosystems and thermophiles, along with a roadmap of the dissertation. Chapter 2 documents a study on the response of specific thermophiles from Gongxiaoshe (GXS) Hot Spring in China to pulses of labile dissolved organic carbon, specifically acetate and aspartate, using quantitative stable isotope probing (qSIP) and metagenomics. The results indicate strong resource partitioning and a wider preference for aspartate incorporation into DNA over acetate. Chapter 3 explores the ecophysiology and evolution of a dominant archaeal species, designated Calditenuis ramacidaminiphagus, from Great Boiling Spring, Nevada, USA. By using fluorescence in situ hybridization coupled with nanoscale secondary ion mass spectrometry (FISH-NanoSIMS), metagenomics, metaproteomics, and laboratory cultures, we demonstrated branched-chain amino acids (BCAAs) specialization in C. ramacidaminiphagus. We also showed that BCAA specialization as a key trait for the genus Calditenuis. Chapter 4 summarizes our research findings and discusses future research perspectives. Chapter 5 describes my contributions to other research projects.