Fluid flow shapes microbial carbon cycling and mineral formation in shallow-water hydrothermal vents

Hydrothermal systems are characterized by steep thermal and chemical gradients, high metal and sulfur concentrations, and high variability in redox and pH. They provide natural laboratories to study microbial adaptation at the limits of habitability and offer insights into early Earth and potential extraterrestrial life. This dissertation investigates how hydrothermal fluid flow shapes microbial carbon cycling, ecosystem transfer, and mineral formation in shallow to transitional systems (8 to 210 m water depth) off Kueishantao (Taiwan) and Milos (Greece). By integrating lipid biomarkers with compound-specific δ13C, Δ14C, and δ2H analyses and mineralogical data, it explores carbon uptake pathways, fossil carbon incorporation, and membrane adaptation under contrasting physicochemical regimes. At Kueishantao, extreme sulfur-rich and acidic fluids promote chemoautotrophy dominated by sulfur-oxidizing Campylobacteria using the reductive tricarboxylic acid (rTCA) cycle, reflected in 13C-enriched fatty acids with minimal isotopic fractionation. These organisms are mostly responsible for vent carbon uptake (as shown by compound-specific 14C and 2H data). At Milos, spatial variations in diffusive versus advective fluid flow control redox conditions, microbial metabolism, and mineral formation. Sulfate-rich diffusive settings favor sulfate reduction linked to pyrite formation, whereas advective flow supports sulfide oxidation and elemental sulfur accumulation. Membrane adaptations, including elongation of bacterial ether lipids and methylation of archaeal tetraethers, reflect increasing environmental stress, particularly in metal-rich chimney deposits. Together, this work demonstrates that shallow hydrothermal systems sustain diverse and metabolically flexible microbial communities that are linked to local geochemical and mineralogical conditions.