Millimetre‐Scale Stratification of Microbial Communities in Hydrothermal Sediments

Resolving the spatial organisation of microbial populations in environments shaped by steep thermal and geochemical gradients remains a challenge in environmental biogeochemistry. Conventional molecular biomarker or gene‐based approaches typically require large volumes of homogenised samples, limiting their ability to depict spatially structured microbial ecosystems, where critical microbial processes occur on millimetre scales. To overcome these limitations, we applied high‐resolution mass spectrometry imaging (MSI) to an 11.5 cm long sediment section from the hydrothermal Cathedral Hill mat complex in the Guaymas Basin, known for its extreme temperatures and sharp geochemical gradients. The μm‐scaled spatial resolution unveiled a nuanced lipidome zonation tightly compressed to a narrow 5‐cm segment below the sediment–water interface. The surface layer (above 1.1 cmbsf) hosts molecular patterns primarily shaped by opposing oxygen and sulphide gradients, followed by a near‐seamless transition to an anoxic zone dominated by anaerobic methane‐oxidising archaea (ANME) and sulphate‐reducing bacteria (SRB). At greater depth, molecular signals indicative of active microbial communities remained below the detection limit except for diverse, potentially ANME‐ and SRB‐related lipids concentrated within a siliceous concretion. The sharp transitions in lipid zonation hint at persistent redox zones and resilient microbial niches under intense fluid flow and dynamic geochemical gradients.