A standardized field framework for integrated microbiological and geochemical sampling of deeply-sourced seeps across large-scale geological gradients

Abstract

Accessing the deep subsurface biosphere remains a major challenge in Earth and planetary sciences. Drilling provides direct access but is costly, spatially restricted, and difficult to deploy at the scales required to investigate interactions between geological processes and microbial ecosystems. Here, we present a standardized field framework for using deeply-sourced thermal springs and natural seeps as natural access points to subsurface systems. Developed across multiple large-scale field programs, the framework integrates microbiological and geochemical sampling within a unified standard operating procedure (SOP) encompassing site and outlet selection, synoptic co-located sampling, sample identification, metadata acquisition, and quality control. The approach supports coordinated collection of fluids, gases, sediments, biofilms, and surface backgrounds together with field geochemical and environmental measurements. A multi-proxy framework explicitly evaluates preservation of the subsurface signal and the extent of surface influence, allowing samples to be interpreted along a subsurface–surface continuum and compared across sites and campaigns. By formalizing sample acquisition, tracking, and assessment, the framework provides a reproducible and scalable approach for investigating geosphere–biosphere interactions without direct drilling. The protocols are modular, adaptable to different scientific questions, and designed around FAIR data principles to facilitate integration and reuse across studies.