When the Lights are Off: Microbial Diversity in Caves

The subsurface is one of the most unexplored and unknown ecosystems on Earth. Cave systems, due to their easier accessibility, offer a window into this hidden biosphere, making them ideal natural laboratories for studying subsurface life. Caves can be hosted in various rock types and form as a result of a range of processes, such as dissolution, mechanical weathering, mechanical movement, melting, and solidification. Despite these differences, caves tend to share several characteristics, including the absence of light, limited nutrient input, and isolation from surrounding environments, making them highly oligotrophic. Nevertheless, previous studies have demonstrated that caves harbor a diverse microbial consortium, relying on chemotrophy and mutualistic interactions to sustain complex communities. We analyzed a dataset of metagenomes representing cave systems worldwide, encompassing diverse cave types (e.g., quartzite, limestone, sulfidic, and basaltic caves), obtaining a curated collection of 2303 medium- to high-quality metagenome-assembled genomes (MAGs). We found a high diversity of bacterial and archaeal phyla, consistent with previous studies, and observed that these communities are distributed according to cave formation types, underpinning the role of cave geochemistry in shaping microbial distribution in these systems. We further explored their roles in major biogeochemical cycles, shedding light on their fundamental contributions to organic matter cycling. Our findings also highlight the role of subterranean systems, particularly karst environments, in global carbon cycling. This study offers deeper insight into life that thrives when the lights are off.