Cave microbial communities are structured by environmental matrix and depth and can be characterized with field-portable assays

Caves and mines represent extreme and isolated environments that harbor unique microbial communities, yet they remain among the least studied environments on Earth. Understanding how these communities are structured across different habitats and locations is essential for both ecological research and public health monitoring. In this study, we surveyed microbiomes across multiple caves and environmental materials to reveal how location, substrate type, and depth shape microbial diversity. We also demonstrated that portable DNA extraction and analysis tools can be used in the field to rapidly detect microorganisms, including potential pathogens, without the need for laboratory infrastructure. These results provide new insight into how microbial life is distributed in subterranean ecosystems and establish practical methods for monitoring microbial diversity and detecting pathogens in remote environments.