Portable Assays Aid Scientists in Cave Exploration

New field-ready genetic tools allow rapid identification of cave microbiomes, including potential health threats.

Mar. 24, 2026 at 12:04am

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A new study has demonstrated that field-portable assays can now be used to study the complex ecosystems of caves in near real-time, enabling rapid response and exploration in subterranean science. The researchers conducted sampling trips to 5 different caves and mines across the U.S., collecting hundreds of environmental samples and using DNA sequencing to identify all bacteria present. They found that geography, material, and depth all impact the microbial populations within a cave, and that the new portable DNA tools work similarly well to a full-scale lab in detecting bacteria of interest, including potential human pathogens.

Why it matters

Our understanding of the microbial life in caves has been limited due to the constraints of slow, lab-based methods. This study shows that field-ready genetic tools can now give scientists answers about cave biodiversity and potential health threats in hours, not weeks, improving public health surveillance and operational risk assessment for military and other decision makers.

The details

The researchers used proven, field-portable nucleic acid extraction and sequencing technology to rapidly identify microbes, including potential disease-causing agents, directly in the field. They gathered samples along regular distance intervals stretching from the sunlit entrances deep into the dark zones of 5 different caves and mines across the U.S., including soil, rock, water, air and animal feces. Back in the lab, they used DNA sequencing to show all bacteria present and compared the results to traditional laboratory methods, finding the portable tools worked similarly well.

  • The study was published on March 24, 2026 in Applied and Environmental Microbiology.

The players

Eric A. Weingarten, Ph.D.

A research biologist at the Environmental Laboratory of the U.S. Army Engineer Research and Development Center (ERDC) and the lead author of the study.

American Society for Microbiology

The publisher of the journal Applied and Environmental Microbiology where the study was published.

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What they’re saying

“We've shown that we're no longer constrained by slow, lab-based methods [for studying caves]. Proven, field-ready genetic tools can give us answers about biodiversity and potential health threats in hours, not weeks, enabling rapid response and exploration in subterranean science.”

— Eric A. Weingarten, Ph.D., Research Biologist, U.S. Army Engineer Research and Development Center

What’s next

The researchers plan to continue expanding their cave sampling efforts to more locations and using the portable assays to build a comprehensive map of microbial ecosystems in caves across the United States.

The takeaway

This study demonstrates how new field-ready genetic tools are revolutionizing the ability to rapidly study and monitor complex cave environments, providing critical data to public health officials, military decision makers, and scientists about potential threats and the overall biodiversity of these unique subterranean ecosystems.