Diana E. Northup(1), Kathy Lavoie (2), Larry Mallory (3)
as printed in April 1997 NSS NEWS


In caves, we have microbes that are resident and microbes that are transient. Transient microbes ride into caves on air currents, in water flows, on insects, on bats, and through humans. Anything or anyone entering a cave may carry transient microbes. Resident microbes, on the other hand, occur as native inhabitants of a cave. Native microbes depend solely on the resources within the cave for survival, but transient microbes tend to thrive where abundant organic materials are available.

Microbes that live by using organic carbon are called chemoheterotrophs. Guano deposits, flowing water, and decaying wood provide organic rich matter for chemoheterotrophic microbes such as fungi. Most fungi found in caves fit this picture and are most likely transients. Bacteria can also be brought in caves as transients. However, current research shows that most native microbes in caves are bacteria.

Within a typical cave, any place with sufficient moisture might contain microbes. If there is a stream running into the cave, you might expect to find algae washed in from the surface, protozoa in the sediments at the bottom of the stream, and bacteria clinging to the surface of the water and air (bacteria like to hang out at interfaces where rock meets water and water meets air). The banks along a stream, with their deposits of sediment, would be home to fungal spores. These spores, the fungal equivalent of seeds, only grow when organic matter is encountered. Bacteria are abundant in deposits of soil or sediment, but most bacteria are dormant unless suitable food is present. Fungal spores and bacteria are found in the surface water film of limestone rock and calcite speleothems. These microbes may contribute to the formation and degradation of speleothems.

Two of the few places where you are likely to see colonies made up of billions and billions of bacterial cells is on limestone or lava tube surfaces. Those reflective white dots, clustered together in moist areas on cave ceilings and walls are actinomycete bacteria. Actinomycetes are responsible for the distinctive odor that caves and soils have, unlike musty basements whose odor is due to fungi. The air we breathe (you won't like this part!) contains millions of fungal spores and floating bacteria. Deep in caves, bacteria are found living in pools and dripwater. These bacteria are specialized to grow in very low nutrient, or oligotrophic, environments.


Bacteria and fungi that make their home in caves are important for several reasons. Because of their long isolation from the surface and because of their existence in very low nutrient environments (we're not talking about the bat guano microbes here!), some cave microbes appear to have evolved to produce specialized chemical compounds, or toxins, with which to fend off neighboring microbes (their own version of assault rifles). These microbial chemical compounds may be useful to humans in the fight against disease or pollution. Preliminary results from Mallory's studies suggest that microbes demonstrating this sort of beneficial activity were collected from pristine sites that were rarely visited by humans.

Our knowledge of the microbial world in general is really quite limited and our knowledge of cave microbial diversity is even more limited. Thus, the potential exists to find novel microbes in caves. Investigation of such organisms may provide new details about the evolutionary relationships of bacteria and fungi.

The study of microbes in caves is also important in elucidating how speleothems are formed. There is good, although limited, evidence that microbes are involved in the formation of iron and manganese oxides, sulfur compounds, saltpeter deposits, and even calcium carbonate.

Finally, scientists are finding bacteria deep within rocks of the earth and in association with deep-sea hydrothermal vents. The deep subsurface environment is difficult to sample; thus, caves provide a more accessible avenue for studying these microbes.


The impact of humans on microbes in caves takes two forms. We import foreign (surface) microbes as we explore caves. Secondly, we bring additional organic matter into the cave in the form of skin, hair, food, lint, urine, and possibly even feces. You are shedding tens of thousands of skin fragments per minute! This additional organic matter does the most harm. Native cave microbes often live in very low nutrient environments and may not even be able to survive in richer environments. If we add too much organic matter, the cave habitat will cease to be a good place for native bacteria to live; and will become, instead, a good place for transient, surface microbes to thrive!


To decrease the number of foreign microbes you bring into the cave:

  • Clean the mud and dirt from your boots, packs, cave clothes and vertical equipment before entering the cave.
  • Wash your hair before going caving.
  • Set up pitchers by drinking sources so that hands and water bottles are not dipped into the pools. Better yet, set up siphon tubes with nylon spigots, diminishing the need for cavers to stand near the water source.
  • Give caves, especially very pristine ones, time to rest between human visits. Give the foreign microbes a chance to die out.

To limit the amount of human-associated organic matter entering the cave (particularly in caves without streams):

  • Carry out all feces, spit, and vomit. Carry a gallon plastic bag, wet wipes, and plastic wrap with you at all times for emergencies (unexpected running from either end).
  • Eat over a bag large enough to catch the crumbs.
  • If you're camping in a cave, use established camps to limit the impact to a small specific area.
  • Don't take a full bath or shower right before caving. Such cleanliness dries out skin and makes it flakier. A reasonable compromise is to shower the night before entering a cave.
  • In very pristine areas, or areas with nutrient sources that might support interesting microbes (e.g., hydrogen sulfide or sulfur), limit the number of persons that can visit the area and the time spent in the area.
  • While in the cave, limit head scratching and avoid hair combing.
  • Cotton clothing is less desirable than synthetics. It creates more lint and its fibers are more readily consumed by microbes.

In conserving microorganisms and the habitat in which they exist, balance is needed. Exploration teams often inform scientists of habitat that might contain microbes of interest. If the care taken by explorers of Lechuguilla Cave can serve as a model for other exploration endeavors, we can preserve microbes that may tell us much about the world in which we live. In order to preserve the more easily impacted microbes, we may wish to establish a few microbial preserves in remote areas of pristine caves and in areas with unique habitats.

If you have comments on the draft pamphlet, please contact Diana Northup at the Biology Department, University of New Mexico, Albuquerque, NM 87131.

1 Department of Biology, University of New Mexico, Albuquerque, NM 87131 dnorthup@unm.edu
2 Department of Biology, University of Michigan-Flint, Flint, MI 48502-2186
3 Biomes, 16720 Cashell Road, Rockville, MD 20853