Endoliths—Microbes Living within Rocks

By Monica Bruckner, Montana State University

What Are Endoliths?

Endoliths are organisms that live inside rocks or in pores between mineral grains. These creatures are thought to have been found in a large range of environments - from rocks on the Earth's surface to miles beneath the subsurface! There are thousands of known species of endoliths, including members from Bacteria, Archaea, and Fungi. Many endoliths are autotrophs, meaning they are able to make their own organic compounds by utilizing gas or dissolved nutrients from water moving through fractured rock. Others may incorporate inorganic compounds found in their rock substrate (possibly by excreting acids to dissolve the rock).

Where on Earth are Endoliths Found?

Cryptoendolith living in Antarctic sandstone.

Endoliths have been found in a variety of environments, from the shallow surface to the deep terrestrial and ocean crust. Endoliths are a type of extremophile, which is an organism that thrives in harsh conditions. For more information about extremophiles, visit the Microbial Life Extremophile Collection.

There are several different types of endoliths, each occupying a different environment. Three major environmental groupings of endoliths are:

  • Cryptoendoliths - Cryptoendoliths are endoliths that live in rock on the Earth's surface. Cryptoendolithic lichen [web definition] communities are the dominant form of cryptoendolithic life and have been found in the dry valleys of Antarctica. These communities grow in porous rocks such as sandstone. Due to their tolerance for extreme conditions, cryptoendoliths have stimulated interest in exobiology, or the idea that life can exist on other planets.

  • Subsurface Endoliths - Subsurface endoliths can be found in groundwater aquifers or caves. These organisms do not necessarily feed on nutrients from the rock, but they may utilize nutrients found in groundwater. Some subsurface microbes may contribute to groundwater quality problems, while others may be used to remediate pollution problems. ( This site may be offline. )
  • Deep-Biosphere Endoliths - These endoliths have been found in deep, extremely hot (over 100° C) or cold (up to -15° C) rock, miles beneath the ocean floor. In addition, researchers have found evidence for endolithic communities surviving in deep mines, such as a South African gold mine. (more info) Organisms living in these environments not only deal with extreme temperatures, but also intense pressures, total darkness, and anoxic conditions. Like cryptoendoliths, deep biosphere endoliths have stimulated interest in exobiology. Nanobacterial fossils may indicate that endolithic life once existed on other planets. For more information about nanobacteria, visit the nanobacteria collection.

What Are the Implications for Endolithic Life?

Recent work with endolithic geomicrobiology may alter our understanding of life. These microbes expand our understanding about the ability of organisms to survive and even thrive in extreme conditions. They also raise new ideas regarding the possibility of extraterrestrial life. Furthermore, these microbes may alter our ideas about the origin of life on Earth, because they have the ability to live within rock thereby escaping damaging UV rays.

Endoliths may also play a role in environmental issues. For instance, microbes living beneath the ocean floor have been suggested to play a role in the carbon cycle and global warming. Endoliths may also have environmental benefits including bioremediation of contaminated sites and mines and improvement of groundwater quality by converting harmful compounds into non-toxic waste products. In addition, these organisms may be responsible for biomineralization of economically important ores.

Deep subsurface microbes are important in our understanding the possibilities for life and have the potential for a wide range of applications that can improve the quality of life. Therefore, continued geomicrobiological research in these deep, dark environments is crucial to understanding the possibilities for life in extreme environments and for remediating environmental problems.

Endolith Collections

General Collection: Resources such as news articles, web sites, and reference pages provide a comprehensive array of information about endoliths for students and non-scientists.

Advanced Collection: Compiled for professionals and advanced learners, this endolith collection includes online resources such as journal articles, academic reviews, and surveys. 

For Educators: This endolith collection includes activities, assignments, and reading materials created specifically for educators.

Additional Resources

For additional resources about endoliths, search the Microbial Life collection.