An endolith is an organism (archaeum, bacterium, fungus, lichen, algae or amoeba) that lives inside rock, coral, animal shells, or in the pores between mineral grains of a rock. Many are extremophiles, living in places previously thought inhospitable to life. They are of particular interest to astrobiologists, who theorize that endolithic environments on Mars and other planets constitute potential refugia for extraterrestrial microbial communities.
The term "endolith", which defines an organism that colonizes the interior of any kind of rock, has been further classified into three subclasses:
- colonizes fissures and cracks in the rock (chasm = cleft)
- colonizes structural cavities within porous rocks, including spaces produced and vacated by euendoliths (crypto = hidden)
- penetrates actively into the interior of rocks forming tunnels that conform with the shape of its body, rock boring organism (eu = good, true)
Endoliths have been found in rock down to a depth of 3 kilometres (1.9 mi), though it is unknown if that is their limit (due to the cost involved in digging so deep). The main threat to their survival seems not to result from the pressure at such depth, but from the increased temperature. Judging from hyperthermophile organisms, the temperature limit is at about 120 °C (Strain 121 can reproduce at 121 °C), which limits the possible depth to 4-4.5 km below the continental crust, and 7 or 7.5 km below the ocean floor. Endolithic organisms have also been found in surface rocks in regions of low humidity (hypolith) and low temperature (psychrophile), including the Dry Valleys and permafrost of Antarctica, the Alps, and the Rocky Mountains.
Endoliths can survive by feeding on traces of iron, potassium, or sulfur. (See lithotroph.) Whether they metabolize these directly from the surrounding rock, or rather excrete an acid to dissolve them first, remains to be seen. The Ocean Drilling Program found microscopic trails in basalt from the Atlantic, Indian, and Pacific oceans that contain DNA. Photosynthetic endoliths have also been discovered.
As water and nutrients are rather sparse in the environment of the endolith, they have a very slow reproduction cycle. Early data suggests that some only engage in cell division once every hundred years. In August 2013 researchers reported evidence of endoliths in the ocean floor with a generation time of 10,000 years. Most of their energy is spent repairing cell damage caused by cosmic rays or racemization, and very little is available for reproduction or growth. It is thought that they weather long ice ages in this fashion, emerging when the temperature in the area warms.
As most endoliths are autotrophs, they can generate organic compounds essential for their survival on their own from inorganic matter. Some endoliths have specialized in feeding on their autotroph relatives. The micro-biotope where these different endolithic species live together has been called a Subsurface Lithotrophic Microbial Ecosystem (SLiME).
Endolithic fungi and algae in marine ecosystems
Only limited research has been done concerning the distribution of marine endolithic fungi and its diversity even though there is a probability that endolithic fungi could perhaps play an important role in the health of coral reefs.
Endolithic fungi have been discovered in shells as early as the year 1889 by Edouard Bornet and Charles Flahault. These two French phycologists specifically provided descriptions for two fungi: Ostracoblabe implexis and Lithopythium gangliiforme. Discovery of endolithic fungi, such as Dodgella priscus and Conchyliastrum, has also been made in the beach sand of Australia by George Zembrowski. Findings have also been made in coral reefs and have been found to be, at times, beneficial to their coral hosts. 
In the wake of worldwide coral bleaching, studies have suggested that the endolithic algae located in the skeleton of the coral may be aiding the survival of coral species by providing an alternative source of energy. Although the role that endolithic Fungi is important in coral reefs, it is often overlooked because much research is focused on the effects of coral bleaching as well as the relationships between coelenterate and endosymbiotic symbiodinia.
According to a study done by Astrid Gunther endoliths were also found in the island of Cozumel (Mexico). The endoliths found there not only included algae and fungi but also included cyanobacteria, sponges as well as many other microborers.
Until the 1990s phototrophic endoliths were thought as somewhat benign but since then evidence has surfaced that phototrophic endoliths (primarily cyanobacteria) have infested 50 to 80% of midshore populations of the mussel species Perna perna located in South Africa.The infestation of Phototrophic endoliths resulted in lethal and sub-lethal effects such as the decrease in strength of the mussel shells. Although the rate of thickening of the shells were faster in more infested areas it is not rapid enough to combat the degradation of the mussel shells.
Endolithic fungi and the mass extinction of Cretaceous dinosaurs
Evidence of endolithic fungi were discovered within dinosaur eggshell found in central China. The endolithic fungi that was found within the eggshells were characterized as being “needle-like, ribbon-like, and silk-like."
Fungus is seldom fossilized and even when it is preserved it can be difficult to distinguish endolithic hyphae from endolithic cyanobacteria and algae. Endolithic microbes can, however, be distinguished based on their distribution, ecology, and morphology. According to a 2008 study, the endolithic fungi that formed on the eggshells would have resulted in the abnormal incubation of the eggs and eventually led to the contribution to the mass extinction of these dinosaurs. It may also have led to the preservation of dinosaur eggs, including some that contained embryos.
- Wierzchos, J., Camara, B., De Los Rios, A., Davila, A. F., Sanchaz Almazo, M., Artieda, O., Wierzchos, K., Gomez-Silva, B., McKay, C., Ascaso, C. (2011). Microbial colonization of Ca-sulfate crusts in the hyperarid core of the Atacama Desert: Implications for the search for life on Mars.Geobiology, 9, 44-60.
- Stjepko Golubic, E.Imre Friedmann, and Jürgen Schneider (June 1981). "The lithobiotic ecological niche, with special reference to microorganisms". Journal of Sedimentary Research 51 (2): 475–478.
- Two miles underground — Gold mines present "ideal environment" for geologists studying subsurface microbes
- Looking for life in all the wrong places — research on cryptoendoliths Discover, May 1997 by Will Hively
- Microbial Diversity of Cryptoendolithic Communities from the McMurdo Dry Valleys, Antarctica
- Horath Th, Bachofen R (2009) Molecular Characterization of an Endolithic Microbial Community in Dolomite Rock in the Central Alps (Switzerland) Microb Ecol 58:290–306
- Walker JJ, Spear JR, Pace NR (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434:1011–1014
- Walker JJ, Pace NR (2007) Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems. Appl Environ Microbiol 73:3497–3504
- Glass Munchers Under the Sea — NASA Astrobiology Institute — Leslie Mullen
- Microbial Populations in Ocean Floor Basalt: Results from ODP Leg 187
- Wierzchos, J., Ascaso, C., and McKay., C. P.(2006). Astrobiology, 6(3): 415-422. doi:10.1089/ast.2006.6.415.
- Bob Yirka Aug 29, 2013
- Frequently Requested Information about the SLiME Hypothesis
- Golubic, Stjepko, Gudrun Radtke, and Therese Le Campion-Alsumard. "Endolithic fungi in marine ecosystems." Trends in microbiology 13.5 (2005): 229-235.
- Fine, M., and Y. Loya. "Endolithic Algae: An Alternative Source of Photoassimilates during Coral Bleaching." Proceedings of the Royal Society B: Biological Sciences 269.1497 (2002): 1205-210. Web.
- Günther, Dipl Biol Astrid. "Distribution and bathymetric zonation of shell-boring endoliths in recent reef and shelf environments: Cozumel, Yucatan (Mexico)." Facies 22.1 (1990): 233-261.
- Kaehler, S., and C. D. McQuaid. "Lethal and sub-lethal effects of phototrophic endoliths attacking the shell of the intertidal mussel Perna perna." Marine Biology 135.3 (1999): 497-503.
- Gong, YiMing, Ran Xu, and Bi Hu. "Endolithic fungi: A possible killer for the mass extinction of Cretaceous dinosaurs." Science in China Series D: Earth Sciences 51.6 (2008): 801-807.
- Gong, YiMing, Ran Xu, and Bi Hu, 2008. p. 806.
- Endoliths General Collection — This collection of online resources such as news articles, web sites, and reference pages provides a comprehensive array of information about endoliths.
- Endolith Advanced Collection — Compiled for professionals and advanced learners, this endolith collection includes online resources such as journal articles, academic reviews, and surveys.