Editing Endolith

{{short description|Organism living inside a rock}}
{{for|the dental term|Pulp stone}}
[[File:Cryptoendolith.jpg|right|thumb|Endolith lifeform found inside an Antarctic rock]]

An '''endolith''' or '''endolithic''' is an [[organism]] ([[Archaea|archaeon]], [[bacterium]], [[fungus]], [[lichen]], [[algae]], [[sponge]], or [[amoeboid|amoeba]]) that is able to acquire the necessary resources for growth in the inner part of a [[Rock (geology)|rock]],<ref>{{cite book |first1=C.R. |last1=Omelon |year=2016 |chapter=Endolithic Microorganisms and Their Habitats |editor1-last=Hurst |editor1-first=C.J. |series=Advances in environmental microbiology, vol. 1| title =Their World: A Diversity of Microbial Environments |location=Cincinnati, USA |publisher=Springer |doi = 10.1007/978-3-319-28071-4_4| pages=171–201 }}</ref> mineral, [[coral]], [[Exoskeleton|animal shell]]s, or in the [[Porosity|pore]]s between [[mineral]] grains of a rock.  Many are [[extremophile]]s, living in places long considered inhospitable to life. The distribution, biomass, and diversity of endolith microorganisms are determined by the physical and chemical properties of the rock substrate, including the mineral composition, permeability, the presence of organic compounds, the structure and distribution of pores, water retention capacity, and the pH.<ref>{{multiref2|{{cite journal |last1=Cockell |first1=C. S. |last2=Olsson |first2=K. |last3=Knowles |first3=F. |last4=Kelly |first4=L. |last5=Herrera |first5=A. |last6=Thorsteinsson |first6=T. |last7=Marteinsson |first7=V. |title=Bacteria  in weathered basaltic glass, Iceland |journal=Geomicrobiology Journal |date=2009 |volume=26 |issue=7 |pages=491–507 |doi=10.1080/01490450903061101|s2cid=131694781 }}|{{cite journal |last1=Herrera |first1=A. |last2=Cockell |first2=C. S. |last3=Self |first3=S. |last4=Blaxter |first4=M. |last5=Reitner |first5=J. |last6=Thorsteinsson |first6=T. |last7=Tindle |first7=A. G. |title=A cryptoendolithic community in volcanic glass |journal=Astrobiology |date=2009 |volume=9 |issue=4 |pages=369–381 |doi=10.1089/ast.2008.0278|pmid=19519213 |bibcode=2009AsBio...9..369H }}|{{cite journal |last1=Kelly |first1=L. C. |last2=Cockell |first2=C. S. |last3=Herrera-Belaroussi |first3=A. |last4=Piceno |first4=Y. |last5=Andersen |first5=G. |last6=DeSantis |first6=T. |last7=LeRoux |first7=X. |title=Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland |journal=Microbial Ecology |date=2011 |volume=62 |issue=1 |pages=69–79 |doi=10.1007/s00248-011-9864-1|pmid=21584756 |s2cid=23356098 }}|{{cite journal |last1=Omelon |first1=C. R. |last2=Pollard |first2=W. H. |last3=Ferris |first3=F. G. |title=Inorganic species distribution and microbial diversity within high Arctic cryptoendolithic habitats. |journal=Microbial Ecology |date=2007 |volume=54 |issue=4 |pages=740–752 |doi=10.1007/s00248-007-9235-0|pmid=17457639 |s2cid=19843927 }}}}</ref> Normally, the endoliths colonize the areas within lithic substrates to withstand intense solar radiation, temperature fluctuations, wind, and desiccation.<ref>{{cite journal |last1=Walker |first1=J. J. |last2=Pace |first2=N. R. |title=Endolithic microbial ecosystems |journal=Annual Review of Microbiology |date=2007 |volume=61 |pages=331–347|doi=10.1146/annurev.micro.61.080706.093302 |pmid=17506683 }}</ref> 
They are of particular interest to [[astrobiology|astrobiologists]], who theorize that endolithic environments on [[Mars]] and other planets constitute potential [[Refugium (population biology)|refugia]] for extraterrestrial microbial communities.<ref name="Wierzchos et al. 2011">{{cite journal |last1=Wierzchos |first1=J. |last2=Camara |first2=B. |last3=De Los Rios |first3=A. |last4=Davila |first4=A. F. |last5=Sanchaz Almazo |first5=M. |last6=Artieda |first6=O. |last7=Wierzchos |first7=K. |last8=Gomez-Silva |first8=B. |last9=McKay |first9=C. |last10=Ascaso |first10=C. |year=2011 |title=Microbial colonization of Ca-sulfate crusts in the hyperarid core of the Atacama Desert: Implications for the search for life on Mars |journal=[[Geobiology (journal)|Geobiology]] |volume=9 |issue=1 |pages=44–60 |doi=10.1111/j.1472-4669.2010.00254.x |pmid=20726901 |s2cid=9458330 }}</ref><ref name="NYT-20160912">{{cite news |last=Chang |first=Kenneth |title=Visions of Life on Mars in Earth's Depths |url=https://www.nytimes.com/2016/09/13/science/south-african-mine-life-on-mars.html |date=12 September 2016 |work=[[The New York Times]] |access-date=12 September 2016}}</ref>

==Subdefinitions==
The term "endolith", which defines an organism that colonizes the interior of any kind of rock, has been further classified into five subclasses:<ref>{{Cite journal |url=http://jsedres.sepmonline.org/cgi/content/abstract/51/2/475 |archive-url=https://web.archive.org/web/20101230015229/http://jsedres.sepmonline.org/cgi/content/abstract/51/2/475 |url-status=dead |archive-date=2010-12-30 |first1=Stjepko |last1=Golubic |first2=E. Imre |last2=Friedmann|author2-link = Imre Friedmann|first3=Jürgen|last3= Schneider |title=The lithobiotic ecological niche, with special reference to microorganisms |journal=SEPM Journal of Sedimentary Research|volume=51 |number=2 |date=June 1981 |pages=475–478|doi=10.1306/212F7CB6-2B24-11D7-8648000102C1865D }}</ref>

;Chasmoendolith: Colonizes fissures and cracks in the rock connected to the surface (''chasm'' = cleft)
;Cryptoendolith: Colonizes structural cavities within natural pore spaces within the rocks. These pores are usually indirectly connected to the rock surface; (''crypto'' = hidden) 
;Euendolith: Penetrates actively into the interior of rocks forming channels and grooves that conform with the shape of its body, rock boring organism (''eu'' = true)
;Hypoendolith: Colonizes the pore spaces located on the underside of the rock and that make contact with the soil (''hypo'' = under)
;Autoendolith: Capable of rocks formation by mineral depositation (''auto'' = self)

==Environment==
Endolithic microorganisms have been reported in many areas around the globe. There are reports in warm hyper-arid and arid deserts such as Mojave and Sonora (USA), Atacama (Chile), Gobi (China, Mongolia), Negev (Israel), Namib (Namibia Angola), Al-Jafr basin (Jordan) and the Depression of Turpan (China),<ref>{{multiref2|{{cite journal |last1=Ascaso |first1=C |title=Ecología microbiana de sustratos líticos |journal=Ciencia y Medio Ambiente |date=2002 |pages=90–103 |hdl=10261/111133 |isbn=9788469979723 |language=es |hdl-access= free}}|{{cite journal |last1=Bungartz |first1=F |last2=Garvie |first2=L. A. |last3=Nash |first3=T. H. |title=Anatomy of the endolithic Sonoran Desert lichen ''Verrucaria rubrocincta'' Breuss: implications for biodeterioration and biomineralization |journal=The Lichenologist |year=2004 |volume=36 |issue=1 |pages=55–73 |doi=10.1017/S0024282904013854|s2cid=86211017 }}|{{cite journal |last1=Dong |first1=H |last2=Rech |first2=J. A. |last3=Jiang |first3=H |last4=Sun |first4=H |last5=Buck |first5=B. J. |title=Endolithic cyanobacteria in soil gypsum: Occurrences in Atacama (Chile), Mojave (United States), and Al-Jafr Basin (Jordan) Deserts |journal=Journal of Geophysical Research: Biogeosciences |date=2007 |volume=112 |issue=G2 |doi=10.1029/2006JG000385|bibcode=2007JGRG..112.2030D |doi-access=free }}|{{cite journal |last1=Lacap |first1=D. C.|author-link=Donnabella Lacap-Bugler |last2=Warren-Rhodes |first2=K. A. |last3=McKay |first3=C. P. |last4=Pointing |first4=S. B. |title=Cyanobacteria and chloroflexi-dominated hypolithic colonization of quartz at the hyper-arid core of the Atacama Desert, Chile. |journal=Extremophiles |date=2011 |volume=15 |issue=1 |pages=31–38 |doi=10.1007/s00792-010-0334-3|pmid=21069402 |pmc=3017302 }}|{{cite journal |last1=Schlesinger |first1=W. H |last2=Pippen |first2=J. S. |last3=Wallenstein |first3=M. D. |last4=Hofmockel |first4=K. S. |last5=Klepeis |first5=D. M. |last6=Mahall |first6=B. E. |title=Community composition and photosynthesis by photoautotrophs under quartz pebbles, southern Mojave Desert |journal=Ecology |date=2003 |volume=84 |issue=12 |pages=3222–3231 |doi=10.1890/02-0549}}|{{cite journal |last1=Stomeo |first1=F |last2=Valverde |first2=A |last3=Pointing |first3=S. B. |last4=McKay |first4=C. P. |last5=Warren-Rhodes |first5=K. A. |last6=Tuffin |first6=M. I. |last7=Cowan |first7=D. A. |title=Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert |journal=Extremophiles |date=2013 |volume=17 |issue=2 |pages=329–337 |doi=10.1007/s00792-013-0519-7|pmid=23397517 |hdl=10566/3555 |s2cid=11175962 |hdl-access=free }}|{{cite journal |last1=Vítek |first1=P. |last2=Ascaso |first2=C |last3=Artieda |first3=O |last4=Wierzchos |first4=J |title=Raman imaging in geomicrobiology: endolithic phototrophic microorganisms in gypsum from the extreme sun irradiation area in the Atacama Desert |journal=Analytical and Bioanalytical Chemistry |date=2016 |volume=408 |issue=15 |pages=4083–4092 |doi=10.1007/s00216-016-9497-9|pmid=27055886 |s2cid=8132118 }}}}</ref><ref name="Cryptoendolithic algae of hot semia">{{cite journal |last1=Bell |first1=R. A. |title=Cryptoendolithic algae of hot semiarid lands and deserts |journal=Journal of Phycology |date=1993 |volume=29 |issue=2 |pages=133–139 |doi=10.1111/j.0022-3646.1993.00133.x|s2cid=85033484 }}</ref> also in cold deserts as Arctic and Antarctic,<ref>{{multiref2|{{cite journal |last1=Ascaso |first1=C |title=Ecología microbiana de sustratos líticos |journal=Ciencia y Medio Ambiente |date=2002 |pages=90–103 |hdl=10261/111133| hdl-access= free|isbn=9788469979723|language= es}}|{{cite journal |last1=Cockell |first1=C. S. |last2=Stokes |first2=M. D. |title=Widespread colonization by polar hypoliths |journal=Nature |date=2004 |volume=431 |issue=7007 |pages=414 |doi=10.1038/431414a|pmid=15386002 |doi-access=free }}|{{cite journal |last1=Cowan |first1=D. A. |last2=Khan |first2=N. |last3=Pointing |first3=S. B. |last4=Cary |first4=S. C. |title=Diverse hypolithic refuge communities in the McMurdo Dry Valleys |journal=Antarctic Science |date=2010 |volume=22 |issue=6 |pages=714–720 |doi=10.1017/S0954102010000507|bibcode=2010AntSc..22..714C |hdl=10289/5090 |s2cid=53558610 |hdl-access=free }}|{{cite journal <!-- Citation bot no --> |last1=Friedmann |first1=E. I.|author1-link =Imre Friedmann |title=Endolithic Microbial Life in Hot and Cold Deserts |doi= 10.1007/BF00928400 |journal=Origins of Life |year=1980 |volume=10 |issue=3 |pages=223–235 |pmid=6774304}}<br />Republication of {{cite conference <!-- Citation bot no --> |last1=Friedmann |first1=E. I.|author1-link =Imre Friedmann |chapter=Endolithic Microbial Life in Hot and Cold Deserts | date= 1978 |doi=10.1007/978-94-009-9085-2_3 |isbn=978-94-009-9087-6 | pages= 33–45 | title= Limits of Life | conference=Proceedings of the Fourth College Park Colloquium on Chemical Evolution | editor1-first= Cyril | editor1-last=Ponnamperuma| editor2-first =Lynn | editor2-last= Margulis }}|{{cite journal |last1=Smith |first1=M. C. |last2=Bowman |first2=J. P. |last3=Scott |first3=F. J. |last4=Line |first4=M. A. |title=Sublithic bacteria associated with Antarctic quartz stones |journal=Antarctic Science |date=2000 |volume=12 |issue=2 |pages=177–184 |doi=10.1017/S0954102000000237|bibcode=2000AntSc..12..177S |s2cid=84337509 }}|{{cite journal |last1=Omelon |first1=C. R. |last2=Pollard |first2=W. H. |last3=Ferris |first3=F. G. |title=Environmental controls on microbial colonization of high Arctic cryptoendolithic habitats |journal=Polar Biology |date=2006 |volume=30 |issue=1 |pages=19–29 |doi=10.1007/s00300-006-0155-0|s2cid=22633158 }}|{{cite book |last1=Makhalanyane |first1=T. P. |last2=Pointing |first2=S. B. |last3=Cowan |first3=D. A. |chapter=Lithobionts: Cryptic and Refuge Niches |title=Antarctic Terrestrial Microbiology |date=2014 |pages=163–179 |doi=10.1007/978-3-642-45213-0_9|isbn=978-3-642-45212-3 }}|{{cite journal |last1=Friedmann |first1=E. I.|author1-link =Imre Friedmann |last2=Weed |first2=R. |title=Microbial trace-fossil formation, biogenous, and abiotic weathering in the Antarctic cold desert |journal=Science |year=1987 |volume=236 |issue=4802 |pages=703–705 |doi=10.1126/science.11536571|pmid=11536571 }}}}</ref> and deep [[subsoil]] and ocean trenches rocks.<ref>{{cite journal |last1=Inagaki |first1=F. |last2=Takai |first2=K. |last3=Komatsu |first3=T. |last4=Sakihama |first4=Y. |last5=Inoue |first5=A. |last6=Horikoshi |first6=K. |title=Profile of microbial community structure and presence of endolithic microorganisms inside a deep-sea rock |journal=Geomicrobiology Journal |date=2015 |volume=19 |issue=6 |pages=535–552 |doi=10.1080/01490450290098577|s2cid=84636295 }}</ref> However, there are reports of endolithic microorganisms in inter-tropical zones,<ref>{{cite journal |last1=Gaylarde |first1=C. |last2=Baptista-Neto |first2=J. A. |last3=Ogawa |first3=A. |last4=Kowalski |first4=M. |last5=Celikkol-Aydin |first5=S. |last6=Beech |first6=I. |title=Epilithic and endolithic microorganisms and deterioration on stone church facades subject to urban pollution in a sub-tropical climate |journal=Biofouling |date=2017 |volume=33 |issue=2 |pages=113–127 |doi=10.1080/08927014.2016.1269893|pmid=28054493 |s2cid=3295932 }}</ref> where humidity and solar radiation are significantly different from the above-mentioned biomes. Endoliths have been found in the rock down to a depth of {{cvt|3|km|mi}}, though it is unknown if that is their limit (due to the cost involved in drilling to such depths).<ref name="two miles underground">{{cite web|last1=Schultz|first1=Steven|title=Two miles underground|url=http://www.princeton.edu/pr/pwb/99/1213/microbe.shtml|publisher=Princeton Weekly Bulletin|archive-url=https://web.archive.org/web/20160113130655/http://www.princeton.edu/pr/pwb/99/1213/microbe.shtml|archive-date=13 January 2016|date=13 December 1999}} — Gold mines present "ideal environment" for geologists studying subsurface microbes</ref><ref name="hively">{{cite news|url=http://discovermagazine.com/1997/may/lookingforlifein1124|title= Looking for life in all the wrong places — research on cryptoendoliths|work=[[Discover (magazine)|Discover]]|date= May 1997 |first1= Will|last1= Hively|access-date=December 5, 2019}}</ref> 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&nbsp;°C ([[Strain 121]] can reproduce at 121&nbsp;°C), which limits the possible depth to 4-4.5&nbsp;km below the [[continent]]al crust, and 7 or 7.5&nbsp;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]],<ref name="dry valleys">{{Cite journal |doi = 10.1128/AEM.69.7.3858-3867.2003|pmid = 12839754|pmc = 165166|title = Microbial Diversity of Cryptoendolithic Communities from the McMurdo Dry Valleys, Antarctica|journal = Applied and Environmental Microbiology|volume = 69|issue = 7|pages = 3858–3867|year = 2003|last1 = de la Torre|first1 = J. R.|last2 = Goebel|first2 = B. M.|last3 = Friedmann|first3 = E. I.|author3-link =Imre Friedmann| last4 = Pace|first4 = N. R.|bibcode = 2003ApEnM..69.3858D}}</ref> the [[Alps]],<ref>{{cite journal|last1=Horath|first1=Thomas|last2=Bachofen|first2=Reinhard|title=Molecular Characterization of an Endolithic Microbial Community in Dolomite Rock in the Central Alps (Switzerland)|journal=Microbial Ecology|date=August 2009|volume=58|issue=2|pages=290–306|doi=10.1007/s00248-008-9483-7|pmid=19172216|s2cid=845383|url=https://www.zora.uzh.ch/id/eprint/18300/34/ZORA_NL_18300.pdf}}</ref> and the [[Rocky Mountains]].<ref>{{Cite journal | doi=10.1038/nature03447| pmid=15846344| title=Geobiology of a microbial endolithic community in the Yellowstone geothermal environment| journal=Nature| volume=434| issue=7036| pages=1011–1014| year=2005| last1=Walker| first1=Jeffrey J.| last2=Spear| first2=John R.| last3=Pace| first3=Norman R.| bibcode=2005Natur.434.1011W| s2cid=4408407}}</ref><ref>{{Cite journal |doi = 10.1128/AEM.02656-06|pmid = 17416689|pmc = 1932665|title = Phylogenetic Composition of Rocky Mountain Endolithic Microbial Ecosystems|journal = Applied and Environmental Microbiology|volume = 73|issue = 11|pages = 3497–3504|year = 2007|last1 = Walker|first1 = J. J.|last2 = Pace|first2 = N. R.|bibcode = 2007ApEnM..73.3497W}}</ref>

==Metabolism and survival==
The metabolism of endolithic microorganisms is versatile; there have been found genes involved in [[Sulfur metabolism|sulphur metabolism]],  [[iron-oxidizing bacteria|iron metabolism]] and [[carbon fixation]] in many endolithic communities. Whether they metabolize directly from the surrounding rock, or excrete an acid to dissolve it first is yet undetermined. According to Meslier & DiRuggiero <ref name="Academic press">{{cite book |first1=V |last1=Meslier |first2=J |last2=DiRuggiero |year=2019 |chapter=7 Endolithic microbial communities as model systems for ecology and astrobiology |editor1-last=Seckbach |editor1-first=J. |editor2-last=Rampelotto |editor2-first=P.H. |title=Model Ecosystems in Extreme Environments |publisher=Academic press | isbn= 978-0-1281-2742-1}}</ref> there are genes found in the endolithic community involved in [[nitrogen fixation]]. The [[Ocean Drilling Program]] found microscopic trails in [[basalt]] from the [[Atlantic Ocean|Atlantic]], [[Indian Ocean|Indian]], and [[Pacific Ocean|Pacific]] oceans that contain [[DNA]].<ref name="glass munchers">{{cite web|last1=Mullen|first1=Leslie|title=Glass Munchers Under the Sea|url=http://www.nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=98|website=NASA Astrobiology Institute|url-status=dead|archive-url=https://web.archive.org/web/20130220141852/http://nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=98|archive-date=20 February 2013}}</ref><ref name="basalt">{{cite journal|last1=Lysnes|first1=Kristine|last2=Torsvik|first2=Terje|last3=Thorseth|first3=Ingunn H.|last4=Pedersen|first4=Rolf B.|title=Microbial Populations in Ocean Floor Basalt: Results from ODP Leg 187|journal=Proc ODP Sci Results|series=Proceedings of the Ocean Drilling Program|date=2004|volume=187|pages=1–27|url=http://www-odp.tamu.edu/publications/187_SR/VOLUME/CHAPTERS/203.PDF|doi=10.2973/odp.proc.sr.187.203.2004 }}</ref> Photosynthetic endoliths have also been discovered.<ref name="photendolith">{{cite journal |last1=Wierzchos |first1=Jacek |last2=Ascaso |first2=Carmen |last3=McKay |first3=Christopher P. |title=Endolithic Cyanobacteria in Halite Rocks from the Hyperarid Core of the Atacama Desert |journal=Astrobiology |date=2006 |volume=6 |issue=3 |pages=415–422 |doi=10.1089/ast.2006.6.415|pmid=16805697 |bibcode=2006AsBio...6..415W |hdl=10261/19099 |hdl-access=free }}</ref>

As water and nutrients are sparse in the endolith's surrounding environment, water limitation is a key factor in the capacity of survival of many endolithic microorganisms. Many of those microorganisms have adaptations to survive in low concentrations of water.<ref name="Academic press"/> Additionally, the presence of pigments, especially in [[cyanobacteria]] and some [[algae]], such as; [[Β-Carotene|beta carotenes]] and [[chlorophyll]] help them to protect against dangerous radiation and act as a way to obtain energy.<ref>{{cite journal |last1=Osterrothová |first1=K |last2=Culka |first2=A |last3=Němečková |first3=K |last4=Kaftan |first4=D |last5=Nedbalová |first5=L |last6=Procházková |first6=L |last7=Jehlička |first7=J |title=Analyzing carotenoids of snow algae by Raman microspectroscopy and high-performance liquid chromatography |journal=Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy |date=2019 |volume=212 |pages=262–271 |doi=10.1016/j.saa.2019.01.013|pmid=30658280 |bibcode=2019AcSpA.212..262O |s2cid=58604046 }}</ref> Another characteristic is the presence of a very slow [[reproduction]] cycle. Early data suggest some only engage in [[cell division]] once every hundred years. In August 2013, researchers reported evidence of endoliths in the ocean floor, perhaps millions of years old and reproducing only once every 10,000 years.<ref>{{cite web|last1=Yirka|first1=Bob|title=Soil beneath ocean found to harbor long-lived bacteria, fungi and viruses|url=http://phys.org/news/2013-08-soil-beneath-ocean-harbor-bacteria.html|website=Phys.org|date=29 August 2013|archive-url=https://web.archive.org/web/20151029144045/http://phys.org/news/2013-08-soil-beneath-ocean-harbor-bacteria.html|archive-date=29 October 2015|url-status=live}}</ref>  Most of their energy is spent repairing [[cell damage]] caused by [[cosmic ray]]s or [[racemization]], and very little is available for reproduction or growth. It is thought that they weather long [[ice age]]s in this fashion, emerging when the temperature in the area warms.<ref name="hively"/>

==Ecology==
As most endoliths are [[autotroph]]s, 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 Lithoautotrophic Microbial Ecosystem|subsurface lithoautotrophic microbial ecosystem]]'' (''SLiME''),<ref name="slime">{{cite web|title=Frequently Requested Information about the SLiME Hypothesis|url=http://www.pnl.gov/slme/SLiME_FAQs.html|archive-url=https://web.archive.org/web/20060930140112/http://www.pnl.gov/slme/SLiME_FAQs.html|archive-date=30 September 2006}}</ref> or ''endolithic systems'' within the subterranean lithic [[biome]].

''Endolithic systems'' are still at an early stage of exploration. In some cases its biota can support simple invertebrates, most organisms are unicellular. Near-surface layers of rock may contain blue-green algae but most energy comes from chemical synthesis of minerals. The limited supply of energy limits the rates of growth and reproduction. In deeper rock layers microbes are exposed to high pressures and temperatures.<ref>{{cite book |first1=DA |last1=Keith |first2=TM |last2=Iliffe |first3=V |last3=Gerovasileiou| first4=B |last4=Gonzalez |first5=D |last5=Brankovits |first6=A |last6=Martínez García |year=2020 |chapter=S1.2 Endolithic systems |chapter-url=https://global-ecosystems.org/explore/groups/S1.2 |editor1-last=Keith |editor1-first=D.A. |editor2-last=Ferrer-Paris |editor2-first=J.R. |editor3-last=Nicholson |editor3-first=E. |editor4-last=Kingsford |editor4-first=R.T. |title=The IUCN Global Ecosystem Typology 2.0: Descriptive profiles for biomes and ecosystem functional groups |location=Gland, Switzerland |publisher=IUCN | doi=10.2305/IUCN.CH.2020.13.en | isbn= 978-2-8317-2077-7|s2cid=241360441 }}</ref>

==Endolithic fungi and algae in marine ecosystems==
Although it is possible that endolithic fungi could play an important role in the health of [[coral reef]]s, only limited research has been conducted on the distribution and diversity of [[Marine fungi|marine endolithic fungi]].

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.<ref>{{cite journal |last1=Golubic |first1=Stjepko |last2=Radtke |first2=Gudrun |last3=Campion-Alsumard |first3=Therese Le |title=Endolithic fungi in marine ecosystems |journal=Trends in Microbiology |date=2005 |volume=13 |issue=5 |pages=229–235 |doi=10.1016/j.tim.2005.03.007|pmid=15866040 }}</ref>

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 play 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 [[Endosymbiont|endosymbiotic]] [[Symbiodinium|Symbiodinia]].<ref>{{cite journal |last1=Fine |first1=Maoz |last2=Loya |first2=Yossi |title=Endolithic algae: an alternative source of photoassimilates during coral bleaching |journal=Proceedings of the Royal Society of London. Series B: Biological Sciences |date=2002 |volume=269 |issue=1497 |pages=1205–1210 |doi=10.1098/rspb.2002.1983|pmid=12065035 |pmc=1691023 }}</ref>

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.<ref>{{cite journal |last1=Günther |first1=Astrid |title=Distribution and bathymetric zonation of shell-boring endoliths in recent reef and shelf environments: Cozumel, Yucatan (Mexico) |journal=Facies |date=1990 |volume=22 |issue=1 |pages=233–261 |doi=10.1007/bf02536953|s2cid=130403994 }}</ref>

==Endolithic parasitism==
Until the 1990s [[Phototrophic autotroph|phototrophic]] endoliths were thought of as somewhat benign, but evidence has since 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.<ref>{{cite journal |last1=Kaehler |first1=S. |last2=McQuaid |first2=C. D. |title=Lethal and sub-lethal effects of phototrophic endoliths attacking the shell of the intertidal mussel ''Perna perna'' |journal=Marine Biology |date=1999 |volume=135 |issue=3 |pages=497–503 |doi=10.1007/s002270050650|s2cid=84103549 }}</ref>

==Endolithic fungi found in the eggs of Cretaceous dinosaurs==
Evidence of endolithic fungi were discovered within dinosaur eggshell found in central China. They were characterized as being “needle-like, ribbon-like, and silk-like.".<ref name=Gong>{{cite journal |last1=Gong |first1=YiMing |last2=Xu |first2=Ran |last3=Hu |first3=Bi |title=Endolithic fungi: A possible killer for the mass extinction of Cretaceous dinosaurs |journal=Science in China Series D: Earth Sciences |date=2008 |volume=51 |issue=6 |pages=801–807 |doi=10.1007/s11430-008-0052-1|bibcode=2008ScChD..51..801G |s2cid=126670640 }}</ref>

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 may have killed the embryos in infected eggs of these dinosaurs. It may also have led to the preservation of dinosaur eggs, including some that contained embryos.<ref name=Gong />

==Relationship with astrobiology==
Endolithic microorganisms have been considered a model for the search for life on other planets by inquiring about what sort of microorganisms on [[Earth]] inhabit specific [[mineral]]s, which helps to propose those lithologies as life detection targets on an extra-terrestrial surface such as [[Mars]]. Several studies have been carried out in extreme places that serve as analogs for Mars's surface and subsurface, and many studies in [[geomicrobiology]] on Earth's hot and cold deserts have been developed.<ref>{{cite journal |last1=Warren-Rhodes |first1=K. A. |last2=Rhodes |first2=K. L. |last3=Pointing |first3=S. B. |last4=Ewing |first4=S. A. |last5=Lacap |first5=D. C. |last6=Gomez-Silva |first6=B. |last7=McKay |first7=C. P. |title=Hypolithic cyanobacteria, dry limit of photosynthesis, and microbial ecology in the hyperarid Atacama Desert |journal=Microbial Ecology |date=2006 |volume=52 |issue=3 |pages=389–398 |doi=10.1007/s00248-006-9055-7|pmid=16865610 |s2cid=1914122 }}</ref> In these [[extreme environment]]s, microorganisms find protection against thermal buffering, UV radiation, and desiccation while living inside pores and fissures of minerals and rocks.<ref name="Cryptoendolithic algae of hot semia">{{cite journal |last1=Bell |first1=R. A. |title=Cryptoendolithic algae of hot semiarid lands and deserts |journal=Journal of Phycology |date=1993 |volume=29 |issue=2 |pages=133–139 |doi=10.1111/j.0022-3646.1993.00133.x|s2cid=85033484 }}</ref><ref name="Wierzchos et al. 2011"/> Life in these endolithic habitats might face similar stress due to the scarcity of water and high UV radiation that rule on modern Mars.<ref name="Academic press"/>

An excellent example of these adaptations is the non-hygroscopic but microporous translucent gypsum crusts, which are found as potential substrates that can mitigate exposure to UV radiation and desiccation and allow microbial colonization in hyper-arid deserts.<ref>{{cite journal |last1=Cockell |first1=C. |last2=Osinski |first2=G. |last3=Lee |first3=P. |title=The impact crater as a habitat: effects of impact processing of target materials |journal=Astrobiology |year=2003 |volume=3 |issue=1 |pages=3181–191 |doi=10.1089/153110703321632507|pmid=12804371 |bibcode=2003AsBio...3..181C }}</ref><ref>{{cite journal |last1=Oren |first1=A. |last2=Kühl |first2=M. |last3=Karsten |first3=U. |title=An endoevaporitic microbial mat within a gypsum crust: zonation of phototrophs, photopigments, and light penetration |journal=Marine Ecology Progress Series |date=1995 |volume=128 |pages=151–159 |doi=10.3354/meps128151|bibcode=1995MEPS..128..151O |doi-access=free }}</ref> In the same way, the ability to grow under high water stress and oligotrophic conditions confer to endolithic microorganisms to survive in conditions similar to those found on Mars. There is evidence of the past existence of water on the red planet; perhaps, these microorganisms could develop adaptations found in current deserts on the Earth. Furthermore, The endolithic structures are a good way to find ancient or current biological activity ([[biosignature]]s) on Mars or other rocky planets.

==Geological evidence==
In 2025, researchers from [[Johannes Gutenberg University Mainz]] reported unusual micro-burrows discovered in [[marble]] and [[limestone]] formations across desert regions of [[Namibia]], [[Oman]], and [[Saudi Arabia]].<ref>{{Cite journal | last1=Passchier | first1=C.W. | last2=Wassenaar | first2=T.M. | last3=Groschopf | first3=N. | last4=Jantschke | first4=A. | last5=Mertz-Kraus | first5=R. | title=Subfossil Fracture-Related Euendolithic Micro-burrows in Marble and Limestone | journal=Geomicrobiology Journal | year=27 February 2025 | doi=10.1080/01490451.2025.2467417 | doi-access=free }}</ref> These micro-tunnels, roughly half a millimeter wide and up to three centimeters long, were aligned vertically in parallel bands and filled with [[calcium carbonate]] powder. Traces of biological material suggest these features were formed by a previously unknown endolithic microorganism capable of penetrating deep into rock, likely to access nutrients. While no DNA was recovered, the structures are estimated to be between one and two million years old and represent possible subfossil evidence of microbial life.<ref>{{cite web |url=https://press.uni-mainz.de/unknown-microorganisms-used-marble-and-limestone-as-a-habitat/ |title=Unknown microorganisms used marble and limestone as a habitat |publisher=Johannes Gutenberg University Mainz |date=19 March 2025 }}</ref>

==In popular culture==
The [[manga]] and [[anime]] [[Land of the Lustrous]] revolves around characters composed of gems given life by endolithic [[inclusion (mineral)|inclusions]].

==See also==
* [[Lithophile]]
* [[Lithotroph]]
* [[Volyn biota]]

==References==
{{reflist|30em}}

==External links==
* [http://serc.carleton.edu/microbelife/extreme/endolith/general.html 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.
* [http://serc.carleton.edu/microbelife/extreme/endolith/advanced.html Endolith Advanced Collection] — Compiled for professionals and advanced learners, this endolith collection includes online resources such as journal articles, academic reviews, and surveys.

{{Extremophile}}
{{Biomes}}
{{Use dmy dates|date=June 2018}}

[[Category:Lithophiles]]