Extremophile

Thermophiles, a type of extremophile, produce some of the bright colors of Grand Prismatic Spring, Yellowstone National Park

An extremophile (from Latin extremus meaning "extreme" and Greek philiā (φιλία) meaning "love") is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth.[1][2] In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles.

Characteristics

In the 1980s and 1990s, biologists found that microbial life has an amazing flexibility for surviving in extreme environments—niches that are extraordinarily hot, or acidic, for example—that would be completely inhospitable to complex organisms. Some scientists even concluded that life may have begun on Earth in hydrothermal vents far under the ocean's surface.[3] According to astrophysicist Dr. Steinn Sigurdsson, "There are viable bacterial spores that have been found that are 40 million years old on Earth—and we know they're very hardened to radiation."[4] On 6 February 2013, scientists reported that bacteria were found living in the cold and dark in a lake buried a half-mile deep under the ice in Antarctica.[5] On 17 March 2013, researchers reported data that suggested microbial life forms thrive in the Mariana Trench, the deepest spot on the Earth.[6][7] Other researchers reported related studies that microbes thrive inside rocks up to 1900 feet below the sea floor under 8500 feet of ocean off the coast of the northwestern United States.[6][8] According to one of the researchers, "You can find microbes everywhere—they're extremely adaptable to conditions, and survive wherever they are."[6]

Morphology

Most known extremophiles are microbes. The domain Archaea contains renowned examples, but extremophiles are present in numerous and diverse genetic lineages of bacteria and archaeans. Furthermore, it is erroneous to use the term extremophile to encompass all archaeans, as some are mesophilic. Neither are all extremophiles unicellular; protostome animals found in similar environments include the Pompeii worm, the psychrophilic Grylloblattidae (insects) and Antarctic krill (a crustacean). Many would also classify tardigrades (water bears) as extremophiles but while tardigrades can survive in extreme environments, they are not considered extremophiles because they are not adapted to live in these conditions. Their chances of dying increase the longer they are exposed to the extreme environment.

Classifications

There are many classes of extremophiles that range all around the globe, each corresponding to the way its environmental niche differs from mesophilic conditions. These classifications are not exclusive. Many extremophiles fall under multiple categories and are classified as polyextremophiles. For example, organisms living inside hot rocks deep under Earth's surface are thermophilic and barophilic such as Thermococcus barophilus.[9] A polyextremophile living at the summit of a mountain in the Atacama Desert might be a radioresistant xerophile, a psychrophile, and an oligotroph. Polyextremophiles are well known for their ability to tolerate both high and low pH levels.

Terms

Acidophile
An organism with optimal growth at pH levels of 3 or below
Alkaliphile
An organism with optimal growth at pH levels of 9 or above
Anaerobe
An organism that does not require oxygen for growth such as Spinoloricus Cinzia. Two sub-types exist: facultative anaerobe and obligate anaerobe. A facultative anaerobe can tolerate anaerobic and aerobic conditions; however, an obligate anaerobe would die in the presence of even trace levels of oxygen
Cryptoendolith
An organism that lives in microscopic spaces within rocks, such as pores between aggregate grains; these may also be called Endolith, a term that also includes organisms populating fissures, aquifers, and faults filled with groundwater in the deep subsurface
Halophile
An organism requiring at least 0.2M concentrations of salt (NaCl) for growth[10]
Hyperthermophile
An organism that can thrive at temperatures above 80 °C, such as those found in hydrothermal systems
Hypolith
An organism that lives underneath rocks in cold deserts
Lithoautotroph
An organism (usually bacteria) whose sole source of carbon is carbon dioxide and exergonic inorganic oxidation (chemolithotrophs) such as Nitrosomonas europaea; these organisms are capable of deriving energy from reduced mineral compounds like pyrites, and are active in geochemical cycling and the weathering of parent bedrock to form soil
Metallotolerant
Capable of tolerating high levels of dissolved heavy metals in solution, such as copper, cadmium, arsenic, and zinc; examples include Ferroplasma sp., Cupriavidus metallidurans and GFAJ-1[11][12][13]
Oligotroph
An organism capable of growth in nutritionally limited environments
Osmophile
An organism capable of growth in environments with a high sugar concentration
Piezophile
(Also referred to as barophile). An organism that lives optimally at high pressures such as those deep in the ocean or underground;[14] common in the deep terrestrial subsurface, as well as in oceanic trenches
Polyextremophile
A polyextremophile (faux Ancient Latin/Greek for 'affection for many extremes') is an organism that qualifies as an extremophile under more than one category
Psychrophile/Cryophile
An organism capable of survival, growth or reproduction at temperatures of -15 °C or lower for extended periods; common in cold soils, permafrost, polar ice, cold ocean water, and in or under alpine snowpack
Radioresistant
Organisms resistant to high levels of ionizing radiation, most commonly ultraviolet radiation, but also including organisms capable of resisting nuclear radiation
Thermophile
An organism that can thrive at temperatures between 45–122 °C
Thermoacidophile
Combination of thermophile and acidophile that prefer temperatures of 70–80 °C and pH between 2 and 3
Xerophile
An organism that can grow in extremely dry, desiccating conditions; this type is exemplified by the soil microbes of the Atacama Desert

In astrobiology

Astrobiology is the field concerned with forming theories, such as panspermia, about the distribution, nature, and future of life in the universe. In it, microbial ecologists, astronomers, planetary scientists, geochemists, philosophers, and explorers cooperate constructively to guide the search for life on other planets. Astrobiologists are particularly interested in studying extremophiles,[15] as many organisms of this type are capable of surviving in environments similar to those known to exist on other planets. For example, Mars may have regions in its deep subsurface permafrost that could harbor endolith communities.[15] The subsurface water ocean of Jupiter's moon Europa may harbor life, especially at hypothesized hydrothermal vents at the ocean floor.

Recent research carried out on extremophiles in Japan involved a variety of bacteria including Escherichia coli and Paracoccus denitrificans being subject to conditions of extreme gravity. The bacteria were cultivated while being rotated in an ultracentrifuge at high speeds corresponding to 403,627 g (i.e. 403,627 times the gravity experienced on Earth). Paracoccus denitrificans was one of the bacteria which displayed not only survival but also robust cellular growth under these conditions of hyperacceleration which are usually found only in cosmic environments, such as on very massive stars or in the shock waves of supernovas. Analysis showed that the small size of prokaryotic cells is essential for successful growth under hypergravity. The research has implications on the feasibility of panspermia.[16][17]

On 26 April 2012, scientists reported that lichen survived and showed remarkable results on the adaptation capacity of photosynthetic activity within the simulation time of 34 days under Martian conditions in the Mars Simulation Laboratory (MSL) maintained by the German Aerospace Center (DLR).[18][19]

On 29 April 2013, scientists at Rensselaer Polytechnic Institute, funded by NASA, reported that, during spaceflight on the International Space Station, microbes seem to adapt to the space environment in ways "not observed on Earth" and in ways that "can lead to increases in growth and virulence".[20]

On 19 May 2014, scientists announced that numerous microbes, like Tersicoccus phoenicis, may be resistant to methods usually used in spacecraft assembly clean rooms. It's not currently known if such resistant microbes could have withstood space travel and are present on the Curiosity rover now on the planet Mars.[21]

On 20 August 2014, scientists confirmed the existence of microorganisms living half a mile below the ice of Antarctica.[22][23]

Examples

New sub-types of -philes are identified frequently and the sub-category list for extremophiles is always growing. For example, microbial life lives in the liquid asphalt lake, Pitch Lake. Research indicates that extremophiles inhabit the asphalt lake in populations ranging between 106 to 107 cells/gram.[24][25] Likewise, until recently boron tolerance was unknown but a strong borophile was discovered in bacteria. With the recent isolation of Bacillus boroniphilus, borophiles came into discussion.[26] Studying these borophiles may help illuminate the mechanisms of both boron toxicity and boron deficiency.

Industrial uses

The thermoalkaliphilic catalase, which initiates the breakdown of hydrogen peroxide into oxygen and water, was isolated from an organism, Thermus brockianus, found in Yellowstone National Park by Idaho National Laboratory researchers. The catalase operates over a temperature range from 30 °C to over 94 °C and a pH range from 6–10. This catalase is extremely stable compared to other catalases at high temperatures and pH. In a comparative study, the T. brockianus catalase exhibited a half life of 15 days at 80 °C and pH 10 while a catalase derived from Aspergillus niger had a half life of 15 seconds under the same conditions. The catalase will have applications for removal of hydrogen peroxide in industrial processes such as pulp and paper bleaching, textile bleaching, food pasteurization, and surface decontamination of food packaging.[27]

DNA modifying enzymes such as Taq DNA polymerase and some Bacillus enzymes used in clinical diagnostics and starch liquefaction are produced commercially by several biotechnology companies.[28]

DNA transfer

Over 65 prokaryotic species are known to be naturally competent for genetic transformation, the ability to transfer DNA from one cell to another cell followed by integration of the donor DNA into the recipient cell’s chromosome.[29] Several extremophiles are able to carry out species-specific DNA transfer, as described below. However, it is not yet clear how common such a capability is among extremophiles.

The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known. This bacterium can also survive cold, dehydration, vacuum and acid and is thus known as a polyextremophile. D. radiodurans is competent to perform genetic transformation.[30] Recipient cells are able to repair DNA damage in donor transforming DNA that had been UV irradiated as efficiently as they repair cellular DNA when the cells themselves are irradiated. The extreme thermophilic bacterium Thermus thermophilus and other related Thermus species are also capable of genetic transformation.[31]

Halobacterium volcanii, an extreme halophilic (saline tolerant) archaeon, is capable of natural genetic transformation. Cytoplasmic bridges are formed between cells that appear to be used for DNA transfer from one cell to another in either direction.[32]

Sulfolobus solfataricus and Sulfolobus acidocaldarius are hyperthermophilic archaea. Exposure of these organisms to the DNA damaging agents UV irradiation, bleomycin or mitomycin C induces species-specific cellular aggregation.[33][34] UV-induced cellular aggregation of S. acidocaldarius mediates chromosomal marker exchange with high frequency.[34] Recombination rates exceed those of uninduced cultures by up to three orders of magnitude. Frols et al.[33] and Ajon et al.[34] hypothesized that cellular aggregation enhances species-specific DNA transfer between Sulfolobus cells in order to repair damaged DNA by means of homologous recombination. Van Wolferen et al.[35] noted that this DNA exchange process may be crucial under DNA damaging conditions such as high temperatures. It has also been suggested that DNA transfer in Sulfolobus may be an early form of sexual interaction similar to the more well-studied bacterial transformation systems that involve species-specific DNA transfer leading to homologous recombinational repair of DNA damage[36] (and see Transformation (genetics)).

Extracellular membrane vesicles (MVs) might be involved in DNA transfer between different hyperthermophilic archaeal species.[37] It has been shown that both plasmids[38] and viral genomes[37] can be transferred via MVs. Notably, a horizontal plasmid transfer has been documented between hyperthermophilic Thermococcus and Methanocaldococcus species, respectively belonging to the orders Thermococcales and Methanococcales.[39]

See also

References

  1. ↑ Rampelotto, P. H. (2010). "Resistance of microorganisms to extreme environmental conditions and its contribution to Astrobiology". Sustainability. 2 (6): 1602–1623. Bibcode:2010Sust....2.1602R. doi:10.3390/su2061602.
  2. ↑ Rothschild, L.J.; Mancinelli, R.L. (2001). "Life in extreme environments". Nature. 409 (6823): 1092–1101. Bibcode:2001Natur.409.1092R. doi:10.1038/35059215. PMID 11234023.
  3. ↑ "Mars Exploration - Press kit" (PDF). NASA. June 2003. Retrieved 14 July 2009.
  4. ↑ BBC Staff (23 August 2011). "Impacts 'more likely' to have spread life from Earth". BBC. Retrieved 24 August 2011.
  5. ↑ Gorman, James (6 February 2013). "Bacteria Found Deep Under Antarctic Ice, Scientists Say". New York Times. Retrieved 6 February 2013.
  6. 1 2 3 Choi, Charles Q. (17 March 2013). "Microbes Thrive in Deepest Spot on Earth". LiveScience. Retrieved 17 March 2013.
  7. ↑ Glud, Ronnie; Wenzhöfer, Frank; Middleboe, Mathias; Oguri, Kazumasa; Turnewitsch, Robert; Canfield, Donald E.; Kitazato, Hiroshi (17 March 2013). "High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth". Nature Geoscience. 6 (4): 284–288. Bibcode:2013NatGe...6..284G. doi:10.1038/ngeo1773. Retrieved 17 March 2013.
  8. ↑ Oskin, Becky (14 March 2013). "Intraterrestrials: Life Thrives in Ocean Floor". LiveScience. Retrieved 17 March 2013.
  9. ↑ "Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent". IJSEM. 49: 351–359. 1999. doi:10.1099/00207713-49-2-351.
  10. ↑ Cavicchioli, R. & Thomas, T. 2000. Extremophiles. In: J. Lederberg. (ed.) Encyclopedia of Microbiology, Second Edition, Vol. 2, pp. 317–337. Academic Press, San Diego.
  11. ↑ "Studies refute arsenic bug claim". BBC News. 9 July 2012. Retrieved 10 July 2012.
  12. ↑ Erb, Tobias J.; Kiefer, Patrick; Hattendorf, Bodo; Günther, Detlef; Vorholt, Julia A. (8 July 2012). "GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism". Science. 337 (6093): 467–70. Bibcode:2012Sci...337..467E. doi:10.1126/science.1218455. PMID 22773139. Retrieved 10 July 2012.
  13. ↑ Reaves, Marshall Louis; Sinha, Sunita; Rabinowitz, Joshua D.; Kruglyak, Leonid; Redfield, Rosemary J. (8 July 2012). "Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells". Science. 337 (6093): 470–3. arXiv:1201.6643Freely accessible. Bibcode:2012Sci...337..470R. doi:10.1126/science.1219861. PMC 3845625Freely accessible. PMID 22773140. Retrieved 10 July 2012.
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  15. 1 2 Chang, Kenneth (12 September 2016). "Visions of Life on Mars in Earth's Depths". New York Times. Retrieved 12 September 2016.
  16. ↑ Than, Ker (25 April 2011). "Bacteria Grow Under 400,000 Times Earth's Gravity". National Geographic- Daily News. National Geographic Society. Retrieved 28 April 2011.
  17. ↑ Deguchi, Shigeru; Hirokazu Shimoshige, Mikiko Tsudome, Sada-atsu Mukai, Robert W. Corkery, Susumu Ito, and Koki Horikoshi; Tsudome, M.; Mukai, S.-a.; Corkery, R. W.; Ito, S.; Horikoshi, K. (2011). "Microbial growth at hyperaccelerations up to 403,627 xg". Proceedings of the National Academy of Sciences. 108 (19): 7997–8002. Bibcode:2011PNAS..108.7997D. doi:10.1073/pnas.1018027108. Retrieved 28 April 2011.
  18. ↑ Baldwin, Emily (26 April 2012). "Lichen survives harsh Mars environment". Skymania News. Retrieved 27 April 2012.
  19. ↑ de Vera, J.-P.; Kohler, Ulrich (26 April 2012). "The adaptation potential of extremophiles to Martian surface conditions and its implication for the habitability of Mars" (PDF). European Geosciences Union. Retrieved 27 April 2012.
  20. ↑ Kim W; et al. (29 April 2013). "Spaceflight Promotes Biofilm Formation by Pseudomonas aeruginosa". Plos One. 8 (4): e6237. Bibcode:2013PLoSO...862437K. doi:10.1371/journal.pone.0062437. Retrieved 5 July 2013.
  21. ↑ Madhusoodanan, Jyoti (19 May 2014). "Microbial stowaways to Mars identified". Nature. doi:10.1038/nature.2014.15249. Retrieved 23 May 2014.
  22. ↑ Fox, Douglas (20 August 2014). "Lakes under the ice: Antarctica's secret garden". Nature. 512 (7514): 244–246. Bibcode:2014Natur.512..244F. doi:10.1038/512244a. Retrieved 21 August 2014.
  23. ↑ Mack, Eric (20 August 2014). "Life Confirmed Under Antarctic Ice; Is Space Next?". Forbes. Retrieved 21 August 2014.
  24. ↑ Microbial Life Found in Hydrocarbon Lake. the physics arXiv blog 15 April 2010.
  25. ↑ Schulze-Makuch, Haque, Antonio, Ali, Hosein, Song, Yang, Zaikova, Beckles, Guinan, Lehto, Hallam. Microbial Life in a Liquid Asphalt Desert.
  26. ↑ Ahmed, Iftikhar; Yokota, Akira; Fujiwara, Toru (2006). "A novel highly boron tolerant bacterium, Bacillus boroniphilus sp. nov., isolated from soil, that requires boron for its growth". Extremophiles. 11 (2): 217–224. doi:10.1007/s00792-006-0027-0. PMID 17072687.
  27. ↑ "Bioenergy and Industrial Microbiology". Idaho National Laboratory. U.S. Department of Energy. Retrieved 3 February 2014.
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  29. ↑ Johnsborg, O; Eldholm, V; Håvarstein, LS. (2007). "Natural genetic transformation: prevalence, mechanisms and function". Res Microbiol. 158 (10): 767–78. doi:10.1016/j.resmic.2007.09.004. PMID 17997281.
  30. ↑ Moseley, BE; Setlow, JK. (1968). "Transformation in Micrococcus radiodurans and the ultraviolet sensitivity of its transforming DNA". Proc Natl Acad Sci U S A. 61 (1): 176–83. Bibcode:1968PNAS...61..176M. doi:10.1073/pnas.61.1.176. PMC 285920Freely accessible. PMID 5303325.
  31. ↑ Koyama, Y; Hoshino, T; Tomizuka, N; Furukawa, K. (1986). "Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp". J Bacteriol. 166 (1): 338–40. PMID 3957870.
  32. ↑ Rosenshine, I; Tchelet, R; Mevarech, M. (1989). "The mechanism of DNA transfer in the mating system of an archaebacterium". Science. 245 (4924): 1387–9. Bibcode:1989Sci...245.1387R. doi:10.1126/science.2818746. PMID 2818746.
  33. 1 2 Fröls, S; Ajon, M; Wagner, M; Teichmann, D; Zolghadr, B; Folea, M; Boekema, EJ; Driessen, AJ; Schleper, C; et al. (2008). "UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation". Mol Microbiol. 70 (4): 938–52. doi:10.1111/j.1365-2958.2008.06459.x. PMID 18990182.
  34. 1 2 3 Ajon, M; Fröls, S; van Wolferen, M; Stoecker, K; Teichmann, D; Driessen, AJ; Grogan, DW; Albers, SV; Schleper, C.; et al. (2011). "UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili". Mol Microbiol. 82 (4): 807–17. doi:10.1111/j.1365-2958.2011.07861.x. PMID 21999488.
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  37. 1 2 Gaudin M, Krupovic M, Marguet E, Gauliard E, Cvirkaite-Krupovic V, Le Cam E, Oberto J, Forterre P; Krupovic; Marguet; Gauliard; Cvirkaite-Krupovic; Le Cam; Oberto; Forterre (2014). "Extracellular membrane vesicles harbouring viral genomes". Environ Microbiol. 16 (4): 1167–75. doi:10.1111/1462-2920.12235. PMID 24034793.
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Further reading

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