Acidophile Explained

Acidophiles or acidophilic organisms are those that thrive under highly acidic conditions (usually at pH 5.0 or below^[1]). These organisms can be found in different branches of the tree of life, including Archaea, Bacteria,^[2] and Eukarya.

Examples

A list of these organisms includes:

Archaea

• Sulfolobales, an order in the Thermoproteota branch^[3] of Archaea

• Thermoplasmatales, an order in the Euryarchaeota branch of Archaea

• ARMAN, in the Euryarchaeota branch of Archaea

• Acidianus brierleyi, A. infernus, facultatively anaerobic thermoacidophilic archaebacteria

• Halarchaeum acidiphilum, acidophilic member of the Halobacteriacaeae^[4]

• Metallosphaera sedula, thermoacidophilic

Bacteria

• Acidobacteriota,^[5] a phylum of Bacteria

• Acidithiobacillales, an order of Pseudomonadota e.g. A. ferrooxidans, A. thiooxidans

• Thiobacillus prosperus, T. acidophilus, T. organovorus, T. cuprinus

• Acetobacter aceti, a bacterium that produces acetic acid (vinegar) from the oxidation of ethanol.

• Alicyclobacillus, a genus of bacteria that can contaminate fruit juices.^[6]

Eukarya

• Mucor racemosus^[7]

• Urotricha^[7]

• Dunaliella acidophila^[7]

• Members of the algal class Cyanidiophyceae, including Cyanidioschyzon merolae

Mechanisms of adaptation to acidic environments

Most acidophile organisms have evolved extremely efficient mechanisms to pump protons out of the intracellular space in order to keep the cytoplasm at or near neutral pH. Therefore, intracellular proteins do not need to develop acid stability through evolution. However, other acidophiles, such as Acetobacter aceti, have an acidified cytoplasm which forces nearly all proteins in the genome to evolve acid stability.^[8] For this reason, Acetobacter aceti has become a valuable resource for understanding the mechanisms by which proteins can attain acid stability.

Studies of proteins adapted to low pH have revealed a few general mechanisms by which proteins can achieve acid stability. In most acid stable proteins (such as pepsin and the soxF protein from Sulfolobus acidocaldarius), there is an overabundance of acidic residues which minimizes low pH destabilization induced by a buildup of positive charge. Other mechanisms include minimization of solvent accessibility of acidic residues or binding of metal cofactors. In a specialized case of acid stability, the NAPase protein from Nocardiopsis alba was shown to have relocated acid-sensitive salt bridges away from regions that play an important role in the unfolding process. In this case of kinetic acid stability, protein longevity is accomplished across a wide range of pH, both acidic and basic.

See also

• Acidophiles in acid mine drainage
• Acidophobe
• Neutrophile
• Acidophile (histology)

Further reading

• Cooper, J. B.. Khan, G.. Taylor, G.. Tickle, I. J.. Blundell, T. L. . July 1990. X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution. J Mol Biol. 214. 1. 199–222. 2115088. 10.1016/0022-2836(90)90156-G .
• Bonisch, H.. Schmidt, C. L.. Schafer, G.. Ladenstein, R. . June 2002. The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution. J Mol Biol . 319. 3. 791–805. 12054871. 10.1016/S0022-2836(02)00323-6 .
• January 2004. X-ray structures of the maltose-maltodextrin-binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins. Journal of Molecular Biology. 335. 1. 261–74. 14659755. 10.1016/j.jmb.2003.10.042. Schafer. K. Magnusson. U. Scheffel. F. Schiefner. A. Sandgren. MO. Diederichs. K. Welte. W. Hülsmann. A. Schneider. E. Mowbray. SL.
• Walter, R. L.. Ealick, S. E.. Friedman, A. M.. Blake, R. C. 2nd. Proctor, P.. Shoham, M.. November 1996. Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability. J Mol Biol. 263. 5. 730–51. 10.1006/jmbi.1996.0612. 8947572. free.
• Botuyan, M. V.. Toy-Palmer, A.. Chung, J.. Blake, R. C. 2nd. Beroza, P.. Case, D. A.. Jane Dyson. Dyson, H. J.. 1996. NMR solution structure of Cu(I) rusticyanin from Thiobacillus ferrooxidans: structural basis for the extreme acid stability and redox potential. J Mol Biol. 263. 752–67. 10.1006/jmbi.1996.0613. 8947573. 5.
• Kelch, B. A.. Eagen, K. P.. Erciyas, F. P.. Humphris, E. L.. Thomason, A. R.. Mitsuiki, S.. Agard, D. A. . May 2007. 368. 3. Structural and mechanistic exploration of acid resistance: kinetic stability facilitates evolution of extremophilic behavior. J Mol Biol . 870–883. 10.1016/j.jmb.2007.02.032. 17382344. 10.1.1.79.3711.

Notes and References

1. Jin . Qusheng . Kirk . Matthew F. . 2018-05-01 . pH as a Primary Control in Environmental Microbiology: 1. Thermodynamic Perspective . Frontiers in Environmental Science . 6 . 21 . 10.3389/fenvs.2018.00021 . 2296-665X. free .
2. Becker, A., Types of Bacteria Living in Acidic pH". Retrieved 10 May 2017.
3. Book: The Prokaryotes: A handbook on the biology of bacteria . Dworkin M, Falkow S . 2006.
4. Book: Singh OV . Extremophiles: Sustainable Resources and Biotechnological Implications . John Wiley & Sons. 2012 . 76–79. 978-1-118-10300-5 .
5. Quaiser. Achim. Ochsenreiter. Torsten. Lanz. Christa. Schuster. Stephan C.. Treusch. Alexander H.. Eck. Jürgen. Schleper. Christa. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Molecular Microbiology. 27 August 2003. 50. 2. 563–575. 10.1046/j.1365-2958.2003.03707.x. 14617179. 25162803.
6. Pettipher GL . Osmundson ME . Murphy JM . Methods for the detection and enumeration of Alicyclobacillus acidoterrestris and investigation of growth and production of taint in fruit juice and fruit juice-containing drinks . Letters in Applied Microbiology . 24 . 3 . 185–189 . March 1997 . 10.1046/j.1472-765X.1997.00373.x . 9080697. 6976998 .
7. Web site: Eukaryotic Acidophiles . Douglas . Rawlings . D. Barrie . Johnson . Encyclopedia of Life Support System (EOLSS) . 3 February 2014 . Eolss Publishers . https://web.archive.org/web/20141013044716/http://www.eolss.net/eolsssamplechapters/c03/e6-73-06-01/E6-73-06-01-TXT-04.aspx#6.%20Eukaryotic%20Acidophiles . 2014-10-13 . dead .
8. Menzel, U.. Gottschalk, G.. 1985. 143. The internal pH of Acetobacterium wieringae and Acetobacter aceti during growth and production of acetic acid. 1. Arch Microbiol. 47–51. 10.1007/BF00414767. 1985ArMic.143...47M. 6477488.