1887

Chapter 4.3.1 : The Microbiology of Extremely Acidic Environments

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

The Microbiology of Extremely Acidic Environments, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch4.3.1-1.gif /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch4.3.1-2.gif

Abstract:

Extremely acidic environments, defined having a pH of <3, are found in locations as diverse as the Arctic and the Tropics. While these be natural phenomena, human activity, most notoriously mining of metals and coals, are often responsible for the severe acidification of localized environments. The indigenous microflora in extremely acidic environments include species of prokaryotes and eukaryotes, many of which are obligately acidophilic. Acidophiles are widely distributed throughout the "tree of life", and include species of Bacteria, Archaea and Eukarya that are often only very distantly related to each other. Various mechanisms are used by acidophiles to adapt to the challenges they face, which include contending with elevated concentrations of transition metals and metalloids, and severely limited bioavailability of macronutrients such as phosphate.

Inorganic energy sources (reduced iron and sulfur) are highly abundant in many extremely acidic environments. Chemolithotrophic acidophiles are the basis of food webs in subterranean and also contribute to net primary production in deep submarine geothermal vents. However, where solar energy is available phototrophic acidophiles, predominantly species of acidophilic eukaryotic microalgae, proliferate and assume the dominant role of primary producers. Acidophilic microorganisms interact with each other in various ways, including via redox transformations of iron and sulfur, generating electron donors and acceptors for prokaryotic metabolisms, and via provision of organic compounds (supporting heterotrophic species) or inorganic carbon (supporting autotrophs). Acidophiles have long been used to extract metals from ores (biomining) and biotechnologies are emerging that harness their abilities to remediate polluted waters and recover metals.

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Acidic environments at geothermal sites: (a) Norris geyser basin, Yellowstone National Park, WY; (b) a hot spring on São Miguel, Azores; (c) prismatic sulfur crystals forming in a volcanic vent, Montserrat, WI. doi:10.1128/9781555818821.ch4.3.1.f1

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Simplified representation of ferrous iron oxidation by the iron-oxidizing acidithiobacilli protons entering the cytoplasm via the membrane-bound ATP synthetase complex (ATPase, shown in purple) are counterbalanced by electrons that derive from the oxidation of ferrous iron, mediated by cytochromes and rusticyanin (shown in green and yellow) located in the acidic periplasm. Cytochrome oxidase (shown in blue) catalyzes the reduction of molecular oxygen by incoming protons and electrons, generating water, the sole metabolic end product of this process.

doi:10.1128/9781555818821.ch4.3.1.f2

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Microbial eukaryotic biofilms found in the Río Tinto: (a) green filaments formed mainly by and ; (b) biofilms of sp.; (c) biofilms formed mostly by euglenoids and diatoms; biofilms of sp. The scale bars represent 5 cm. doi:10.1128/9781555818821.ch4.3.1.f3

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Light micrographs of different eukaryotic species isolated from the Río Tinto: (a) sp. (filamentous green algae); (b) sp. (Heliozoa); (c) sp. (red algae); (d) ; (e) amoebae (protoctista) (f) sp. (green algae). The scale bar represents 10 μm. doi:10.1128/9781555818821.ch4.3.1f4

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

(Top): schematic representation of the “overlay” technique for isolating and enumerating different physiological groups of acidophilic prokaryotes. A two-layered gel is prepared, with the underlay being inoculated either with a strain (e.g., SJH) of (to cultivate autotrophic acidophiles), or (to cultivate heterotrophic acidophiles, as this acidophile “detoxifies” the medium but does not use organic compounds such as glycerol and yeast extract which are used by most other acidophilic heterotrophs). (Bottom): (a) colonies of iron-oxidizing acidophiles, isolated from the Río Tinto on ferrous iron overlay plates; (b) colonies of heterotrophic acidophiles, isolated from an abandoned copper mine (Roeros) in Norway on yeast extract–containing overlay plates. doi:10.1128/9781555818821.ch4.3.1.f5

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6
FIGURE 6

(a) the Río Tinto in the Iberian Peninsula Belt, Spain; (b) a pit lake in the abandoned São Domingos copper mine, Portugal. doi:10.1128/9781555818821.ch4.3.1.f6

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 7
FIGURE 7

Microbial growth and geochemical transformations of iron, sulfur, and carbon in an acidic (pH 2.5) stream draining a small abandoned copper mine (Cantareras) in the Iberian Pyrite Belt. Algal surface streamers overlie a bacterial mat that is light brown in color (and populated by iron-reducing acidophiles) which in turn overlies a charcoal-colored mat, which contains sulfate-reducing and other heterotrophic acidophiles. Most fixation of inorganic carbon in the stream community is mediated by acidophilic algae, though autotrophic iron- and sulfur-oxidizing bacteria also contribute to net primary production. doi:10.1128/9781555818821.ch4.3.1.f7

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818821.ch4.3.1
1. Johnson DB,. 2009. Extremophiles: acid environments, p 107 126. In Schaechter M (ed), Encyclopaedia of Microbiology. Elsevier, Oxford.
2. Reysenbach A-L, Liu Y, Banta AB, Beveridge TJ, Kirshtein JD, Schouten S, Tivey MK, von Damm KL, Voytek MA. 2006. A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature 442 : 444 447.[PubMed][CrossRef]
3. Langdahl BR, Ingvorsen K. 1997. Temperature characteristics of bacterial iron solubilisation and 14C assimilation in naturally exposed sulfide ore material at Citronen Fjord, Greenland (83°N). FEMS Microbiol Ecol 23 : 275 283.[CrossRef]
4. Vera M, Schippers A, Sand W. 2013. Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation part A. Appl Microbiol Biotechnol 97 : 7529 7541.[PubMed][CrossRef]
5. Stumm W, Morgan JJ. 1981. Aquatic chemistry: an introduction emphasizing chemical equilibria in natural waters. Wiley, New York.
6. González-Toril E, Llobet-Brossa E, Casamayor EO, Amman R, Amils R. 2003. Microbial ecology of an extreme acidic environment, the Tinto River. Appl Environ Microbiol 69 : 4853 4865.[CrossRef]
7. Johnson DB. 2006. Biohydrometallurgy and the environment: intimate and important associations. Hydrometallurgy 83 : 153 166.[CrossRef]
8. Nordstrom DK, Alpers CN, Ptacek CJ, Blowes DW. 2000. Negative pH and extremely acidic mine-waters from Iron Mountain, California. Environ Sci Technol 34 : 254 258.[CrossRef]
9. Norris PR, Ingledew WJ,. 1992. Acidophilic bacteria: adaptations and applications, p 115 142. In Herbert RA, Sharp RJ (eds), Molecular biology and biotechnology of extremophiles. Blackie, Glasgow.
10. Matin A. 1999. pH homeostasis in acidophiles, p 152 166. In Bacterial responses to pH. Novartis Foundation Symposium 221. Wiley, Chichester, UK.
11. Golyshina OV, Golyshin PN, Timmis KN, Ferrer M. 2006. The “pH optimum anomaly” of intracellular enzymes of Ferroplasma acidiphilum. Environ Microbiol 8 : 416 425.[PubMed][CrossRef]
12. Schouten S, Hopmans EC, Damsté JSS. 2013. The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: a review. Org Geochem 54 : 19 61.[CrossRef]
13. Alexander B, Leach S, Ingledew WJ. 1987. The relationship between chemiosmotic parameters and sensitivity to anions and organic acids in the acidophile Thiobacillus ferrrooxidans. J Gen Microbiol 133 : 1171 1179.
14. Bonnefoy V, Holmes DS. 2012. Genomic insights into microbial oxidation and iron uptake strategies in extremely acidic environments. Environ Microbiol 14 : 1597 1611.[PubMed][CrossRef]
15. Messerli MA, Amaral-Zettler LA, Zettler E, Jung S, Smith PJS, Sogin ML. 2005. Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile. J Exp Biol 208 : 2569 2579.[PubMed][CrossRef]
16. Albertano P, Pinto G, Santisi S, Taddei R. 1982. Spermatosopsis acidophila Kalina, a little known alga from highly acidic environment. G Bot Ital 115 : 65 76.[CrossRef]
17. Gimmler H, Weis U, Weiss C, Kugel H, Treffny B. 1989. Dunaliella acidophila (Kalina) Masyuk-an alga with a positive membrane potential. New Phytol 113 : 175 184.[CrossRef]
18. Sekler I, Glaser HU, Pick U. 1991. Characterization of a plasma membrane H +-ATPase from the extremely acidophilic alga Dunaliella acidophila. J Membr Biol 121 : 51 57.[PubMed][CrossRef]
19. Sekler I, Pick U. 1993. Purification and properties of a plasma membrane H +-ATPase from the extremely acidophilic alga Dunaliella acidophila. Plant Physiol 101 : 1055 1061.[PubMed]
20. Sekler I, Weiss M, Pick U. 1994. Activation of the Dunaliella acidophila plasma membrane H +-ATPase by trypsin cleavage of a fragment that contains a phosphorylation site. Plant Physiol 105 : 1125 1132.[PubMed][CrossRef]
21. Gimmler H, Schieder M, Kowalski M, Zimmermann U, Pick U. 1991. Dunaliella acidophila: an algae with a positive zeta potential at its optimal pH for growth. Plant Cell Environ 14 : 261 269.[CrossRef]
22. Jannson M. 1981. Induction of high phosphatase activity by aluminium in acid lakes. Arch Hydrobiol 93 : 32 44.
23. Boavida MJ, Heath RT. 1986. Phosphatase activity of Chlamydomonas acidophila Negoro (Volvocales, Chlorophyceae). Phycologia 25 : 400 404.[CrossRef]
24. Spijkerman E. 2007. Phosphorus acquisition by Chlamydomonas acidophila under autotrophic and osmo-mixotrophic growth conditions. J Exp Bot 58 : 4195 4202.[PubMed][CrossRef]
25. Lessmann D, Fyson A, Nixdorf B. 2000. Phytoplankton of the extremely acidic mining lakes of Lusatia (Germany) with pH ≤3. Hydrobiologia 433 : 123 128.[CrossRef]
26. Nishikawa K, Tominaga N. 2001. Isolation, growth, ultrastructure, and metal tolerance of the green alga, Chlamydomonas acidophila (Chlorophyta). Biosci Biotechnol Biochem 65 : 2650 2656.[PubMed][CrossRef]
27. Nishikawa K, Yamakoshi Y, Uemura I, Tominaga N. 2003. Ultrastructural changes in Chlamydomonas acidophila (Chlorophyta) induced by heavy metals and polyphosphate metabolism. FEMS Microbiol Ecol 44 : 253 259.[PubMed][CrossRef]
28. Aguilera A, Amils R. 2005. Tolerance to cadmium in Chlamydomonas sp. (Chlorophyta) strains isolated from an extreme acidic environment, the Tinto River (SW, Spain). Aquat Toxicol 75 : 316 329.[PubMed][CrossRef]
29. Gerloff-Elias A, Barua D, Molich A, Spijkerman E. 2006. Temperature- and pH-dependent accumulation of heat-shock proteins in the acidophilic green alga Chlamydomonas acidophila. FEMS Microbiol Ecol 56 : 345 354.[PubMed][CrossRef]
30. Spijkerman E, Barua D, Gerloff-Elias A, Kern J, Gaedke U, Heckathorn SA. 2007. Stress responses and metal tolerance of Chlamydomonas acidophila in metal-enriched lake water and artificial medium. Extremophiles 11 : 551 562.[PubMed][CrossRef]
31. Cid C, Garcia-Descalzo L, Casado-Lafuente V, Amils R, Aguilera A. 2010. proteomic analysis of the response of an acidophilic strain of Chlamydomonas sp. (Chlorophyta) to natural metal-rich water. Proteomics 10 : 2026 2036.[PubMed][CrossRef]
32. Rodríguez-Zavala JS, García-García JD, Ortiz-Cruz MA, Moreno-Sánchez R. 2007. Molecular mechanisms of resistance to heavy metals in the protist Euglena gracilis. J Environ Sci Health A Tox Hazard Subst Environ Eng 42 : 1365 1378.[CrossRef]
33. Perales-Vela HG, Peña-Castro JM, Cañizares-Villanueva RO. 2006. Heavy metal detoxification in eukaryotic microalgae. Chemosphere 64 : 1 10.[PubMed][CrossRef]
34. Qin J, Lehr CR, Yuan C, Le XC, McDermott TR, Rosen BP. 2009. Biotransformation of arsenic by a Yellowstone thermoacidophilic eukaryotic alga. Proc Natl Acad Sci USA 106 : 5213 5217.[PubMed][CrossRef]
35. Halter D, Casiot C, Heipieper HJ, Plewniak F, Marchal M, Simon S, Arsène-Ploetze F, Bertin PN. 2012. Surface properties and intracellular speciation revealed an original adaptive mechanism to arsenic in the acid mine drainage bio-indicator Euglena mutabilis. Appl Microbiol Biotechnol 93 : 1735 1744.[PubMed][CrossRef]
36. Casiot C, Bruneel O, Personné JC, Leblanc M, Elbaz-Poulichet F. 2004. Arsenic oxidation and bioaccumulation by the acidophilic protozoan, Euglena mutabilis, in acid mine drainage (Carnoulès, France). Sci Total Environ 320 : 259 267.[PubMed][CrossRef]
37. Brock T. 1978. Thermophilic Microorganisms and Life at High Temperatures. Springer, New York.
38. Roberts DML,. 1999. Eukaryotic cells under extreme conditions, p 165 173. In Seckbach J (ed), Enigmatic Microorganisms and Life in Extreme Environments. Kluwer Academic, London.
39. Caron DA, Countway PD, Brown MV. 2004. The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools. J Eukaryot Microbiol 51 : 38 48.[PubMed][CrossRef]
40. Deneke R. 2000. Review of rotifers and crustaceans in highly acidic environments of pH ≤3. Hydrobiologia 433 : 176 172.[CrossRef]
41. Bell EM, Weithoff G. 2003. Benthic recruitment of zooplankton in an acidic lake. J Exp Mar Biol Ecol 285–286 : 205 219.[CrossRef]
42. Aguilera A, Souza-Egipsy V, Gomez F, Amils R. 2007. Development and structure of eukaryotic biofilms in an extreme acidic environment, Río Tinto (SW, Spain). Microb Ecol 53 : 294 305.[PubMed][CrossRef]
43. Aguilera A, Souza-Egipsy V, San Martín-Úriz P, Amils R. 2008. Extracellular matrix assembly in extreme acidic eukaryotic biofilms and their possible implications in heavy metal adsorption. Aquat Toxicol 88 : 257 266.[PubMed][CrossRef]
44. Nixdorf B, Mischke U, Lessmann D. 1998. Chrysophytes and chlamydomonads: pioneer colonists in extremely acidic mining lakes (pH ≤3) in Lusatia (Germany). Hydrobiologia 369/370 : 315 327.[CrossRef]
45. Beulker C, Lessmann D, Nixdorf B. 2003. Aspects of phytoplankton succession and spatial distribution in an acidic mining lake (Plessa 117, Germany). Acta Oecologica 24 : 25 31.[CrossRef]
46. Nixdorf B, Krumbeck H, Jander J, Beulker C. 2003. Comparison of bacterial and phytoplankton productivity in extremely acidic mining lakes and eutrophic hard water lakes. Acta Oecologica 24 : 281 288.[CrossRef]
47. Moser M, Weisse T. 2011. The most acidified Austrian lake in comparison to a neutralized mining lake. Limnolog 41 : 303 316.[CrossRef]
48. Amaral-Zettler L, Gomez F, Zettler E, Keenan B, Amils R, Sogin M. 2002. Eukaryotic diversity in Spain's river of fire. Nature 417 : 137.[PubMed][CrossRef]
49. Aguilera A, Zettler E, Gomez F, Amaral-Zettler L, Rodrıguez N, Amilsa R. 2007. Distribution and seasonal variability in the benthic eukaryotic community of Río Tinto (SW, Spain), an acidic, high metal extreme environment. Syst Appl Microbiol 30 : 531 546.[PubMed][CrossRef]
50. De Nicola D. 2000. A review of diatoms found in highly acidic environments. Hydrobiologia 433 : 111 122.[CrossRef]
51. Laliberte G, Dela Noue J. 1993. Auto-, hetero- and mixotrophic growth of Chlamydomonas humicola (Chlorophyceae) on acetate. J Phycol 29 : 612 620.[CrossRef]
52. Seckbach J,. 1999. The cyanidiophyceae: hot spring and acidophilic algae, p 427 435. In Seckbach J (ed), Enigmatic Microorganisms and Life in Extreme Environments. Kluwer Academic, London.
53. Pinto G, Albertano P, Ciniglia C. 2003. Comparative approaches to the taxonomy of the genus Galdieria merola (Cyanidiales, Rhodophyta). Cryptogam Algol 24 : 13 32.
54. Aguilera A, Manrubia SC, Gómez F, Rodríguez N, Amils R. 1996. Eukaryotic community distribution and its relationship to water physicochemical parameters in an extreme acidic environment, Rio Tinto (SW, Spain). Appl Environ Microbiol 72 : 5325 5330.[CrossRef]
55. Albertano P, Ciniglia C, Pinto G, Pollio A. 2000. The taxonomic position of Cyanidium, Cyanidioschyzon and Galdieria: an update. Hydrobiologia 433 : 137 143.[CrossRef]
56. Müller KM, Oliveira MC, Sheath RG, Bhattacharya D. 2001. Ribosomal DNA phylogeny of the Bangiophycidae (Rhodophyta) and the origin of secondary plastids. Am J Bot 88 : 1390 400.[CrossRef]
57. Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D. 2004. A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol 21 : 809 818.[PubMed][CrossRef]
58. Toplin JA, Norris TB, Lehr CR, McDermott TR, Castenholz RW. 2008. Biogeographic and phylogenetic diversity of thermoacidophilic cyanidiales in Yellowstone National Park, Japan, and New Zealand. Appl Environ Microbiol 74 : 2822 2833.[PubMed][CrossRef]
59. Schleper C, Puehler G, Kuhlmorgen B, Zillig W. 1995. Life at extremely low pH. Nature 375 : 741 742.[PubMed][CrossRef]
60. Gross W, Schnarrenberger C. 1995. Heterotrophic growth of two strains of the acido-thermophilic red alga Galdieria sulphuraria. Plant Cell Physiol 36 : 633 638.
61. Reeb V, Bhattacharya D,. 2010. The thermo-acidophilic Cyanidiophyceae (Cyanidiales), p 409 426. In Seckbach J, Chapman DJ (eds), Red Algae in the Genomic Age. Springer, Netherlands.
62. Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP. 2013. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science 339 : 1207 1210.[CrossRef]
63. Wolfe GR, Cunningham FX, Durnford D, Green BR, Gantt E. 1994. Evidence for a common origin of chloroplasts with light-harvesting complexes of different pigmentation. Nature 367 : 566 568.[CrossRef]
64. Scheller HV, Jensen PE, Haldrup A, Lunde C, Knoetzel J. 2001. Role of subunits in eukaryotic photosystem I. Biochim Biophys Acta 1507 : 41 60.[PubMed][CrossRef]
65. Vanselow C, Weber AP, Krause K, Fromme P. 2009. Genetic analysis of the photosystem I subunits from the red alga, Galdieria sulphuraria. Biochim Biophys Acta 1787 : 46 59.[PubMed][CrossRef]
66. Grobbelaar J, Neddal L, Tichy V, Setlik I. 1995. Variation in some photosynthetic characteristics of microalgae cultured in outdoor thin-layered sloping reactors. J Appl Phycol 7 : 175 184.[CrossRef]
67. Oesterhelt C, Schmalzlin E, Schmitt JM, Lokstein H. 2007. Regulation of photosynthesis in the unicellular acidophilic red alga Galdieria sulphuraria. Plant J 51 : 500 511.[PubMed][CrossRef]
68. Thangaraj B, Jolley CC, Sarrou I, Bultema JB, Greyslak J, Whitelegge JP, Lin S, Kouřil R, Subramanyam R, Boekema EJ, Fromme P. 2011. Efficient light harvesting in a dark, hot, acidic environment: the structure and function of PSI-LHCI from Galdieria sulphuraria. Biophys J 100 : 135 143.[PubMed][CrossRef]
69. Sittenfeld A, Mora M, Ortega JM, Albertazzi F, Cordero A, Roncel M. 2002. Characterization of a photo- synthetic Euglena strain isolated from an acidic hot mud pool of a volcanic area of Costa Rica. FEMS Microbiol Ecol 42 : 151 161.[PubMed]
70. Johnson DB, Hallberg KB. 2003. The microbiology of acidic mine waters. Res Microbiol 154 : 466 473.[PubMed][CrossRef]
71. Ňancucheo I, Johnson DB. 2012. Acidophilic algae isolated from mine-impacted environments and their roles in sustaining heterotrophic acidophiles. Front Microbiol 3 : 325.[CrossRef]
72. Halter D, Goulhen-Chollet F, Gallien S, Casiot C, Hamelin J, Gilard F, Heintz D, Schaeffer C, Carapito C, Van Dorsselaer A, Tcherkez G, Arsene-Ploetze F, Bertin PN. 2012. In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis. ISME J 6 : 1391 1402.[PubMed][CrossRef]
73. Brake SS, Hasiotis ST, Dannelly HK, Connors KA. 2002. Eukaryotic stromatolite builders in acid mine drainage: implications for Precambrian iron formations and oxygenation of the atmosphere? Geology 30 : 599 602.[CrossRef]
74. Packroff G. 2000. Protozooplankton in acídic mining lakes with special respect to ciliates. Hydrobiologia 433 : 157 166.[CrossRef]
75. Moser M, Weisse T. 2011. Combined stress effect of pH and temperature narrows the niche width of flagellates in acid mining lakes. J Plank Res 33 : 1023 1032.[CrossRef]
76. Wollmann K, Deneke R, Nixdor B, Packroff G. 2000. Dynamics of planktonic food webs in three mining lakes across a pH gradient. Hydrobiologia 433 : 3 14.[CrossRef]
77. Weisse T, Moser M, Scheffel U, Stadler P, Berendonk T, Weithoff G, Berger H. 2013. Systematics and species-specific response to pH of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) from acid mining lakes. Eur J Protistol 49 : 255 271.[PubMed][CrossRef]
78. Johnson DB, Rang L. 1993. Effects of acidophilic protozoa on populations of metal-mobilizing bacteria during the leaching of pyritic coal. J Gen Microbiol 139 : 1417 1423.[CrossRef]
79. Gross S, Robbins EI. 2000. Acidophilic and acid-tolerant fungi and yeasts. Hydrobiologia 433 : 91 109.[CrossRef]
80. Armstrong GM. 1921. Studies in the physiology of the fungi-sulfur nutrition, the use of thiosulphate as influenced by hydrogen ion concentration. Ann Missouri Bot Garden 8 : 237 248.[CrossRef]
81. Gadanho M, Sampaio JP. 2006. Microeukaryotic diversity in the extreme environments of the Iberian Pyrite Belt: a comparison between universal and fungi-specific primer sets, temperature gradient gel electrophoresis and cloning. FEMS Microbiol Ecol 57 : 139 148.[PubMed][CrossRef]
82. Duran C, Marin I, Amils R,. 1999. Specific metal sequestering acidophilic fungi, p 521 530. In Amils R, Ballester A (eds), Biohydrometallurgy and the Environment, Towards the Mining of the 21st cCentury, Proc Int Biohydrometal Symp. Elsevier, Amsterdam.
83. Fournier D, Lemieux R, Couillard D. 1998. Essential interactions between Thiobacillus ferrooxidans and heterotrophic microorganisms during a wastewater sludge bioleaching process. Environ Pollut 101 : 303 309.[PubMed][CrossRef]
84. Oggerin M, Tornos F, Rodríguez N, del Moral C, Sánchez-Román M, Amils R. 2013. Specific jarosite biomineralization by Purpureocillium lilacinum, an acidophilic fungi isolated from Río Tinto. Environ Microbiol 15 : 2228 2237. 10.1111/1462-2920.12094.[PubMed][CrossRef] http://dx.doi.org/10.1111/1462-2920.12094
85. Russo G, Libkind D, Sampaio JP, VanBrock MR. 2008. Yeast diversity in the acidic Río Agrio-Lake Caviahue volcanic environment (Patagonia, Argentina). FEMS Microbiol Ecol 65 : 415 424.[PubMed][CrossRef]
86. Gadanho M, Libkind D, Sampaio JP. 2006. Yeast diversity in the extreme acidic environments of the Iberian Pyrite Belt. Microb Ecol 2 : 552 563.[CrossRef]
87. Gadanho M, Sampaio JP. 2009. Cryptococcus ibericus sp. nov., Cryptococcus aciditolerans sp. nov. and Cryptococcus metallitolerans sp. nov., a new ecoclade of anamorphic basidiomycetous yeast species from an extreme environment associated with acid rock drainage in São Domingos pyrite mine, Portugal. Int J Syst Evol Micr 59 : 2375 2379.[CrossRef]
88. Johnson DB, Hallberg KB. 2009. Carbon, iron and sulfur metabolism in acidophilic micro-organisms. Adv Microb Physio 54 : 202 256.
89. Rohwerder T, Sand W. 2007. Oxidation of inorganic sulfur compounds in acidophilic prokaryotes. Eng Life Sci 7 : 301 309.[CrossRef]
90. Hedrich S, Johnson DB. 2013. Aerobic and anaerobic oxidation of hydrogen by acidophilic bacteria. FEMS Microbiol Lett 349 : 40 45.[PubMed]
91. Kelly DP,. 1978. Bioenergetics of chemolithotrophic bacteria, p 363 386. In Bull AT, Meadow PM (eds), Companion to Microbiology; Selected Topics for Further Discussion. Longman, London.
92. Bond PL, Druschel GK, Banfield JF. 2000. Comparison of acid mine drainage communities in physically and geochemically distinct ecosystems. Appl Environ Microbiol 66 : 4962 4971.[PubMed][CrossRef]
93. Kimura S, Bryan CG, Hallberg KB, Johnson DB. 2011. Biodiversity and geochemistry of an extremely acidic, low temperature subterranean environment sustained by chemolithotrophy. Environ Microbiol 13 : 2092 2104.[PubMed][CrossRef]
94. Kay CM, Rowe OF, Rocchetti L, Coupland K, Hallberg KB, Johnson DB. 2013. Evolution of microbial “streamer” growths in an acidic, metal-contaminated stream draining an abandoned underground copper mine. Life 3 : 189 210.[PubMed][CrossRef]
95. Yarzabal A, Appia-Ayme C, Ratouchniak J, Bonnefoy V. 2004. Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology 150 : 2113 2123.[PubMed][CrossRef]
96. Johnson DB, Kanao T, Hedrich S. 2012. Redox transformations of iron at extremely low pH: fundamental and applied aspects. Front Microbiol 3 : 96.[PubMed][CrossRef]
97. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. 2005. Genome-directed isolation of the key nitrogen-fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol 71 : 6319 6324.[PubMed][CrossRef]
98. Kelly DP. 1999. Thermodynamic aspects of energy conservation by chemolithotrophic sulfur bacteria in relation to the sulfur oxidation pathways. Arch Microbiol 171 : 219 229.[CrossRef]
99. Dopson M, Johnson DB. 2012. Biodiversity, metabolism and applications of acidophilic sulfur- metabolizing micro-organisms. Environ Microbiol 14 : 2620 2631.[PubMed][CrossRef]
100. Quatrini R, Appia-Ayme C, Denis Y, Jedlicki E, Holmes D, Bonnefoy V. 2009. Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics 10 : 394.[PubMed][CrossRef]
101. Kletzin A. 1992. Molecular characterization of the sor gene, which encodes the sulfur oxygenase/reductase of the thermophilic archaeum Desulfurolobus ambivalens. J Bacteriol 174 : 5854 5859.[PubMed]
102. Osorio H, Mangold S, Denis Y, Ňancucheo I, Esparza M, Johnson DB, Bonnefoy V, Dopson M, Holmes DS. 2013. Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans. Appl Environ Microbiol 79 : 2172 2181.[PubMed][CrossRef]
103. Brock TD, Brock KM, Belly RT, Weiss RL. 1972. Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Microbiol 84 : 54 68.[CrossRef]
104. Stetter KO, Segerer A, Zillig W, Huber G, Fiala G, Huber R, Konig H. 1986. Extremely thermophilic sulfur-metabolizing archaebacteria. Syst Appl Microbiol 7 : 393 397.[CrossRef]
105. Drobner E, Huber H, Stetter KO. 1990. Thiobacillus ferrooxidans, a facultative hydrogen oxidizer. Appl Environ Microbiol 56 : 2922 2923.[PubMed]
106. Shima S, Suzuki KI. 1993. Hydrogenobacter acidophilus sp. nov., a thermoacidophilic, aerobic, hydrogen-oxidizing bacterium requiring elemental sulfur for growth. Int J Syst Bacteriol 43 : 703 708.[CrossRef]
107. Ňancucheo I, Johnson DB. 2010. Production of glycolic acid by chemolithotrophic iron- and sulfur-oxidizing bacteria and its role in delineating and sustaining acidophilic sulfide mineral-oxidizing consortia. Appl Environ Microbiol 76 : 461 467.[CrossRef]
108. Kermer R, Hedrich S, Taubert M, Baumann S, Schlömann M, Johnson DB, von Bergen M, Seifert J. 2012. Elucidation of carbon transfer in a mixed culture of Acidiphilium cryptum and Acidithiobacillus ferrooxidans using protein-based stable isotope probing. J Integr OMICS 2 : 37 45.
109. Prokofeva MI, Miroshnichenko ML, Kostrikina NA, Chernyh NA, Kuznetsov BB, Tourova TP, Bonch-Osmolovskaya EA. 2000. Acidilobus aceticus gen. nov., sp. nov., a novel anaerobic thermoacidophilic archaeon from continental hot vents in Kamchatka. Int J Syst Evol Micr 50 : 2001 2008.[CrossRef]
110. Johnson DB, Bacelar-Nicolau P, Okibe N, Thomas A, Hallberg KB. 2009. Characteristics of Ferrimicrobium acidiphilum gen. nov., sp. nov., and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic iron-oxidizing, extremely acidophilic Actinobacteria. Int J Syst Evol Micr 59 : 1082 1089.[CrossRef]
111. Jones RM, Hedrich S, Johnson DB. 2013. Acidocella aromatica sp. nov.: an acidophilic heterotrophic alphaproteobacterium with unusual phenotypic traits. Extemophiles 17 : 841 850.[CrossRef]
112. Shuttleworth KL, Unz RF, Wichlacz PL. 1985. Glucose catabolism in strains of acidophilic, heterotrophic bacteria. Appl Environ Microbiol 50 : 573 579.[PubMed]
113. Johnson DB, McGinness S. 1991. Ferric iron reduction by acidophilic heterotrophic bacteria. Appl Environ Microbiol 57 : 207 211.[PubMed]
114. Coupland K, Johnson DB. 2008. Evidence that the potential for dissimilatory ferric iron reduction is widespread among acidophilic heterotrophic bacteria. FEMS Microbiol Lett 279 : 30 35.[PubMed][CrossRef]
115. Sanz JL, Rodriguez N, Diaz EE, Amils R. 2011. Methanogenesis in the sediments of Rio Tinto, an extreme acidic river. Environ Microbiol 13 : 2336 2341.[PubMed][CrossRef]
116. Johnson DB. 2012. Geomicrobiology of extremely acidic subsurface environments. FEMS Microbiol Ecol 81 : 2 12.[PubMed][CrossRef]
117. Shively JM, van Keulen G, Meijer WG. 1998. Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Ann Rev Microbiol 52 : 191 230.[CrossRef]
118. Levican G, Ugalde JA, Ehrenfeld N, Maass A, Pareda P. 2008. Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics 9 : 581.[PubMed][CrossRef]
119. Dopson M, Baker-Austin C, Hind A, Bowman JP, Bond PL. 2004. Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp. nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments. Appl Environ Microbiol 70 : 2079 2088.[PubMed][CrossRef]
120. Johnson DB, Hallberg KB, Hedrich S. 2014. Uncovering a microbial enigma: isolation and characterization of the streamer-generating, iron-oxidizing acidophilic bacterium, “ Ferrovum myxofaciens. Appl Environ Microbiol 80 : 672 680.[PubMed][CrossRef]
121. Waksman SA, Joffe JS. 1922. Microorganisms concerned in the oxidation of sulfur in the soil. II. Thiobacillus thioooxidans, a new sulfur-oxidizing organism. J Bacteriol 7 : 239 256.[PubMed]
122. Johnson DB, Hallberg KB,. 2007. Techniques for detecting and identifying acidophilic mineral-oxidising microorganisms, p 237 262. In Rawlings DE, Johnson DB (eds), Biomining. Springer, Heidelberg, Germany.
123. Haraishi A, Shimada K. 2001. Aerobic anoxygenic photosynthetic bacteria with zinc-bacteriochlorophyll. J Gen Appl Microbiol 47 : 161 180.[CrossRef]
124. Urakami T, Tamaoko J, Suzuki K, Komagata K. 1989. Acidomonas gen. nov., incorporating Acetobacter methanolicus as Acidomonas methanolica comb. nov. Int J Syst Bacteriol 39 : 50 55.[CrossRef]
125. Chase JM, Holland SM, Greenberg DE, Marshall-Batty K, Zelazny AM, Church JA. 2012. Acidomonas methanolica-associated necrotizing lymphadenitis in a patient with chronic granulomatous disease. J Clin Immun 32 : 1193 1196.[PubMed][CrossRef]
126. Johnson DB, Stallwood B, Kimura S, Hallberg KB. 2006. Isolation and characterization of Acidicaldus organovorus, gen. nov., sp. nov.; a novel sulfur-oxidizing, ferric iron-reducing thermo-acidophilic heterotrophic Proteobacterium. Arch Microbiol 185 : 212 221.[PubMed][CrossRef]
127. Lane DJ, Harrison AP Jr, Stahl D, Pace B, Giovannoni SJ, Olsen GJ, Pace NR. 1992. Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J Bacteriol 174 : 269 278.[PubMed]
128. Kelly DP, Wood AP. 2000. Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov., and Thermothiobacillus gen. nov. Int J System Evol Micr 50 : 511 516.[CrossRef]
129. Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW. 2010. Phylogeny of gammaproteobacteria. J Bacteriol 192 : 2305 2314.[PubMed][CrossRef]
130. Williams KP, Kelly DP. 2013. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. Int J Syst Evol Micr 63 : 2901 2906.[CrossRef]
131. Colmer AR, Temple KL, Hinkle ME. 1950. An iron-oxidizing bacterium from the acid drainage of some bituminous coal mines. J Bacteriol 59 : 317 328.[PubMed]
132. Amouric A, Brochier-Armanet C, Johnson DB, Bonnefoy V, Hallberg KB. 2011. Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways. Microbiology 157 : 111 122.[PubMed][CrossRef]
133. Hallberg KB, González-Toril E, Johnson DB. 2010. Acidithiobacillus ferrivorans sp. nov.; facultatively anaerobic, psychrotolerant, iron- and sulfur-oxidizing acidophiles isolated from metal mine-impacted environments. Extremophiles 14 : 9 19.[PubMed][CrossRef]
134. Hedrich S, Johnson DB. 2013. Acidithiobacillus ferridurans, sp. nov.; an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium. Int J Syst Evol Microbiol 63 : 4018 4025.[PubMed][CrossRef]
135. Hallberg KB, Lindstrom EB. 1994. Characterization of Thiobacillus caldus sp. nov., a moderately thermophilic acidophile. Microbiology 140 : 3451 3456.[PubMed][CrossRef]
136. Bryant RD, McGroarty KM, Costerton JW, Laishley EJ. 1983. Isolation and characterization of a new Thiobacillus species ( T. albertis). Can J Microbiol 29 : 1159 1170.[CrossRef]
137. Harrison AP Jr. 1982. Genomic and physiological diversity amongst strains of Thiobacillus ferrooxidans, and genomic comparison with Thiobacillus thiooxidans. Arch Microbiol 131 : 68 76.[CrossRef]
138. Hallberg KB, Hedrich S, Johnson DB. 2011. Acidiferribacter thiooxydans, gen. nov. sp. nov.; an acidophilic, thermo-tolerant, facultatively anaerobic iron- and sulfur-oxidizer of the family Ectothiorhodospiraceae. Extremophiles 15 : 271 279.[PubMed][CrossRef]
139. Hou S, Makarova KS,, Saw JH,, Senin P,, Ly BV,, Zhou Z,, Ren Y,, Wang J,, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M. 2008. Complete genome sequence of the extremely acidophilic isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3 : 26.[PubMed][CrossRef]
140. Markosyan GE. 1972. A new iron-oxidizing bacterium, Leptospirillum ferrooxidans gen. et. sp. nov. Biol J Armenia 25 : 26 29 (in Russian).
141. Coram NJ, Rawlings DE. 2002. Molecular relationship between two groups of the genus Leptospirillum and the finding that Leptospirillum ferriphilum sp. nov. dominates South African commercial biooxidation tanks that operate at 40°C. Appl Environ Microbiol 68 : 838 845.[PubMed][CrossRef]
142. Goltsman DSA, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CJ, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF. 2009. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 75 : 4599 4615.[PubMed][CrossRef]
143. Goltsman DSA, Dasari M, Thomas BC, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF. 2013. New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics and transcriptomics of the new species “ Leptospirillum Group IV UBA BS”. Appl Environ Microbiol 79 : 5384 5393.[PubMed][CrossRef]
144. Okibe N, Gericke M, Hallberg KB, Johnson DB. 2003. Enumeration and characterization of acidophilic microorganisms isolated from a pilot plant stirred tank bioleaching operation. Appl Environ Microbiol 69 : 1936 1943.[PubMed][CrossRef]
145. Kinnunen H-M, Puhakka JA. 2004. High-rate ferric sulfate generation by a Leptospirillum ferriphilum-dominated biofilm and the role of jarosite in biomass retainment in a fluidized-bed reactor. Biotechnol Bioeng 85 : 697 705.[PubMed][CrossRef]
146. Clark DA, Norris PR. 1996. Acidimicrobium ferrooxidans gen. nov., sp. nov.: mixed culture ferrous iron oxidation with Sulfobacillus species. Microbiology 142 : 785 90.[CrossRef]
147. Norris PR, Davis-Belmar CS, Brown CF, Calvo-Bado LA. 2011. Autotrophic, sulfur-oxidizing actinobacteria in acidic environments. Extremophiles 15 : 155 163.[PubMed][CrossRef]
148. Jones RM, Johnson DB. 2015. Acidithrix ferrooxidans gen. nov., sp. nov.; a filamentous and obligately heterotrophic, acidophilic member of the Actinobacteria that catalyzes the dissimilatory oxido-reduction of iron. Res Microbiol 166 : 111 120.[PubMed][CrossRef]
149. Itoh T, Yamonoi K, Kudo T, Ohkuma M, Takashina T. 2011. Aciditerrimonas ferrireducens gen. nov., sp. nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field. Int J Syst Evol Micr 61 : 1281 1285.[CrossRef]
150. Rawlings DE, Johnson DB. 2007. The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology 153 : 315 324.[PubMed][CrossRef]
151. Yahya A, Hallberg KB, Johnson DB. 2008. Iron and carbon metabolism by a mineral-oxidizing Alicyclobacillus-like bacterium. Arch Microbiol 189 : 305 312.[PubMed][CrossRef]
152. Wakeman K, Auvinen H, Johnson DB. 2008. Microbiological and geochemical dynamics in simulated heap leaching of a polymetallic sulfide ore. Biotechnol Bioeng 101 : 739 750.[PubMed][CrossRef]
153. Golyshina OV, Pivovarova TA, Karavaiko GI, Kondrat'eva TF, Moore ERB, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM, Golyshin PN. 2000. Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea. Int J Syst Evol Micr 50 : 997 1006.[CrossRef]
154. Darland G, Brock TD, Samsonoff W, Conti SF. 1970. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 170 : 1416 1418.[PubMed][CrossRef]
155. Schleper C, Puehle G, Holz I, Gambacorta A, Janekovic D, Santarius U, Klenk H-P, Zillig W. 1995. Picrophilus gen. nov., fam. nov.: a novel aerobic, heterotrophic, thermoacidophilic genus and family comprising archaea capable of growth around pH 0. J Bacteriol 177 : 7050 7059.[PubMed]
156. Edwards KJ, Bond PL, Gihring TM, Banfield JF. 2000. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287 : 1796 1799.[PubMed][CrossRef]
157. Zhou H, Zhang R, Hu P, Zeng W, Xie Y, Wu C, Qiu G. 2008. Isolation and characterization of Ferroplasma thermophilum sp. nov., a novel extremely acidophilic, moderately thermophilic archaeon and its role in bioleaching of chalcopyrite. J Appl Microbiol 105 : 591 601.[PubMed][CrossRef]
158. Golyshina OV, Yakimov MM, Heinrich Lünsdorf H, Ferrer M, Nimtz M, Timmis KN, Wray V, Tindall BJ, Golyshin PN. 2009. Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov. Int J Syst Evol Micr 59 : 2815 2823.[CrossRef]
159. Itoh T, Yoshikawa N, Takashina T. 2007. Thermogymnomonas acidicola gen. nov., sp. nov., a novel thermoacidophilic, cell wall-less archaeon in the order Thermoplasmatales, isolated from a solfataric soil in Hakone, Japan. Int J Syst Evol Micr 57 : 2557 61.[CrossRef]
160. Huber G, Stetter KO. 1991. Sulfolobus metallicus, sp. nov., a novel strictly chemolithoautotrophic thermophilic archaeal species of metal-mobilizers. System Appl Microbiol 14 : 372 378.[CrossRef]
161. Norris PR, Burton NP, Clark DA. 2013. Mineral sulfide concentrate leaching in high temperature bioreactors. Miner Eng 48 : 10 19.[CrossRef]
162. Plumb JJ, Haddad CM, Gibson JAE, Franzmann PD. 2007. Acidianus sulfidivorans sp. nov., an extremely acidophilic, thermophilic archaeon isolated from a solfatara on Lihir, Papua New Guinea, and emendation of the genus description. Int J Syst Evol Micr 57 : 1418 1423.[CrossRef]
163. Brierley CL, Brierley JA. 2013. Progress in bioleaching: part B: applications of microbial processes by the minerals industries. Appl Microbiol Biotechnol 97 : 7543 7552.[PubMed][CrossRef]
164. Johnson DB. 1998. Biodiversity and ecology of acidophilic microorganisms. FEMS Microbiol Ecol 27 : 307 317.[CrossRef]
165. Johnson DB,. 2007. Physiology and ecology of acidophilic microorganisms, p 257 270. In Gerday C, Glansdorff N (eds), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC.
166. García-Moyano A, González-Toril E, Aguilera Á, Amils R. 2012. Comparative microbial ecology study of the sediments and the water column of the Río Tinto, an extreme acidic environment. FEMS Microbiol Ecol 81 : 303 14.[CrossRef]
167. Sánchez-Andrea I, Rodríguez N, Amils R, Sanz JL. 2011. Microbial diversity in anaerobic sediments at Rio Tinto, a naturally acidic environment with a high heavy metal content. Appl Environ Microbiol 77 : 6085 6093.[CrossRef]
168. Geller W, Schultze M, Kleinmann R, Wolkersdorfer C (eds) 2012. Acidic Pit Lakes: The Legacy of Coal and Metal Surface Mines. Environmental Science and Engineering, Environmental Science, Springer, Berlin.
169. Santofimia E, González-Toril E, López-Pamo E, Gomariz M, Amils R, Aguilera A. 2013. Microbial diversity and its relationship to physicochemical characteristics of the water in two extreme acidic pit lakes from the Iberian Pyrite Belt (SW Spain). PLoS One 8 : e66746.[PubMed][CrossRef]
170. Falagan C, Sanchez-Espana J, Johnson DB. 2013. New insights into the biogeochemistry of extremely acidic environments revealed by a combined cultivation-based and culture-independent study of two stratified pit lakes. FEMS Microbiol Ecol 87 : 231 243. 10.1111/1574-6941.12218.[PubMed][CrossRef] http://dx.doi.org/10.1111/1574-6941.12218
171. Rowe OF, Sánchez-España J, Hallberg KB, Johnson DB. 2007. Microbial communities and geochemical dynamics in an extremely acidic, metal-rich stream at an abandoned sulfide mine (Huelva, Spain) underpinned by two functional primary production systems. Environ Microbiol 9 : 1761 1771.[PubMed][CrossRef]
172. Justice BN, Pan C, Mueller R, Spaulding SE, Shah V, Sun CL, Yelton AP, Miller CS, Thomas BC, Shah M, VerBerkmoes N, Hettich R, Banfield JF. 2012. Heterotrophic archaea contribute to carbon cycling in low-pH suboxic biofilm communities. Appl Environ Microbiol 78 : 8321 8330.[PubMed][CrossRef]
173. Ziegler S, Ackermann S, Majzian J, Gescher J. 2009. Matrix composition and community structure analysis of a novel bacterial leaching community. Environ Microbiol 11 : 2329 2338.[PubMed][CrossRef]
174. Macalady JL, Dattagupta S, Schaperdoth I, Jones DS, Druschel GK, Eastman D. 2008. Niche differentiation among sulfur-oxidizing bacterial populations. ISME J 2 : 590 601.[PubMed][CrossRef]
175. Bond PL, Smriga SP, Banfield JF. 2000. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl Environ Microbiol 66 : 3842 3849.[PubMed][CrossRef]
176. Johnson DB. 2013. Development and application of biotechnologies in the metal mining industry. Environ Sci Pollut Res 11 : 7768 7776.[CrossRef]
177. Rawlings DE. 2002. Heavy metal mining using microbes. Ann Rev Microbiol 56 : 65 91.[CrossRef]
178. Rawlings DE, Johnson DB (eds) 2007. Biomining. Springer, Heidelberg.
179. Brierley JA. 2008. A perspective on developments in biohydrometallurgy. Hydrometallurgy 94 : 2 7.[CrossRef]
180. Morin D, d'Hugues P,. 2007. Bioleaching of a cobalt-containing pyrite in stirred reactors: a case study from laboratory scale to industrial applications, p 35 56. In Rawlings DE, Johnson DB (eds), Biomining. Springer, Heidelberg.
181. Johnson DB, Grail BM, Hallberg KB. 2013. A new direction for biomining: extraction of metals by reductive dissolution of oxidized ores. Minerals 3 : 49 58.[CrossRef]
182. Heinzel E, Janneck E, Glombitza F, Schlömann M, Seifert J. 2009. Population dynamics of iron-oxidizing communities in pilot plants for the treatment of acid mine waters. Environ Sci Technol 43 : 6138 6144.[PubMed][CrossRef]
183. Hedrich S, Johnson DB. 2012. A modular continuous flow reactor system for the selective bio-oxidation and precipitation of iron in mine-impacted waters. Biores Technol 106 : 44 49.[CrossRef]
184. Liljeqvist M, Sundkvist J-E, Saleh A, Dopson M. 2011. Low temperature removal of inorganic sulfur compounds from mining process waters. Biotechnol Bioeng 108 : 1251 1259.[PubMed][CrossRef]
185. Ňancucheo I, Johnson DB. 2012. Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria. Microbial Biotechnol 5 : 34 44.[CrossRef]

Tables

Generic image for table
TABLE 1

Comparison of free energy changes associated with the oxidation of electron donors used by acidophilic prokaryotes ( )

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Generic image for table
TABLE 2

Contrasting physiological properties of spp.

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1
Generic image for table
TABLE 3

Physiological properties of acidophilic actinobacteria

Citation: Barrie Johnson D, Aguilera A. 2016. The Microbiology of Extremely Acidic Environments, p 4.3.1-1-4.3.1-24. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.3.1

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error