Acidophiles in acid mine drainage
Encyclopedia
Acidophiles are not just present in exotic environments such as Yellowstone National Park
or deep-sea hydrothermal vents. Genera such as Acidithiobacillus
and Leptospirillum bacteria, and Thermoplasmales archaea
, are present in syntrophic
relationships in the more mundane environments of concrete sewer pipes and implicated in the heavy-metal-containing, sulfurous waters of rivers such as the Rheidol.
Such microorganisms are responsible for the phenomenon of acid mine drainage
(AMD) and thus are important both economically and from a conservation perspective. Control of these acidophiles and their harnessing for industrial biotechnology shows their effect need not be entirely negative.
The use of acidophilic
organisms in mining
is a nascent technique for extracting trace metals through bioleaching
, and offers solutions for the phenomenon of acid mine drainage
(AMD) in mining spoils.
(O2) and water
(H2O), metal sulfide
s undergo oxidation to produce metal-rich acidic effluent. If the pH is low enough to overcome the natural buffer
ing capacity of the surrounding rocks (‘calcium carbonate equivalent’ or ‘acid neutralising capacity’), the surrounding area may become acidic, as well as contaminated with high levels of heavy metals
(Costigan, Bradshaw & Gemmell, 1981)(Mills). Though acidophiles have an important place in the iron
and sulfur biogeochemical cycles
, strongly acidic environments are overwhelmingly anthropogenic in cause, primarily created at the cessation of mining operations where sulfide minerals, such as pyrite
(iron disulfide or FeS2), are present.
Acid mine drainage may occur in the mine itself, the spoil heap (particularly colliery spoils from coal mining
), or through some other activity that exposes metal sulfides at a high concentration, such as at major construction sites (Akcil, & Koldas, 2006). Banks et al. provide a basic summary of the processes that occur:
(synonym Thiobacillus ferrooxidans) (Kelly & Wood, 2000). These bacteria can accelerate pyritic oxidation by 10^6 times (Mielke, Pace, Porter & Southam, 2003). In that study, a proposal for the rate at which A.ferrooxidans can oxidise pyrite is the ability to use ferrous iron to generate a ferric iron catalyst :
Under the above acidic conditions, ferric iron (Fe3+) is a more potent oxidant than oxygen, resulting in faster pyrite oxidation rates.
A.ferrooxidans is a chemolithoautotrophic bacteria, due to the oligotroph
ic nature (low dissolved organic carbon concentration) of acidic environments, and their lack of illumination for phototrophy. Even when in vadose conditions, A.ferrooxidans can survive, if the rock retains moisture and the mine is aerated. In fact in this situation, with pioneer microorganisms, the limiting factor is likely to be the environmental circumneutral pH
, which inhibits many acidophile’s growth. However, favourable geochemical conditions quickly develop with an acidic interface between the bacteria and the mineral surface, and pH is lowered to a level closer to acidophilic optimum (Mielke et al., 2003).
The process proceeds through A.ferrooxidans exhibiting a quorum
level for the trigger of acid mine drainage
(AMD). At first colonisation of metal sulfides there is no AMD, and as the bacteria grow into microcolonies, AMD remains absent, then at a certain colony size, the population begins to produce a measurable change in water chemistry, and AMD escalates (Mielke et al., 2003). This means pH is not a clear measure of a mine’s liability to AMD; culturing A.ferrooxidans (or others) gives a definite indication of a future AMD issue (Mielke et al., 2003).
Other bacteria also implicated in AMD include Leptospirillum ferrooxidans, Acidithiobacillus thiooxidans and Sulfobacillus thermosulfidooxidans.
display impressive acid tolerance, most retain a circumneutral cytoplasm
to avoid denaturation
of their acid-labile cell constituents. Archaea such as Ferroplasma acidiphilum, which oxidises ferrous iron, have a number of intracellular
enzymes with an optimum similar to that of their external acidic environment (Golyshina & Timmis, 2005). This may explain their ability to survive pH as low as 1.3 (Golyshina, Pivovarova, Karavaiko, Kondrat’eva et al., 2000). The differing cell membrane
s in the archaeal domain compared to the bacterial domain may hold part of the explanation; ether
lipids that link isoprene
, compared to proteobacteria’s di-ester linkage (Albers, 2000), are central to the difference. Though lacking a cell wall, F. acidiphilum cell membranes contain caldarchaetidylglycerol tetraether lipids, which effectively block almost all proton
access (Golyshina & Timmis, 2005), Thermoplasma acidophilum also uses these bulky isoprenoid cores in its phospholipid bilayer (Nemoto, Shida, Shimada, Oshima & Yamagishi, 2003).
It has been suggested by Golyshina & Timmis (2005) that the family Ferroplasmaceae
may in fact be more important in AMD than the current paradigm, Acidithiobacillaceae. From a practical viewpoint this changes little, as despite the myriad physiological differences between archaea and bacteria, treatments would remain the same; if pH is kept high, and water and oxygen are prohibited from the pyrite, the reaction will be negligible.
The isolation from solfataric soils of two Picrophilus
species of archaea P.oshimae and P.torridus are of note for their record low of survival at pH 0 (Schleper, Puehler, Holz, Gambacorta et al., 1995), indicating that further AMD microorganisms may remain to be found which operate at an even lower pH. Though the genus Picrophilus is not known to be involved in AMD (Edwards, Bond, Gihring & Banfield, 2000), its extreme acidophily is of interest, for instance its proton-resistant liposomes, which could be present in AMD acidophiles (Driessen, van de Vossenberg & Konings, 1996).
, then ferric-reducing heterotrophs use iron as an electron-acceptor.
Another more synergistic behaviour is the faster oxidation of ferrous iron when A.ferrooxidans and Sulfobacillus thermosulfidooxidans are combined in low-CO2
culture (Clark & Norris, 1996). S.thermosulfidooxidans is a more efficient iron-oxidiser, but this is usually inhibited by low-CO2 uptake. A.ferrooxidans has a higher affinity
for the gas, but a lower iron oxidation speed, and so can supply S.thermosulfidooxidans for mutual benefit.
The community possesses diversity beyond the bacteria and archaea however; the approximately constant pH present during acid mine drainage make for a reasonably stable environment, with a community that spans a number of trophic level
s, and includes obligate
ly acidophilic eukaryotes such as fungi, yeasts, algae
and protozoa
.
production. A large amount of energy is available to the acidophile through proton movement across the membrane, but with it comes cytoplasmic acidity. Instead ions such as sodium can be used as a substitute energy transducer to avoid this pH increase (ATPase
s are often Na+ linked, rather than H+ linked) (Driessen, van de Vossenberg & Konings, 1996).
(ETC).
On the subject of the ETC, an adaptation to living in the mine environment is in the use of different ETC electron-acceptors to neutralophiles; sulfur
, arsenic
, selenium
, uranium
, iron
, and manganese
in solid form (Ruebush, Icopini, Brantley & Tien, 2006) rather than O2 (most commonly Fe in dissimilatory iron reduction, frequent in AMD).
and thermophilic. For instance, this Order
expresses an increased concentration of purine
-containing codons for heat-stability, whilst increasing pyramidine codons in long open reading frame
s for protection from acid-stress. More generally, and presumably to reduce the chances of an acid-hydrolysis
mutation, all obligate hyperacidophiles have truncated genomes when compared to neutralophile microorganisms. Picrophilus torridus, for instance, has the highest coding density of any non-parasitic aerobic microorganism living on organic substrates (Fütterer, Angelov, Liesegang, Gottschalk et al., 2004).
. The P.torridus genome just mentioned contains a large numbers of genes concerned with repair proteins.
is the primary biotech issue created by the AMD acidophiles. There are a number of methods for dealing with AMD, some crude (such as raising pH through liming, removing water, binding iron with organic wastes) and some less so (application of bactericides, biocontrol with other bacteria/archaea, offsite wetland creation, use of metal-immobilising bacteria, galvanic suppression). A number of other neutralising agents are available (pulverised fuel ash
-based grouts, cattle manure, whey
, brewer's yeast) many which solve a waste disposal problem from another industry.
As supplies of some metals dwindle, other methods of extraction are being explored, including the use of acidophiles, in a process known as bioleaching
. Though slower than conventional methods, the microorganisms (which can also include fungi) enable the exploitation of extremely low grade ores with minimum expense (Mohapatra, Bohidar, Pradhan, Kar, & Sukla, 2007). Projects include nickel extraction with A.ferrooxidans and Aspergillus sp. fungi (Mohapatra et al., 2007) and sulfur removal from coal with Acidithiobacillus sp. (Dugan & Apel, 1984). The extraction can occur at the mine site, from waste water streams (or the main watercourse if the contamination has reached that far), in bioreactors, or at a power station (for instance to remove sulfur from coal before combustion to avoid sulfuric acid rain).
, which contains 38 of the 50 worst polluting metal mines in Wales.
Slightly further afield, the government endorsement of a return to coal as an energy source (Department of Trade and Industry white paper, 2007) brings with it the return of mining (for instance the open-cast pit at Ffos-y-fran
, Merthyr Tydfil
), and so potential AMD. Much preventative work needs to be done, rather than curative, to avoid the problems associated with the last generation of coal mines.
The fast and efficient protein and DNA repair
systems show promise for human medical uses, particularly with regard to cancer and ageing. However further research is required to determine whether these systems really are qualitatively different, and how that can be applied from microorganisms to humans.
As discussed earlier, acidophiles can have the option to use non-O2 electron acceptors. Johnson (1998) points out that facultative anaerobism
of acidophiles, previously dismissed, have major implications for AMD control. Further research is needed to determine how far current methods to separate the reduced material from oxygen are working, in light of the fact that the reaction may be able to continue, albeit at an impeded rate.
Albers, S.V., van de Vossenberg, J.L.C.M., Driessen, A.J.M. & Konings, W.M. (2000) Adaptations of the Archaeal cell membrane to heat stress. Frontiers in Bioscience 5: 813-820
Clark, D.A. & Norris, P.R. (1996) Acidimicrobium ferrooxidans gen. nov., sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus species. Microbiology 141: 785–790.
Costigan, P.A., Bradshaw, A.D. & Gemmell, R.P. (1981) The Reclamation of Acidic Colliery Spoil. I. Acid Production Potential. The Journal of Applied Ecology 18: 865-878
Department of Trade and Industry (2007) Meeting the Energy Challenge: a white paper on energy. pp.111-112. http://www.berr.gov.uk/energy/whitepaper/page39534.html Accessed 27/02/08
Driessen, A.J.M., van de Vossenberg, J.L.C.M. & Konings, W.N. (1996) Membrane composition and ion-permeability in extremophiles. FEMS Microbiology Reviews 18: 2-3
Dugan, P.R. & Apel, W.A. (1984) Microbiological desulfurization of coal. Patent number: 4456688 http://www.google.com/patents?id=uhMsAAAAEBAJ Accessed 29/02/08
Edwards, K.J., Bond, P.L., Gihring, T.M. & Banfield, J.F. (2000) An Archaeal Iron-Oxidizing Extreme Acidophile Important in Acid Mine Drainage. Science 287: 1796-1799
Fütterer, O., Angelov, A., Liesegang, H., Gottschalk, G., Schleper, C., Schepers, B., Dock, C., Antranikian, G. & Liebl, W. (2004) Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proceedings of the National Academy of Science U. S. A. 101: 9091–9096
Golyshina, O.V., Pivovarova, T.A., Karavaiko, G.I., Kondrat’eva, T.F., Moore, E.R.B., Abraham, W.R., Lünsdorf, H., Timmis, K.N., Yakimov, M.M. & Golyshin, P.N. (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. International Journal of Systematic and Evolutionary Microbiology 50: 997–1006
Golyshina, O.V. & Timmis, K.N. (2005) Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments Environmental Microbiology 7: 1277–1288
Kelly, D.P. & Wood, A.P. (2000) Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. International Journal of Systematic and Evolutionary Microbiology 50: 511–516
Mielke, R.E., Pace, D.L., Porter, T. & Southam, G. (2003) A critical stage in the formation of acid mine drainage: Colonization of pyrite by Acidithiobacillus ferrooxidans under pH-neutral conditions. Geobiology 1: 81–90
Mohapatra, S., Bohidar, S., Pradhan, N., Kar, R.N., & Sukla, L.B. (2007) Microbial extraction of nickel from Sukinda chromite overburden by Acidithiobacillus ferrooxidans and Aspergillus strains. Hydrometallurgy 85: 1-8
Nemoto, N., Shida, Y., Shimada, H., Oshima, T. & Yamagishi, A. (2003) Characterization of the precursor of tetraether lipid biosynthesis in the thermoacidophilic archaeon Thermoplasma acidophilum. Extremophiles 7: 235–243
Pearce, N.J.G., Hartley, S., Perkins, W.T., Dinelli, E., Edyvean, R.G.J., Priestman, G., Bachmann, R. & Sandlands, L. (2007) Dealginated seaweed for the bioremediation of mine waters in mid-wales: Results of field trials from the “BIOMAN” EU life environment project. IMWA Symposium 2007: Water in Mining Environments, Cagliari, Italy, 27-31 May,
Ruebush, S.S., Icopini GA, Brantley SL. & Tien M. (2006) In vitro enzymatic reduction kinetics of mineral oxides by membrane fractions from Shewanella Oneidensis MR-1. Geochim et Cosmochimica Acta 70: 56-70
Schleper, C., Puehler, G.A., 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. Journal of Bacteriology 177: 7050–7059
Yellowstone National Park
Yellowstone National Park, established by the U.S. Congress and signed into law by President Ulysses S. Grant on March 1, 1872, is a national park located primarily in the U.S. state of Wyoming, although it also extends into Montana and Idaho...
or deep-sea hydrothermal vents. Genera such as Acidithiobacillus
Acidithiobacillus
Acidithiobacillus is a genus of Proteobacteria. Like all Proteobacteria, Acidithiobacillus is Gram-negative. The members of this genus used to belong to Thiobacillus, before they were reclassified in the year 2000....
and Leptospirillum bacteria, and Thermoplasmales archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
, are present in syntrophic
Symbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...
relationships in the more mundane environments of concrete sewer pipes and implicated in the heavy-metal-containing, sulfurous waters of rivers such as the Rheidol.
Such microorganisms are responsible for the phenomenon of acid mine drainage
Acid mine drainage
Acid mine drainage , or acid rock drainage , refers to the outflow of acidic water from metal mines or coal mines. However, other areas where the earth has been disturbed may also contribute acid rock drainage to the environment...
(AMD) and thus are important both economically and from a conservation perspective. Control of these acidophiles and their harnessing for industrial biotechnology shows their effect need not be entirely negative.
The use of acidophilic
Acidophile (organisms)
Acidophilic organisms are those that thrive under highly acidic conditions . These organisms can be found in different branches of the tree of life, including Archaea, Bacteria, and Eukaryotes...
organisms in mining
Mining
Mining is the extraction of valuable minerals or other geological materials from the earth, from an ore body, vein or seam. The term also includes the removal of soil. Materials recovered by mining include base metals, precious metals, iron, uranium, coal, diamonds, limestone, oil shale, rock...
is a nascent technique for extracting trace metals through bioleaching
Bioleaching
Bioleaching is the extraction of specific metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide...
, and offers solutions for the phenomenon of acid mine drainage
Acid mine drainage
Acid mine drainage , or acid rock drainage , refers to the outflow of acidic water from metal mines or coal mines. However, other areas where the earth has been disturbed may also contribute acid rock drainage to the environment...
(AMD) in mining spoils.
Introduction
Upon exposure to oxygenOxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
(O2) and water
Water
Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...
(H2O), metal sulfide
Sulfide mineral
The sulfide minerals are a class of minerals containing sulfide as the major anion. Some sulfide minerals are economically important as metal ores. The sulfide class also includes the selenides, the tellurides, the arsenides, the antimonides, the bismuthinides, the sulfarsenides and the sulfosalts...
s undergo oxidation to produce metal-rich acidic effluent. If the pH is low enough to overcome the natural buffer
Buffering agent
A buffering agent is a weak acid or base used to maintain the acidity of a solution at a chosen value. The function of a buffering agent is to prevent a rapid change in pH when acids or bases are added to the solution. Buffering agents have variable properties—some are more soluble than others;...
ing capacity of the surrounding rocks (‘calcium carbonate equivalent’ or ‘acid neutralising capacity’), the surrounding area may become acidic, as well as contaminated with high levels of heavy metals
Heavy metals
A heavy metal is a member of a loosely-defined subset of elements that exhibit metallic properties. It mainly includes the transition metals, some metalloids, lanthanides, and actinides. Many different definitions have been proposed—some based on density, some on atomic number or atomic weight,...
(Costigan, Bradshaw & Gemmell, 1981)(Mills). Though acidophiles have an important place in the iron
Iron cycle
In ecology or geoscience, the iron cycle is the biogeochemical cycle of iron through landforms, the atmosphere, and oceans. The iron cycle affects dust deposition and aerosol iron bioavailability..- References :...
and sulfur biogeochemical cycles
Sulfur cycle
The sulfur cycle are the collection of processes by which sulfur moves to and from minerals and living systems. Such biogeochemical cycles are important in geology because they affect many minerals...
, strongly acidic environments are overwhelmingly anthropogenic in cause, primarily created at the cessation of mining operations where sulfide minerals, such as pyrite
Pyrite
The mineral pyrite, or iron pyrite, is an iron sulfide with the formula FeS2. This mineral's metallic luster and pale-to-normal, brass-yellow hue have earned it the nickname fool's gold because of its resemblance to gold...
(iron disulfide or FeS2), are present.
Acid mine drainage may occur in the mine itself, the spoil heap (particularly colliery spoils from coal mining
Coal mining
The goal of coal mining is to obtain coal from the ground. Coal is valued for its energy content, and since the 1880s has been widely used to generate electricity. Steel and cement industries use coal as a fuel for extraction of iron from iron ore and for cement production. In the United States,...
), or through some other activity that exposes metal sulfides at a high concentration, such as at major construction sites (Akcil, & Koldas, 2006). Banks et al. provide a basic summary of the processes that occur:
- 2FeS2 + 2H2O + 7O2 = 2Fe2+ + 4SO42– + 4H+(aq)
- Pyrite + water + oxygen = ferrous iron + sulfate + acid
Bacterial influences on acid mine drainage
The oxidation of metal sulfide (by oxygen) is slow without colonization by acidophiles, particularly Acidithiobacillus ferrooxidansAcidithiobacillus
Acidithiobacillus is a genus of Proteobacteria. Like all Proteobacteria, Acidithiobacillus is Gram-negative. The members of this genus used to belong to Thiobacillus, before they were reclassified in the year 2000....
(synonym Thiobacillus ferrooxidans) (Kelly & Wood, 2000). These bacteria can accelerate pyritic oxidation by 10^6 times (Mielke, Pace, Porter & Southam, 2003). In that study, a proposal for the rate at which A.ferrooxidans can oxidise pyrite is the ability to use ferrous iron to generate a ferric iron catalyst :
- Fe2+ + 1/4O2 + H+ → Fe3+ + 1/2H2O
Under the above acidic conditions, ferric iron (Fe3+) is a more potent oxidant than oxygen, resulting in faster pyrite oxidation rates.
A.ferrooxidans is a chemolithoautotrophic bacteria, due to the oligotroph
Oligotroph
An oligotroph is an organism that can live in an environment that offers very low levels of nutrients. They may be contrasted with copiotrophs, which prefer nutritionally rich environments...
ic nature (low dissolved organic carbon concentration) of acidic environments, and their lack of illumination for phototrophy. Even when in vadose conditions, A.ferrooxidans can survive, if the rock retains moisture and the mine is aerated. In fact in this situation, with pioneer microorganisms, the limiting factor is likely to be the environmental circumneutral pH
PH
In chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...
, which inhibits many acidophile’s growth. However, favourable geochemical conditions quickly develop with an acidic interface between the bacteria and the mineral surface, and pH is lowered to a level closer to acidophilic optimum (Mielke et al., 2003).
The process proceeds through A.ferrooxidans exhibiting a quorum
Quorum
A quorum is the minimum number of members of a deliberative assembly necessary to conduct the business of that group...
level for the trigger of acid mine drainage
Acid mine drainage
Acid mine drainage , or acid rock drainage , refers to the outflow of acidic water from metal mines or coal mines. However, other areas where the earth has been disturbed may also contribute acid rock drainage to the environment...
(AMD). At first colonisation of metal sulfides there is no AMD, and as the bacteria grow into microcolonies, AMD remains absent, then at a certain colony size, the population begins to produce a measurable change in water chemistry, and AMD escalates (Mielke et al., 2003). This means pH is not a clear measure of a mine’s liability to AMD; culturing A.ferrooxidans (or others) gives a definite indication of a future AMD issue (Mielke et al., 2003).
Other bacteria also implicated in AMD include Leptospirillum ferrooxidans, Acidithiobacillus thiooxidans and Sulfobacillus thermosulfidooxidans.
Archaean acidophiles
Though proteobacteriaProteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....
display impressive acid tolerance, most retain a circumneutral cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...
to avoid denaturation
Denaturation (biochemistry)
Denaturation is a process in which proteins or nucleic acids lose their tertiary structure and secondary structure by application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent , or heat...
of their acid-labile cell constituents. Archaea such as Ferroplasma acidiphilum, which oxidises ferrous iron, have a number of intracellular
Intracellular
Not to be confused with intercellular, meaning "between cells".In cell biology, molecular biology and related fields, the word intracellular means "inside the cell".It is used in contrast to extracellular...
enzymes with an optimum similar to that of their external acidic environment (Golyshina & Timmis, 2005). This may explain their ability to survive pH as low as 1.3 (Golyshina, Pivovarova, Karavaiko, Kondrat’eva et al., 2000). The differing cell membrane
Cell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...
s in the archaeal domain compared to the bacterial domain may hold part of the explanation; ether
Ether
Ethers are a class of organic compounds that contain an ether group — an oxygen atom connected to two alkyl or aryl groups — of general formula R–O–R'. A typical example is the solvent and anesthetic diethyl ether, commonly referred to simply as "ether"...
lipids that link isoprene
Isoprene
Isoprene , or 2-methyl-1,3-butadiene, is a common organic compound with the formula CH2=CCH=CH2. Under standard conditions it is a colorless liquid...
, compared to proteobacteria’s di-ester linkage (Albers, 2000), are central to the difference. Though lacking a cell wall, F. acidiphilum cell membranes contain caldarchaetidylglycerol tetraether lipids, which effectively block almost all proton
Proton
The proton is a subatomic particle with the symbol or and a positive electric charge of 1 elementary charge. One or more protons are present in the nucleus of each atom, along with neutrons. The number of protons in each atom is its atomic number....
access (Golyshina & Timmis, 2005), Thermoplasma acidophilum also uses these bulky isoprenoid cores in its phospholipid bilayer (Nemoto, Shida, Shimada, Oshima & Yamagishi, 2003).
It has been suggested by Golyshina & Timmis (2005) that the family Ferroplasmaceae
Ferroplasmaceae
In taxonomy, the Ferroplasmaceae are a family of the Thermoplasmatales.-External links:...
may in fact be more important in AMD than the current paradigm, Acidithiobacillaceae. From a practical viewpoint this changes little, as despite the myriad physiological differences between archaea and bacteria, treatments would remain the same; if pH is kept high, and water and oxygen are prohibited from the pyrite, the reaction will be negligible.
The isolation from solfataric soils of two Picrophilus
Picrophilus
In taxonomy, Picrophilus is an archaean genus of the family Picrophilaceae.Picrophilus is an extremely acidophilic genus within Euryarchaeota. These microbes are the most acidophilic organisms currently known, with the ability to grow at a pH of -0.06. They are obligate acidophiles and are unable...
species of archaea P.oshimae and P.torridus are of note for their record low of survival at pH 0 (Schleper, Puehler, Holz, Gambacorta et al., 1995), indicating that further AMD microorganisms may remain to be found which operate at an even lower pH. Though the genus Picrophilus is not known to be involved in AMD (Edwards, Bond, Gihring & Banfield, 2000), its extreme acidophily is of interest, for instance its proton-resistant liposomes, which could be present in AMD acidophiles (Driessen, van de Vossenberg & Konings, 1996).
Interactions in the mine community
Tentatively, there may be examples of syntrophy between acidophilic species, and even cross-domain cooperation between archaea and bacteria. One mutalistic example is the rotation of iron between species; ferrous-oxidising chemolithotrophs use iron as an electron donorElectron donor
An electron donor is a chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process....
, then ferric-reducing heterotrophs use iron as an electron-acceptor.
Another more synergistic behaviour is the faster oxidation of ferrous iron when A.ferrooxidans and Sulfobacillus thermosulfidooxidans are combined in low-CO2
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
culture (Clark & Norris, 1996). S.thermosulfidooxidans is a more efficient iron-oxidiser, but this is usually inhibited by low-CO2 uptake. A.ferrooxidans has a higher affinity
Chemical affinity
In chemical physics and physical chemistry, chemical affinity is the electronic property by which dissimilar chemical species are capable of forming chemical compounds...
for the gas, but a lower iron oxidation speed, and so can supply S.thermosulfidooxidans for mutual benefit.
The community possesses diversity beyond the bacteria and archaea however; the approximately constant pH present during acid mine drainage make for a reasonably stable environment, with a community that spans a number of trophic level
Trophic level
The trophic level of an organism is the position it occupies in a food chain. The word trophic derives from the Greek τροφή referring to food or feeding. A food chain represents a succession of organisms that eat another organism and are, in turn, eaten themselves. The number of steps an organism...
s, and includes obligate
Obligate
Obligate means "by necessity" and is used mainly in biology in phrases such as:* Obligate aerobe, an organism that cannot survive without oxygen* Obligate anaerobe, an organism that cannot survive in the presence of oxygen...
ly acidophilic eukaryotes such as fungi, yeasts, algae
Algae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...
and protozoa
Protozoa
Protozoa are a diverse group of single-cells eukaryotic organisms, many of which are motile. Throughout history, protozoa have been defined as single-cell protists with animal-like behavior, e.g., movement...
.
Physiology and biochemistry
Acidophiles display a great range of adaptations to not just tolerating, but thriving in an extreme pH environment (the definition of an acidophile being an organism that has a pH optimum below pH 3). Principal in these is the necessity of maintaining a large pH gradient, to ensure a circumneutral cytoplasm (normally, however not in Picrophilus species). The archaeans have already been discussed above, and further information on their and bacterial adaptations are in basic form in the Figure. To elaborate upon the figure, the bacteria also use membrane proton blocking to maintain a high cytoplasmic pH, which is a passive system as even non-respiring A.ferrooxidans exhibit it. Acidophiles are also able to extrude protons against the pH gradient with unique transport proteins, a process more difficult for moderate- and hyper-thermophiles; a higher temperature causes cell membranes to become more permeable to protons, necessarily leading to increased H+ influx, in the absence of other membrane alterations (Driessen, van de Vossenberg & Konings, 1996).Proton motive force
Acidophiles harness the strong proton motive force (PMF), caused by the pH gradient across their cell membrane, for ATPAdenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
production. A large amount of energy is available to the acidophile through proton movement across the membrane, but with it comes cytoplasmic acidity. Instead ions such as sodium can be used as a substitute energy transducer to avoid this pH increase (ATPase
ATPase
ATPases are a class of enzymes that catalyze the decomposition of adenosine triphosphate into adenosine diphosphate and a free phosphate ion. This dephosphorylation reaction releases energy, which the enzyme harnesses to drive other chemical reactions that would not otherwise occur...
s are often Na+ linked, rather than H+ linked) (Driessen, van de Vossenberg & Konings, 1996).
Expelling H+ containing vesicles
Alternatively bacteria can use H+ containing vesicles to avoid cytoplasmic acidity (see Figure), but most require that any H+ taken in must be extruded after use in the electron transport chainElectron transport chain
An electron transport chain couples electron transfer between an electron donor and an electron acceptor with the transfer of H+ ions across a membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate...
(ETC).
On the subject of the ETC, an adaptation to living in the mine environment is in the use of different ETC electron-acceptors to neutralophiles; sulfur
Sulfur
Sulfur or sulphur is the chemical element with atomic number 16. In the periodic table it is represented by the symbol S. It is an abundant, multivalent non-metal. Under normal conditions, sulfur atoms form cyclic octatomic molecules with chemical formula S8. Elemental sulfur is a bright yellow...
, arsenic
Arsenic
Arsenic is a chemical element with the symbol As, atomic number 33 and relative atomic mass 74.92. Arsenic occurs in many minerals, usually in conjunction with sulfur and metals, and also as a pure elemental crystal. It was first documented by Albertus Magnus in 1250.Arsenic is a metalloid...
, selenium
Selenium
Selenium is a chemical element with atomic number 34, chemical symbol Se, and an atomic mass of 78.96. It is a nonmetal, whose properties are intermediate between those of adjacent chalcogen elements sulfur and tellurium...
, uranium
Uranium
Uranium is a silvery-white metallic chemical element in the actinide series of the periodic table, with atomic number 92. It is assigned the chemical symbol U. A uranium atom has 92 protons and 92 electrons, of which 6 are valence electrons...
, iron
Iron
Iron is a chemical element with the symbol Fe and atomic number 26. It is a metal in the first transition series. It is the most common element forming the planet Earth as a whole, forming much of Earth's outer and inner core. It is the fourth most common element in the Earth's crust...
, and manganese
Manganese
Manganese is a chemical element, designated by the symbol Mn. It has the atomic number 25. It is found as a free element in nature , and in many minerals...
in solid form (Ruebush, Icopini, Brantley & Tien, 2006) rather than O2 (most commonly Fe in dissimilatory iron reduction, frequent in AMD).
Genomic adaptations
Genomic adaptations are also present, but not without complications in organisms like Thermoplasmatales archaea, which is both acidophilicAcidophile (organisms)
Acidophilic organisms are those that thrive under highly acidic conditions . These organisms can be found in different branches of the tree of life, including Archaea, Bacteria, and Eukaryotes...
and thermophilic. For instance, this Order
Order (biology)
In scientific classification used in biology, the order is# a taxonomic rank used in the classification of organisms. Other well-known ranks are life, domain, kingdom, phylum, class, family, genus, and species, with order fitting in between class and family...
expresses an increased concentration of purine
Purine
A purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
-containing codons for heat-stability, whilst increasing pyramidine codons in long open reading frame
Reading frame
In biology, a reading frame is a way of breaking a sequence of nucleotides in DNA or RNA into three letter codons which can be translated in amino acids. There are 3 possible reading frames in an mRNA strand: each reading frame corresponding to starting at a different alignment...
s for protection from acid-stress. More generally, and presumably to reduce the chances of an acid-hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
mutation, all obligate hyperacidophiles have truncated genomes when compared to neutralophile microorganisms. Picrophilus torridus, for instance, has the highest coding density of any non-parasitic aerobic microorganism living on organic substrates (Fütterer, Angelov, Liesegang, Gottschalk et al., 2004).
Improved repair
Acidophiles also benefit from improved DNA and protein repair systems such as chaperones involved in protein refoldingProtein folding
Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
. The P.torridus genome just mentioned contains a large numbers of genes concerned with repair proteins.
Biotechnology applications
BioremediationBioremediation
Bioremediation is the use of microorganism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated...
is the primary biotech issue created by the AMD acidophiles. There are a number of methods for dealing with AMD, some crude (such as raising pH through liming, removing water, binding iron with organic wastes) and some less so (application of bactericides, biocontrol with other bacteria/archaea, offsite wetland creation, use of metal-immobilising bacteria, galvanic suppression). A number of other neutralising agents are available (pulverised fuel ash
Pulverised Fuel Ash
Pulverised fuel ash , is a by product of pulverised fuel fired power stations. The fuel is pulverised into a fine powder, mixed with heated air and burned. Approximately 18% of the fuel forms fine glass spheres, the lighter of which are borne aloft by the combustion process...
-based grouts, cattle manure, whey
Whey
Whey or Milk Serum is the liquid remaining after milk has been curdled and strained. It is a by-product of the manufacture of cheese or casein and has several commercial uses. Sweet whey is manufactured during the making of rennet types of hard cheese like cheddar or Swiss cheese...
, brewer's yeast) many which solve a waste disposal problem from another industry.
As supplies of some metals dwindle, other methods of extraction are being explored, including the use of acidophiles, in a process known as bioleaching
Bioleaching
Bioleaching is the extraction of specific metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide...
. Though slower than conventional methods, the microorganisms (which can also include fungi) enable the exploitation of extremely low grade ores with minimum expense (Mohapatra, Bohidar, Pradhan, Kar, & Sukla, 2007). Projects include nickel extraction with A.ferrooxidans and Aspergillus sp. fungi (Mohapatra et al., 2007) and sulfur removal from coal with Acidithiobacillus sp. (Dugan & Apel, 1984). The extraction can occur at the mine site, from waste water streams (or the main watercourse if the contamination has reached that far), in bioreactors, or at a power station (for instance to remove sulfur from coal before combustion to avoid sulfuric acid rain).
Future of the technique
AMD continues to be important locally in the River Rheidol, and in the near future further treatment will be needed in the area around AberystwythAberystwyth
Aberystwyth is a historic market town, administrative centre and holiday resort within Ceredigion, Wales. Often colloquially known as Aber, it is located at the confluence of the rivers Ystwyth and Rheidol....
, which contains 38 of the 50 worst polluting metal mines in Wales.
Slightly further afield, the government endorsement of a return to coal as an energy source (Department of Trade and Industry white paper, 2007) brings with it the return of mining (for instance the open-cast pit at Ffos-y-fran
Ffos-y-fran
The Ffos-y-fran Land Reclamation Scheme is a major opencast coaling operation to the north-east of Merthyr Tydfil in South Wales. It is a joint development undertaken by Miller Argent Ltd, a jointly owned company between The Miller Group Ltd, Argent Group PLC and Bernard J. Llewellyn JP...
, Merthyr Tydfil
Merthyr Tydfil
Merthyr Tydfil is a town in Wales, with a population of about 30,000. Although once the largest town in Wales, it is now ranked as the 15th largest urban area in Wales. It also gives its name to a county borough, which has a population of around 55,000. It is located in the historic county of...
), and so potential AMD. Much preventative work needs to be done, rather than curative, to avoid the problems associated with the last generation of coal mines.
The fast and efficient protein and DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
systems show promise for human medical uses, particularly with regard to cancer and ageing. However further research is required to determine whether these systems really are qualitatively different, and how that can be applied from microorganisms to humans.
As discussed earlier, acidophiles can have the option to use non-O2 electron acceptors. Johnson (1998) points out that facultative anaerobism
Facultative anaerobic organism
A facultative anaerobic organism is an organism, usually a bacterium, that makes ATP by aerobic respiration if oxygen is present but is also capable of switching to fermentation...
of acidophiles, previously dismissed, have major implications for AMD control. Further research is needed to determine how far current methods to separate the reduced material from oxygen are working, in light of the fact that the reaction may be able to continue, albeit at an impeded rate.
See also
- Microbial metabolismMicrobial metabolismMicrobial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics...
- Extremophiles
- BacTech Environmental Corp.
Footnotes
Akcil, A. & Koldas, S. (2006) Improving Environmental, Economic and Ethical Performance in the Mining Industry. Part 2: Life cycle and process analysis and technical issues. Journal of Cleaner Production 14: 1139-1145Albers, S.V., van de Vossenberg, J.L.C.M., Driessen, A.J.M. & Konings, W.M. (2000) Adaptations of the Archaeal cell membrane to heat stress. Frontiers in Bioscience 5: 813-820
Clark, D.A. & Norris, P.R. (1996) Acidimicrobium ferrooxidans gen. nov., sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus species. Microbiology 141: 785–790.
Costigan, P.A., Bradshaw, A.D. & Gemmell, R.P. (1981) The Reclamation of Acidic Colliery Spoil. I. Acid Production Potential. The Journal of Applied Ecology 18: 865-878
Department of Trade and Industry (2007) Meeting the Energy Challenge: a white paper on energy. pp.111-112. http://www.berr.gov.uk/energy/whitepaper/page39534.html Accessed 27/02/08
Driessen, A.J.M., van de Vossenberg, J.L.C.M. & Konings, W.N. (1996) Membrane composition and ion-permeability in extremophiles. FEMS Microbiology Reviews 18: 2-3
Dugan, P.R. & Apel, W.A. (1984) Microbiological desulfurization of coal. Patent number: 4456688 http://www.google.com/patents?id=uhMsAAAAEBAJ Accessed 29/02/08
Edwards, K.J., Bond, P.L., Gihring, T.M. & Banfield, J.F. (2000) An Archaeal Iron-Oxidizing Extreme Acidophile Important in Acid Mine Drainage. Science 287: 1796-1799
Fütterer, O., Angelov, A., Liesegang, H., Gottschalk, G., Schleper, C., Schepers, B., Dock, C., Antranikian, G. & Liebl, W. (2004) Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proceedings of the National Academy of Science U. S. A. 101: 9091–9096
Golyshina, O.V., Pivovarova, T.A., Karavaiko, G.I., Kondrat’eva, T.F., Moore, E.R.B., Abraham, W.R., Lünsdorf, H., Timmis, K.N., Yakimov, M.M. & Golyshin, P.N. (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. International Journal of Systematic and Evolutionary Microbiology 50: 997–1006
Golyshina, O.V. & Timmis, K.N. (2005) Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments Environmental Microbiology 7: 1277–1288
Kelly, D.P. & Wood, A.P. (2000) Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. International Journal of Systematic and Evolutionary Microbiology 50: 511–516
Mielke, R.E., Pace, D.L., Porter, T. & Southam, G. (2003) A critical stage in the formation of acid mine drainage: Colonization of pyrite by Acidithiobacillus ferrooxidans under pH-neutral conditions. Geobiology 1: 81–90
Mohapatra, S., Bohidar, S., Pradhan, N., Kar, R.N., & Sukla, L.B. (2007) Microbial extraction of nickel from Sukinda chromite overburden by Acidithiobacillus ferrooxidans and Aspergillus strains. Hydrometallurgy 85: 1-8
Nemoto, N., Shida, Y., Shimada, H., Oshima, T. & Yamagishi, A. (2003) Characterization of the precursor of tetraether lipid biosynthesis in the thermoacidophilic archaeon Thermoplasma acidophilum. Extremophiles 7: 235–243
Pearce, N.J.G., Hartley, S., Perkins, W.T., Dinelli, E., Edyvean, R.G.J., Priestman, G., Bachmann, R. & Sandlands, L. (2007) Dealginated seaweed for the bioremediation of mine waters in mid-wales: Results of field trials from the “BIOMAN” EU life environment project. IMWA Symposium 2007: Water in Mining Environments, Cagliari, Italy, 27-31 May,
Ruebush, S.S., Icopini GA, Brantley SL. & Tien M. (2006) In vitro enzymatic reduction kinetics of mineral oxides by membrane fractions from Shewanella Oneidensis MR-1. Geochim et Cosmochimica Acta 70: 56-70
Schleper, C., Puehler, G.A., 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. Journal of Bacteriology 177: 7050–7059