Mineral–Microbe Interactions

and Implications for

Remediation
Hailiang Dong1, 2 and Anhuai Lu3

1811-5209/12/0008-0095$2.50 DOI: 10.2113/gselements.8.2.95

M
inerals and microbes have coevolved throughout much of Earth COEVOLUTION
history. They interact at the microscopic scale, but their effects are OF MINERALS
manifested macroscopically. Minerals support microbial growth by AND MICROBES
Minerals and microbes have
providing essential nutrients, and microbial activity alters mineral solubility
coevolved over much of Earth’s
and the oxidation state of certain constituent elements. Microbially mediated history. The origin and evolution
dissolution, precipitation, and transformation of minerals are either directly of life is thought to have been cata-
controlled by microorganisms or induced by biochemical reactions that usually lyzed by minerals. The prebiotic
synthesis of primordial life-forms
take place outside the cell. All these reactions alter metal mobility, leading on early Earth was catalyzed by
to the release or sequestration of heavy metals and radionuclides. These m i ne r a l s s uc h as p y r ite
processes therefore have implications for ore formation and the bioremedia- (Wächtershäuser 1988) and clays.
Self-replicating building blocks of
tion of contaminated sites.
organic molecules have been
Keywords : biosignature, coevolution, heavy metal, mineral–microbe synthesized autocatalytically on
interactions, remediation pyrite surfaces, forming surface
metabolists, a primitive, two-
dimensional life-form. Polymer­
INTRODUCTION ization of RNA monomers to oligomers can be catalyzed
Microbes and minerals interact at all time and spatial by the clay mineral montmorillonite (Ferris 2005).
scales. Microbes have been found in a number of Earth’s
extreme environments. In spite of the diverse geological Once life emerged on Earth, it began to interact with
environments in which microbes are found and the varied minerals in a variety of ways and has continuously and
approaches taken to study them, a common thread—the often irreversibly transformed Earth’s surface mineralogy.
interplay between minerals and microbes—connects all Sulfur-metabolizing bacteria may have existed around 3.5
these environments and experimental approaches. Minerals billion years ago (Ga) and were responsible for pyrite
and rocks provide microbes with nutrients and livable habi- precipitation and sulfur isotope fractionation (Wacey et al.
tats, and microbes impact mineral weathering and diagen- 2011). Cyanobacterial communities formed patchy
esis through their effects on mineral solubility. By contrast, carbonate buildups in shallow seas as early as the
microbes form minerals as a by-product of either their Paleoarchean (3.5 Ga), and by the Neoarchean, they had
surface reactivity towards soluble metals or as a conse- become the principal builders of carbonate platforms
quence of their metabolism. The recognition of the impor- (Altermann et al. 2006).
tance of mineral–microbe interactions has revived the The “Great Oxidation Event” (GOE), a consequence of
classical discipline of mineralogy, and many modern oxygenic photosynthesis by cyanobacteria starting at
mineralogists study minerals in the broad field of “envi- 2.45 Ga (Konhauser et al. 2011), raised the atmospheric
ronmental mineralogy.” The unique and diverse microbes oxygen level to >1% of the modern value and greatly diver-
discovered in various Earth habitats have also provided sified the species of minerals, from about 1500 to more
microbiologists with unique opportunities for study. In than 4000 (Hazen and Ferry 2010). Many of these minerals,
this introductory article, we first review the coevolution such as sulfates, oxyhydroxides, and nitrates, would not
of minerals and microbes, and then discuss various modes have developed in abundance in the anoxic environment
of mineral–microbe interaction and the consequences of prior to the GOE. Carbonate deposits formed between 2.25
these interactions in the context of remediation of heavy and 2.06 Ga, which contain the greatest diversity in stro-
metals and radionuclides in groundwater and soils at many matolite types in Earth’s history, indicate robust microbial
contaminated sites around the world. The article ends with carbonate and phosphate biomineralization (Hazen et al.
a brief discussion of mineral–microbe interactions 2008). Likewise, the deposition of abundant banded iron
throughout geological history. formations around this time (mostly 2.4–1.8 Ga) has been
ascribed in part to Fe(II)-oxidizing bacterial activity
(Konhauser et al. 2011).
1 Department of Geology and Environmental Earth Science
Miami University, Oxford, OH 45056, USA The Neoproterozoic Era saw dramatic fluctuations of
E-mail: [email protected] climate and atmospheric composition. Despite severe envi-
2 State Key Laboratory of Biogeology and Environmental Geology ronmental variability, microbes persisted and continued
China University of Geosciences, Beijing 100083, China to interact with minerals. Increasing deposition of clay
3 School of Earth and Space Sciences, Peking University minerals during the Neoproterozoic might have been
Beijing 100871, China caused by microbial activity in soil (Kennedy et al. 2006).

E lements , V ol . 8, pp. 95–100 95 A pr il 2012

Meanwhile, microbes in the marine environment, including nutrients to support their growth (Fig. 1a). A good example
phototrophic bacteria, could have biomineralized phos- is the microbial dissolution of basalt and volcanic glass to
phorite when rivers began to carry large quantities of phos- release phosphorus and other nutrients essential for growth
phorus to the oceans (Hazen et al. 2008). (Fig. 1b) (Rogers and Bennett 2004). Under favorable condi-
tions, microbes will also precipitate a number of biogenic
The dominant role of biology in the mineralogical diversity minerals, such as carbonates, silicates, phosphates, sulfides,
of the Earth’s surface is further illustrated by the multipli- oxides, and even native elements (Konhauser 2007; Dong
cations of biological forms in the Phanerozoic, when et al. 2009; Lu and Wang 2012 this issue). Many studies
microbes, as well as plants, invertebrates, and vertebrates, have focused on minerals with redox-sensitive elements,
mediated the formation of numerous minerals (Hazen et such as iron (Lovley 2000; Konhauser et al. 2011) and sulfur
al. 2008). Skeletal minerals, dominantly carbonates and (Dahl and Friedrich 2008). Transformation of these
phosphates, appeared in the early Cambrian. Some exam- elements from one valence state to another provides energy
ples of minerals biologically generated during the for driving the metabolic system of many microorganisms.
Phanerozoic are jarosite, goethite, hazenite, γ-sulfur, and In these redox reactions, varying amounts of energy are
intracellular magnetic grains of greigite (Fe3S 4) (Hazen et released, depending on the nature of the reactants and
al. 2008). products and on the metabolic pathways employed by the
The diversification of mineral landscapes on Earth’s surface, microorganisms (Chapelle 2000).
in turn, exerted a profound influence on the evolution of The electrons transferred during redox processes can also
life. Because of the abundance of oxidized minerals after be harnessed to produce energy through bioelectrochem-
the GOE, those microbes that could respire on oxidants ical systems, such as the “microbial fuel cell” (Logan 2008).
such as sulfate, ferric iron, and other oxidized metals, that It has been suggested that electrically conductive pili or
is, microbes such as sulfate-reducing bacteria and iron- pilus-like appendages (nanowires) establish electron trans-
reducing bacteria, may have taken advantage of vast port not only between bacteria and minerals but also
reserves of energy stored in chemical disequilibria between among different microorganisms in a community (Gorby
oxidants and organic/inorganic carbon. The activity of
these organisms would have altered the global biogeo-
chemical cycles of carbon, sulfur, nitrogen, and iron.

Although the interactions occurred largely on the micro- A

scopic scale, the results were often macroscopic, with
consequences both adverse and beneficial. Many of these
consequences are recorded in sedimentary rocks, to serve
as reminders of the powerful interactions that once
occurred, and as biosignatures that reveal the mineral–
microbe interaction history. It is to our advantage to learn
from the rock record and to make use of the positive side
effects of mineral–microbe interactions to remove heavy
metals and radionuclides from contaminated environ-
ments, degrade organic contaminants, sequester CO2, and
generate energy.

MAJOR MODES OF MINERAL–MICROBE

INTERACTION
Modes of mineral–microbe interaction can be classified B
from the perspective of either microbes or minerals. From
the microbial perspective, the interaction can result in
either biologically controlled mineralization (BCM) or
biologically induced mineralization (BIM) (Frankel and
Bazylinski 2003). In BCM, the nucleation and growth of
crystals are genetically controlled by microbes; a typical
example is magnetite in magnetosomes produced by
magnetotactic bacteria. Carbonates, phosphates, and silica
in marine animals are other examples (Dove 2010). Broadly
speaking, mineralization controlled by protein templates
belongs to BCM as well. BCM minerals have specific func-
tions, such as for navigation (magnetite) or for providing
a skeleton (carbonates, phosphate, and silica). In BIM,
however, mineralization is not genetically controlled and
occurs as a result of changes in microenvironments through
microbial metabolism. Many examples of the products of
BIM exist, such as clay minerals, (hydr)oxides, sulfides,
carbonates, and phosphates (Frankel and Bazylinski 2003;
(A) Schematic diagram showing mineral–microbe
Konhauser 2007; Dong 2012 this issue). Figure 1 interactions. Microbes dissolve minerals and release
nutrients that become available for uptake. These nutrients are
From the mineralogical perspective, mineral–microbe portrayed as delicious “chocolate, ice cream and beer” available
interactions can be classified into microbially mediated to the microbes to stimulate their growth. D rawing courtesy of
mineral dissolution, precipitation, or both (i.e. transforma- P. A. B ennett (B) Scanning electron microscope photomicrograph
of rod-shaped cells on a basalt surface; dissolution pits are visible
tion and change in redox state). Minerals contain nutrients
underneath the bodies of the microbes (Roberts et al. 2004). Scale
and energy that microbes need to sustain their metabolism bar is 0.5 μm. Image courtesy of J. A. Roberts, with permission from the
and growth. Microbes break down minerals and release G eological Society of A merica

E lements 96 A pr il 2012
et al. 2006; Lu et al. 2012 this issue). Conductive networks IMPLICATIONS OF MINERAL–MICROBE
have been found to be established in soil between microbial INTERACTIONS FOR REMEDIATION OF
populations and iron oxides (Kato et al. 2010). These extra- HEAVY METALS AND RADIONUCLIDES
cellular electron-transfer processes have led to speculation
Mineral–microbe interactions indirectly affect the
that novel modes of bacterial networking, interaction, and
geochemical fluxes and biogeochemical cycling of a large
energy-sharing with the surroundings may play important
number of elements. Among them are toxic heavy metals
roles in nature (Nielsen et al. 2010).
(e.g. chromium) and radionuclides (uranium and techne-
On Earth, a predominant renewable energy source for tium). Some of the radioactive elements entered the envi-
powering natural bioactivity is solar light, and photo- ronment from mining activity and from nuclear weapons
trophic microorganisms are adapted to capture this energy. testing in the 1950s and 1960s. Some metallurgical and
Nonphototrophic microorganisms have been excluded chemical industries produce large amounts of chromium
from light-centered metabolism due to their lack of photo- slag and contaminate local soil and groundwater (Fig. 3).
sensitive cellular compounds. Nonetheless, this deficiency Another important source of heavy metals and radionu-
does not necessarily preclude an ability to derive energy clides is nuclear power plant operations that release
indirectly from the Sun through semiconducting minerals. contaminants either by accident (such as Chernobyl in
Upon solar irradiation, semiconducting minerals, such as 1986 and the Fukushima Daiichi nuclear disaster in Japan
rutile (TiO2 ), sphalerite (ZnS), and goethite (FeOOH), can in 2011) or due to improper long-term storage of radioactive
give off electrons, and these electrons can be transferred materials. Other metals, such as lead, arsenic, antimony,
to nonphototrophic microbes to support their growth and cadmium, are enriched in certain environments by
(Fig. 2a). Alternatively, microorganisms in the biochemical either natural or anthropogenic processes. Because many
chamber of a fuel cell can catalyze the oxidation of organic of these metals and radionuclides are carcinogens, their
carbon, and the electrons produced can be transferred to release into the environment and their fate cause intense
the photocatalytic chamber to reduce electron acceptors scientific and public concern and are the subject of substan-
(such as heavy metals and radionuclides) (Fig. 2b). Since tial research. For example, an issue of Geomicrobiology
the net energy consumed in such an integrated electro- Journal dedicated to the topic of the geomicrobiology of
chemical cell is light energy, it is referred to as a light fuel radionuclides was published in July 2011. Heavy metals/
cell (LFC) (Fig. 2) to distinguish it from a bioelectrochem- radionuclides and their environmental effects have been
ical cell (Lu et al. 2012). In essence, LFCs exhibit an alter- highlighted in past issues of Elements: “The Nuclear Fuel
native mineral–microbe interactive pathway, which is Cycle: Environmental Aspects,” published in December
fundamentally a natural, solar-driven biogeochemical 2006, and “Mine Wastes,” published in December 2011.
process.
The mobility of these metals and radionuclides in ground-
water aquifers, soils, and sediments is largely controlled by
their interactions with minerals and microbes (Lovley
2000; Dong et al. 2009; Cheng et al. 2012 this issue). Heavy
A metals and radionuclides can be removed from solution
through adsorption, coprecipitation, and redox transforma-
tions. Both microbes and minerals have large surface areas,
and a range of metals and radionuclides can sorb onto their
surfaces via electrostatic attraction and surface complex-
ation. A number of metals and radionuclides can also
substitute for other elements in mineral structures or form
their own minerals (Cheng et al. 2012; Lu and Wang 2012;

Figure 3 A chromium slag dump and wastewater near Yuezhou

Township, Qujing City, Yunnan Province, China.
Approximately 5000 tons of chromium slag were illegally disposed
of in the last 10 years, leaving the slag exposed to air and water.
Schematic diagram of a light fuel cell. (A) Electrons Wastewaters with high concentrations of Cr(VI) and other metals
Figure 2 generated from the photocatalysis of a semicon- are potentially discharged into the underlying soil and the Nanpan
ducting mineral are transferred via an external circuit (R) to the River, an upstream tributary of the Pearl River. This incident was
biochemical chamber, where they act as a source of energy to reported in June 2011, and it took nearly a week to remove all the
support the growth of microorganisms. (B) Microorganisms in the accumulated chromium slag and contaminated soil (~9000 tons) to
biochemical chamber catalyze the oxidation of organic carbon and special treatment facilities. Nearly 100 cubic meters of wastewater
promote the transfer of electrons to the photocatalytic chamber, were pumped and disposed of appropriately. All downstream water
where they reduce electron acceptors (such as heavy metals and bodies have been either isolated from any contaminant source or
radionuclides). cleaned up. Photo : http ://news.sina .com, A ugust 14, 2011

E lements 97 A pr il 2012
Southam 2012 this issue). Thus any microbial activity that This level of understanding of past microbial activities and
either dissolves or precipitates minerals would have major their mineralogical consequences requires the search for
implications for the mobility of these metals. biomarkers that have been preserved in the geological
record. Most biological molecules cannot survive diagenesis
Uranium, chromium, and technetium are three important and metamorphism, but lipid biomarkers are an exception:
heavy metals with different sources and pathways (Cheng they can be preserved in sedimentary rocks and used to
et al. 2012). A common feature of these three elements is infer past microbial communities (Olcott et al. 2005).
that they are highly soluble and mobile in natural environ- Compound-specific stable isotope fractionation is a
ments when they occur in their oxidized states [i.e. U(VI), powerful tool for understanding the role of microbial
Cr(VI), and Tc(VII)], but once they are reduced to lower metabolisms in the formation of minerals that have been
oxidation states [i.e. U(IV), Cr(III), and Tc(IV)], their mobil- preserved in the rock record. For ancient and highly altered
ities are greatly decreased because they occur as solids such rocks, however, geochemical biomarkers may be more
as uraninite (UO2), Cr(OH) 3, and TcO2. A common strategy robust.
for removing these metals is to manipulate redox condi-
tions in order to reduce the metals either chemically or Among geochemical biomarkers, morphological evidence
biologically (Cheng et al. 2012). Biological reduction can is direct and often intuitive. Good examples include stalks
be promoted by adding nutrients to stimulate native micro- produced by Fe(II)-oxidizing bacteria (Chan et al. 2010)
bial activity (called biostimulation) or by injecting certain and tubular textures in basaltic glass (Staudigel et al. 2006).
bacteria (bioaugmentation) (Fig. 4). A number of metal- The extracellular, twisted, ribbon-like stalks produced by
reducing and sulfate-reducing bacteria are capable of Fe(II)-oxidizing bacteria have a physiological role in
reducing these metals enzymatically. When locally preventing the encrustation of cells by iron hydroxides.
enriched, these reduced metals can form economically Likewise, the tubular textures in basaltic glass are produced
valuable deposits. by microbes that colonize nutrient-containing glass and
grow perpendicular to previously existing fractures
(Staudigel et al. 2006).

Biogenic minerals are robust biomarkers, but only a few

minerals are known to be exclusively biogenic, including
rosickýite (γ-sulfur) and hazenite [KNaMg2 (PO4) 2 ·14H2O]
(Hazen et al. 2008). A potentially promising method for
revealing the biogenicity of some minerals is thermal treat-
ment followed by spectroscopic characterization. Untreated
biogenic carbonates (aragonite and calcite) show the same
characteristics as abiotic carbonates in infrared spectra,
but after heating, the biogenic spectra are different (Orofino
et al. 2010). A third line of geochemical evidence is the
elemental composition and isotopic fractionation that are
often characteristic of biotic processes. Enzymatic and
biochemical activities prefer one element or isotope over
another, resulting in measurable element or isotope frac-
tionation. In addition to the research on conventional
isotopes, such as C, N, and S, recent studies have focused
on nontraditional isotopes, such as Mg, Ca, Cr, Mo, Fe, Cu,
Zn, Cd, and Hg (Bullen and Eisenhauer 2009).

Figure 4 Schematic diagram showing the biostimulation IN THIS ISSUE

strategy. A dilute acetate solution is injected into a
uranium-contaminated site, and anoxic conditions are created Because of the broad nature of mineral–microbe interac-
following consumption of oxygen by heterotrophic microorganisms. tions, it is impossible to provide a comprehensive coverage
Under these conditions, metal-reducing bacteria couple the oxida- of the topic in a single issue of Elements. The articles in
tion of acetate to carbon dioxide with the reduction of U(VI) to
U(IV) (see inset). Because U(IV) is insoluble in groundwater and
this issue represent a small subset of mineral–microbe
precipitates as a solid, uranium is removed from the groundwater. studies, as they focus on modern environments. We have
The zone of U(VI) removal is shown in the down-gradient direction strived to achieve a balanced coverage between funda-
of groundwater flow for the purpose of clarity. In practice, U(VI) mental and applied science and in terms of microbial versus
removal should take place at or close to the zone of acetate
injection.
mineral perspectives. Southam takes on a prokaryotic
perspective; he describes mineral substrates as a source of
nutrients and energy and discusses the resulting secondary
mineral transformations that have important implications
for the bioremediation of metals. Cheng, Holman, and Lin
GEOLOGICAL RECORD OF MINERAL– focus on some practical aspects of mineral–microbe inter-
MICROBE INTERACTIONS: BIOSIGNATURES actions—the potential and limitations of the bioremedia-
Much of our knowledge about mineral–microbe interac- tion of chromium and uranium—and highlight the
tions is derived from laboratory experiments and observa- importance of biologically mediated transformations,
tions in modern systems. However, since the emergence of immobilization, and mineralization of toxic metals in the
life on Earth, minerals and microbes have coevolved context of remediation. In the paper on clay mineral–
through mutual interactions on Earth’s surface. To under- microbe interaction, Dong discusses the microbial dissolu-
stand this coevolution and its effects on the biogeochem- tion, formation, and transformation of clay minerals, and
ical cycles of elements essential to life, such as C, N, S, Fe, the microbial oxidation and reduction of iron in clay
and P, it is important to deduce the modes of mineral– minerals. Lu and Wang highlight the role of microorgan-
microbe interactions in the past, the types of microbes and isms in the oxidation of sulfides and heavy metal release/
minerals involved, and even the rates of their interactions. sequestration in mine tailings, and they describe some

E lements 98 A pr il 2012
engineered treatment technologies. Last, Lu, Li, and Jin A combined approach using lipid, morphological, miner-
report a pathway in which nonphototrophic organisms are alogical, elemental, and isotopic biomarkers is promising
able to harness solar energy via photocatalysis of semicon- for identifying the footprints of ancient microbes in the
ducting minerals. geological record. Regardless of whether the processes are
ancient or modern, microbial activity can cause significant
CONCLUSIONS changes in the mobility of heavy metals and radionuclides,
which can result in the formation of metal deposits over
The interactions of minerals and microbes are complex,
geologic time or the immobilization of metals in modern
and studying such a broad topic requires expertise in
contaminated sites.
mineralogy, geochemistry, microbiology, and environ-
mental engineering. Despite the fact that many observa-
tions and experimental studies have focused on modern ACKNOWLEDGMENTS
interactions, ancient processes are equally exciting, as This work was supported by grants from the U.S. Department
minerals and microbes have coevolved throughout much of Energy (DOE FG02-07ER64369 and DOE-SC0005333)
of Earth’s history. Studies of ancient mineral–microbe to HD and by the National Basic Research Program of China
interaction processes are often much more challenging (973 Program) (2007CB815602) to AL.
because of the lack of easily discernible biomarkers.

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GLOSSARY diated semiconductor photocathode. Natural attenuation – a naturally occurring
Electrons can be used to reduce metals for process, without any human intervention,
Bioelectrochemical system (BES) – a system that the purpose of remediation. that can reduce the toxicity, mobility, mass,
contains an anode, a cathode, a conductive Magnetotactic bacteria – a group of bacteria that or concentration of contaminants in water
circuit (e.g. water, minerals, wires), and at orient along the magnetic field lines of or soils. These processes include a variety of
least one bacterial species Earth’s magnetic field using intracellular physical, chemical, and biological processes.
Biomineralization – the process by which organ- organelles called magnetosomes that contain Photocatalysis – acceleration of a photoreaction
isms produce minerals, often resulting in magnetic crystals such as magnetite or in the presence of a catalyst.
fossilization of cellular structure greigite Phototrophic microorganisms – microorganisms
Bioremediation – the use of biological agents, Metal-reducing bacteria – a group of bacteria that that use light as an energy source in the
such as bacteria or plants, to remove or can reduce oxidized forms of metals to process of photosynthesis. Nonphototrophic
immobilize contaminants in polluted soil or reduced forms under anoxic conditions. microorganisms use either inorganic or
water These bacteria include DIR. organic substrates as a source of energy.
Biologically induced mineralization (BIM) – Methanogens – members of the Euryarchaea that Proton motive force – an energized state of a
mineral formation outside or on the cell as produce methane as a metabolic by-product membrane created by the expulsion of
a result of the indirect effect of the microor- during anaerobic respiration on low-molec- protons from the inner to the outer membrane
ganism’s metabolism ular-weight oxidized forms of carbon surface through the action of an electron-
Biologically controlled mineralization (BCM) – transport chain
nucleation and growth of mineral particles Microbes or microorganisms – microscopic Radionuclide – an atom with an unstable nucleus
where an organism exerts a high degree of organisms that are comprised of either a that undergoes decay and emits gamma rays
crystallochemical control single cell (unicellular) or a group of cells and/or subatomic particles
Diagenesis – any chemical, physical, or biological (multicellular). Microbes include bacteria, Secondary mineral – a mineral formed by the
change undergone by sediment after its fungi, archaea, protists, some plants (such alteration of preexisting primary minerals
initial deposition and during and after its as green algae), and some animals (such through weathering, metamorphic activity,
lithification. These changes happen at rela- as plankton). They are usually invisible fluid–rock interaction, or biological activity
tively low temperatures and pressures and to the naked eye.
Semiconducting mineral – a mineral of interme-
result in changes to the rock’s original miner- In 1990 Carl Woese proposed the three- diate electrical conductivity, between that of
alogy and texture. domain system that divides all living a metal and that of an insulator. Such
Dissimilatory iron reduction (DIR) – the process by things: bacteria, archaea, and eukaryotes minerals are characterized by a distinctive
which bacteria respire on Fe(III), resulting in (the latter includes fungi, protists, plants, electronic structure with a filled valence
the production of Fe(II). This process is and animals). Bacteria and archaea band and an empty conduction band. Some
linked to the oxidation of either organic or together constitute the prokaryotes, semiconducting minerals are light sensitive
inorganic compounds. organisms that lack a cell nucleus and and can carry out photocatalysis.
other membrane-bound organelles, in
Extracellular polymeric substances – polysaccha- contrast to eukaryotes. Bacteria and Semiconductor photocatalysis – light-induced
rides, proteins, and nucleic acids secreted by archaea function and reproduce as indi- reactions on the surface of a semiconductor.
microorganisms. These substances form vidual cells. Archaea differ from bacteria When light with energy higher than the
extracellular matrix and promote cell aggre- in genetics and biochemistry as well as band gap of a semiconductor irradiates it,
gation and biofilm formation. cell-membrane composition. Archaea negatively charged electrons and positively
Great Oxidation Event –the biologically induced were originally thought to live in extreme charged holes are generated in the conduc-
appearance of free oxygen in Earth’s atmo- environments, such as hot springs, but tion band and valence band, respectively, of
sphere around 2.4 billion years ago due to recently, archaea have been found in a the semiconductor. These electron–hole pairs
photosynthesis number of common habitats, such as undergo further redox reactions.
Heavy metal – a member of a loosely defined oceans and soils. Siderophore – a compound that forms strong
subset of elements that includes transition Eukaryotes contain organelles inside a complexes with Fe(III) and may contribute
metals, some metalloids, lanthanides, and cell and can be either unicellular or multi- to the weathering of Fe oxides and silicate
actinides; these normally have a high atomic cellular. Many eukaryotes are macro- minerals
weight and a specific gravity greater than 5.0. scopic, such as plants and animals, and Smectite – a group of clay minerals with a 2:1
They can be toxic or poisonous to life often visible to the naked eye. However, a structure (i.e. one octahedral layer sand-
at very low concentration. number of eukaryotes are also microbes, wiched between two tetrahedral layers) and
Illite – a clay mineral with a similar structure to including protists (such as algae species that display the property of expansion and
muscovite and smectite (2:1 structure). Its and slime molds) and fungi (such as contraction of their structure during a
composition lies between that of muscovite yeast). wetting and drying cycle
and that of smectite. Because of its high net Microbes live in normal Earth habitats, Smectite-to-illite reaction – smectite is stable at
negative charge (0.6–0.9 per half unit cell), such as groundwater and soils, as well as low temperature and pressure and is a major
its structure is not expandable. in a number of extreme environments, constituent of surface soils and sediments.
Iron chelators – small organic molecules that including deserts, saline lakes, the deep As these materials are buried, temperature
complex and increase the solubility and subsurface, hot springs, and the deep and pressure increase, and smectite becomes
mobility of Fe ocean f loor under high pressure. unstable and transforms to illite.
Microorganisms play important roles in
Iron hardpan – a laterally extensive or discon- Sulfate-reducing bacteria (SRB) – bacteria and
the biogeochemical cycling of carbon,
tinuous surface or subsurface layer covering archaea that obtain energy from the transfer
nitrogen, and other elements in both
tailings. In this layer, sulfates and iron oxides of electrons from hydrogen or organic
modern and ancient environments.
and (oxy)hydroxides produced by the weath- compounds to sulfate
Microbial diversity and abundance
ering of the top portion of the tailings fill usually decrease, and their biogeochem- Superoxide dismutases (SODs) – a class of enzymes
the intergranular pores and cement the ical functions become less active, in that catalyze the dismutation of superoxide
tailings. response to extreme environmental into oxygen and hydrogen peroxide. As such,
Light fuel cell (LFC) – an electrochemical system conditions. they are an important antioxidant defence
that converts solar energy into chemical and in nearly all cells exposed to oxygen.
electrical energy (Lu et al. 2012). The system Microbial fuel cell (MFC) – a type of bioelectro- Thermophile – an organism that prefers tempera-
consists of a semiconductor photocatalytic chemical system that consists of anodic and tures between 45 and 122 oC for growth
anode (photoanode) and a biological cathode cathodic chambers, usually separated by a
(biocathode), or a bioanode and a semicon- proton-exchange membrane. The two elec-
ductor photocathode. In an LFC, a semicon- trodes are connected by a conductive wire.
ductor photoanode generates photoelectrons Microbes biodegrade (oxidize) substrates in
upon irradiation by light, and the photoelec- the anodic chamber and transfer electrons
trons flow through a circuit into a biocathode. through a circuit to a terminal electron
Alternatively, a bioanode oxidizes organic acceptor at the cathode. This process can
substrates and transfers electrons to an irra- generate electricity.

E lements 100 A pr il 2012