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Geomicrobiology is the scientific field at the intersection of geology and microbiology and is a major subfield of
geobiology Geobiology is a field of scientific research that explores the interactions between the physical Earth and the biosphere. It is a relatively young field, and its borders are fluid. There is considerable overlap with the fields of ecology, evolutio ...
. It concerns the role of
microbe A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
s on geological and geochemical processes and effects of minerals and metals to microbial growth, activity and survival. Such interactions occur in the
geosphere There are several conflicting usages of geosphere, variously defined. It may be taken as the collective name for the lithosphere, the hydrosphere, the cryosphere, and the atmosphere. The different collectives of the geosphere are able to exchange ...
(rocks, minerals, soils, and sediments), the
atmosphere An atmosphere () is a layer of gas or layers of gases that envelop a planet, and is held in place by the gravity of the planetary body. A planet retains an atmosphere when the gravity is great and the temperature of the atmosphere is low. A s ...
and the
hydrosphere The hydrosphere () is the combined mass of water found on, under, and above the surface of a planet, minor planet, or natural satellite. Although Earth's hydrosphere has been around for about 4 billion years, it continues to change in shape. This ...
. Geomicrobiology studies microorganisms that are driving the Earth's
biogeochemical cycle A biogeochemical cycle (or more generally a cycle of matter) is the pathway by which a chemical substance cycles (is turned over or moves through) the biotic and the abiotic compartments of Earth. The biotic compartment is the biosphere and the ...
s, mediating mineral precipitation and dissolution, and sorbing and concentrating metals. The applications include for example
bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi, and plants), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluent ...
, mining,
climate change mitigation Climate change mitigation is action to limit climate change by reducing emissions of greenhouse gases or removing those gases from the atmosphere. The recent rise in global average temperature is mostly caused by emissions from fossil fuels bu ...
and public drinking water supplies.


Rocks and minerals


Microbe-aquifer interactions

Microorganisms are known to impact
aquifer An aquifer is an underground layer of water-bearing, permeable rock, rock fractures, or unconsolidated materials (gravel, sand, or silt). Groundwater from aquifers can be extracted using a water well. Aquifers vary greatly in their characteris ...
s by modifying their rates of dissolution. In the
karst Karst is a topography formed from the dissolution of soluble rocks such as limestone, dolomite, and gypsum. It is characterized by underground drainage systems with sinkholes and caves. It has also been documented for more weathering-resistant ...
ic
Edwards Aquifer The Edwards Aquifer is one of the most prolific artesian aquifers in the world. Located on the eastern edge of the Edwards Plateau in the U.S. state of Texas, it is the source of drinking water for two million people, and is the primary water s ...
, microbes colonizing the aquifer surfaces enhance the dissolution rates of the host rock. In the
oceanic crust Oceanic crust is the uppermost layer of the oceanic portion of the tectonic plates. It is composed of the upper oceanic crust, with pillow lavas and a dike complex, and the lower oceanic crust, composed of troctolite, gabbro and ultramafic c ...
al aquifer, the largest aquifer on Earth, microbial communities can impact ocean productivity, sea water chemistry as well as geochemical cycling throughout the
geosphere There are several conflicting usages of geosphere, variously defined. It may be taken as the collective name for the lithosphere, the hydrosphere, the cryosphere, and the atmosphere. The different collectives of the geosphere are able to exchange ...
. The mineral make-up of the rocks affects the composition and abundance of these subseafloor microbial communities present. Through
bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi, and plants), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluent ...
some microbes can aid in decontaminating freshwater resources in aquifers contaminated by waste products.


Microbially precipitated minerals

Some bacteria use
metal A metal (from Greek μέταλλον ''métallon'', "mine, quarry, metal") is a material that, when freshly prepared, polished, or fractured, shows a lustrous appearance, and conducts electricity and heat relatively well. Metals are typica ...
ion An ion () is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by conv ...
s as their energy source. They convert (or chemically reduce) the dissolved metal ions from one electrical state to another. This reduction releases energy for the bacteria's use, and, as a side product, serves to concentrate the metals into what ultimately become
ore deposits Ore is natural rock or sediment that contains one or more valuable minerals, typically containing metals, that can be mined, treated and sold at a profit.Encyclopædia Britannica. "Ore". Encyclopædia Britannica Online. Retrieved 7 April ...
.
Biohydrometallurgy Biohydrometallurgy is a technique in the world of metallurgy that utilizes biological agents (bacteria) to recover and treat metals such as copper. Modern biohydrometallurgy advances started with the bioleaching of copper more efficiently in the 195 ...
or ''in situ'' mining is where low-grade ores may be attacked by well-studied microbial processes under controlled conditions to extract metals. Certain iron, copper, uranium and even gold ores are thought to have formed as the result of microbe action. Subsurface environments, like aquifers, are attractive locations when selecting repositories for nuclear waste, carbon dioxide (See
carbon sequestration Carbon sequestration is the process of storing carbon in a carbon pool. Carbon dioxide () is naturally captured from the atmosphere through biological, chemical, and physical processes. These changes can be accelerated through changes in lan ...
), or as artificial reservoirs for
natural gas Natural gas (also called fossil gas or simply gas) is a naturally occurring mixture of gaseous hydrocarbons consisting primarily of methane in addition to various smaller amounts of other higher alkanes. Low levels of trace gases like carbon di ...
. Understanding microbial activity within the aquifer is important since it may interact with and effect the stability of the materials within the underground repository. Microbe-mineral interactions contribute to
biofouling Biofouling or biological fouling is the accumulation of microorganisms, plants, algae, or small animals where it is not wanted on surfaces such as ship and submarine hulls, devices such as water inlets, pipework, grates, ponds, and rivers tha ...
and microbially induced corrosion. Microbially induced corrosion of materials, such as carbon steel, have serious implications in the safe storage of radioactive waste within repositories and storage containers.


Environmental remediation

Microbes are being studied and used to degrade organic and even nuclear waste pollution (see
Deinococcus radiodurans ''Deinococcus radiodurans'' is an extremophilic bacterium and one of the most radiation-resistant organisms known. It can survive cold, dehydration, vacuum, and acid, and therefore is known as a polyextremophile. It has been listed as the world ...
) and assist in environmental cleanup. An application of geomicrobiology is
bioleaching Bioleaching is the extraction of metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide. Bioleaching is one of several applications within biohydrometallurgy and several ...
, the use of microbes to extract metals from mine waste.


Soil and sediment: microbial remediation

Microbial remediation is used in soils to remove contaminants and pollutants. Microbes play a key role in many
biogeochemistry Biogeochemistry is the scientific discipline that involves the study of the chemical, physical, geological, and biological processes and reactions that govern the composition of the natural environment (including the biosphere, the cryosphere ...
cycles and can effect a variety of soil properties, such as
biotransformation Biotransformation is the biochemical modification of one chemical compound or a mixture of chemical compounds. Biotransformations can be conducted with whole cells, their lysates, or purified enzymes. Increasingly, biotransformations are effected w ...
of mineral and metal speciation, toxicity, mobility, mineral precipitation, and mineral dissolution. Microbes play a role in the immobilization and detoxification of a variety of elements, such as
metals A metal (from Greek μέταλλον ''métallon'', "mine, quarry, metal") is a material that, when freshly prepared, polished, or fractured, shows a lustrous appearance, and conducts electricity and heat relatively well. Metals are typicall ...
,
radionuclide A radionuclide (radioactive nuclide, radioisotope or radioactive isotope) is a nuclide that has excess nuclear energy, making it unstable. This excess energy can be used in one of three ways: emitted from the nucleus as gamma radiation; transferr ...
s, sulfur and phosphorus, in the soil. Thirteen metals are considered priority pollutants (Sb, As, Be, Cd, Cr, Cu, Pb, Ni, Se, Ag, Tl, Zn, Hg). Soils and sediment act as sinks for metals which originate from both natural sources through rocks and minerals as well as anthropogenic sources through agriculture, industry, mining, waste disposal, among others. Many heavy metals, such as
chromium Chromium is a chemical element with the symbol Cr and atomic number 24. It is the first element in group 6. It is a steely-grey, lustrous, hard, and brittle transition metal. Chromium metal is valued for its high corrosion resistance and hardne ...
(Cr), at low concentrations are essential micronutrients in the soil, however they can be toxic at higher concentrations. Heavy metals are added into soils through many anthropogenic sources such industry and/or fertilizers. Heavy metal interaction with microbes can increase or decrease the toxicity. Levels of chromium toxicity, mobility and
bioavailability In pharmacology, bioavailability is a subcategory of absorption and is the fraction (%) of an administered drug that reaches the systemic circulation. By definition, when a medication is administered intravenously, its bioavailability is 100%. H ...
depend on oxidation states of chromium. Two of the most common chromium species are Cr(III) and Cr(VI). Cr(VI) is highly mobile, bioavailable and more toxic to
flora Flora is all the plant life present in a particular region or time, generally the naturally occurring ( indigenous) native plants. Sometimes bacteria and fungi are also referred to as flora, as in the terms '' gut flora'' or ''skin flora''. ...
and fauna, while Cr(III) is less toxic, more immobile and readily precipitates in soils with pH >6. Utilizing microbes to facilitate the transformation of Cr(VI) to Cr(III) is an environmentally friendly, low cost bioremediation technique to help mitigate toxicity in the environment.


Acid mine drainage

Another application of geomicrobiology is
bioleaching Bioleaching is the extraction of metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide. Bioleaching is one of several applications within biohydrometallurgy and several ...
, the use of microbes to extract metals from mine waste. For example, sulfate-reducing bacteria (SRB) produce H2S which precipitates metals as a metal sulfide. This process removed heavy metals from mine waste which is one of the major environmental issues associated with acid mine drainage (along with a low pH). Bioremediation techniques are also used on contaminated surface water and
ground water Groundwater is the water present beneath Earth's surface in rock and soil pore spaces and in the fractures of rock formations. About 30 percent of all readily available freshwater in the world is groundwater. A unit of rock or an unconsolidate ...
often associated with acid mine drainage. Studies have shown that the production of
bicarbonate In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogencarbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula . Bicarbonate serves a crucial biochemic ...
by microbes such as sulfate-reducing bacteria adds
alkalinity Alkalinity (from ar, القلوي, al-qaly, lit=ashes of the saltwort) is the capacity of water to resist acidification. It should not be confused with basicity, which is an absolute measurement on the pH scale. Alkalinity is the strength o ...
to neutralize the acidity of the mine drainage waters.
Hydrogen ion A hydrogen ion is created when a hydrogen atom loses or gains an electron. A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle ...
s are consumed while bicarbonate is produced which leads to an increase in pH (decrease in acidity).


Microbial degradation of hydrocarbons

Microbes can affect the quality of
oil and gas A fossil fuel is a hydrocarbon-containing material formed naturally in the Earth's crust from the remains of dead plants and animals that is extracted and burned as a fuel. The main fossil fuels are coal, oil, and natural gas. Fossil fuels ...
deposits through their metabolic processes. Microbes can influence the development of hydrocarbons by being present at the time of deposition of the source sediments or by dispersing through the rock column to colonize reservoir or source lithologies after the generation of hydrocarbons.


Early Earth history and astrobiology

A common field of study within geomicrobiology is origin of life on earth or other planets. Various rock-water interactions, such as
serpentinization Serpentinization is a hydration and metamorphic transformation of ferromagnesian minerals, such as olivine and pyroxene, in mafic and ultramafic rock to produce serpentinite. Minerals formed by serpentinization include the serpentine group miner ...
and water radiolysis, are possible sources of metabolic energy to support chemolithoautotrophic microbial communities on Early Earth and on other planetary bodies such as Mars, Europa and Enceladus. Interactions between microbes and sediment record some of the earliest evidence of life on earth. Information on the life during
Archean The Archean Eon ( , also spelled Archaean or Archæan) is the second of four geologic eons of Earth's history, representing the time from . The Archean was preceded by the Hadean Eon and followed by the Proterozoic. The Earth during the Archea ...
Earth is recorded in bacterial fossils and
stromatolites Stromatolites () or stromatoliths () are layered sedimentary formations (microbialite) that are created mainly by photosynthetic microorganisms such as cyanobacteria, sulfate-reducing bacteria, and Pseudomonadota (formerly proteobacteria). The ...
preserved in precipitated lithologies such as chert or carbonates. Additional evidence of early life on land around 3.5 billion years ago can be found in the Dresser formation of Australia in a hot spring facies, indicating that some of Earth's earliest life on land occurred in hot springs.
Microbially induced sedimentary structure Microbially induced sedimentary structures (MISS) are primary sedimentary structures formed by the interaction of microbes with sediment and physical agents of erosion, deposition, and transportation. The structures commonly form when microbial ma ...
s (MISS) are found throughout the geologic record up to 3.2 billion years old. They are formed by the interaction of microbial mats and physical sediment dynamics, and record paleoenvironmental data as well as providing evidence of early life. The paleoenvironments of early life on Earth also serve as models when searching for potential fossil life on Mars.


Extremophiles

Another area of investigation in geomicrobiology is the study of
extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme tem ...
organisms, the microorganisms that thrive in environments normally considered hostile to life. Such environments may include extremely hot ( hot springs or mid-ocean ridge
black smoker A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspot ...
) environments, extremely saline environments, or even space environments such as Martian soil or
comet A comet is an icy, small Solar System body that, when passing close to the Sun, warms and begins to release gases, a process that is called outgassing. This produces a visible atmosphere or coma, and sometimes also a tail. These phenomena are ...
s. Observations and research in hyper-saline
lagoon A lagoon is a shallow body of water separated from a larger body of water by a narrow landform, such as reefs, barrier islands, barrier peninsulas, or isthmuses. Lagoons are commonly divided into ''coastal lagoons'' (or ''barrier lagoons'' ...
environments in Brazil and Australia as well as slightly saline, inland lake environments in NW China have shown that
anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: * Anaerobic adhesive, a bonding a ...
sulfate-reducing bacteria may be directly involved in the formation of
dolomite Dolomite may refer to: *Dolomite (mineral), a carbonate mineral *Dolomite (rock), also known as dolostone, a sedimentary carbonate rock *Dolomite, Alabama, United States, an unincorporated community *Dolomite, California, United States, an unincor ...
. This suggests the alteration and replacement of limestone sediments by
dolomitization Dolomitization is a geological process by which the carbonate mineral dolomite is formed when magnesium ions replace calcium ions in another carbonate mineral, calcite. It is common for this mineral alteration into dolomite to take place due to ...
in ancient rocks was possibly aided by ancestors to these anaerobic bacteria. In July 2019, a scientific study of Kidd Mine in Canada discovered
sulfur-breathing organisms Sulfate-reducing microorganisms (SRM) or sulfate-reducing prokaryotes (SRP) are a group composed of sulfate-reducing bacteria (SRB) and sulfate-reducing archaea (SRA), both of which can perform anaerobic respiration utilizing sulfate () as termi ...
which live 7900 feet below the surface, and which breathe sulfur in order to survive. these organisms are also remarkable due to eating rocks such as pyrite as their regular food source.Strange life-forms found deep in a mine point to vast 'underground Galapagos'
By Corey S. Powell, Sept. 7, 2019, nbcnews.com.


See also

* Bacterial oxidation * Desulforudis audaxviator * Deep biosphere


References


Further reading

* * * * *


External links


Gold mines may be formed by bacteria - PDF file
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