Geomicrobiology is the scientific field at the intersection of
geology and
microbiology and is a major subfield of
geobiology. It concerns the role of
microbes on geological and
geochemical processes and effects of minerals and metals to microbial growth, activity and survival.[2] Such interactions occur in the
geosphere (rocks, minerals, soils, and sediments), the
atmosphere and the
hydrosphere.[3] Geomicrobiology studies microorganisms that are driving the Earth's
biogeochemical cycles, mediating mineral precipitation and dissolution, and sorbing and concentrating metals.[4] The applications include for example
bioremediation,[5]mining,
climate change mitigation[6] and public
drinking water supplies.[7]
Rocks and minerals
Microbe-aquifer interactions
Microorganisms are known to impact
aquifers by modifying their rates of dissolution. In the
karsticEdwards Aquifer, microbes colonizing the aquifer surfaces enhance the dissolution rates of the host rock.[8]
In the
oceanic crustal aquifer, the largest aquifer on Earth,[9] microbial communities can impact ocean
productivity, sea water chemistry as well as geochemical cycling throughout the
geosphere. The mineral make-up of the rocks affects the composition and abundance of these subseafloor microbial communities present.[10] Through
bioremediation some microbes can aid in decontaminating freshwater resources in aquifers contaminated by waste products.
Some bacteria use
metalions 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.
Biohydrometallurgy 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.[11]
Subsurface environments, like aquifers, are attractive locations when selecting repositories for
nuclear waste,
carbon dioxide (See
carbon sequestration), or as artificial reservoirs for
natural gas. Understanding microbial activity within the aquifer is important since it may interact with and effect the stability of the materials within the underground repository.[12] Microbe-mineral interactions contribute to
biofouling 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.[13]
Environmental remediation
Microbes are being studied and used to degrade organic and even
nuclear waste pollution (see
Deinococcus radiodurans) and assist in environmental cleanup. An application of geomicrobiology is
bioleaching, the use of microbes to extract metals from
mine waste.
Microbial remediation is used in soils to remove contaminants and pollutants. Microbes play a key role in many
biogeochemistry cycles and can effect a variety of soil properties, such as
biotransformation 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,
radionuclides,
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).[2] 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 (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 depend on oxidation states of chromium.[14] Two of the most common chromium species are Cr(III) and Cr(VI). Cr(VI) is highly mobile, bioavailable and more toxic to
flora and
fauna, while Cr(III) is less toxic, more immobile and readily precipitates in soils with
pH >6.[15] 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.[16]
Another application of geomicrobiology is
bioleaching, 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).[17]
Bioremediation techniques are also used on contaminated
surface water and
ground water often associated with acid mine drainage. Studies have shown that the production of
bicarbonate by microbes such as sulfate-reducing bacteria adds
alkalinity to neutralize the acidity of the mine drainage waters.[5]Hydrogen ions are consumed while bicarbonate is produced which leads to an increase in pH (decrease in acidity).[18]
Microbes can affect the quality of
oil and gas deposits through their metabolic processes.[19] 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 and water
radiolysis,[12] 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.[20][21]
Interactions between microbes and sediment record some of the earliest evidence of life on earth. Information on the life during
Archean Earth is recorded in bacterial fossils and
stromatolites preserved in precipitated lithologies such as chert or carbonates.[22][23] 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.[24]Microbially induced sedimentary structures (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.[25] 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 organisms, the microorganisms that thrive in environments normally considered hostile to life. Such environments may include extremely hot (
hot springs or
mid-ocean ridgeblack smoker) environments, extremely
saline environments, or even space environments such as
Martian soil or
comets.[4]
Observations and research in hyper-saline
lagoon environments in
Brazil and
Australia as well as slightly saline, inland lake environments in NW
China have shown that
anaerobicsulfate-reducing bacteria may be directly involved in the formation of
dolomite.[27] This suggests the alteration and replacement of
limestone sediments by
dolomitization in ancient rocks was possibly aided by ancestors to these anaerobic bacteria.[28]
In July 2019, a scientific study of
Kidd Mine in Canada discovered
sulfur-breathing organisms 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.[29][30][31]
^
abKonhauser, K. (2007). Introduction to geomicrobiology. Malden, MA: Blackwell Pub.
ISBN978-1444309027.
^
abKaksonen, A.H.; Puhakka, J.A (2007). "Sulfate Reduction Based Bioprocesses for the Treatment of Acid Mine Drainage and the Recovery of Metals". Engineering in Life Sciences. 7 (6): 541–564.
doi:
10.1002/elsc.200720216.
S2CID95354248.
^McCollom, Thomas M.; Christopher, Donaldson (2016). "Generation of hydrogen and methane during experimental low-temperature reaction of ultramafic rocks with water". Astrobiology. 16 (6): 389–406.
Bibcode:
2016AsBio..16..389M.
doi:
10.1089/ast.2015.1382.
PMID27267306.
^Deng, S; Dong, H; Hongchen, J; Bingsong, Y; Bishop, M (2010). "Microbial dolomite precipitation using sulfate reducing and halophilic bacteria: results from Quighai Lake, Tibetan Plateau, NW China". Chemical Geology. 278 (3–4): 151–159.
Bibcode:
2010ChGeo.278..151D.
doi:
10.1016/j.chemgeo.2010.09.008.
^Dillon, Jesse (2011). "The Role of Sulfate Reduction in Stromatolites and Microbial Mats: Ancient and Modern Perspectives". In Tewari, V.; Seckbach, J. (eds.). STROMATOLITES: Interaction of Microbes with Sediments. Cellular Origin, Life in Extreme Habitats and Astrobiology. Vol. 18. pp. 571–590.
doi:
10.1007/978-94-007-0397-1_25.
ISBN978-94-007-0396-4.
^Lollar, Garnet S.; Warr, Oliver; Telling, Jon; Osburn, Magdalena R.; Lollar, Barbara Sherwood (2019). "'Follow the Water': Hydrogeochemical Constraints on Microbial Investigations 2.4 km Below Surface at the Kidd Creek Deep Fluid and Deep Life Observatory". Geomicrobiology Journal. 36 (10): 859–872.
doi:
10.1080/01490451.2019.1641770.
S2CID199636268.