Geomicrobiology

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The coccolithophore Gephyrocapsa oceanica may become an important carbon sink as the acidity of the ocean increases. Gephyrocapsa oceanica color.jpg
The coccolithophore Gephyrocapsa oceanica may become an important carbon sink as the acidity of the ocean increases.

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]

Contents

Rocks and minerals

Microbe-aquifer interactions

Microorganisms are known to impact aquifers by modifying their rates of dissolution. In the karstic Edwards 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.

Microbially precipitated minerals

Some bacteria use metal ions 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.

Soil and sediment: microbial remediation

Two scientists prepare samples of soil mixed with oil to test a microbe's ability to clean up contaminated soil. PNNL soil tests.jpg
Two scientists prepare samples of soil mixed with oil to test a microbe's ability to clean up contaminated soil.

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]

Acid mine drainage

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]

Microbial degradation of hydrocarbons

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

Paleoarchean (3.35-3.46 billion years old) stromatolite from Western Australia. Stromatolite (Strelley Pool Formation, Paleoarchean, 3.35-3.46 Ga; East Strelley Greenstone Belt, Pilbara Craton, Western Australia) 1 (17346619166).jpg
Paleoarchean (3.35-3.46 billion years old) stromatolite from Western Australia.

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

The colors of Grand Prismatic Spring in Yellowstone National Park are due to mats of thermophilic bacteria. Aerial image of Grand Prismatic Spring (view from the south).jpg
The colors of Grand Prismatic Spring in Yellowstone National Park are due to mats of thermophilic bacteria.

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 ridge black 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 anaerobic sulfate-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]

See also

Related Research Articles

<span class="mw-page-title-main">Extremophile</span> Organisms capable of living in extreme environments

An extremophile is an organism that is able to live in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, pressure, radiation, salinity, or pH level.

<span class="mw-page-title-main">Bioremediation</span> Process used to treat contaminated media such as water and soil

Bioremediation broadly refers to any process wherein a biological system, living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluents etc., in natural or artificial settings. The natural ability of organisms to adsorb, accumulate, and degrade common and emerging pollutants has attracted the use of biological resources in treatment of contaminated environment. In comparison to conventional physicochemical treatment methods bioremediation may offer advantages as it aims to be sustainable, eco-friendly, cheap, and scalable.

Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.

Biological augmentation is the addition of archaea or bacterial cultures required to speed up the rate of degradation of a contaminant. Organisms that originate from contaminated areas may already be able to break down waste, but perhaps inefficiently and slowly.

<i>Acidithiobacillus</i> Genus of bacteria

Acidithiobacillus is a genus of the Acidithiobacillia in the phylum "Pseudomonadota". This genus includes ten species of acidophilic microorganisms capable of sulfur and/or iron oxidation: Acidithiobacillus albertensis, Acidithiobacillus caldus, Acidithiobacillus cuprithermicus, Acidithiobacillus ferrianus, Acidithiobacillus ferridurans, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, Acidithiobacillus sulfuriphilus, and Acidithiobacillus thiooxidans.A. ferooxidans is the most widely studied of the genus, but A. caldus and A. thiooxidans are also significant in research. Like all "Pseudomonadota", Acidithiobacillus spp. are Gram-negative and non-spore forming. They also play a significant role in the generation of acid mine drainage; a major global environmental challenge within the mining industry. Some species of Acidithiobacillus are utilized in bioleaching and biomining. A portion of the genes that support the survival of these bacteria in acidic environments are presumed to have been obtained by horizontal gene transfer.

<span class="mw-page-title-main">Sulfate-reducing microorganism</span> Microorganisms that "breathe" sulfates

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 (SO2−
4) as terminal electron acceptor, reducing it to hydrogen sulfide (H2S). Therefore, these sulfidogenic microorganisms "breathe" sulfate rather than molecular oxygen (O2), which is the terminal electron acceptor reduced to water (H2O) in aerobic respiration.

<span class="mw-page-title-main">Sulfur cycle</span> Biogeochemical cycle of sulfur

The important sulfur cycle is a biogeochemical cycle in which the sulfur moves between rocks, waterways and living systems. It is important in geology as it affects many minerals and in life because sulfur is an essential element (CHNOPS), being a constituent of many proteins and cofactors, and sulfur compounds can be used as oxidants or reductants in microbial respiration. The global sulfur cycle involves the transformations of sulfur species through different oxidation states, which play an important role in both geological and biological processes. Steps of the sulfur cycle are:

Microbial 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. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

<span class="mw-page-title-main">Gammaproteobacteria</span> Class of bacteria

Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota. It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically important groups of bacteria belong to this class. All members of this class are Gram-negative. It is the most phylogenetically and physiologically diverse class of the Pseudomonadota.

Biomining refers to any process that uses living organisms to extract metals from ores and other solid materials. Typically these processes involve prokaryotes, however fungi and plants may also be used. Biomining is one of several applications within biohydrometallurgy with applications in ore refinement, precious metal recovery, and bioremediation. The largest application currently being used is the treatment of mining waste containing iron, copper, zinc, and gold allowing for salvation of any discarded minerals. It may also be useful in maximizing the yields of increasingly low grade ore deposits. Biomining has been proposed as a relatively environmentally friendly alternative and/or supplementation to traditional mining. Current methods of biomining are modified leach mining processes. These aptly named bioleaching processes most commonly includes the inoculation of extracted rock with bacteria and acidic solution, with the leachate salvaged and processed for the metals of value. Biomining has many applications outside of metal recovery, most notably is bioremediation which has already been used to clean up coastlines after oil spills. There are also many promising future applications, like space biomining, fungal bioleaching and biomining with hybrid biomaterials.

<span class="mw-page-title-main">Microbial mat</span> Multi-layered sheet of microorganisms

A microbial mat is a multi-layered sheet of microorganisms, mainly bacteria and archaea, or bacteria alone. Microbial mats grow at interfaces between different types of material, mostly on submerged or moist surfaces, but a few survive in deserts. A few are found as endosymbionts of animals.

<i>Nitratidesulfovibrio vulgaris</i> Species of bacterium

Nitratidesulfovibrio vulgaris is a species of Gram-negative sulfate-reducing bacteria in the Desulfovibrionaceae family. It is also an anaerobic sulfate-reducing bacterium that is an important organism involved in the bioremediation of heavy metals in the environment. Nitratidesulfovibrio vulgaris is often used as a model organism for sulfur-reducing bacteria and was the first of such bacteria to have its genome sequenced. It is ubiquitous in nature and has also been implicated in a variety of human bacterial infections, although it may only be an opportunistic pathogen. This microbe also has the ability to endure high salinity environments, which is done through the utilization of osmoprotectants and efflux systems.

<span class="mw-page-title-main">Redox gradient</span> Variation of the redox potential with distance (or depth)

A redox gradient is a series of reduction-oxidation (redox) reactions sorted according to redox potential. The redox ladder displays the order in which redox reactions occur based on the free energy gained from redox pairs. These redox gradients form both spatially and temporally as a result of differences in microbial processes, chemical composition of the environment, and oxidative potential. Common environments where redox gradients exist are coastal marshes, lakes, contaminant plumes, and soils.

Arsenate-reducing bacteria are bacteria which reduce arsenates. Arsenate-reducing bacteria are ubiquitous in arsenic-contaminated groundwater (aqueous environment). Arsenates are salts or esters of arsenic acid (H3AsO4), consisting of the ion AsO43−. They are moderate oxidizers that can be reduced to arsenites and to arsine. Arsenate can serve as a respiratory electron acceptor for oxidation of organic substrates and H2S or H2. Arsenates occur naturally in minerals such as adamite, alarsite, legrandite, and erythrite, and as hydrated or anhydrous arsenates. Arsenates are similar to phosphates since arsenic (As) and phosphorus (P) occur in group 15 (or VA) of the periodic table. Unlike phosphates, arsenates are not readily lost from minerals due to weathering. They are the predominant form of inorganic arsenic in aqueous aerobic environments. On the other hand, arsenite is more common in anaerobic environments, more mobile, and more toxic than arsenate. Arsenite is 25–60 times more toxic and more mobile than arsenate under most environmental conditions. Arsenate can lead to poisoning, since it can replace inorganic phosphate in the glyceraldehyde-3-phosphate --> 1,3-biphosphoglycerate step of glycolysis, producing 1-arseno-3-phosphoglycerate instead. Although glycolysis continues, 1 ATP molecule is lost. Thus, arsenate is toxic due to its ability to uncouple glycolysis. Arsenate can also inhibit pyruvate conversion into acetyl-CoA, thereby blocking the TCA cycle, resulting in additional loss of ATP.

Bioremediation of petroleum contaminated environments is a process in which the biological pathways within microorganisms or plants are used to degrade or sequester toxic hydrocarbons, heavy metals, and other volatile organic compounds found within fossil fuels. Oil spills happen frequently at varying degrees along with all aspects of the petroleum supply chain, presenting a complex array of issues for both environmental and public health. While traditional cleanup methods such as chemical or manual containment and removal often result in rapid results, bioremediation is less labor-intensive, expensive, and averts chemical or mechanical damage. The efficiency and effectiveness of bioremediation efforts are based on maintaining ideal conditions, such as pH, RED-OX potential, temperature, moisture, oxygen abundance, nutrient availability, soil composition, and pollutant structure, for the desired organism or biological pathway to facilitate reactions. Three main types of bioremediation used for petroleum spills include microbial remediation, phytoremediation, and mycoremediation. Bioremediation has been implemented in various notable oil spills including the 1989 Exxon Valdez incident where the application of fertilizer on affected shoreline increased rates of biodegradation.

Mars habitability analogue environments on Earth are environments that share potentially relevant astrobiological conditions with Mars. These include sites that are analogues of potential subsurface habitats, and deep subsurface habitats.

<span class="mw-page-title-main">Frederick Colwell</span>

Frederick (Rick) Colwell is a microbial ecologist specializing in subsurface microbiology and geomicrobiology. He is a professor of ocean ecology and biogeochemistry at Oregon State University, and an adjunct and affiliate faculty member at Idaho State University.

<span class="mw-page-title-main">Hydrothermal vent microbial communities</span> Undersea unicellular organisms

The hydrothermal vent microbial community includes all unicellular organisms that live and reproduce in a chemically distinct area around hydrothermal vents. These include organisms in the microbial mat, free floating cells, or bacteria in an endosymbiotic relationship with animals. Chemolithoautotrophic bacteria derive nutrients and energy from the geological activity at Hydrothermal vents to fix carbon into organic forms. Viruses are also a part of the hydrothermal vent microbial community and their influence on the microbial ecology in these ecosystems is a burgeoning field of research.

The deep biosphere is the part of the biosphere that resides below the first few meters of the surface. It extends down at least 5 kilometers below the continental surface and 10.5 kilometers below the sea surface, at temperatures that may reach beyond 120 °C (248 °F) which is comparable to the maximum temperature where a metabolically active organism has been found. It includes all three domains of life and the genetic diversity rivals that on the surface.

<span class="mw-page-title-main">Gold cycle</span>

The gold cycle is the biogeochemical cycling of gold through the lithosphere, hydrosphere, atmosphere, and biosphere. Gold is a noble transition metal that is highly mobile in the environment and subject to biogeochemical cycling, driven largely by microorganisms. Gold undergoes processes of solubilization, stabilization, bioreduction, biomineralization, aggregation, and ligand utilization throughout its cycle. These processes are influenced by various microbial populations and cycling of other elements such as carbon, nitrogen, and sulfur. Gold exists in several forms in the Earth's surface environment including Au(I/III)-complexes, nanoparticles, and placer gold particles. The gold biogeochemical cycle is highly complex and strongly intertwined with cycling of other metals including silver, copper, iron, manganese, arsenic, and mercury. Gold is important in the biotech field for applications such as mineral exploration, processing and remediation, development of biosensors and drug delivery systems, industrial catalysts, and for recovery of gold from electronic waste.

References

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  29. ↑ 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. S2CID   199636268.
  30. ↑ World's Oldest Groundwater Supports Life Through Water-Rock Chemistry Archived 2019-09-10 at the Wayback Machine , July 29, 2019, deepcarbon.net.
  31. ↑ Strange life-forms found deep in a mine point to vast 'underground Galapagos', By Corey S. Powell, Sept. 7, 2019, nbcnews.com.

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