Geomicrobiology is the scientific field at the intersection of geology and microbiology. It concerns the role of microbes on geological and geochemical processes and effects of minerals and metals to microbial growth, activity and survival. Such interactions occur in the geosphere (rocks, minerals, soils, and sediments), the atmosphere and the hydrosphere. Geomicrobiology studies microorganisms that are driving the Earth's biogeochemical cycles, mediating mineral precipitation and dissolution, and sorbing and concentrating metals.  The applications include for example bioremediation, mining, climate change mitigation and public drinking water supplies.
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.
In the oceanic crustal aquifer, the largest aquifer on Earth, 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. Through bioremediation some microbes can aid in decontaminating freshwater resources in aquifers contaminated by waste products.
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.
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. 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.
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). 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. 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. 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.
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).
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. Hydrogen ions are consumed while bicarbonate is produced which leads to an increase in pH (decrease in acidity).
Microbes can affect the quality of oil and gas 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.
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, 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 Earth is recorded in bacterial fossils and stromatolites 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 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. The different paleoenvironments of early life on Earth also serves as model when searching for potential fossil life on Mars.
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.
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. This suggests the alteration and replacement of limestone sediments by dolomitization 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 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. 
Antje Boetius (born 5 March 1967) is a German marine biologist presently serving as professor of geomicrobiology at the Max Planck Institute for Marine Microbiology, University of Bremen. She received the Gottfried Wilhelm Leibniz Prize, with 2.5 million euros in funding, in March 2009 for her study of sea bed microorganisms that affect the global climate. She was the first person to describe anaerobic oxidation of methane, and believes the Earth's earliest life forms may have subsisted on methane in the absence of molecular oxygen (instead reducing oxygen-containing compounds such as nitrate or sulfate). She has also suggested such life forms may be able to reduce the rate of climate change in future. She is one the laureate of the 2018 Environment Prize (German Environment Foundation)Applied and Environmental Microbiology
Applied and Environmental Microbiology is a biweekly peer-reviewed scientific journal published by the American Society for Microbiology. It was established in 1953 as Applied Microbiology and obtained its current name in 1975. Articles older than six months are available free of cost from the website, however, the newly published articles within six months are available to subscribers only. According to the Journal Citation Reports, the journal has a 2017 impact factor of 3.633. The journal has been ranked as one of the top 100 journals over the past 100 years in the fields of biology and medicine. The current editor-in-chief is Harold L. Drake (University of Bayreuth).
The journal's scope includes "(a) applied microbiology, including biotechnology, protein engineering, bioremediation, and food microbiology, (b) microbial ecology, including environmental, organismic, and genomic microbiology, and (c) interdisciplinary microbiology, including invertebrate microbiology, plant microbiology, aquatic microbiology, and geomicrobiology".Astrobiology (journal)
Astrobiology is a peer-reviewed scientific journal covering research on the origin, evolution, distribution and future of life across the universe. The journal's scope includes astrophysics, astropaleontology, bioastronomy, cosmochemistry, ecogenomics, exobiology, extremophiles, geomicrobiology, gravitational biology, life detection technology, meteoritics, origins of life, planetary geoscience, planetary protection, prebiotic chemistry, space exploration technology and terraforming.Biogeophysics
Biogeophysics is a subdiscipline of geophysics concerned with how plants, microbial activity and other organisms alter geologic materials and affect geophysical signatures.Biosignature
A biosignature (sometimes called chemical fossil or molecular fossil) is any substance – such as an element, isotope, or molecule – or phenomenon that provides scientific evidence of past or present life. Measurable attributes of life include its complex physical or chemical structures and its use of free energy and the production of biomass and wastes. A biosignature can provide evidence for living organisms outside the Earth and can be directly or indirectly detected by searching for their unique byproducts.Blood Falls
Blood Falls is an outflow of an iron oxide-tainted plume of saltwater, flowing from the tongue of Taylor Glacier onto the ice-covered surface of West Lake Bonney in the Taylor Valley of the McMurdo Dry Valleys in Victoria Land, East Antarctica.
Iron-rich hypersaline water sporadically emerges from small fissures in the ice cascades. The saltwater source is a subglacial pool of unknown size overlain by about 400 metres (1,300 ft) of ice several kilometers from its tiny outlet at Blood Falls.
The reddish deposit was found in 1911 by the Australian geologist Griffith Taylor, who first explored the valley that bears his name. The Antarctica pioneers first attributed the red color to red algae, but later it was proven to be due to iron oxides.Charles S. Cockell
Charles Seaton Cockell (born 21 May 1967) is a British astrobiologist who is the current professor of astrobiology in the School of Physics and Astronomy at the University of Edinburgh and Director of the UK Centre for Astrobiology. . He was previously the Professor of Geomicrobiology with the Open University and a microbiologist with the British Antarctic Survey, Cambridge, UK. His scientific interests have focused on astrobiology, geomicrobiology and life in extreme environments. He has published over 300 scientific papers and books in these areas . He has contributed to plans for the human exploration of Mars. For example, he led the design study Project Boreas, which planned and designed a research station for the Martian polar ice caps. He was the first Chair of the Astrobiology Society of Britain.Deep biosphere
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. It includes all three domains of life and the genetic diversity rivals that on the surface.Extremophile
An extremophile (from Latin extremus meaning "extreme" and Greek philiā (φιλία) meaning "love") is an organism with optimal growth in environmental conditions considered extreme in comparison to the environmental conditions that are comfortable to humans. In contrast, organisms that live in more moderate environmental conditions, according to an anthropocentric view, may be termed mesophiles or neutrophiles.Frederick Colwell
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.GFAJ-1
GFAJ-1 is a strain of rod-shaped bacteria in the family Halomonadaceae. It is an extremophile that was isolated from the hypersaline and alkaline Mono Lake in eastern California by geobiologist Felisa Wolfe-Simon, a NASA research fellow in residence at the US Geological Survey. In a 2010 Science journal publication, the authors claimed that the microbe, when starved of phosphorus, is capable of substituting arsenic for a small percentage of its phosphorus to sustain its growth. Immediately after publication, other microbiologists and biochemists expressed doubt about this claim which was robustly criticized in the scientific community. Subsequent independent studies published in 2012 found no detectable arsenate in the DNA of GFAJ-1, refuted the claim, and demonstrated that GFAJ-1 is simply an arsenate-resistant, phosphate-dependent organism.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, evolutionary biology, microbiology, paleontology, and particularly soil science and biogeochemistry. Geobiology applies the principles and methods of biology, geology, and soil science to the study of the ancient history of the co-evolution of life and Earth as well as the role of life in the modern world. Geobiologic studies tend to be focused on microorganisms, and on the role that life plays in altering the chemical and physical environment of the pedosphere, which exists at the intersection of the lithosphere, atmosphere, hydrosphere and/or cryosphere. It differs from biogeochemistry in that the focus is on processes and organisms over space and time rather than on global chemical cycles.
Geobiological research synthesizes the geologic record with modern biologic studies. It deals with process - how organisms affect the Earth and vice versa - as well as history - how the Earth and life have changed together. Much research is grounded in the search for fundamental understanding, but geobiology can also be applied, as in the case of microbes that clean up oil spills.Geobiology employs molecular biology, environmental microbiology, chemical analyses, and the geologic record to investigate the evolutionary interconnectedness of life and Earth. It attempts to understand how the Earth has changed since the origin of life and what it might have been like along the way. Some definitions of geobiology even push the boundaries of this time frame - to understanding the origin of life and to the role that man has played and will continue to play in shaping the Earth in the Anthropocene.Halomonadaceae
Halomonadaceae is a family of halophilic Proteobacteria.Halotolerance
Halotolerance is the adaptation of living organisms to conditions of high salinity. Halotolerant species tend to live in areas such as hypersaline lakes, coastal dunes, saline deserts, salt marshes, and inland salt seas and springs. Halophiles are organisms that live in highly saline environments, and require the salinity to survive, while halotolerant organisms (belonging to different domains of life) can grow under saline conditions, but do not require elevated concentrations of salt for growth. Halophytes are salt-tolerant higher plants. Halotolerant microorganisms are of considerable biotechnological interest.Katrina Edwards
Katrina Jane Edwards (15 March 1968 - 26 October 2014) was a pioneering geomicrobiologist known for her studies of organisms living below the ocean floor, specifically exploring the interactions between the microbes and their geological surroundings, and how global processes were influenced by these interactions. She spearheaded the Center for Dark Energy Biosphere Investigation (C-DEBI) project at the University of Southern California, which is ongoing. Edwards also helped organize the deep biosphere research community by heading the Fe-Oxidizing Microbial Observatory Project on Loihi Seamount, and serving on several program steering committees involving ocean drilling. Edwards taught at the Woods Hole Oceanographic Institute (WHOI) and later became a professor at the University of Southern California.Nanobacterium
Nanobacterium ( NAN-oh-bak-TEER-ee-əm, pl. nanobacteria NAN-oh-bak-TEER-ee-ə) is the unit or member name of a proposed class of living organisms, specifically cell-walled microorganisms with a size much smaller than the generally accepted lower limit for life (about 200 nm for bacteria, like mycoplasma). Originally based on observed nano-scale structures in geological formations (including one meteorite), the status of nanobacteria has been controversial, with some researchers suggesting they are a new class of living organism capable of incorporating radiolabeled uridine, and others attributing to them a simpler, abiotic nature. One skeptic dubbed them "the cold fusion of microbiology", in reference to a notorious episode of supposed erroneous science. The term "calcifying nanoparticles" (CNPs) has also been used as a conservative name regarding their possible status as a life form.
Research tends to agree that these structures exist, and appear to replicate in some way. However, the idea that they are living entities has now largely been discarded, and the particles are instead thought to be nonliving crystallizations of minerals and organic molecules.Penelope Boston
Penelope J. Boston is a speleologist. She is associate director of the National Cave and Karst Research Institute in Carlsbad, New Mexico, and founder and director of the Cave and Karst Studies Program at New Mexico Institute of Mining and Technology in Socorro. Among her research interests are geomicrobiology of caves and mines, extraterrestrial speleogenesis, and space exploration and astrobiology generally.In the mid-1980s, Boston (then a graduate student at the University of Colorado Boulder) was one of the founders of the Mars Underground and helped organize a series of conferences called The Case for Mars. In March 2016 Boston was named the Director for NASA Astrobiology Institute. Her appointment is effective May 31, 2016.Sulfate-reducing microorganisms
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 (SO42–) 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.
Most sulfate-reducing microorganisms can also reduce some other oxidized inorganic sulfur compounds, such as sulfite (SO32–), dithionite (S2O42–), thiosulfate (S2O32–), trithionate (S3O62–), tetrathionate (S4O62−), elemental sulfur (S8), and polysulfides (Sn2−). Depending on the context, "sulfate-reducing microorganisms" can be used in a broader sense (including all species that can reduce any of these sulfur compounds) or in a narrower sense (including only species that reduce sulfate, and excluding strict thiosulfate and sulfur reducers, for example).
Sulfate-reducing microorganisms can be traced back to 3.5 billion years ago and are considered to be among the oldest forms of microbes, having contributed to the sulfur cycle soon after life emerged on Earth.Many organisms reduce small amounts of sulfates in order to synthesize sulfur-containing cell components; this is known as assimilatory sulfate reduction. By contrast, the sulfate-reducing microorganisms considered here reduce sulfate in large amounts to obtain energy and expel the resulting sulfide as waste; this is known as dissimilatory sulfate reduction. They use sulfate as the terminal electron acceptor of their electron transport chain. Most of them are anaerobes; however there are examples of sulfate-reducing microorganisms that are tolerant of oxygen, and some of them can even perform aerobic respiration. No growth is observed when oxygen is used as the electron acceptor.
In addition, there are sulfate-reducing microorganisms that can also reduce other electron acceptors, such as fumarate, nitrate (NO3−), nitrite (NO2−), ferric iron [Fe(III)], and dimethyl sulfoxide.In terms of electron donor, this group contains both organotrophs and lithotrophs. The organotrophs oxidize organic compounds, such as carbohydrates, organic acids (e.g., formate, lactate, acetate, propionate, and butyrate), alcohols (methanol and ethanol), aliphatic hydrocarbons (including methane), and aromatic hydrocarbons (benzene, toluene, ethylbenzene, and xylene). The lithotrophs oxidize molecular hydrogen (H2), for which they compete with methanogens and acetogens in anaerobic conditions. Some sulfate-reducing microorganisms can directly utilize metallic iron [Fe(0)] as electron donor, oxidizing it to ferrous iron [Fe(II)].Zetaproteobacteria
The class Zetaproteobacteria is the sixth and most recently described class of the Proteobacteria. Zetaproteobacteria can also refer to the group of organisms assigned to this class. The Zetaproteobacteria are represented by a single described species, Mariprofundus ferrooxydans, which is an iron-oxidizing neutrophilic chemolithoautotroph originally isolated from Loihi Seamount in 1996 (post-eruption). Molecular cloning techniques focusing on the small subunit ribosomal RNA gene have also been used to identify a more diverse majority of the Zetaproteobacteria that have as yet been unculturable.Regardless of culturing status, the Zetaproteobacteria show up worldwide in estuarine and marine habitats associated with opposing steep redox gradients of reduced (ferrous) iron and oxygen, either as a minor detectable component or as the dominant member of the microbial community. Zetaproteobacteria have been most commonly found at deep-sea hydrothermal vents, though recent discovery of members of this class in near-shore environments has led to the reevaluation of Zetaproteobacteria distribution and significance.
|History of geology|
|Сomposition and structure|