Geobacter
Encyclopedia
Geobacter is a genus of proteobacteria
. Geobacter are an anaerobic respiration
bacterial species which have capabilities that make them useful in bioremediation
. The geobacter was found to be the first organism with the ability to oxidize organic compounds and metals, including iron
, radioactive metals and petroleum compounds into environmentally benign carbon dioxide
while using iron oxide
or other available metals as electron acceptor.
in Washington D.C. The first strain was deemed strain GS-15. Geobacter have been found in anaerobic conditions in soils and aquatic sediment.
out of groundwater. Geobacter metabolize the material by creating pili
between itself and the food material.
It has been shown that species of Geobacter are able to cooperate in metabolizing a mixture of chemicals that neither could process alone. Provided with ethanol and sodium fumarate, G. metallireducens broke down the ethanol generating an excess of electrons which were passed to G. sulfurreducens via "nanowires" grown between the species, enabling G. sulfurreducens to break down the fumarate ions.
The production of electricity
during this process has also led scientists to theorize that Geobacter could act as a natural battery
. This natural battery could use renewable biomass such as compost materials, or be used to convert human and animal solid waste into electricity. There are also potential applications in the field of nanotechnology
for the creation of microbial nanowires
in very small circuits and electronic devices. The nanowires could also be connected, creating a microscopic power grid.
of recalcitrant organic pollutant
s is of great environmental significance and involves intriguing novel biochemical reactions. In particular, hydrocarbon
s and halogenated compounds have long been doubted to be degradable in the absence of oxygen, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria
during the last decades provided ultimate proof for these processes in nature. Many novel biochemical reactions were discovered enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was rather slow, since genetic systems are not readily applicable for most of them. However, several complete genome sequences are now available for bacteria capable of anaerobic organic pollutant degradation. The genome of the hydrocarbon degrading and iron-reducing species Geobacter metallireducens (accession nr. NC_007517) was determined recently. The genome revealed the presence of genes for reductive dehalogenases, suggesting a wide dehalogenating spectrum of the organisms. Moreover, genome sequences provided unprecedented insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.
Geobacter species are often the predominant organisms when extracellular electron transfer
is an important bioremediation
process in subsurface environments. Therefore, a systems biology approach to understanding and optimizing bioremediation with Geobacter species has been initiated with the ultimate goal of developing in silico models that can predict the growth and metabolism of Geobacter species under a diversity of subsurface conditions. To date, these studies have included sequencing the genome
s of multiple Geobacter species and detailed functional genomic/physiological studies on one species, Geobacter sulfurreducens . Genome-based models of several Geobacter species that are able to predict physiological responses under different environmental conditions are now available. Quantitative analysis of gene transcript levels during in situ uranium
bioremediation has demonstrated that it is possible to track in situ rates of metabolism and the in situ metabolic state of Geobacter in the subsurface. Initial attempts to link in silico Geobacter models with existing subsurface hydrological and geochemical models are underway. It is expected that this systems approach to bioremediation with Geobacter will provide the opportunity to evaluate multiple Geobacter -catalyzed bioremediation strategies in silico prior to field implementation, thus providing substantial savings when initiating large-scale in situ bioremediation projects for groundwater
polluted with uranium and/or organic contaminants.
.
Proteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....
. Geobacter are an anaerobic respiration
Anaerobic respiration
Anaerobic respiration is a form of respiration using electron acceptors other than oxygen. Although oxygen is not used as the final electron acceptor, the process still uses a respiratory electron transport chain; it is respiration without oxygen...
bacterial species which have capabilities that make them useful in bioremediation
Bioremediation
Bioremediation is the use of microorganism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated...
. The geobacter was found to be the first organism with the ability to oxidize organic compounds and metals, including iron
Iron
Iron is a chemical element with the symbol Fe and atomic number 26. It is a metal in the first transition series. It is the most common element forming the planet Earth as a whole, forming much of Earth's outer and inner core. It is the fourth most common element in the Earth's crust...
, radioactive metals and petroleum compounds into environmentally benign carbon dioxide
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
while using iron oxide
Iron oxide
Iron oxides are chemical compounds composed of iron and oxygen. All together, there are sixteen known iron oxides and oxyhydroxides.Iron oxides and oxide-hydroxides are widespread in nature, play an important role in many geological and biological processes, and are widely utilized by humans, e.g.,...
or other available metals as electron acceptor.
History
Geobacter metallireducens was first isolated by Derek Lovley in 1987 in sand sediment from the Potomac RiverPotomac River
The Potomac River flows into the Chesapeake Bay, located along the mid-Atlantic coast of the United States. The river is approximately long, with a drainage area of about 14,700 square miles...
in Washington D.C. The first strain was deemed strain GS-15. Geobacter have been found in anaerobic conditions in soils and aquatic sediment.
Potential and actual applications
Research on the potential of Geobacter is underway and on-going. Geobacters ability to consume oil-based pollutants and radioactive material with carbon dioxide as waste byproduct has already been used in environmental clean-up for underground petroleum spills and for the precipitation of uraniumUranium
Uranium is a silvery-white metallic chemical element in the actinide series of the periodic table, with atomic number 92. It is assigned the chemical symbol U. A uranium atom has 92 protons and 92 electrons, of which 6 are valence electrons...
out of groundwater. Geobacter metabolize the material by creating pili
Pilus
right|thumb|350px|Schematic drawing of bacterial conjugation. 1- Donor cell produces pilus. 2- Pilus attaches to recipient cell, brings the two cells together. 3- The mobile plasmid is nicked and a single strand of DNA is then transferred to the recipient cell...
between itself and the food material.
It has been shown that species of Geobacter are able to cooperate in metabolizing a mixture of chemicals that neither could process alone. Provided with ethanol and sodium fumarate, G. metallireducens broke down the ethanol generating an excess of electrons which were passed to G. sulfurreducens via "nanowires" grown between the species, enabling G. sulfurreducens to break down the fumarate ions.
The production of electricity
Electricity
Electricity is a general term encompassing a variety of phenomena resulting from the presence and flow of electric charge. These include many easily recognizable phenomena, such as lightning, static electricity, and the flow of electrical current in an electrical wire...
during this process has also led scientists to theorize that Geobacter could act as a natural battery
Battery (electricity)
An electrical battery is one or more electrochemical cells that convert stored chemical energy into electrical energy. Since the invention of the first battery in 1800 by Alessandro Volta and especially since the technically improved Daniell cell in 1836, batteries have become a common power...
. This natural battery could use renewable biomass such as compost materials, or be used to convert human and animal solid waste into electricity. There are also potential applications in the field of nanotechnology
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
for the creation of microbial nanowires
Bacterial Nanowires
Bacterial nanowires are electrically conductive appendages produced by a number of bacteria most notably from the Geobacter and Shewanella genera...
in very small circuits and electronic devices. The nanowires could also be connected, creating a microscopic power grid.
Biodegradation and Bioremediation
Microbial biodegradationMicrobial biodegradation
Interest in the microbial biodegradation of pollutants has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments...
of recalcitrant organic pollutant
Pollutant
A pollutant is a waste material that pollutes air, water or soil, and is the cause of pollution.Three factors determine the severity of a pollutant: its chemical nature, its concentration and its persistence. Some pollutants are biodegradable and therefore will not persist in the environment in the...
s is of great environmental significance and involves intriguing novel biochemical reactions. In particular, hydrocarbon
Hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons from which one hydrogen atom has been removed are functional groups, called hydrocarbyls....
s and halogenated compounds have long been doubted to be degradable in the absence of oxygen, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
during the last decades provided ultimate proof for these processes in nature. Many novel biochemical reactions were discovered enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was rather slow, since genetic systems are not readily applicable for most of them. However, several complete genome sequences are now available for bacteria capable of anaerobic organic pollutant degradation. The genome of the hydrocarbon degrading and iron-reducing species Geobacter metallireducens (accession nr. NC_007517) was determined recently. The genome revealed the presence of genes for reductive dehalogenases, suggesting a wide dehalogenating spectrum of the organisms. Moreover, genome sequences provided unprecedented insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.
Geobacter species are often the predominant organisms when extracellular electron transfer
Electron transfer
Electron transfer is the process by which an electron moves from an atom or a chemical species to another atom or chemical species...
is an important bioremediation
Bioremediation
Bioremediation is the use of microorganism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated...
process in subsurface environments. Therefore, a systems biology approach to understanding and optimizing bioremediation with Geobacter species has been initiated with the ultimate goal of developing in silico models that can predict the growth and metabolism of Geobacter species under a diversity of subsurface conditions. To date, these studies have included sequencing the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s of multiple Geobacter species and detailed functional genomic/physiological studies on one species, Geobacter sulfurreducens . Genome-based models of several Geobacter species that are able to predict physiological responses under different environmental conditions are now available. Quantitative analysis of gene transcript levels during in situ uranium
Uranium
Uranium is a silvery-white metallic chemical element in the actinide series of the periodic table, with atomic number 92. It is assigned the chemical symbol U. A uranium atom has 92 protons and 92 electrons, of which 6 are valence electrons...
bioremediation has demonstrated that it is possible to track in situ rates of metabolism and the in situ metabolic state of Geobacter in the subsurface. Initial attempts to link in silico Geobacter models with existing subsurface hydrological and geochemical models are underway. It is expected that this systems approach to bioremediation with Geobacter will provide the opportunity to evaluate multiple Geobacter -catalyzed bioremediation strategies in silico prior to field implementation, thus providing substantial savings when initiating large-scale in situ bioremediation projects for groundwater
Groundwater
Groundwater is water located beneath the ground surface in soil pore spaces and in the fractures of rock formations. A unit of rock or an unconsolidated deposit is called an aquifer when it can yield a usable quantity of water. The depth at which soil pore spaces or fractures and voids in rock...
polluted with uranium and/or organic contaminants.
Popular culture
Geobacter are used as a plot device in the first episode of the third season of ReGenesisReGenesis
ReGenesis is a Canadian television program produced by The Movie Network and Movie Central in conjunction with Shaftesbury Films. The series, which ran for four seasons, revolves around the scientists of NorBAC , a fictional organization with a lab based in Toronto...
.