HOME

TheInfoList



OR:

''Geobacter'' is a genus of bacteria. ''Geobacter'' species are
anaerobic respiration 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. In aerobic organisms undergoing re ...
bacterial species which have capabilities that make them useful in
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 ...
. ''Geobacter'' was found to be the first organism with the ability to
oxidize Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or ...
organic compounds and metals, including iron, radioactive metals, and petroleum compounds into environmentally benign
carbon dioxide Carbon dioxide ( chemical formula ) is a chemical compound made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature. In the air, carbon dioxide is tr ...
while using
iron oxide Iron oxides are chemical compounds composed of iron and oxygen. Several iron oxides are recognized. All are black magnetic solids. Often they are non-stoichiometric. Oxyhydroxides are a related class of compounds, perhaps the best known of which ...
or other available metals as electron acceptors. ''Geobacter'' species are also found to be able to respire upon a
graphite Graphite () is a crystalline form of the element carbon. It consists of stacked layers of graphene. Graphite occurs naturally and is the most stable form of carbon under standard conditions. Synthetic and natural graphite are consumed on lar ...
electrode An electrode is an electrical conductor used to make contact with a nonmetallic part of a circuit (e.g. a semiconductor, an electrolyte, a vacuum or air). Electrodes are essential parts of batteries that can consist of a variety of materials de ...
. They have been found in anaerobic conditions in soils and aquatic sediment.


History

''
Geobacter metallireducens ''Geobacter metallireducens'' is a gram-negative metal-reducing proteobacterium. It is a strict anaerobe that oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. It can al ...
'' was first isolated by Derek Lovley in 1987 in sand sediment from the
Potomac River The Potomac River () drains the Mid-Atlantic United States, flowing from the Potomac Highlands into Chesapeake Bay. It is long,U.S. Geological Survey. National Hydrography Dataset high-resolution flowline dataThe National Map. Retrieved Augu ...
in Washington D.C. The first strain was deemed strain GS-15.


Metabolic mechanisms

For quite some time, it was thought that ''Geobacter'' species lacked c-cytochromes that can be utilized to reduce metal ions, hence it was assumed that they required direct physical contact in order to use metal ions as terminal electron acceptors (TEAs). The discovery of the highly conductive pili in ''Geobacter'' species, and the proposal of using them as biological nano-wires further strengthened this view. Nevertheless, recent discoveries have revealed that many ''Geobacter'' species, such as '' Geobacter uraniireducens,'' not only do not possess highly conductive pili, but also do not need direct physical contact in order to utilize the metal ions as TEAs, suggesting that there is a great variety of extracellular electron transport mechanisms among the ''Geobacter'' species. For example, one other way of transporting electrons is via a quinone-mediated electron shuttle, which is observed in '' Geobacter sulfurreducens''. Another observed metabolic phenomenon is the cooperation between ''Geobacter''
species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
, in which several species cooperate in
metabolizing Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...
a mixture of chemicals that neither could process alone. Provided with
ethanol Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an alcohol with the chemical formula . Its formula can be also written as or (an ethyl group linked to a ...
and sodium fumarate, ''G. metallireducens'' broke down the ethanol, generating an excess of
electrons The electron ( or ) is a subatomic particle with a negative one elementary electric charge. Electrons belong to the first generation of the lepton particle family, and are generally thought to be elementary particles because they have no ...
that were passed to ''G. sulfurreducens'' via
nanowires A nanowire is a nanostructure in the form of a wire with the diameter of the order of a nanometre (10−9 metres). More generally, nanowires can be defined as structures that have a thickness or diameter constrained to tens of nanometers or les ...
grown between them, enabling ''G. sulfurreducens'' to break down the fumarate ions. The nanowires are made of proteins with metal-like conductivity.


Applications


Biodegradation and bioremediation

''Geobacters ability to consume oil-based pollutants and radioactive material with
carbon dioxide Carbon dioxide ( chemical formula ) is a chemical compound made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature. In the air, carbon dioxide is tr ...
as waste byproduct has been used in environmental clean-up for underground
petroleum Petroleum, also known as crude oil, or simply oil, is a naturally occurring yellowish-black liquid mixture of mainly hydrocarbons, and is found in geological formations. The name ''petroleum'' covers both naturally occurring unprocessed crude ...
spills and for the precipitation of
uranium Uranium is a chemical element with the symbol U and atomic number 92. It is a silvery-grey metal in the actinide series of the periodic table. A uranium atom has 92 protons and 92 electrons, of which 6 are valence electrons. Uranium is weak ...
out of groundwater. ''Geobacter'' degrade the material by creating electrically conductive pili between itself and the pollutant material, using it as an electron source. Microbial biodegradation of recalcitrant organic
pollutant A pollutant or novel entity is a substance or energy introduced into the environment that has undesired effects, or adversely affects the usefulness of a resource. These can be both naturally forming (i.e. minerals or extracted compounds like o ...
s is of great environmental significance and involves intriguing novel biochemical reactions. In particular,
hydrocarbon In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons are generally colourless and hydrophobic, and their odors are usually weak ...
s and halogenated compounds have long been doubted to be anaerobically degradable, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria documented these processes in nature. Novel biochemical reactions were discovered, enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was slowed by the absence of genetic systems for most of them. However, several complete genome sequences later became available for such bacteria. The genome of the hydrocarbon degrading and iron-reducing species ''G. metallireducens'' (accession nr. NC_007517) was determined in 2008. The genome revealed the presence of genes for reductive
dehalogenase A dehalogenase is a type of enzyme that catalyzes the removal of a halogen atom from a substrate. Examples include: * Reductive dehalogenases * 4-chlorobenzoate dehalogenase * 4-chlorobenzoyl-CoA dehalogenase * Dichloromethane dehalogenase * ...
s, suggesting a wide dehalogenating spectrum. Moreover, genome sequences provided 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 (ET) occurs when an electron relocates from an atom or molecule to another such chemical entity. ET is a mechanistic description of certain kinds of redox reactions involving transfer of electrons. Electrochemical processes ar ...
is an important
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 ...
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 In biology and other experimental sciences, an ''in silico'' experiment is one performed on computer or via computer simulation. The phrase is pseudo-Latin for 'in silicon' (correct la, in silicio), referring to silicon in computer chips. It ...
'' models that can predict the growth and metabolism of ''Geobacter'' species under a diversity of subsurface conditions. The
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
s of multiple ''Geobacter'' species have been sequenced. Detailed functional genomic/physiological studies on one species, ''G. sulfurreducens'' was conducted.
Genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
-based models of several ''Geobacter'' species that are able to predict physiological responses under different environmental conditions are available. Quantitative analysis of gene transcript levels during ''in situ''
uranium Uranium is a chemical element with the symbol U and atomic number 92. It is a silvery-grey metal in the actinide series of the periodic table. A uranium atom has 92 protons and 92 electrons, of which 6 are valence electrons. Uranium is weak ...
bioremediation demonstrated that it is possible to track ''in situ'' rates of metabolism and the ''in situ'' metabolic state of ''Geobacter'' in the subsurface.


Biofilm conductivity

Many ''Geobacter'' species, such as ''G. sulfureducens'', are capable of creating thick networks of
biofilm A biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular p ...
s on
microbial fuel cell Microbial fuel cell (MFC) is a type of bioelectrochemical fuel cell system that generates electric current by diverting electrons produced from the microbial oxidation of reduced compounds (also known as fuel or electron donor) on the anode to oxid ...
anodes for extracellular electron transfer. Cytochromes within the biofilm associate with pili to form extracellular structures called
nanowire A nanowire is a nanostructure in the form of a wire with the diameter of the order of a nanometre (10−9 metres). More generally, nanowires can be defined as structures that have a thickness or diameter constrained to tens of nanometers or less ...
s, which facilitate extracellular electron transfer throughout the biofilm. These cytochromes accept electrons from the microorganisms as well as from other reduced cytochromes present in the biofilm. Electric currents are produced when the transfer of these electrons to anodes is coupled to the oxidation of intracellular organic wastes. Previous research has proposed that the high conductivity of ''Geobacter'' biofilms can be used to power microbial fuel cells and to generate electricity from organic waste products. In particular, ''G. sulfureducens'' holds one of the highest records for microbial fuel cell current density that researchers have ever been able to measure in vitro. This ability can be attributed to biofilm conductivity, as highly conductive biofilms have been found to be positively correlated with high current densities in microbial fuel cells. At the moment, the development of microbial fuel cells for power generation purposes is partly restricted by its inefficiency compared to other sources of power and an insufficient understanding of extracellular electron transfer. As such, many researchers are currently studying how we can utilize biofilm conductivity to our advantage to produce even higher current densities. Low pH environments have been found to change redox potentials, thus inhibiting electron transfer from microorganisms to cytochromes. In addition, biofilms have been found to become less conductive with decreasing temperature, although raising the temperature back up again can restore biofilm conductivity without any adverse effects. The presence of pili or flagella on ''Geobacter'' species has been found to increase electric current generation by enabling more efficient electron transfer. These different factors can be tweaked to produce maximum electricity and to optimize bioremediation in the future.


Neuromorphic memristor

In a University of Massachusetts Amherst study, a neuromorphic memory (memristor) utilized Geobacter biofilm cut into thin nanowire strands. The nanowire strands conduct a low voltage similar to that of a neurons in a human brain. In a paper co-authored by Derek Lovely, Jun Yao observed that his team can "modulate the conductivity, or the plasticity of the nanowire-memristor synapse so it can emulate biological components for brain-inspired computing....". The breakthrough observation came as they monitored voltage activity at a sub 1 volt level.


Phylogeny

The currently accepted taxonomy is based on the
List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical ...
(LPSN) and
National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. Th ...
(NCBI)


Popular culture

''Geobacter'' has become an icon for teaching about microbial electrogenesis and microbial fuel cells and has appeared in educational kits that are available for students and hobbyists. ''Geobacter'' is also used to generate electricity via electrode grid in Amazon, Peru.


See also

* '' Shewanella'' *
List of bacterial orders This article lists the orders of the Bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16 ...
*
List of bacteria genera This article lists the genera of the bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). However many taxonomic names a ...


References


External links

*
LPSN List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bou ...

Genus: Geobacter
*

* [https://web.archive.org/web/20090318063410/http://www.israel21c.org/bin/en.jsp?enDispWho=Articles%5El2303&enPage=BlankPage&enDisplay=view&enDispWhat=object&enVersion=0&enZone=Technology An electrifying solution] {{Taxonbar, from=Q1979991 Thermodesulfobacteriota Bacteria genera