Geobacter Benzoatilyticus
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''Geobacter'' is a genus of
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
. ''Geobacter'' species use
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 ...
to alter the redox state of minerals and many pollutants, a trait that makes them useful in
bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, wate ...
. ''Geobacter'' was the first organism described with the ability to completely
oxidize Redox ( , , reduction–oxidation or oxidation–reduction) is a type of chemical reaction in which the oxidation states of the reactants change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is ...
organic compounds to carbon dioxide, and transfer these electrons to metals such as Fe(III), Mn(IV), and U(VI). ''Geobacter'' species are also found to be able to transfer electrons to conductive surfaces such as
graphite Graphite () is a Crystallinity, crystalline allotrope (form) of the element carbon. It consists of many stacked Layered materials, layers of graphene, typically in excess of hundreds of layers. Graphite occurs naturally and is the most stable ...
electrodes 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 a gas). In electrochemical cells, electrodes are essential parts that can consist of a variety ...
. They are found in anaerobic habitats including wetlands, subsurface aquifers, 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 R Lovley in 1987 in sand sediment from the
Potomac River The Potomac River () is in the Mid-Atlantic (United States), Mid-Atlantic region of the United States and flows from the Potomac Highlands in West Virginia to Chesapeake Bay in Maryland. It is long,U.S. Geological Survey. National Hydrography D ...
in Washington D.C. The first strain was deemed strain GS-15.


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 of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...
(LPSN) and
National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the 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. The NCBI is lo ...
(NCBI). Species incertae sedis: * "''Ca.'' G. eutrophica" corrig. Mei et al. 2018 * "''G. hephaestius''" Janssen 2004 * "''G. humireducens''" Holmes et al. 2003 Assigned to different genera: *''
Geobacter argillaceus ''Geobacter argillaceus'' is a non-spore-forming and motile bacterium from the genus ''Geobacter ''Geobacter'' is a genus of bacteria. ''Geobacter'' species use anaerobic respiration to alter the redox state of minerals and many pollutants, ...
'' Shelobolina et al. 2007 (Shelobolina et al. 2007) Xu et al. 2021">''Geomobilibacter argillaceus''" (Shelobolina et al. 2007) Xu et al. 2021*''
Geobacter lovleyi ''Geobacter lovleyi'' is a gram-negative metal-reducing and tetrachloroethene- dechlorinating proteobacterium. It has potential as a bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria ...
'' Sung et al. 2009 'Trichlorobacter lovleyi'' (Sung et al. 2009) Waite et al. 2020*''
Geobacter psychrophilus ''Geobacter psychrophilus'' is a Fe(III)-reducing bacterium. It is Gram-negative, slightly curved, rod-shaped and motile via means of monotrichous flagella A flagellum (; : flagella) (Latin for 'whip' or 'scourge') is a hair-like appendage t ...
'' Nevin et al. 2005 (Nevin et al. 2005) Waite et al. 2020">''Pseudopelobacter psychrophilus''" (Nevin et al. 2005) Waite et al. 2020*''
Geobacter thiogenes ''Geobacter thiogenes'' is a bacterium from the genus ''Geobacter ''Geobacter'' is a genus of bacteria. ''Geobacter'' species use anaerobic respiration to alter the redox state of minerals and many pollutants, a trait that makes them useful ...
'' (De Wever et al. 2001) Nevin et al. 2007 'Trichlorobacter thiogenes'' De Wever et al. 2001


Metabolic mechanisms

Based on experiments physically separating Fe(III) oxides from cells, using dialysis menbranes or gels to sequester the metals, evidence suggested cells required direct physical contact in order to use metal ions as terminal electron acceptors (TEAs). The discovery of conductive filaments extending from ''Geobacter'' species, and the finding that mutations eliminating these filaments decreased growth with metals led to the proposal of "
bacterial nanowires Bacterial nanowires (also known as microbial nanowires) are electrically conductive appendages produced by a number of bacteria most notably from the ''Geobacter'' and '' Shewanella'' genera. Conductive nanowires have also been reported in the oxy ...
" able to connect cells to metals. These nanowires were first proposed to be pili, but have since been shown to be made of cytochromes assembled into long conductive fibers. Recent discoveries have revealed that some ''Geobacter'' species, such as ''
Geobacter uraniireducens ''Geobacter uraniireducens'' (more recently known as ''Geotalea uraniireducens'') is a gram-negative, rod-shaped, anaerobicchemolithotrophic mesophilic, and motile bacterium from the genus of ''Geobacter''. G. ''uraniireducens'' has been found t ...
,'' not only do not seem to possess conductive filaments, but also do not need direct physical contact in order to utilize the metal ions, suggesting some ''Geobacter'' species may secrete soluble molecules that carry electrons beyond the cell. For example, one other way of transporting electrons is via a flavin-mediated electron shuttle, which is observed in ''Shewanella'' ''.'' Another observed metabolic phenomenon is the cooperation between ''Geobacter''
species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...
, in which several species cooperate in metabolizing a mixture of chemicals that neither could process alone. For example, when supplied with
ethanol Ethanol (also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound with the chemical formula . It is an Alcohol (chemistry), alcohol, with its formula also written as , or EtOH, where Et is the ps ...
as an electron donor and fumarate as the electron acceptor, ''G. metallireducens'' oxidized the ethanol, generating an excess of
electrons The electron (, or in nuclear reactions) is a subatomic particle with a negative one elementary charge, elementary electric charge. It is a fundamental particle that comprises the ordinary matter that makes up the universe, along with up qua ...
that were passed through direct electrical transfer to ''G. sulfurreducens'' via
nanowires upright=1.2, Crystalline 2×2-atom tin selenide nanowire grown inside a single-wall carbon nanotube (tube diameter ≈1 nm). A nanowire is a nanostructure in the form of a wire with the diameter of the order of a nanometre (10−9 m). Mor ...
grown between them, enabling ''G. sulfurreducens'' to reduce the fumarate .


Applications


Biodegradation and bioremediation

''Geobacters ability to oxidize oil-based pollutants and reduce radioactive materials 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 chemical mixture found in geological formations, consisting mainly of hydrocarbons. The term ''petroleum'' refers both to naturally occurring un ...
spills and for the precipitation of reduced
uranium Uranium is a chemical element; it has chemical symbol, 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. Ura ...
out of groundwater.
Microbial biodegradation Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons (e ...
of recalcitrant organic
pollutant A pollutant or novel entity is a substance or energy introduced into the environment that has undesired effect, or adversely affects the usefulness of a resource. These can be both naturally forming (i.e. minerals or extracted compounds like oi ...
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 Hydrophobe, hydrophobic; their odor is usually fain ...
s and
halogenated In chemistry, halogenation is a chemical reaction which introduces one or more halogens into a chemical compound. Halide-containing compounds are pervasive, making this type of transformation important, e.g. in the production of polymers, drugs ...
compounds have long been doubted to be anaerobically degradable, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
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 The halogens () are a group in the periodic table consisting of six chemically related elements: fluorine (F), chlorine (Cl), bromine (Br), iodine (I), and the radioac ...
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, ion, or molecule, to another such chemical entity. ET describes the mechanism by which electrons are transferred in redox reactions. Electrochemical processes are ET reactio ...
is an important
bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, wate ...
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 a computer or via computer simulation software. The phrase is pseudo-Latin for 'in silicon' (correct ), referring to silicon in computer chips. It was c ...
'' models that can predict the growth and metabolism of ''Geobacter'' species under a diversity of subsurface conditions. The
genome 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 genes, other functional regions of the genome such as ...
s of multiple ''Geobacter'' species have been sequenced. Detailed functional genomic/physiological studies on one species, ''G. sulfurreducens'' was conducted.
Genome 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 genes, other functional regions of the genome such as ...
-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; it has chemical symbol, 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. Ura ...
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 is a Syntrophy, syntrophic Microbial consortium, community of microorganisms in which cell (biology), cells cell adhesion, stick to each other and often also to a surface. These adherent cells become embedded within a slimy ext ...
s on the anodes of
microbial fuel cell Microbial fuel cell (MFC) is a type of bioelectrochemical fuel cell system also known as micro fuel cell that generates electric current by diverting electrons produced from the microbial oxidation of reduced compounds (also known as fuel or ele ...
for extracellular electron transfer. While prior imaging experiments suggested cytochromes within the biofilm associate with pili to form extracellular structures called
nanowire file:SnSe@SWCNT.jpg, upright=1.2, Crystalline 2×2-atom tin selenide nanowire grown inside a single-wall carbon nanotube (tube diameter ≈1 nm). A nanowire is a nanostructure in the form of a wire with the diameter of the order of a nanometre ( ...
s, when the structures of nanowires were solved it was found that these filaments were actually composed only of cytochromes. These cytochrome nanowires carry electrons from one microorganism to the next, and ultimately are accepted by the electrode, allowing the entire biofilm to respire. 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 measured 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 low current density (mA per square centimeter of electrode) compared to industrial sources of power, and an poor understanding of what limits extracellular electron transfer over long distances in biofilms. 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 proposed to form inside biofilms, limiting electron transfer from microorganisms to cytochromes. The presence of nonconductive filaments such as pili or flagella on ''Geobacter'' species has been proposed to affect current generation by interfering with efficient electron transfer. Factors limiting the individual turnover rate of cells, and how many cells can link together in a biofilm, will both need to be understood to maximize electricity production in the future.


Neuromorphic memristor

In a University of Massachusetts Amherst study, a neuromorphic memory (memristor) utilized Geobacter biofilm cut into thin nanowire strands, although the proteins or DNA making up the nanowires remains unknown. 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....".


Popular culture

''Geobacter'' has become an icon for teaching about microbial
electrogenesis Electroreception and electrogenesis are the closely related biological abilities to perceive electrical stimuli and to generate electric fields. Both are used to locate prey; stronger electric discharges are used in a few groups of fishes, such ...
and microbial fuel cells and has appeared in educational kits that are available for students and hobbyists.


See also

*
Forest ring Forest rings are large, circular patterns of low tree density in the boreal forests of northern Canada. These rings can range from to nearly in diameter, with rims about in thickness. The origin of forest rings is not known, despite several me ...
*
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 Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, ...
* ''
Shewanella ''Shewanella'' is the sole genus included in the marine bacteria family Shewanellaceae. Some species within it were formerly classed as '' Alteromonas''. ''Shewanella'' consists of facultatively anaerobic Gram-negative rods, most of which are fou ...
''


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 image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practi ...

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