Geobacter

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Geobacter
Geobacter sulfurreducens.TIF
Geobacter sulfurreducens
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Phylum: Thermodesulfobacteriota
Class: Desulfuromonadia
Order: Geobacterales
Family: Geobacteraceae
Genus: Geobacter
Lovley et al. 1995 [1]
Type species
Geobacter metallireducens
Lovley et al. 1995
Species

See text

Geobacter is a genus of bacteria. Geobacter species are anaerobic respiration bacterial species which have capabilities that make them useful in bioremediation. 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 acceptors. [2] Geobacter species are also found to be able to respire upon a graphite electrode. [3] They have been found in anaerobic conditions in soils and aquatic sediment. [4]

Contents

History

Geobacter metallireducens was first isolated by Derek R Lovley in 1987 in sand sediment from the Potomac River in Washington D.C. The first strain was deemed strain GS-15. [5]

Geobacter spp. and methanotrophs, such as Candidatus Methylomirabilis and Methylobacter, were highly abundant in samples from the 'Bean' and the 'Thorn North' ring, in Ontario, Canada. [6]

Species

Currently accepted species based on the List of Prokaryotic names with Standing in Nomenclature (LPSN). [1]

Metabolic mechanisms

For quite some time,[ when? ] 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). [7] The discovery of the highly conductive pili in Geobacter species, and the proposal of using them as biological nano-wires further strengthened this view. [7] 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. [8] For example, one other way of transporting electrons is via a quinone-mediated electron shuttle, which is observed in Geobacter sulfurreducens . [9]

Another observed metabolic phenomenon is the cooperation between Geobacter species, in which several species 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 that were passed to G. sulfurreducens via nanowires grown between them, enabling G. sulfurreducens to break down the fumarate ions. [10] The nanowires are made of proteins with metal-like conductivity. [11]

Applications

Biodegradation and bioremediation

Geobacter's ability to consume oil-based pollutants and radioactive material with carbon dioxide as waste byproduct has been used in environmental clean-up for underground petroleum spills and for the precipitation of uranium out of groundwater. [12] [13] Geobacter degrade the material by creating electrically conductive pili between itself and the pollutant material, using it as an electron source. [14]

Microbial biodegradation of recalcitrant organic pollutants is of great environmental significance and involves intriguing novel biochemical reactions. In particular, hydrocarbons 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 dehalogenases, suggesting a wide dehalogenating spectrum. Moreover, genome sequences provided insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation. [15]

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. The genomes of multiple Geobacter species have been sequenced. Detailed functional genomic/physiological studies on one species, G. sulfurreducens was conducted. Genome-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 bioremediation demonstrated that it is possible to track in situ rates of metabolism and the in situ metabolic state of Geobacter in the subsurface. [16]

Biofilm conductivity

Many Geobacter species, such as G. sulfureducens, are capable of creating thick networks of biofilms on microbial fuel cell anodes for extracellular electron transfer. [17] Cytochromes within the biofilm associate with pili to form extracellular structures called nanowires, which facilitate extracellular electron transfer throughout the biofilm. [18] These cytochromes accept electrons from the microorganisms as well as from other reduced cytochromes present in the biofilm. [18]

Electric currents are produced when the transfer of these electrons to anodes is coupled to the oxidation of intracellular organic wastes. [18] 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. [19] [20] 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. [20] 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. [19]

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. [21] 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. [18] 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. [22] The presence of pili or flagella on Geobacter species has been found to increase electric current generation by enabling more efficient electron transfer. [23] These different factors can be tweaked to produce maximum electricity and to optimize bioremediation in the future. [21]

Neuromorphic memristor

In a University of Massachusetts Amherst study, a neuromorphic memory (memristor) utilized Geobacter biofilm cut into thin nanowire strands. [24] 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....". [25] 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 (LPSN) [1] and National Center for Biotechnology Information (NCBI) [26]

16S rRNA based LTP_08_2023 [27] [28] [29] 120 marker proteins based GTDB 08-RS214 [30] [31] [32]
Geobacter

G. sulfurreducens Caccavo et al. 1995

G. anodireducens Sun et al. 2014

G. soliZhou et al. 2014

G. argillaceus Shelobolina et al. 2007

G. pickeringiiShelobolina et al. 2007

G. hydrogenophilusCoates et al. 2001

G. benzoatilyticusYang et al. 2022

G. grbiciaeCoates et al. 2001

G. metallireducens Lovley et al. 1995

Geobacter

G. pickeringii

G. benzoatilyticus

G. hydrogenophilus

G. metallireducens [incl. G. grbiciae]

Species incertae sedis:

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. [33] Geobacter is also used to generate electricity via electrode grid in Amazon, Peru.[ citation needed ]

See also

Related Research Articles

<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.

In biology, syntrophy, syntrophism, or cross-feeding is the cooperative interaction between at least two microbial species to degrade a single substrate. This type of biological interaction typically involves the transfer of one or more metabolic intermediates between two or more metabolically diverse microbial species living in close proximity to each other. Thus, syntrophy can be considered an obligatory interdependency and a mutualistic metabolism between different microbial species, wherein the growth of one partner depends on the nutrients, growth factors, or substrates provided by the other(s).

<i>Shewanella</i> Genus of bacteria

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 found in extreme aquatic habitats where the temperature is very low and the pressure is very high. Shewanella bacteria are a normal component of the surface flora of fish and are implicated in fish spoilage. Shewanella chilikensis, a species of the genus Shewanella commonly found in the marine sponges of Saint Martin's Island of the Bay of Bengal, Bangladesh.

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, polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds, pharmaceutical substances, radionuclides and metals.

<i>Shewanella oneidensis</i> Species of bacterium

Shewanella oneidensis is a bacterium notable for its ability to reduce metal ions and live in environments with or without oxygen. This proteobacterium was first isolated from Lake Oneida, NY in 1988, hence its name.

<span class="mw-page-title-main">Bacterial nanowires</span> Electrically conductive appendages produced by a number of bacteria

Bacterial nanowires are electrically conductive appendages produced by a number of bacteria most notably from the Geobacter and Shewanella genera. Conductive nanowires have also been confirmed in the oxygenic cyanobacterium Synechocystis PCC6803 and a thermophilic, methanogenic coculture consisting of Pelotomaculum thermopropionicum and Methanothermobacter thermoautotrophicus. From physiological and functional perspectives, bacterial nanowires are diverse. The precise role microbial nanowires play in their biological systems has not been fully realized, but several proposed functions exist. Outside of a naturally occurring environment, bacterial nanowires have shown potential to be useful in several fields, notably the bioenergy and bioremediation industries.

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

An exoelectrogen normally refers to a microorganism that has the ability to transfer electrons extracellularly. While exoelectrogen is the predominant name, other terms have been used: electrochemically active bacteria, anode respiring bacteria, and electricigens. Electrons exocytosed in this fashion are produced following ATP production using an electron transport chain (ETC) during oxidative phosphorylation. Conventional cellular respiration requires a final electron acceptor to receive these electrons. Cells that use molecular oxygen (O2) as their final electron acceptor are described as using aerobic respiration, while cells that use other soluble compounds as their final electron acceptor are described as using anaerobic respiration. However, the final electron acceptor of an exoelectrogen is found extracellularly and can be a strong oxidizing agent in aqueous solution or a solid conductor/electron acceptor. Two commonly observed acceptors are iron compounds (specifically Fe(III) oxides) and manganese compounds (specifically Mn(III/IV) oxides). As oxygen is a strong oxidizer, cells are able to do this strictly in the absence of oxygen.

In the taxonomy of microorganisms, the Methanothrix is a genus of methanogenic archaea within the Euryarchaeota. Methanothrix cells were first isolated from a mesophilic sewage digester but have since been found in many anaerobic and aerobic environments. Methanothrix were originally understood to be obligate anaerobes that can survive exposure to high concentrations of oxygen, but recent studies have shown at least one Candidatus operational taxonomic unit proposed to be in the Methanothrix genus not only survives but remains active in oxic soils. This proposed species, Ca. Methanothrix paradoxum, is frequently found in methane-releasing ecosystems and is the dominant methanogen in oxic soils.

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 also use uranium for its growth and convert U(VI) to U(IV).

<i>Geobacter sulfurreducens</i> Species of bacterium

Geobacter sulfurreducens is a gram-negative metal- and sulphur-reducing proteobacterium. It is rod-shaped, aerotolerant anaerobe, non-fermentative, has flagellum and type four pili, and is closely related to Geobacter metallireducens. Geobacter sulfurreducens is an anaerobic species of bacteria that comes from the family of bacteria called Geobacteraceae. Under the genus of Geobacter, G. sulfurreducens is one out of twenty different species. The Geobacter genus was discovered by Derek R. Lovley in 1987. G. sulfurreducens was first isolated in Norman, Oklahoma, USA from materials found around the surface of a contaminated ditch.

Geopsychrobacter electrodiphilus is a species of bacteria, the type species of its genus. It is a psychrotolerant member of its family, capable of attaching to the anodes of sediment fuel cells and harvesting electricity by oxidation of organic compounds to carbon dioxide and transferring the electrons to the anode.

Geobacter psychrophilus is a Fe(III)-reducing bacterium. It is Gram-negative, slightly curved, rod-shaped and motile via means of monotrichous flagella. Its type strain is P35T.

OmcS nanowires are conductive filaments found in some species of bacteria, including Geobacter sulfurreducens, where they catalyze the transfer of electrons. They are multiheme c-Type cytochromes localized outside of the cell of some exoelectrogenic bacterial species, serving as mediator of extracellular electron transfer from cells to Fe(III) oxides and other extracellular electron acceptors.

Dissimilatory metal-reducing microorganisms are a group of microorganisms (both bacteria and archaea) that can perform anaerobic respiration utilizing a metal as terminal electron acceptor rather than molecular oxygen (O2), which is the terminal electron acceptor reduced to water (H2O) in aerobic respiration. The most common metals used for this end are iron [Fe(III)] and manganese [Mn(IV)], which are reduced to Fe(II) and Mn(II) respectively, and most microorganisms that reduce Fe(III) can reduce Mn(IV) as well. But other metals and metalloids are also used as terminal electron acceptors, such as vanadium [V(V)], chromium [Cr(VI)], molybdenum [Mo(VI)], cobalt [Co(III)], palladium [Pd(II)], gold [Au(III)], and mercury [Hg(II)].

<span class="mw-page-title-main">Forest ring</span> Patterns of low tree density in northern Canada

Forest rings are large, circular patterns of low tree density in the boreal forests of northern Canada. These rings can range from 50 metres (160 ft) to nearly 2 kilometres (1.2 mi) in diameter, with rims about 20 metres (66 ft) in thickness. The origin of forest rings is not known, despite several mechanisms for their creation having been proposed. Such hypotheses include radially growing fungus, buried kimberlite pipes, trapped gas pockets, and meteorite impact craters.

Geobacter anodireducens is a Gram-negative, aerotolerant, exoelectrogenic, anaerobic, non-spore-forming and non-motile bacterium from the genus of Geobacter Like others in its genus, it is commonly found in soil and uses iron as its electron acceptor. Due to its ability to generate current, it is an organism of note for Microbial fuel cell research. G. anodireducens was first isolated in 2014, and characterized in 2019, both by Dan Sun.

Geobacter daltonii is a Gram-negative, Fe(III)- and Uranium(IV)-reducing and non-spore-forming bacterium from the genus of Geobacter. It was isolated from sediments from the Oak Ridge Field Research Center in Oak Ridge, Tennessee in the United States. The specific epithet "daltonii" was refers to Dava Dalton, who performed the initial isolation of the strain, but died shortly thereafter.

Geobacter uraniireducens is a gram-negative, rod-shaped, anaerobic, chemolithotrophic, mesophilic, and motile bacterium from the genus of Geobacter. G. uraniireducens has been found to reduce iron and uranium in sediment and soil. It is being studied for use in bioremediation projects due to its ability to reduce uranium and arsenic.

Gemma Reguera is a Spanish-American microbiologist and professor at Michigan State University. She is the editor-in-chief of the journal Applied and Environmental Microbiology and was elected fellow of the American Academy of Microbiology in 2019. She is the recipient of the 2022 Alice C. Evans Award for Advancement of Women from the American Society for Microbiology. Her lab's research is focused on electrical properties of metal-reducing microorganisms.

Microbial electrochemical technologies (METs) use microorganisms as electrochemical catalyst, merging the microbial metabolism with electrochemical processes for the production of bioelectricity, biofuels, H2 and other valuable chemicals. Microbial fuel cells (MFC) and microbial electrolysis cells (MEC) are prominent examples of METs. While MFC is used to generate electricity from organic matter typically associated with wastewater treatment, MEC use electricity to drive chemical reactions such as the production of H2 or methane. Recently, microbial electrosynthesis cells (MES) have also emerged as a promising MET, where valuable chemicals can be produced in the cathode compartment. Other MET applications include microbial remediation cell, microbial desalination cell, microbial solar cell, microbial chemical cell, etc.,.

References

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  2. ↑ Childers, Susan (2002). "Geobacter metallireducens accesses insoluble Fe (III) oxide by chemotaxis". Nature. 416 (6882): 767–769. Bibcode:2002Natur.416..767C. doi:10.1038/416767a. PMID   11961561. S2CID   2967856.
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