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Geobacter

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Geobacter
Geobacter sulfurreducens
Scientific classification Edit this classification
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]

History

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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]

Metabolic mechanisms

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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

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Biodegradation and bioremediation

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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

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See also: Biofilm and Electric bacteria

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

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See also: Bacterial nanowires § Other significant applications

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

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The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[26] and National Center for Biotechnology Information (NCBI)[27]

16S rRNA based LTP_08_2023[28][29][30] 120 marker proteins based GTDB 08-RS214[31][32][33]
Geobacter

G. sulfurreducens Caccavo et al. 1995

G. anodireducens Sun et al. 2014

G. soli Zhou et al. 2014

G. argillaceus Shelobolina et al. 2007

G. pickeringii Shelobolina et al. 2007

G. hydrogenophilus Coates et al. 2001

G. benzoatilyticus Yang et al. 2022

G. grbiciae Coates et al. 2001

G. metallireducens Lovley et al. 1995

Geobacter

G. pickeringii

G. benzoatilyticus

G. hydrogenophilus

G. metallireducens [incl. G. grbiciae]

Species incertae sedis:

  • "Ca. G. eutrophica" corrig. Mei et al. 2018
  • "G. hephaestius" Janssen 2004
  • "G. humireducens" Holmes et al. 2003
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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.[34] Geobacter is also used to generate electricity via electrode grid in Amazon, Peru.[citation needed]

See also

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References

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  1. ^ "Genus: Geobacter". lpsn.dsmz.de.
  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.
  3. ^ Bond, Daniel (Mar 2003). "Electricity Production by Geobacter sulfurreducens Attached to Electrodes". Applied and Environmental Microbiology. 69 (3): 1548–1555. Bibcode:2003ApEnM..69.1548B. doi:10.1128/AEM.69.3.1548-1555.2003. PMC 150094. PMID 12620842.
  4. ^ Lovley DR, Stolz JF, Nord GL, Phillips EJP (1987). "Anaerobic Production of Magnetite by a Dissimilatory Iron-Reducing Microorganism" (PDF). Nature. 350 (6145): 252–254. Bibcode:1987Natur.330..252L. doi:10.1038/330252a0. S2CID 4234140.
  5. ^ Lovley DR, Stolz JF, Nord GL, Phillips, EJP (1987). "Anaerobic Production of Magnetite by a Dissimilatory Iron-Reducing Microorganism" (PDF). Nature. 350 (6145): 252–254. Bibcode:1987Natur.330..252L. doi:10.1038/330252a0. S2CID 4234140.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ von Gunten, Konstantin; Hamilton, Stewart M.; Zhong, Cheng; Nesbø, Camilla; Li, Jiaying; Muehlenbachs, Karlis; Konhauser, Kurt O.; Alessi, Daniel S. (December 2018). "Electron donor-driven bacterial and archaeal community patterns along forest ring edges in Ontario, Canada: Electron donor-driven microbial community patterns along forest ring edges". Environmental Microbiology Reports. 10 (6): 663–672. doi:10.1111/1758-2229.12678. PMID 30014579. S2CID 51650191. Retrieved 24 January 2023.
  7. ^ a b Reguera, Gemma; McCarthy, Kevin D.; Mehta, Teena; Nicoll, Julie S.; Tuominen, Mark T.; Lovley, Derek R. (2005-06-23). "Extracellular electron transfer via microbial nanowires". Nature. 435 (7045): 1098–1101. Bibcode:2005Natur.435.1098R. doi:10.1038/nature03661. ISSN 1476-4687. PMID 15973408. S2CID 4425287.
  8. ^ Tan, Yang; Adhikari, Ramesh Y.; Malvankar, Nikhil S.; Ward, Joy E.; Nevin, Kelly P.; Woodard, Trevor L.; Smith, Jessica A.; Snoeyenbos-West, Oona L.; Franks, Ashley E. (2016-06-28). "The Low Conductivity of Geobacter uraniireducens Pili Suggests a Diversity of Extracellular Electron Transfer Mechanisms in the Genus Geobacter". Frontiers in Microbiology. 7: 980. doi:10.3389/fmicb.2016.00980. ISSN 1664-302X. PMC 4923279. PMID 27446021.
  9. ^ Pat-Espadas, Aurora M.; Razo-Flores, Elías; Rangel-Mendez, J. Rene; Cervantes, Francisco J. (2014). "Direct and Quinone-Mediated Palladium Reduction by Geobacter sulfurreducens: Mechanisms and Modeling". Environmental Science & Technology. 48 (5): 2910–2919. Bibcode:2014EnST...48.2910P. doi:10.1021/es403968e. PMID 24494981.
  10. ^ Williams, Caroline (2011). "Who are you calling simple?". New Scientist. 211 (2821): 38–41. doi:10.1016/S0262-4079(11)61709-0.
  11. ^ Malvankar, Nikhil; Vargas, Madeline; Nevin, Kelly; Tremblay, Pier-Luc; Evans-Lutterodt, Kenneth; Nykypanchuk, Dmytro; Martz, Eric; Tuominen, Mark T; Lovley, Derek R (2015). "Structural Basis for Metallic-Like Conductivity in Microbial Nanowires". mBio. 6 (2): e00084. doi:10.1128/mbio.00084-15. PMC 4453548. PMID 25736881.
  12. ^ Anderson RT, Vrionis HA, Ortiz-Bernad I, Resch CT, Long PE, Dayvault R, Karp K, Marutzky S, Metzler DR, Peacock A, White DC, Lowe M, Lovley DR (2003). "Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer". Applied and Environmental Microbiology. 69 (10): 5884–91. Bibcode:2003ApEnM..69.5884A. doi:10.1128/aem.69.10.5884-5891.2003. PMC 201226. PMID 14532040.
  13. ^ Cologgi, Dena (2014). "Enhanced uranium immobilization and reduction by Geobacter sulfurreducens biofilms". Applied and Environmental Microbiology. 80 (21): 6638–6646. Bibcode:2014ApEnM..80.6638C. doi:10.1128/AEM.02289-14. PMC 4249037. PMID 25128347.
  14. ^ "Experiment and theory unite at last in debate over microbial nanowires". Phys.org. Retrieved 5 January 2016.
  15. ^ Heider J, Rabus R (2008). "Genomic Insights in the Anaerobic Biodegradation of Organic Pollutants". Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2.
  16. ^ Diaz E, ed. (2008). Microbial Biodegradation: Genomics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 978-1-904455-17-2.
  17. ^ Yates, Matthew D.; Strycharz-Glaven, Sarah M.; Golden, Joel P.; Roy, Jared; Tsoi, Stanislav; Erickson, Jeffrey S.; El-Naggar, Mohamed Y.; Barton, Scott Calabrese; Tender, Leonard M. (2016-11-08). "Measuring conductivity of living Geobacter sulfurreducens biofilms". Nature Nanotechnology. 11 (11): 910–913. Bibcode:2016NatNa..11..910Y. doi:10.1038/nnano.2016.186. ISSN 1748-3395. PMID 27821847.
  18. ^ a b c d Bond, Daniel R.; Strycharz-Glaven, Sarah M.; Tender, Leonard M.; Torres, César I. (21 May 2012). "On Electron Transport through Geobacter Biofilms". ChemSusChem. 5 (6): 1099–1105. doi:10.1002/cssc.201100748. PMID 22615023.
  19. ^ a b Malvankar, Nikhil S.; Tuominen, Mark T.; Lovley, Derek R. (25 January 2012). "Biofilm conductivity is a decisive variable for high-current-density Geobacter sulfurreducens microbial fuel cells". Energy & Environmental Science. 5 (2): 5790. doi:10.1039/C2EE03388G. ISSN 1754-5706.
  20. ^ a b Yi, Hana; Nevin, Kelly P.; Kim, Byoung-Chan; Franks, Ashely E.; Klimes, Anna; Tender, Leonard M.; Lovley, Derek R. (15 August 2009). "Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells". Biosensors & Bioelectronics. 24 (12): 3498–3503. doi:10.1016/j.bios.2009.05.004. ISSN 1873-4235. PMID 19487117.
  21. ^ a b Logan, Bruce E. (2009-03-30). "Exoelectrogenic bacteria that power microbial fuel cells". Nature Reviews Microbiology. 7 (5): 375–381. doi:10.1038/nrmicro2113. ISSN 1740-1534. PMID 19330018. S2CID 2560062.
  22. ^ Yates, Matthew D.; Golden, Joel P.; Roy, Jared; Strycharz-Glaven, Sarah M.; Tsoi, Stanislav; Erickson, Jeffrey S.; El-Naggar, Mohamed Y.; Barton, Scott Calabrese; Tender, Leonard M. (2015-12-02). "Thermally activated long range electron transport in living biofilms". Physical Chemistry Chemical Physics. 17 (48): 32564–32570. Bibcode:2015PCCP...1732564Y. doi:10.1039/c5cp05152e. ISSN 1463-9084. PMID 26611733.
  23. ^ Reguera, Gemma; Nevin, Kelly P.; Nicoll, Julie S.; Covalla, Sean F.; Woodard, Trevor L.; Lovley, Derek R. (1 November 2006). "Biofilm and Nanowire Production Leads to Increased Current in Geobacter sulfurreducens Fuel Cells". Applied and Environmental Microbiology. 72 (11): 7345–7348. Bibcode:2006ApEnM..72.7345R. doi:10.1128/AEM.01444-06. ISSN 0099-2240. PMC 1636155. PMID 16936064.
  24. ^ "Researchers unveil electronics that mimic the human brain in efficient learning". Phys.org. April 20, 2020. Retrieved April 20, 2020.
  25. ^ Fu, Tianda (April 20, 2020). "Bioinspired bio-voltage memristors". Nature Communications. 11 (1): 1861. Bibcode:2020NatCo..11.1861F. doi:10.1038/s41467-020-15759-y. PMC 7171104. PMID 32313096.
  26. ^ A.C. Parte; et al. "Geobacter". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
  27. ^ Sayers; et al. "Geobacter". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.
  28. ^ "The LTP". Retrieved 20 November 2023.
  29. ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
  30. ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  31. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  32. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  33. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  34. ^ "MudWatt: Grow a Living Fuel Cell". Magical Microbes.
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