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Geobacter
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<h2 id="history">History</h2> <p><i><a href="/facts/Geobacter_metallireducens/U2sl8LQT">Geobacter metallireducens</a></i> was first isolated by Derek R Lovley in 1987 in sand sediment from the <a href="/facts/Potomac_River/a6pTbEn0">Potomac River</a> in Washington D.C. The first strain was deemed strain GS-15.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> </p><p><i>Geobacter</i> spp. and <a href="/facts/Methanotroph/fsFp7HDD">methanotrophs</a>, such as Candidatus Methylomirabilis and Methylobacter, were highly abundant in samples from the <a href="/facts/Forest_ring/mlAkmKfx">'Bean' and the 'Thorn North' ring</a>, in Ontario, Canada.<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a> </p> <h2 id="phylogeny">Phylogeny</h2> <p>The currently accepted taxonomy is based on the <a href="/facts/List_of_Prokaryotic_names_with_Standing_in_Nomenclature/9djL152L">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN)<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> and <a href="/facts/National_Center_for_Biotechnology_Information/6Xj5wCbu">National Center for Biotechnology Information</a> (NCBI)<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> </p> <table><tbody><tr><th colspan="1">16S rRNA based <a href="/facts/The_All-Species_Living_Tree_Project/txMadzJv">LTP</a>_10_2024<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a><a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a><a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a></th><th colspan="1">120 marker proteins based <a href="/facts/Genome_Taxonomy_Database/hnEgBvVx">GTDB</a> 09-RS220<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a><a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a><a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a></th></tr><tr><td><table><tbody><tr><td><i>Geobacter</i></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i>G. pickeringii</i> Shelobolina et al. 2007</p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i><a href="/facts/Geobacter_sulfurreducens/HFUUdElR">G. sulfurreducens</a></i> Caccavo et al. 1995</p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i><a href="/facts/Geobacter_anodireducens/dF9fafum">G. anodireducens</a></i> Sun et al. 2014</p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><p><i>G. soli</i> Zhou et al. 2014</p></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i>G. benzoatilyticus</i> Yang et al. 2022</p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i>G. hydrogenophilus</i> Coates et al. 2001</p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i>G. grbiciae</i> Coates et al. 2001</p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><p><i><a href="/facts/Geobacter_metallireducens/U2sl8LQT">G. metallireducens</a></i> Lovley et al. 1995</p></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td><td><table><tbody><tr><td><i>Geobacter</i></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i>G. pickeringii</i></p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i><a href="/facts/Geobacter_anodireducens/dF9fafum">G. anodireducens</a></i> [incl. <i>G. soli</i>]</p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><p><i><a href="/facts/Geobacter_sulfurreducens/HFUUdElR">G. sulfurreducens</a></i></p></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i>G. benzoatilyticus</i></p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><table><tbody><tr><td></td><td rowspan="2"><p><i>G. hydrogenophilus</i></p></td></tr><tr><td></td></tr><tr><td></td><td rowspan="2"><p><i><a href="/facts/Geobacter_metallireducens/U2sl8LQT">G. metallireducens</a></i> [incl. <i>G. grbiciae</i>]</p></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr><tr><td></td></tr></tbody></table></td></tr></tbody></table> <p>Species incertae sedis: </p> <ul><li>"<i>Ca.</i> G. eutrophica" corrig. Mei et al. 2018</li> <li>"<i>G. hephaestius</i>" Janssen 2004</li> <li>"<i>G. humireducens</i>" Holmes et al. 2003</li></ul> <p>Assigned to different genera: </p> <ul><li><i><a href="/facts/Geobacter_argillaceus/uRpqI2AV">Geobacter argillaceus</a></i> Shelobolina et al. 2007 ["<i>Geomobilibacter argillaceus</i>" (Shelobolina et al. 2007) Xu et al. 2021]</li> <li><i><a href="/facts/Geobacter_lovleyi/Bgzmy9vj">Geobacter lovleyi</a></i> Sung et al. 2009 [<i>Trichlorobacter lovleyi</i> (Sung et al. 2009) Waite et al. 2020]</li> <li><i><a href="/facts/Geobacter_psychrophilus/DxKg8gtL">Geobacter psychrophilus</a></i> Nevin et al. 2005 ["<i>Pseudopelobacter psychrophilus</i>" (Nevin et al. 2005) Waite et al. 2020]</li> <li><i><a href="/facts/Geobacter_thiogenes/Pgu86R7h">Geobacter thiogenes</a></i> (De Wever et al. 2001) Nevin et al. 2007 [<i>Trichlorobacter thiogenes</i> De Wever et al. 2001]</li></ul> <h2 id="metabolic-mechanisms">Metabolic mechanisms</h2> <p>For quite some time,[<i>when?</i>] it was thought that <i>Geobacter</i> species lacked <a href="/facts/Cytochrome_c/8gXbxw9z">c-cytochromes</a> 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 <a href="/facts/Electron_acceptor/sRvhMXqH">terminal electron acceptors</a> (TEAs).<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> The discovery of the highly conductive pili in <i>Geobacter</i> species, and the proposal of using them as biological nano-wires further strengthened this view.<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> Nevertheless, recent discoveries have revealed that many <i>Geobacter</i> species, such as <i><a href="/facts/Geobacter_uraniireducens/eaasr5ho">Geobacter uraniireducens</a>,</i> 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 <i>Geobacter</i> species.<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> For example, one other way of transporting electrons is via a <a href="/facts/Quinone/RY00GqrL">quinone</a>-mediated electron shuttle, which is observed in <i><a href="/facts/Geobacter_sulfurreducens/HFUUdElR">Geobacter sulfurreducens</a></i>.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> </p><p>Another observed metabolic phenomenon is the cooperation between <i>Geobacter</i> <a href="/facts/Species/oDg6b96r">species</a>, in which several species cooperate in <a href="/facts/Metabolizing/WxDrm8k5">metabolizing</a> a mixture of chemicals that neither could process alone. Provided with <a href="/facts/Ethanol/3lCLfBSP">ethanol</a> and <a href="/facts/Sodium_fumarate/8basr9ju">sodium fumarate</a>, <i>G. metallireducens</i> broke down the ethanol, generating an excess of <a href="/facts/Electrons/L0KBo5cW">electrons</a> that were passed to <i>G. sulfurreducens</i> via <a href="/facts/Bacterial_nanowires/YrMbD8F8">nanowires</a> grown between them, enabling <i>G. sulfurreducens</i> to break down the fumarate ions.<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> The nanowires are made of proteins with metal-like conductivity.<a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a> </p> <h2 id="applications">Applications</h2> <h3>Biodegradation and bioremediation</h3> <p><i>Geobacter'</i>s ability to consume oil-based pollutants and radioactive material with <a href="/facts/Carbon_dioxide/xGzpppEp">carbon dioxide</a> as waste byproduct has been used in environmental clean-up for underground <a href="/facts/Petroleum/IQV0bHVd">petroleum</a> spills and for the precipitation of <a href="/facts/Uranium/n2sGWBzU">uranium</a> out of groundwater.<a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a><a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> <i>Geobacter</i> degrade the material by creating electrically conductive <a href="/facts/Pilus/xCNEXUdy">pili</a> between itself and the pollutant material, using it as an electron source.<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a> </p><p><a href="/facts/Microbial_biodegradation/S9oSxF6n">Microbial biodegradation</a> of recalcitrant organic <a href="/facts/Pollutant/4f9kmFzq">pollutants</a> is of great environmental significance and involves intriguing novel biochemical reactions. In particular, <a href="/facts/Hydrocarbon/Dcg95Ju5">hydrocarbons</a> and <a href="/facts/Halogenated/vYrGVWcJ">halogenated</a> compounds have long been doubted to be anaerobically degradable, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating <a href="/facts/Bacteria/wC8xSCsU">bacteria</a> 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 <i>G. metallireducens</i> (accession nr. NC_007517) was determined in 2008. The genome revealed the presence of genes for reductive <a href="/facts/Dehalogenase/WnjrPjQ5">dehalogenases</a>, suggesting a wide dehalogenating spectrum. Moreover, genome sequences provided insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.<a class="footnote-ref" id="fnref:23" href="#fn:23"><sup>23</sup></a> </p><p><i>Geobacter</i> species are often the predominant organisms when extracellular <a href="/facts/Electron_transfer/BIdASS9R">electron transfer</a> is an important <a href="/facts/Bioremediation/zft68Ez9">bioremediation</a> process in subsurface environments. Therefore, a systems biology approach to understanding and optimizing bioremediation with <i>Geobacter</i> species has been initiated with the ultimate goal of developing <i><a href="/facts/In_silico/g2Cz0ejg">in silico</a></i> models that can predict the growth and metabolism of <i>Geobacter</i> species under a diversity of subsurface conditions. The <a href="/facts/Genome/31Sm08JT">genomes</a> of multiple <i>Geobacter</i> species have been sequenced. Detailed functional genomic/physiological studies on one species, <i>G. sulfurreducens</i> was conducted. <a href="/facts/Genome/31Sm08JT">Genome</a>-based models of several <i>Geobacter</i> species that are able to predict physiological responses under different environmental conditions are available. Quantitative analysis of gene transcript levels during <i>in situ</i> <a href="/facts/Uranium/n2sGWBzU">uranium</a> bioremediation demonstrated that it is possible to track <i>in situ</i> rates of metabolism and the <i>in situ</i> metabolic state of <i>Geobacter</i> in the subsurface.<a class="footnote-ref" id="fnref:24" href="#fn:24"><sup>24</sup></a> </p> <h3>Biofilm conductivity</h3> <p class="note">See also: <a href="/facts/Biofilm/zg93x2w4">Biofilm</a> and <a href="/facts/Electric_bacteria/hewEdTYN">Electric bacteria</a></p> <p>Many <i>Geobacter</i> species, such as <i>G. sulfureducens</i>, are capable of creating thick networks of <a href="/facts/Biofilm/zg93x2w4">biofilms</a> on <a href="/facts/Microbial_fuel_cell/cPaa7FtW">microbial fuel cell</a> anodes for extracellular electron transfer.<a class="footnote-ref" id="fnref:25" href="#fn:25"><sup>25</sup></a> Cytochromes within the biofilm associate with pili to form extracellular structures called <a href="/facts/Bacterial_nanowires/YrMbD8F8">nanowires</a>, which facilitate extracellular electron transfer throughout the biofilm.<a class="footnote-ref" id="fnref:26" href="#fn:26"><sup>26</sup></a> These cytochromes accept electrons from the microorganisms as well as from other reduced cytochromes present in the biofilm.<a class="footnote-ref" id="fnref:27" href="#fn:27"><sup>27</sup></a> </p><p>Electric currents are produced when the transfer of these electrons to anodes is coupled to the oxidation of intracellular organic wastes.<a class="footnote-ref" id="fnref:28" href="#fn:28"><sup>28</sup></a> Previous research has proposed that the high conductivity of <i>Geobacter</i> biofilms can be used to power microbial fuel cells and to generate electricity from organic waste products.<a class="footnote-ref" id="fnref:29" href="#fn:29"><sup>29</sup></a><a class="footnote-ref" id="fnref:30" href="#fn:30"><sup>30</sup></a> In particular, <i>G. sulfureducens</i> holds one of the highest records for microbial fuel cell current density that researchers have ever been able to measure in vitro.<a class="footnote-ref" id="fnref:31" href="#fn:31"><sup>31</sup></a> 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.<a class="footnote-ref" id="fnref:32" href="#fn:32"><sup>32</sup></a> </p><p>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.<a class="footnote-ref" id="fnref:33" href="#fn:33"><sup>33</sup></a> 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.<a class="footnote-ref" id="fnref:34" href="#fn:34"><sup>34</sup></a> 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.<a class="footnote-ref" id="fnref:35" href="#fn:35"><sup>35</sup></a> The presence of pili or flagella on <i>Geobacter</i> species has been found to increase electric current generation by enabling more efficient electron transfer.<a class="footnote-ref" id="fnref:36" href="#fn:36"><sup>36</sup></a> These different factors can be tweaked to produce maximum electricity and to optimize bioremediation in the future.<a class="footnote-ref" id="fnref:37" href="#fn:37"><sup>37</sup></a> </p> <h3>Neuromorphic memristor</h3> <p class="note">See also: <a href="/facts/Bacterial_nanowires/YrMbD8F8">Bacterial nanowires § Other significant applications</a></p> <p>In a University of Massachusetts Amherst study, a neuromorphic memory (memristor) utilized Geobacter biofilm cut into thin nanowire strands.<a class="footnote-ref" id="fnref:38" href="#fn:38"><sup>38</sup></a> 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....".<a class="footnote-ref" id="fnref:39" href="#fn:39"><sup>39</sup></a> The breakthrough observation came as they monitored voltage activity at a sub 1 volt level. </p> <h2 id="popular-culture">Popular culture</h2> <p><i>Geobacter</i> has become an icon for teaching about microbial <a href="/facts/Electrogenesis/t2DvkguA">electrogenesis</a> and <a href="/facts/Microbial_fuel_cells/cPaa7FtW">microbial fuel cells</a> and has appeared in educational kits that are available for students and hobbyists.<a class="footnote-ref" id="fnref:40" href="#fn:40"><sup>40</sup></a> <i>Geobacter</i> is also used to generate electricity via electrode grid in Amazon, Peru. </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Forest_ring/mlAkmKfx">Forest ring</a></li> <li><a href="/facts/List_of_bacterial_orders/ujvD930b">List of bacterial orders</a></li> <li><a href="/facts/List_of_bacteria_genera/a25ukgSb">List of bacteria genera</a></li> <li><i><a href="/facts/Shewanella/pX19qqsH">Shewanella</a></i></li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="/facts/List_of_Prokaryotic_names_with_Standing_in_Nomenclature/9djL152L">LPSN</a>, <a href="https://lpsn.dsmz.de/genus/geobacter">Genus: Geobacter</a></li> <li><a href="https://web.archive.org/web/20090503122255/http://www.geobacter.org/">"Geobacter project"</a>. Archived from <a href="http://www.geobacter.org">the original</a> on May 3, 2009. Retrieved August 13, 2005.</li> <li><a href="http://www.horizonpress.com/gateway/biodegradation.html">Microbial Biodegradation, Bioremediation and Biotransformation</a></li> <li><a href="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</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>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. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC150094" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC150094</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>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. <a href="http://www.geobacter.org/publications/Nature_1987_Nov.pdf" target="_blank">http://www.geobacter.org/publications/Nature_1987_Nov.pdf</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>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) <a href="http://www.geobacter.org/publications/Nature_1987_Nov.pdf" target="_blank">http://www.geobacter.org/publications/Nature_1987_Nov.pdf</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>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. <a href="https://pubmed.ncbi.nlm.nih.gov/30014579/" target="_blank">https://pubmed.ncbi.nlm.nih.gov/30014579/</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>A.C. Parte; et al. "Geobacter". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2 December 2024. <a href="https://www.bacterio.net/genus/geobacter" target="_blank">https://www.bacterio.net/genus/geobacter</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Sayers; et al. "Geobacter". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09. <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=28231&lvl=3&keep=1&srchmode=1&unlock" target="_blank">https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=28231&lvl=3&keep=1&srchmode=1&unlock</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>"The LTP". 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