@article {3069, title = {Bioinspired bio-voltage memristors.}, journal = {Nat Commun}, volume = {11}, year = {2020}, month = {2020 Apr 20}, pages = {1861}, abstract = {

Memristive devices are promising candidates to emulate biological computing. However, the typical switching voltages (0.2-2 V) in previously described devices are much higher than the amplitude in biological counterparts. Here we demonstrate a type of diffusive memristor, fabricated from the protein nanowires harvested from the bacterium Geobacter sulfurreducens, that functions at the biological voltages of 40-100 mV. Memristive function at biological voltages is possible because the protein nanowires catalyze metallization. Artificial neurons built from these memristors not only function at biological action potentials (e.g., 100 mV, 1 ms) but also exhibit temporal integration close to that in biological neurons. The potential of using the memristor to directly process biosensing signals is also demonstrated.

}, keywords = {Action Potentials, Biosensing Techniques, Electricity, Electronics, Equipment Design, Geobacter, Humans, Molecular Dynamics Simulation, Nanotechnology, Nanowires, Neural Networks, Computer, Neurons, Synapses, Wearable Electronic Devices}, issn = {2041-1723}, doi = {10.1038/s41467-020-15759-y}, author = {Fu, Tianda and Liu, Xiaomeng and Gao, Hongyan and Ward, Joy E and Liu, Xiaorong and Yin, Bing and Wang, Zhongrui and Zhuo, Ye and Walker, David J F and Joshua Yang, J and Chen, Jianhan and Lovley, Derek R and Yao, Jun} } @article {3093, title = {Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis.}, journal = {PLoS One}, volume = {12}, year = {2017}, month = {2017}, pages = {e0170406}, abstract = {

The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na+ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.

}, keywords = {Biofilms, Biomass, Carbon, Clostridium, Culture Media, Culture Techniques, Fimbriae, Bacterial, Flagella, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Glass, Graphite, Osmotic Pressure, RNA, Bacterial, RNA, Ribosomal, Sodium Chloride, Spores, Bacterial, Stress, Physiological}, issn = {1932-6203}, doi = {10.1371/journal.pone.0170406}, author = {Philips, Jo and Rabaey, Korneel and Lovley, Derek R and Vargas, Madeline} } @article {3153, title = {Bioremediation of uranium-contaminated groundwater: a systems approach to subsurface biogeochemistry.}, journal = {Curr Opin Biotechnol}, volume = {24}, year = {2013}, month = {2013 Jun}, pages = {489-97}, abstract = {

Adding organic electron donors to stimulate microbial reduction of highly soluble U(VI) to less soluble U(IV) is a promising strategy for immobilizing uranium in contaminated subsurface environments. Studies suggest that diagnosing the in situ physiological status of the subsurface community during uranium bioremediation with environmental transcriptomic and proteomic techniques can identify factors potentially limiting U(VI) reduction activity. Models which couple genome-scale in silico representations of the metabolism of key microbial populations with geochemical and hydrological models may be able to predict the outcome of bioremediation strategies and aid in the development of new approaches. Concerns remain about the long-term stability of sequestered U(IV) minerals and the release of co-contaminants associated with Fe(III) oxides, which might be overcome through targeted delivery of electrons to select microorganisms using in situ electrodes.

}, keywords = {Biodegradation, Environmental, Electrodes, Ferric Compounds, Genomics, Groundwater, Proteomics, Uranium, Water Pollutants, Radioactive}, issn = {1879-0429}, doi = {10.1016/j.copbio.2012.10.008}, author = {Williams, Kenneth H and Bargar, John R and Lloyd, Jonathan R and Lovley, Derek R} } @article {427, title = {Biochemical characterization of purified OmcS, a c-type cytochrome required for insoluble Fe(III) reduction in Geobacter sulfurreducens.}, journal = {Biochim Biophys Acta}, volume = {1807}, year = {2011}, month = {2011 Apr}, pages = {404-12}, abstract = {Previous studies with Geobacter sulfurreducens have demonstrated that OmcS, an abundant c-type cytochrome that is only loosely bound to the outer surface, plays an important role in electron transfer to Fe(III) oxides as well as other extracellular electron acceptors. In order to further investigate the function of OmcS, it was purified from a strain that overproduces the protein. Purified OmcS had a molecular mass of 47015 Da, and six low-spin bis-histidinyl hexacoordinated heme groups. Its midpoint redox potential was -212 mV. A thermal stability analysis showed that the cooperative melting of purified OmcS occurs in the range of 65-82 {\textdegree}C. Far UV circular dichroism spectroscopy indicated that the secondary structure of purified OmcS consists of about 10\% α-helix and abundant disordered structures. Dithionite-reduced OmcS was able to transfer electrons to a variety of substrates of environmental importance including insoluble Fe(III) oxide, Mn(IV) oxide and humic substances. Stopped flow analysis revealed that the reaction rate of OmcS oxidation has a hyperbolic dependence on the concentration of the studied substrates. A ten-fold faster reaction rate with anthraquinone-2,6-disulfonate (AQDS) (25.2 s$^{-}${\textonesuperior}) was observed as compared to that with Fe(III) citrate (2.9 s$^{-}${\textonesuperior}). The results, coupled with previous localization and gene deletion studies, suggest that OmcS is well-suited to play an important role in extracellular electron transfer.}, keywords = {Circular Dichroism, Cytochrome c Group, Geobacter, Heme, Iron, Kinetics, Molecular Weight, Oxidation-Reduction, Solubility}, issn = {0006-3002}, doi = {10.1016/j.bbabio.2011.01.003}, author = {Qian, Xinlei and Mester, T{\"u}nde and Morgado, Leonor and Arakawa, Tsutomu and Sharma, Manju L and Inoue, Kengo and Joseph, Crisjoe and Salgueiro, Carlos A and Maroney, Michael J and Lovley, Derek R} } @article {514, title = {Biofilm and nanowire production leads to increased current in Geobacter sulfurreducens fuel cells.}, journal = {Appl Environ Microbiol}, volume = {72}, year = {2006}, month = {2006 Nov}, pages = {7345-8}, abstract = {Geobacter sulfurreducens developed highly structured, multilayer biofilms on the anode surface of a microbial fuel cell converting acetate to electricity. Cells at a distance from the anode remained viable, and there was no decrease in the efficiency of current production as the thickness of the biofilm increased. Genetic studies demonstrated that efficient electron transfer through the biofilm required the presence of electrically conductive pili. These pili may represent an electronic network permeating the biofilm that can promote long-range electrical transfer in an energy-efficient manner, increasing electricity production more than 10-fold.}, keywords = {Acetates, Bioelectric Energy Sources, Biofilms, Electricity, Electrodes, Electron Transport, Fimbriae, Bacterial, Geobacter, Microscopy, Confocal, Mutation, Nanowires}, issn = {0099-2240}, doi = {10.1128/AEM.01444-06}, author = {Reguera, Gemma and Nevin, Kelly P and Nicoll, Julie S and Covalla, Sean F and Woodard, Trevor L and Lovley, Derek R} } @article {519, title = {Bug juice: harvesting electricity with microorganisms.}, journal = {Nat Rev Microbiol}, volume = {4}, year = {2006}, month = {2006 Jul}, pages = {497-508}, abstract = {It is well established that some reduced fermentation products or microbially reduced artificial mediators can abiotically react with electrodes to yield a small electrical current. This type of metabolism does not typically result in an efficient conversion of organic compounds to electricity because only some metabolic end products will react with electrodes, and the microorganisms only incompletely oxidize their organic fuels. A new form of microbial respiration has recently been discovered in which microorganisms conserve energy to support growth by oxidizing organic compounds to carbon dioxide with direct quantitative electron transfer to electrodes. These organisms, termed electricigens, offer the possibility of efficiently converting organic compounds into electricity in self-sustaining systems with long-term stability.}, keywords = {Bacteria, Bioelectric Energy Sources, Electricity, Electrodes, Electron Transport, Oxidation-Reduction}, issn = {1740-1526}, doi = {10.1038/nrmicro1442}, author = {Lovley, Derek R} } @article {576, title = {Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens.}, journal = {Biochem J}, volume = {369}, year = {2003}, month = {2003 Jan 1}, pages = {153-61}, abstract = {A 9.6 kDa periplasmic c -type cytochrome, designated PpcA, was purified from the Fe(III)-reducing bacterium Geobacter sulfurreducens and characterized. The purified protein is basic (pI 9.5), contains three haems and has an N-terminal amino acid sequence closely related to those of the previously described trihaem c (7) cytochromes of Geobacter metallireducens and Desulfuromonas acetoxidans. The gene encoding PpcA was identified from the G. sulfurreducens genome using the N-terminal sequence, and encodes a protein of 71 amino acids (molecular mass 9.58 kDa) with 49\% identity to the c (7) cytochrome of D. acetoxidans. In order to determine the physiological role of PpcA, a knockout mutant was prepared with a single-step recombination method. Acetate-dependent Fe(III) reduction was significantly inhibited in both growing cultures and cell suspensions of the mutant. When ppcA was expressed in trans, the full capacity for Fe(III) reduction with acetate was restored. The transfer of electrons from acetate to anthraquinone 2,6-disulphonate (AQDS; a humic acid analogue) and to U(VI) was also compromised in the mutant, but acetate-dependent reduction of fumarate was not altered. The rates of reduction of Fe(III), AQDS, U(VI) and fumarate were also the same in the wild type and ppcA mutant when hydrogen was supplied as the electron donor. When taken together with previous studies on other electron transport proteins in G. sulfurreducens, these results suggest that PpcA serves as an intermediary electron carrier from acetate to terminal Fe(III) reductases in the outer membrane, and is also involved in the transfer of electrons from acetate to U(VI) and humics.}, keywords = {Amino Acid Sequence, Base Sequence, Cytochrome c Group, DNA, Bacterial, Molecular Sequence Data, Periplasm, Proteobacteria, Sequence Homology, Amino Acid}, issn = {0264-6021}, doi = {10.1042/BJ20020597}, author = {Lloyd, Jon R and Leang, Ching and Hodges Myerson, Allison L and Coppi, Maddalena V and Cuifo, Stacey and Methe, Barb and Sandler, Steven J and Lovley, Derek R} } @article {561, title = {Biotechnological application of metal-reducing microorganisms.}, journal = {Adv Appl Microbiol}, volume = {53}, year = {2003}, month = {2003}, pages = {85-128}, keywords = {Archaea, Biodegradation, Environmental, Bioreactors, Environmental Microbiology, Geobacter, Gram-Negative Anaerobic Bacteria, Metals, Heavy, Water Pollutants, Chemical}, issn = {0065-2164}, author = {Lloyd, Jonathan R and Lovley, Derek R and Macaskie, Lynne E} }