Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic-abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution. R eduction-oxidation (redox) reactions and electron transport are essential to the energy conversion pathways of living cells (1). Respiratory organisms generate ATP molecules-life's universal energy currency-by harnessing the free energy of electron transport from electron donors (fuels) to electron acceptors (oxidants) through biological redox chains. In contrast to most eukaryotes, which are limited to relatively few carbon compounds as electron donors and oxygen as the predominant electron acceptor, prokaryotes have evolved into versatile energy scavengers. Microbes can wield an astounding number of metabolic pathways to extract energy from diverse organic and inorganic electron donors and acceptors, which has significant consequences for global biogeochemical cycles (2-4).

Microorganisms overcome the considerable hurdle of respiring extracellular solid substrates by deploying large multiheme cytochrome complexes that form 20 nanometer conduits to traffic electrons through the periplasm and across the cellular outer membrane. Here we report the first kinetic Monte Carlo simulations and single‐molecule scanning tunneling microscopy (STM) measurements of the Shewanella oneidensis MR‐1 outer membrane decaheme cytochrome MtrF, which can perform the final electron transfer step from cells to minerals and microbial fuel cell anodes. We find that the calculated electron transport rate through MtrF is consistent with previously reported in vitro measurements of the Shewanella Mtr complex, as well as in vivo respiration rates on electrode surfaces assuming a reasonable (experimentally verified) coverage of cytochromes on the cell surface. The simulations also reveal a rich phase diagram in the overall electron occupation density of the hemes as a function of electron injection and ejection rates. Single‐molecule tunneling spectroscopy confirms MtrF’s ability to mediate electron transport between an STM tip and an underlying Au(111) surface, but at rates higher than expected from previously calculated heme‐to‐heme electron transfer rates for solvated molecules.

Bacterial nanowires offer a pathway for extracellular electron transfer (EET) by linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Specifically, nanowires of the model metal-reducing bacterium Shewanella oneidensis MR-1 were previously shown to be conductive under non-physiological conditions. Despite the global, environmental, and technological consequences of bacterial nanowire-mediated EET, the composition, electron transport mechanism, and physiological relevance of these appendages remain unclear. The nanowires of S. oneidensis MR-1 were previously thought, but never shown, to be bacterial pili. In addition, the transport mechanism through bacterial nanowires has been the subject of intense debate, with ''metallic-like'' band transport and multistep redox hopping between multiheme cytochromes as the two proposed mechanisms. Here we report the first in vivo observations of the formation and respiratory impact of nanowires in S. oneidensis MR-1. Using live fluorescence measurements and quantitative gene expression analysis, we demonstrate that S. oneidensis MR-1 nanowires are extensions of the outer membrane and periplasm, rather than pilin-based structures. We show, through immunolabeling, that multiheme cytochromes localize to nanowires, in turn supporting the multistep redox hopping model as the transport mechanism. Furthermore, these bacterial nanowires are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and occasionally appear as membrane vesicle chains that transition to smoother filaments. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution.

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantummechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Recently, we presented a computational framework named VizBET to simulate and visualize biological electron-transfer (ET) dynamics. The visualization process was encapsulated as a plugin to the Visual Molecular Dynamics (VMD) software. However, the user's ability to understand complex, multidimensional ET pathways was severely limited when visualized in 2D on traditional computer monitors. To provide a more accurate representation with enhanced depth perception, we here present an extension of VizBET named iBET to render the VMD model of ET dynamics in a commodity virtual reality (VR) platform. The paper describes detailed procedures to export VMD models into the Unity game engine and render it in an Oculus Rift head mounted display. With the increasing availability of low-cost VR systems like the Rift and rich programmability of game engines, the iBET framework provides a powerful means to explore and understand not only biological ET processes but also a unique experiential tool for broad scientific communities.