About

Joshua Atkinson is an Assistant Professor of Civil and Environmental Engineering and a member of the Omenn-Darling Bioengineering Institute at Princeton University. He earned his PhD in Systems, Synthetic, and Physical Biology from Rice University in 2019 and his BS in Microbiology from the University of Michigan in 2012. His research focuses on using approaches from synthetic biology, protein engineering, biophysics, and electrochemistry to understand and control how microbes and proteins transport electrons. The Atkinson Lab aims to elucidate the critical role of electron transport in energy and information processing within cells and microbial communities, with the goal of engineering new biotechnologies to address societal challenges related to sustainability, environmental monitoring and remediation, chemical synthesis, and resource recovery and extraction. His work emphasizes developing design rules for microbial electron transfer regulation, understanding how electron flows influence microbial community structures and geochemical cycles, and creating living electronic materials that integrate biological information processing with electrochemical devices.

Research topics

• Computer Science
• Nanotechnology
• Materials science
• Computational biology
• Chemistry
• Artificial Intelligence
• Biology
• Environmental chemistry
• Biochemical engineering
• Composite material
• Engineering
• Electrical engineering
• Computer hardware

Selected publications

• Artificial sediments enable reproducible cultivation and recapitulate ecological interactions of cable bacteria

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-16

  articleSenior author

  Abstract Cable bacteria are filamentous microbes that couple sulfide oxidation to oxygen reduction over centimeter distances via long-distance electron transport. While their activity creates characteristic biogeochemical gradients that shape sediment ecology, the study of cable bacteria has been constrained by the chemical and physical heterogeneity of the natural sediments they inhabit. To date, laboratory cultivation efforts have relied on these undefined environmental matrices. Here, we established a reproducible enrichment and cultivation platform using an artificial sediment matrix coupled with chemically defined media. This matrix successfully supported the growth of both freshwater and marine cable bacteria and enabled serial propagation over multiple transfers. Microsensor profiling confirmed that the incubations recapitulated hallmark geochemical signatures, including the sulfide, oxygen and pH gradients associated with electrogenic sulfur oxidation. Scanning electron microscopy confirmed the presence of cable bacteria, while 16S rRNA sequencing confirmed enrichment of the cable bacteria together with a stable co-enriched community that included taxa associated with sulfur and iron cycling as well as cellulose decomposition. This defined cultivation system eliminates the variability inherent to natural samples, providing a controlled platform for dissecting the physiology, genetics, and microbial interactions of cable bacteria.

  PublisherDOI

• Biofilm Patterning Reveals the Functional Contributions of Periplasmic Cytochromes to the Electrochemical Activity of <i>Shewanella oneidensis</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-08

  articleOpen access

  Abstract Shewanella oneidensis MR-1 is a model electroactive bacterium whose extracellular electron transfer (EET) pathway includes a sequential network of c -type cytochromes that span the inner membrane, periplasm, and outer membrane. While electrochemical studies revealed the critical role of outer-membrane cytochromes in mediating both outward EET from cells to external surfaces and lateral biofilm conduction across cells, the specific functional role of the periplasmic cytochromes in these processes is less understood. Dissecting the contributions of the periplasmic components has been challenged by the complexity of the periplasmic cytochrome network and the inherent variability of native biofilms, which confounds the electrochemical comparison of cytochrome mutants. Here, we overcome these limitations with a synthetic biology approach combining targeted deletion of genes encoding key periplasmic cytochromes with light-induced biofilm patterning to create uniform, geometrically defined biofilms on electrodes for robust electrochemical comparisons. Voltammetric measurements of patterned S. oneidensis mutant biofilms confirmed the essential role of periplasmic cytochromes in facilitating outward EET, a contribution that becomes apparent when flavins are present to accelerate interfacial electron transfer between outer-membrane cytochromes and the electrode. In contrast to this crucial role in routing outward EET across the periplasm, electrochemical gating measurements of lateral biofilm conductivity revealed that the periplasmic cytochromes do not contribute to long-distance electron transport along cellular layers bridging electrodes. These findings provide new insights into the role of periplasmic cytochromes in S. oneidensis , and distinguish their contributions to routing outward EET across the cell envelope versus biofilm conductivity. Importance Microbes capable of extracellular electron transfer (EET) are central to global biogeochemical cycles and emerging bioelectrochemical technologies. In the important model EET bacterium Shewanella oneidensis MR-1, the outer-membrane components that interface with external surfaces are well-characterized. However, the functional role of the periplasmic components linking the inner and outer membranes has remained obscured by the complex network of multiple cytochromes and biofilm heterogeneity limiting precise comparisons across mutants. By combining light-induced biofilm patterning with electrochemical analysis, we successfully revealed the specific contributions of periplasmic cytochromes: these components are essential for facilitating the outward EET across the cell envelope but do not impact lateral long-distance electron transport across the biofilm. The results refine our understanding of extracellular respiration and provide design rules for engineering living electronic materials.

  PublisherOA PDFDOI

• The Internet of Biofilm Living AI Devices

  IEEE Communications Magazine · 2025-07-28

  article

  As the world searches for groundbreaking, unconventional computing technologies, especially for intelligent edge applications, biological AI is emerging as an energy-efficient, robust, and reliable alternative. Researchers have unveiled the immense computing capacity inherent in biocomputing elements such as bacterial cells. The computing power of bacteria can be harnessed through Gene Regulatory Neural Networks (GRNNs). Biofilms, acting as sophisticated collections of GRNNs, leverage the natural distributed computing architecture with capabilities like parallel processing and analog computing in individual cells while consuming very little energy relative to conventional computing systems. This study introduces the concept of Biofilm Living AI Devices (BLAIDs), which proposes engineering biofilms using optogenetics to function as self-sustaining AI edge devices that interface with modern telecommunications architectures. Our simulation-based analysis demonstrates the computing complexity and reliability of BLAID, establishing it as a compelling candidate for the next generation of low-energy computing and advanced AI technologies.

  PublisherDOI

• Inter-kingdom electromechanical communication

  Nature Chemical Biology · 2024-07-19 · 2 citations

  article1st authorCorresponding
  PublisherDOI

• Red-Light-Induced Genetic System for Control of Extracellular Electron Transfer

  ACS Synthetic Biology · 2024-05-02 · 9 citations

  article

  Optogenetics is a powerful tool for spatiotemporal control of gene expression. Several light-inducible gene regulators have been developed to function in bacteria, and these regulatory circuits have been ported to new host strains. Here, we developed and adapted a red-light-inducible transcription factor for Shewanella oneidensis. This regulatory circuit is based on the iLight optogenetic system, which controls gene expression using red light. A thermodynamic model and promoter engineering were used to adapt this system to achieve differential gene expression in light and dark conditions within a S. oneidensis host strain. We further improved the iLight optogenetic system by adding a repressor to invert the genetic circuit and activate gene expression under red light illumination. The inverted iLight genetic circuit was used to control extracellular electron transfer within S. oneidensis. The ability to use both red- and blue-light-induced optogenetic circuits simultaneously was also demonstrated. Our work expands the synthetic biology capabilities in S. oneidensis, which could facilitate future advances in applications with electrogenic bacteria.

  PublisherDOI

• The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation

  Biochemistry · 2024-02-15

  articleSenior authorCorresponding

  Adenylate kinases (AKs) have evolved AMP-binding and lid domains that are encoded as continuous polypeptides embedded at different locations within the discontinuous polypeptide encoding the core domain. A prior study showed that AK homologues of different stabilities consistently retain cellular activity following circular permutation that splits a region with high energetic frustration within the AMP-binding domain into discontinuous fragments. Herein, we show that mesophilic and thermophilic AKs having this topological restructuring retain activity and substrate-binding characteristics of the parental AK. While permutation decreased the activity of both AK homologues at physiological temperatures, the catalytic activity of the thermophilic AK increased upon permutation when assayed >30 °C below the melting temperature of the native AK. The thermostabilities of the permuted AKs were uniformly lower than those of native AKs, and they exhibited multiphasic unfolding transitions, unlike the native AKs, which presented cooperative thermal unfolding. In addition, proteolytic digestion revealed that permutation destabilized each AK in differing manners, and mass spectrometry suggested that the new termini within the AMP-binding domain were responsible for the increased proteolysis sensitivity. These findings illustrate how changes in contact order can be used to tune enzyme activity and alter folding dynamics in multidomain enzymes.

  PublisherDOI

• The energetics and evolution of oxidoreductases in deep time

  2023-05-18

  preprintOpen access

  The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation-reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox ([https://protein-redox-potential.web.app](https://protein-redox-potential.web.app)), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation-reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep-time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.

  PublisherOA PDFDOI

• The energetics and evolution of oxidoreductases in deep time

  Proteins Structure Function and Bioinformatics · 2023-08-19 · 11 citations

  articleOpen access

  The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation-reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox (https://protein-redox-potential.web.app), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation-reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.

  PublisherOA PDFDOI

• A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase

  Protein Science · 2023-08-08 · 8 citations

  articleOpen access

  Flavodoxins (Flds) mediate the flux of electrons between oxidoreductases in diverse metabolic pathways. To investigate whether Flds can support electron transfer to a sulfite reductase (SIR) that evolved to couple with a ferredoxin, we evaluated the ability of Flds to transfer electrons from a ferredoxin-NADP reductase (FNR) to a ferredoxin-dependent SIR using growth complementation of an Escherichia coli strain with a sulfur metabolism defect. We show that Flds from cyanobacteria complement this growth defect when coexpressed with an FNR and an SIR that evolved to couple with a plant ferredoxin. When we evaluated the effect of peptide insertion on Fld-mediated electron transfer, we observed a sensitivity to insertions within regions predicted to be proximal to the cofactor and partner binding sites, while a high insertion tolerance was detected within loops distal from the cofactor and within regions of helices and sheets that are proximal to those loops. Bioinformatic analysis showed that natural Fld sequence variability predicts a large fraction of the motifs that tolerate insertion of the octapeptide SGRPGSLS. These results represent the first evidence that Flds can support electron transfer to assimilatory SIRs, and they suggest that the pattern of insertion tolerance is influenced by interactions with oxidoreductase partners.

  PublisherOA PDFDOI

• A red light-induced genetic system for control of extracellular electron transfer

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-12-02

  preprintOpen access

  Abstract Optogenetics is a powerful tool for spatiotemporal control of gene expression. Several light-inducible gene regulators have been developed to function in bacteria, and these regulatory circuits have been ported into new host strains. Here, we developed and adapted a red light-inducible transcription factor for Shewanella oneidensis . This regulatory circuit is based on the iLight optogenetic system, which controls gene expression using red light. Promoter engineering and a thermodynamic model were used to adapt this system to achieve differential gene expression in light and dark conditions within a S. oneidensis host strain. We further improved the iLight optogenetic system by adding a repressor to invert the genetic circuit and activate gene expression under red light illumination. The inverted iLight genetic circuit was used to control extracellular electron transfer (EET) within S. oneidensis . The ability to use both red and blue light-induced optogenetic circuits simultaneously was demonstrated. Our work expands the synthetic biology toolbox of Shewanella , which could facilitate future advances in applications with electrogenic bacteria.

  PublisherOA PDFDOI

Recent grants

• NSF Postdoctoral Fellowship in Biology FY 2020

  NSF · $276k · 2020–2024

Frequent coauthors

• Jonathan J. Silberg

  Rice University

  31 shared

• Ian Campbell

  University of Washington

  12 shared

• Jeffrey A. Gralnick

  Biotechnology Institute

  10 shared

• George N. Bennett

  9 shared

• Vikas Nanda

  Johnson University

  8 shared

• Benjamin M. Bonis

  University of Minnesota

  8 shared

• Lin Su

  Southeast University

  7 shared

• Caroline M. Ajo‐Franklin

  6 shared

Labs

• Atkinson LabPI

  Focuses on using protein engineering and synthetic biology approaches to program electroactive proteins and cells to interface bacteria with electronic devices and control geochemical cycles by altering how electrons flow through microbial ecosystems.

Awards & honors

• NSF Postdoctoral Research Fellowship in Biology - Integrativ…
• Best Presentation – International Society of Microbial Elect…
• Lodieska Stockbridge Vaughn Fellowship (2018)
• DOE Office of Science Graduate Research Fellowship (2017)
• NSF Graduate Research Fellowship (2014)