Digital holographic microscopy enhances Shewanella oneidensis MR-1 motility electrostimulation characterization
Data files
Mar 26, 2026 version files 261.10 MB
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2024_03_03_00-16.zip
32.60 MB
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2024_03_03_00-22.zip
32.52 MB
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2024_03_07_9-36.zip
32.66 MB
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2024_03_07_9-41.zip
32.64 MB
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2024_03_08_8-34.zip
32.40 MB
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2024_03_08_8-39.zip
32.37 MB
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2024_03_09_20-50.zip
32.92 MB
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2024_03_09_20-58.zip
32.99 MB
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README.md
3.17 KB
Abstract
Microbial motility is a reliable biosignature of extant life, serving as a measurable indicator of active metabolism, structural integrity, and environmental responsiveness — a relationship recognized since Leeuwenhoek’s earliest observations and regularly used in modern life-detection strategies. Shewanella oneidensis MR-1’s unique capacity for extracellular electron transport (EET) makes it an ideal model organism for investigating how an indium tin oxide (ITO) electrode functioning as an insoluble electron acceptor (IEA) stimulus can modulate microbial motility and improve biosignature detection. Prior studies characterizing electrokinesis, energy taxis, and congregation behaviors in MR-1 have been limited to two-dimensional observations, which fault to capture the full spatial complexity of microbial swimming and often constrain organisms to surface-influenced environments inconsistent with natural conditions. We developed a custom Mach-Zehnder Digital Holographic Microscope (MZ-DHM) paired with an electrochemical sample chamber to characterize the three-dimensional motility response of S. oneidensis MR-1 to applied electric potentials under anaerobic conditions. Motility metrics — including swimming speed, number of motile cells, and reversal rates — were quantified as a function of both electrode activation (0.0 V vs. 0.6 V) and distance from the ITO electrode surface across four independent trials. Applying 0.6 V to the working electrode produced a 3.6-fold increase in the total number of motile cells (57 to 208) over four trials and a 2.6-fold increase in average swimming speed [± SD of instantaneous speeds] (13.2 ± 11.6 μm/s to 33.8 ± 18.6 μm/s). Both motile cell counts and swimming speeds showed a clear spatial gradient, with the strongest responses concentrated within 50 μm of the electrode surface and progressively declining with distance, this is consistent with previous IEA stimuli studies using S. oneidensis but now resolved in three dimensions. The total number of reversal events as well as the reversal rate per microbe increased near the electrode surface. This indicates that electrokinesis and congregation are true phenomenon and are not just a aberration due to the two-dimensional. These results validate the use of IEAs as a reliable stimulus method for enhancing detection of motility-based biosignatures, and establish a proof-of-concept platform (i.e., DHM and electrochemical sample chamber) that is well suited for deployment in extreme terrestrial environments to understand the impacts of IEAs on extreme environmental samples.
Dataset DOI: 10.5061/dryad.1ns1rn97v
Description of the data and file structure
Raw holographic recordings underpinning all quantitative analyses reported in this study are available upon reasonable request to the corresponding author. Each of the four experimental trials comprised two separate recordings: one captured immediately prior to electrode activation (pre-activation) and one captured three minutes after the working electrode was poised at 0.6 V (post-activation). All recordings were acquired at 48 frames per second (fps) for 2500 frames using PFViewer software, but only the first ~2.5 seconds were analyzed. From each recording, the first 120 hologram TIFs were selected, with every other frame retained for processing, yielding a temporally subsampled dataset of 60 images per recording. The datasets listed below therefore each consist of alternating frames drawn from the first 120 images collected. Recording identifiers follow the format YYYY_MM_DD HH-MM, representing the acquisition date and time. Table S2 provides a complete index of recording identifiers for all trials.
| Trial | Pre-Activation Recording ID | Post-Activation Recording ID |
|---|---|---|
| 1 | 2024_03_03 00-16 | 2024_03_03 00-22 |
| 2 | 2024_03_07 9-36 | 2024_03_07 9-41 |
| 3 | 2024_03_08 8-34 | 2024_03_08 8-39 |
| 4 | 2024_03_09 20-50 | 2024_03_09 20-58 |
Table S5. Raw hologram recording index. All recordings were acquired at 48 fps using a Photon Focus MV0-D1920-S01-G2 camera (Sony IMX174 sensor, 1920 × 1200 pixels). Raw holograms were cropped to 800 × 800 pixels prior to angular spectrum method (ASM) reconstruction as described in the main text. Recording ID follows the format YYYY_MM_DD HH-MM, representing the acquisition date and time.
Files and variables
File: 2024_03_03_00-16.zip
Description: Pre-activation trial 1
File: 2024_03_03_00-22.zip
Description: Post-activation trial 1
File: 2024_03_07_9-36.zip
Description: Pre-activation trial 2
File: 2024_03_07_9-41.zip
Description: Post-activation trial 2
File: 2024_03_08_8-34.zip
Description: Pre-activation trial 3
File: 2024_03_08_8-39.zip
Description: Post-activation trial 3
File: 2024_03_09_20-50.zip
Description: Pre-activation trial 4
File: 2024_03_09_20-58.zip
Description: Post-activation trial 4
Code/software
Image processing was done on ImageJ to improve SNR.
Tracking of microbes was done using Open source software that exists here on github, https://github.com/carldsnyder/3D-DHM-Manual-Tracking
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA
