Data from: Multiscale mechanics of granular biofilms
Data files
Jan 03, 2026 version files 679.27 MB
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2025-10-26-ManssonWarsawDataDryad.zip
679.26 MB
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README.md
8.38 KB
Abstract
Biofilms produce and maintain extracellular polymeric substances (EPS) essential for their form and function. While biofilms are commonly lamellar and frequently targets of removal, granular biofilms are increasingly incorporated into water treatment strategies. In both cases, the EPS (mainly consisting of proteins, polysaccharides, and extracellular DNA) is largely responsible for their persistence. Unlike many granular biofilms, which are formed in engineered industrial bioreactors, the “pink berry” consortia is a naturally-occurring and robust granular biofilm of photosynthetic bacteria, found only in intertidal pools of salt marshes around Woods Hole, Massachusetts (USA). The pink berry biofilm’s unique ecological niche has sparked over three decades of study, yet its mechanical properties are completely unknown. Here, we characterized the structural and mechanical landscape of pink berry granules to determine the extent to which microscale heterogeneity influences macroscale material properties. We performed microindentation measurements on intact granules and nanoindentation measurements on thin sections. We report that intact pink berry granules exhibited low reduced elastic moduli (E*pink berry ≈ 0.5–10 kPa) and fast stress relaxation times (τ1/2 ≈ seconds), consistent with previous investigations of soft and viscoelastic biofilms. Nanomechanical measurements of thin pink berry sections revealed two mechanically-distinct domains: a very soft extracellular polymeric substance (EPS) matrix surrounding stiffer microcolonies of purple sulfur bacteria (PSB). Light sheet fluorescence microscopy revealed the spatial organization and distribution of cell-dense PSB microcolonies (34 vol. %) within EPS matrix (66 vol. %), suggesting the nanomechanical behavior of EPS dominates macroscale pink berry mechanics. Our multiscale experimental approach combining mechanics and imaging may be broadly applicable to investigations of complex soft materials, from synthetic hydrogel composites to biologically heterogeneous spheroids, organoids, and tissues.
Dataset DOI: 10.5061/dryad.gtht76j14
Description of the data and file structure
Data from peer-reviewed article:
Title: Multiscale Mechanics of Granular Biofilms
Journal: Tribology Letters
Authors: Lisa K. Mansson, Anna Warsaw, Elizabeth G. Wilbanks, and Angela A. Pitenis
Corresponding authors: Angela Pitenis, apitenis@ucsb.edu and Elizabeth G. Wilbanks, ewilbanks@ucsb.edu
Files and variables
File: 2025-10-26-ManssonWarsawDataDryad.zip
Description:
File List
1) fig1a1.jpg
2) fig1a2.jpg
3) fig1b.jpg
4) fig1c.tiff
5) fig1d.tiff
6) fig2b.csv
7) fig2c.csv
8) fig3b.csv
9) fig3c.csv
10) fig4b.tiff
11) fig4c.csv
12) fig4d.csv
13) fig5a.tif
14) fig5b.tif
15) fig5c1.tif
16) fig5c2.tif
17) fig5c3.tif
18) fig5d1.tif
19) fig5d2.tif
20) fig5d3.tif
21) fig5d4.tif
22) fig5d5.tif
23) fig5d6.tif
24) fig5d7.tif
25) fig6a.tif
26) fig6b.tif
27) fig6c.tif
28) fig6d.tif
29) fig6e.tif
30) fig6f.tif
31) SI_figA1.jpg
32) SI_figA2.csv
33) SI_figA3.jpg
34) SI_figA4.csv
35) SI_figA5.csv
36) SI_figB1.jpg
37) SI_figB2b.csv
38) SI_figB3bc1.tif
39) SI_figB3bc2.tif
40) SI_figC1_C2.csv
-- Data description for non-image files --
FIGURE 2: Microindentation measurements of whole pink berries.
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B) fig2b.csv: Indentation curves (time stamp, Normal force, z-displacement of probe) for all N=7 pink berries indented, all 3 cycles per pink berry. Note for data compliance correction in processing: the penetration depth = displacement - (normal force / normal spring constant k_N).
- row 1: Sample number
- row 2: Cycle number
- row 3: Data header (time (s), force (uN), displacement (um))
- row 4 to end: Data
C) fig2c.csv: Reduced elastic modulus (Estar) estimates from Hertz mechanics contact model fit to data in 2b, and diameter measurements for each pink berry
- row 1: Data header (Sample name, Estar (kPa), diameter (mm))
- row 2 to end: Data
FIGURE 3: Pink berry granular biofilms exhibit fast relaxation during compression.
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B) fig3b.csv: stress relaxation curves (time stamp, Normal force, z-displacement of probe) for all N=6 pink berries indented.
- row 1: Sample number
- row 2: Data header (time (s), force (uN), displacement (um))
- row 3 to end: Data
C) fig3c.csv: Stress relaxation time constant (tau_1/2) from data in 3b, and diameter measurements for each pink berry
- row 1: Data header (Sample number, tauhalf (s), diameter (mm))
- row 2 to end: Data
FIGURE 4: Nanoindentations of sliced pink berries reveal heterogeneity in mechanical properties at the micrometer scale.
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C) fig4c.csv: Indentation curves (time stamp, Normal force, cantilever displacement, piezo stage displacement) for all locations indented, all 3-5 cycles per location. Note that for this indentation measurement, the z-displacement of probe is z_stage = displacement of piezo - displacement of cantilever, both given in the raw data.
- row 1: Indentation location category (PSB microcolony or EPS matrix)
- row 2: Location number
- row 3: Cycle number
- row 4: Data header (Time (s), Load (uN), Cantilever (nm), Piezo (nm))
- row 5 to end: Data
D) fig4d.csv: Reduced elastic modulus (Estar) estimated with the Hertz contact mechanics model from indentation data in fig4c, per indentation location and cycle for all locations indented mapped out visually on images in SI Fig. 3B.
- row 1: Indentation location category (PSB microcolony or EPS matrix)
- row 2: Data header (Sample number per category as match with map in SI Fig. B3, Indentation cycle, Estar (kPa))
- row 3 to end: Data
--- SUPPLEMENTARY INFORMATION ---
SI FIGURE A1: Images of pink berries used for microindentation measurements taken from below the indentation setup with the inverted digital microscope.
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SI_figA1.jpg: Ordered from upper left to bottom right in the sample number order as given in the csv-files for each measurement.
SI FIGURE A2: Force-displacement curves plotted together with F~d3/2 scaling at low strains for three consecutive cycles of indentation of a pink berry.
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SI_figA2.csv: Thee consecutive indentation curves (time stamp, Normal force, z-displacement of probe) for one of the pink berries indented, all 3 cycles. Note for data compliance correction in processing: the penetration depth = displacement - (normal force / normal spring constant k_N).
- row 1: Sample number
- row 2: Cycle number
- row 3: Data header (time (s), force (uN), displacement (um))
- row 4 to end: Data
SI FIGURE A3: Images of pink berries used for stress relaxation measurements taken from below the indentation setup with the inverted digital microscope.
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SI_figA3.jpg: Ordered from upper left to bottom right in the sample number order as given in the csv-files for each measurement.
SI FIGURE A4: Serial indentation of pink berries shows unchanged elastic modulus values between cycles.
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SI_figA4.csv: Thee consecutive indentation curves (time stamp, Normal force, z-displacement of probe) for one pink berry indented, all 3 cycles. Note for data compliance correction in processing: the penetration depth = displacement - (normal force / normal spring constant k_N).
- row 1: Sample number
- row 2: Cycle number
- row 3: Data header (time (s), force (uN), displacement (um))
- row 4 to end: Data
SI FIGURE A5: Pink berries do not show indentation speed-dependent trends for reduced elastic modulus values.
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SI_figA5.csv: Indentation curves (time stamp, Normal force, z-displacement of probe) for N=3 pink berries indented at different indentation velocities, all (3+) cycles per pink berry included. Note for data compliance correction in processing: the penetration depth = displacement - (normal force / normal spring constant k_N).
- row 1: Sample number
- row 2: Indentation velocity (um/s)
- row 3: Cycle number
- row 4: Data header (time (s), force (uN), displacement (um))
- row 5 to end: Data
Pink berries do not show indentation speed-dependent trends for reduced elastic modulus values.
SI FIGURE B2: Agarose nanoindentation shows much larger reduced elastic modulus values compared to PSB microcolonies and EPS matrix in pink berry.
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B) SI_figB2b.csv: Indentation curves (time stamp, Normal force, cantilever displacement, piezo stage displacement) for all locations indented on agarose, all 3-5 cycles per location. Note that for this indentation measurement, the z-displacement of probe is z_stage = displacement of piezo - displacement of cantilever, both given in the raw data.
- row 1: Location number
- row 2: Cycle number
- row 3: Data header (Time (s), Load (uN), Cantilever (nm), Piezo (nm))
- row 4 to end: Data
SI FIGURE B3: Overview of all positions indented with nanoindentation on pink berry sections together with their reduced elastic modulus values.
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D) Same data as FIGURE 4c: fig4c.csv
SI FIGURE C1 and C2: Viscoelastic model fitting
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SI_figC1_C2.csv: stress relaxation curves (time stamp, Normal force, z-displacement of probe) for all N=6 pink berries indented.
- row 1: Sample number
- row 2: Data header (time (s), force (uN), displacement (um))
- row 3 to end: Data