DOI: 10.5061/dryad.gtht76j14
title: Data from: Multiscale mechanics of granular biofilms

description: 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.
description: # Data from: Multiscale mechanics of granular biofilms Dataset DOI:
 [10.5061/dryad.gtht76j14](https://doi.org/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](mailto:apitenis@ucsb.edu) and Elizabeth G. Wilbanks,
 [ewilbanks@ucsb.edu](mailto: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.
 \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \------------------------------------------------------------------------------------------- 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. \--------------------------------------------------------------------------- D) Same data as FIGURE 4c: fig4c.csv ### SI FIGURE C1 and C2: Viscoelastic model fitting \------------------------------------------------------------------------------------------- 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