DOI: 10.5281/zenodo.15735347
title: Context-Dependent Adaptation in Structured Environments

description: Supplementary Movies, Spreadsheets, and Scripts for the bioRxiv preprint "Context-Dependent Adaptation in Structured Environments" by Karita et al., 2025.

Supplementary Movies



Supplementary Movie 1: Inoculum-dependent failure of mat formation by an adaptive Wrinkly Spreader type (WS). Mono-culture of WS could not form a mat structure when started from a low inoculum density (dilution factor 10^4). 3 mL of the cell suspension was statically cultured in a well of a 12-well plate at 28C. The movie was taken with a stereo microscope (Axio Zoom V16, Zeiss) in dark-field illumination with 16X magnification. The time unit is [hour:minute].

Supplementary Movie 2: Successful mat formation by WS. Mono-culture of WS could develop a robust mat when started from a high inoculum density(dilution factor 10^2). 3 mL of the cell suspension was statically cultured in a well of a 12-well plate at 28C. The movie was taken with a stereo microscope (AxioZoom) in dark-field illumination with 16X magnification. The time unit is [hour:minute].

Supplementary Movie 3: Representative observation of microcolony collapse at the air-liquid interface with high magnification. WS microcolony collapse was captured at the center of a well with 140X magnification. 3 mL of WS low-inoculum culture (dilution factor 10^7) was statically cultured in a well of a 12-well plate at 28C. The movie was taken with a stereo microscope (AxioZoom) in dark-field illumination.

Supplementary Movie 4: Phase separation of active fluid-like regions and sessile regions at the air-liquid interface of a co-culture of SM and WS. A mixture of SM and WS was cultured under static conditions. The movie was taken at t = 10.5 h for 5 seconds with bright-field imaging. The same data is also shown in figure S4a.


Spreadsheets



Surface_density_data.xlsx: The surface density of cells at an air-liquid interface was measured across strains and inoculum densities. The data was used to produce Figs 1b and S1a of the manuscript.

Motility_assay_2024_01_30.xlsx: The expansion of bacterial suspension on a soft agar was measured for various mutants. The data was used to produce Figs 1b and S1b of the manuscript.

Motility_assay_2024_03_12.xlsx: The expansion of bacterial suspension on a soft agar was measured for various mutants. The data was used to produce Figs 1b and S1b of the manuscript.

Pellicle_success.xlsx: The frequency of successful pellicle formation was recorded for various inoculum densities. The data was used to produce Fig 1c of the manuscript.

Collapsing_colony_size.xlsx: The size and the position of collapsing microcolonies from an air-liquid interface were semi-manually measured by a cutstom-built MATLAB script. The data was used to produce Fig 1d of the manuscript.

PcdrA-evo-count_2024_10_08.xlsx: The color and morph of colonies on plates were scored. The data was used to produce Fig 4c of the manuscript.

SM-mixevo_count_2024_10_02.xlsx: The color and morph of colonies on plates were scored. The data was used to produce Fig 6c of the manuscript.


Scripts



4state-model.ipynb: A Jupyter notebook for the four-state model in the manuscript. The code was used to produce Fig 5d-f of the manuscript.

Spatial_Model_LBOX500.c: A representative c code for the sptial model in the manuscript for Fig 2. MT.h (developed by Makoto Matsumoto and Takuji Nishimura) was used to generate random numbers.

input.txt: A sample input file to operate  "Spatial_Model_LBOX500.c".