Soil Community Growth and Diversity Simulations under Low and High Connectivity Conditions

Readme file content

The files stored here contain the following material as supplementary and source data for the manuscript under final review for Communications in Biology

Environmental Connectivity Controls Diversity in Soil Microbial Communities

Manupriyam Dubey1, Noushin Hadadi1, Serge Pelet1, Nicolas Carraro1, David R. Johnson2,
and Jan R. van der Meer1*

1 Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
2 Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, CH 8600 Dübendorf, Switzerland

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MATLAB community simulations
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These scripts have the codes for the various community simulations described in the paper and its supplementary information, for growth under low connectivity (cells in isolation in beads), or for growth in mixed suspension (liquid).

The version of MATLAB for which the scripts was developed is 2016a.

Bead_LogOTU_growth_cell_death_biased_negative_interactions.m
Bead_LogOTU_growth_cell_death_biased_positive_interactions.m
Bead_LogOTU_growth_cell_death_bimodal.m
Bead_LogOTU_growth_cell_death_pos_on_slow_interactions.m
Bead_LogOTU_growth_cell_death_random_interactions.m

Liquid_logOTU_no_cell_death.m
Liquid_logOTU_prop_cell_death.m
Liquid_logOTU_random_cell_death.m
Liquid_random_growth_no_cell_death.m

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MATLAB imaging script
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The following script has the general code for the image analysis of microcolonies in beads, observed by two fluorescent colors (SYTO9 and mCherry), as described in the main paper.

Imaging_script.m

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MATLAB data set
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This file contains a data set of soil OTUs in log10 absolute abundance, used for the simulations as described in the main paper and its supplementary information

SC_clean.mat