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. Author manuscript; available in PMC: 2024 Jan 29.
Published in final edited form as: Nat Protoc. 2021 Oct 11;16(11):5030–5082. doi: 10.1038/s41596-021-00593-3

Figure 8. Soil-air interface simulation.

Figure 8.

A two-species community colonizes a soil microhabitat (Procedure 6). a) Schematic detailing common features of a soil microhabitat, which are set in COMETS using simple commands to specify metabolite concentrations, and different ways of maintaining or supplementing those concentrations, in specific spatial locations. b) The initial state of the COMETS simulation, showing impenetrable barriers (gray) and the founder locations of the iJN1463 model (green) and the iYO844 model (blue). c) Time series showing biomass of the two models over time, integrated over the whole spatially structured environment. d) Snapshots of biomass and three key metabolites (f) succinate, f) O2, g) NH4) from 100 hours into the simulation. In the biomass snapshot, green is the iJN1463 model and blue is the iYO844 model. In e-g, the color scale denotes relative metabolite concentration, with bright yellow the maximum and dull purple the minimum. The scale bar shows 2mm.