Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

摘要

Author summary Soil bacterial communities are key players in global biogeochemical cycles and drive other soil regulatory and provisional ecosystem functions. Despite the relatively high bacterial abundance found in fertile soil, bacteria occupy only a small fraction of the soil surfaces and often form hotspots with disproportionate contributions to observed biogenic fluxes. As soil opacity and complexity limit detailed observations of such hotspots in situ, we have developed a modeling platform, IndiMeSH (Individual-based Metabolic network model for Soil Habitats), to enable systematic study of dense multispecies bacterial communities within a structured habitat resembling (but not limited) to soil. The model is capable of representing multispecies trophic interactions and spatial self-organization in response to nutrient gradients, as confirmed in comparison with published results. IndiMeSH offers new opportunities for quantifying bacterial hotspot formation and dynamics and observe their resilience and response to perturbations in hydration and nutrient conditions.