Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

Authored by Dani Or, Minsu Kim

Date Published: 2016

DOI: 10.1371/journal.pone.0147394

Sponsors: Swiss National Science Foundation (SNSF) European Research Council (ERC)

Platforms: No platforms listed

Model Documentation: Other Narrative Mathematical description

Model Code URLs: Model code not found

Abstract

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils.

Tags

Diversity chemotaxis Climate-change Escherichia-coli Community structure Saturated porous-media Water-retention function Solid fractal model Bacterial motility Hydraulic conductivity