Agent-based model for simulating microbial movement with a preferred target for agricultural biologicals

Agricultural biologicals utilize beneficial microorganisms to enhance crop health and productivity, representing a rapidly growing sector of sustainable agriculture, offering environmentally friendly alternatives to synthetic chemicals. A key determinant of their efficacy is the ability of inoculated microbes to navigate through complex soil environments and reach plant roots, a process that is challenging to study empirically. To address this, we developed and validated a flexible Agent-Based Model (ABM) that simulates microbial spatial dynamics in soil. Each agent is characterized by unique attributes, including age, location, and parameters describing its behavior and interactions with the surroundings. Microbial behavior is governed by two core mechanisms: (1) logistic-based birth-death processes for population dynamics, and (2) directional preference for movement. Directional preference is driven by resource attraction toward plant root exudates, modeled with an attraction strength parameter (σ), and density-dependent interactions, modeled with a repulsion intensity parameter (γ). Validation used both in silico simulation and laboratory growth experiments. Simulations confirmed that the ABM reproduced theoretical population dynamic curves and realistic environmental responses. Lower σ values produced tight clustering around resources, while higher γ values resulted in avoidance of high density area. Laboratory experiments confirmed preferential fungal growth toward nutrient sources, with simulated results best matching observed growth patterns at σ values between 2.5 and 3.5. This ABM provides a computationally tractable framework for investigating microbial behavior in agricultural systems, with potential applications in screening and optimizing microbial candidates for agricultural biological products.