Spatial structure and pathogen epidemics: the influence of management and stochasticity in agroecosystems

Organisms susceptible to disease, from humans to crops, inevitably have spatial geometry that influence disease dynamics. Understanding how spatial structure emerges through time in ecological systems and how that structure influences disease dynamics is of practical importance for natural and human management systems. Here we use the annual crop, coffee, Coffea arabica , along with its pathogen, the coffee leaf rust, Haemelia vastatrix , as a model system to understand how spatial structure is created in agroecosystems and its subsequent influence on the dynamics of the system. Here, we create a simple null model of the socio-ecological process of death and stochastic replanting of coffee plants on a plot. We then use spatial networks to quantify the spatial structures and make comparisons of our stochastic null model to empirically observed spatial distributions of coffee. We then present a simple model of pathogen spread on spatial networks across a range of spatial geometries emerging from our null model and show how both local and regional management of agroecosystems interact with space and time to alter disease dynamics. Our results suggest that our null model of evolving spatial structure can capture many critical features of how the spatial arrangement of plants changes through time in coffee agroecosystems. Additionally, we find that small changes in management practices that influence the scale of pathogen transmission, such as shade tree removal, can result in a rapid transition to epidemics with lattice-like spatial arrangements but not irregular planting geometries. The results presented here may have practical implications for farmers in Latin America who are in the process of replanting and overhauling management of their coffee farms in response to a coffee leaf rust epidemic in 2013. We suggest that shade reduction in conjunction with more lattice-like planting schemes may result in coffee being more prone to epidemic-like dynamics of the coffee leaf rust in the future.