Analyzing pathogen suppressiveness in bioassays with natural soils using integrative maximum likelihood methods in R

PeerJ. 2016 Nov 3;4:e2615. doi: 10.7717/peerj.2615. eCollection 2016.

Abstract

The potential of soils to naturally suppress inherent plant pathogens is an important ecosystem function. Usually, pathogen infection assays are used for estimating the suppressive potential of soils. In natural soils, however, co-occurring pathogens might simultaneously infect plants complicating the estimation of a focal pathogen's infection rate (initial slope of the infection-curve) as a measure of soil suppressiveness. Here, we present a method in R correcting for these unwanted effects by developing a two pathogen mono-molecular infection model. We fit the two pathogen mono-molecular infection model to data by using an integrative approach combining a numerical simulation of the model with an iterative maximum likelihood fit. We show that in presence of co-occurring pathogens using uncorrected data leads to a critical under- or overestimation of soil suppressiveness measures. In contrast, our new approach enables to precisely estimate soil suppressiveness measures such as plant infection rate and plant resistance time. Our method allows a correction of measured infection parameters that is necessary in case different pathogens are present. Moreover, our model can be (1) adapted to use other models such as the logistic or the Gompertz model; and (2) it could be extended by a facilitation parameter if infections in plants increase the susceptibility to new infections. We propose our method to be particularly useful for exploring soil suppressiveness of natural soils from different sites (e.g., in biodiversity experiments).

Keywords: Biodiversity; DeSolve; Infected control treatments; Maximum likelihood estimation; Mono-molecular infection model; Ordinary differential equation; Programming manual; R; Soil resistance; bbmle.

Grant support

This study was supported by the German Centre for integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig funded by the German Research Foundation (FZT 118). EL was funded by the German Research Foundation (JO 935/2-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.