Model-Based Community Analyses Identify Fungal Endophytes that May Modulate Symptom Development of Charcoal Rot Disease in Soybean

Abstract

Charcoal rot disease of soybean is a major threat to soybean harvests in the United States. This disease, caused by the fungal pathogen Macrophomina phaseolina (MP), cannot be economically treated in agronomic field conditions, and breeding of resistant cultivars has been largely unsuccessful due to multiple gene resistance. For difficult-to-treat phytopathogens, nascent research has emphasized the potential utility of endophyte modulation of disease symptoms. Most research into biocontrol of MP in soybeans has focused on in vitro or limited greenhouse/pot experiments, which may not emulate field conditions. Here, using a paired framework of diseased and asymptomatic soybeans exposed to MP in a production field setting, coupled with model-based community analyses, we identify several fungal endophytic taxa that apparently modulate disease pathogenicity. We use a multilevel analytical framework to provide evidence of taxa that respond to the disease state by querying plants across years and plant compartments. Additional work is needed to test the mechanisms by which these identified taxa may modulate MP, but this work provides the strongest evidence to date that endophytes may modulate charcoal rot disease levels in production field conditions. We posit that breeding for improved colonization of disease-modulating endophytes is a promising option to manage charcoal rot in soybean. [Figure: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Keywords

• disease modulation
• fungi
• generalized linear models
• Macrophomina phaseolina
• paired analysis