Physiological and metabolomic characterization of biocontrol efficacy against toxigenic fungi: from Trichoderma strains to community-driven interventions

open_access
Open Access
Author:
Irakoze, Zilfa
Graduate Program:
Food Science
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
June 05, 2026
Committee Members:
Paul Esker, Outside Unit & Field Member
Helene Hopfer, Major Field Member
Joshua Lambert, Major Field Member
Josephine Wee, Chair & Dissertation Advisor
Robert Roberts, Program Head/Chair
Keywords:
Biocontrol
Plant extract
Biochemometrics
Ancestral knowledge
Aflatoxin
Mycotoxins
Aspergillus spp
Trichoderma spp.
Antifungal
Fusarium spp.
Volatile organic compounds
Antibiosis
International agriculture
Climate change
Abiotic stress
Outreach and extension
Community engagement
Metabolomics
Abstract:
Mycotoxin contamination of staple crops continues to burden global food safety and food security. Aflatoxins produced by toxigenic Aspergillus spp. are some of the most dangerous mycotoxins and aflatoxin incidences are projected to increase with rising global temperatures and drought. Thus, there is an urgent need for effective and sustainable biocontrol interventions to reduce mycotoxin-producing fungi in the food supply. This dissertation presents a framework that integrates physiological and metabolomic approaches to evaluate two complementary biocontrol interventions against toxigenic fungi, guided by three aims: (1) characterizing metabolite-mediated Trichoderma-Aspergillus interactions, (2) evaluating Trichoderma resilience under climate-relevant environmental stress, and (3) documenting and validating traditional plant-based biocontrol knowledge as a community-driven intervention for mycotoxin management. To achieve these aims, this work uses fungal culture-based assays, untargeted metabolomics, statistical modeling, and human subject research methodologies. In vitro screening of eight Trichoderma spp. against Aspergillus flavus and Aspergillus parasiticus demonstrated multiple Trichoderma strains with antifungal and antiaflatoxigenic activities through competition and metabolite production. Metabolomic profiling of volatile-mediated Trichoderma-Aspergillus interactions identified four discriminant compounds correlated with Trichoderma antifungal efficacy, providing potential targets for Trichoderma strain selection. Response surface modeling showed that adverse temperature and water activity (aw) combinations significantly decreased Trichoderma growth and antifungal activity. No Trichoderma spp. grew at 40°C and aw 0.90. T. asperellum growth inhibition of A. flavus decreased from 49% at 30°C to 0% at 35°C, with aw as the dominant limiting factor. To complement Trichoderma-based biocontrol intervention, bioactivity-guided metabolomics of BioCC+, a community-informed polyherbal formulation from Côte d’Ivoire, demonstrated strong antifungal activity against toxigenic Fusarium graminearum and Fusarium verticilloides (MIC 12-25mg/mL), with biochemometrics identifying six putative antifungal candidates. Ethnobotanical documentation of this practice in the Haut-Sassandra region of Côte d’Ivoire further revealed 23 traditionally used plant species, some of which have been validated to inhibit toxigenic A. flavus by up to 47% in vitro, alongside an alarming loss of this knowledge and a lack of mycotoxin awareness among farming communities. Together, this dissertation highlights that the development of effective and practical biocontrol interventions against toxigenic fungi in food requires complementary insights from laboratory mechanisms, environmental validation, and community engagement.