Multilocus Identification of Indigenous Trichoderma Isolates and Their Biocontrol Mechanisms Against Macrophomina in...

Charcoal rot, caused by the pathogen Macrophomina, is becoming an increasing challenge in Australia's northern cropping systems, with few effective management options available. The use of non-indigenous biocontrol agents raises ecological and regulatory concerns, which highlights the need to identify locally adapted microbial antagonists. In this study, indigenous Trichoderma isolates were collected from rhizosphere soils across Queensland and northern New South Wales and characterised using multilocus sequencing (ITS, tef-1α, rpb2) coupled with phylogenetic analysis. Twenty-six isolates were resolved into six species, dominated by T. azevedoi and T. afroharzianum. Dual-culture assays revealed substantial variation in antagonistic capacity, with several isolates achieving >70% inhibition of Macrophomina growth and maintaining consistent performance across pathogen genotypes. Functional screening indicated that enzyme-associated antibiosis was widespread, whereas volatile-mediated inhibition was restricted to a small subset of isolates. These findings demonstrate that biocontrol potential in indigenous Trichoderma populations is highly strain-dependent rather than species-driven. By integrating multilocus identification with functional screening, this study provides a practical framework for selecting locally adapted biocontrol candidates. This work establishes a foundation for developing region-specific biological control strategies and supports a shift toward targeted, strain-level selection for effective management of charcoal rot.