Exploring the Effects of <i>Trichoderma virens</i> Biofungicide on Carrot Cavity Spot and Soil Fungal Community Dynamics

Carrot cavity spot (CCS) has conventionally been managed with fungicides. However, fungicide resistance, their potential risks to human health and the environment, and the increasing demand for organic produce necessitate the exploration of biofungicides as alternatives. In this study, we evaluated varying concentrations of SoilGard (Certis USA, Columbia, MD), a Trichoderma virens-based biofungicide, for efficacy against different CCS-causing Pythium species in vitro. Additionally, its effects on taxonomic and functional diversities of soil fungal communities were studied in vivo in the greenhouse. To our knowledge, this is the first study reporting SoilGard's effectiveness against CCS, with emphasis on its potential as an alternative for fungicide-resistant Pythium isolates. Our in vitro study revealed that SoilGard efficacy was significantly dose-dependent and isolate-specific, thus highlighting the importance of selecting its application rate and the target isolate. Analysis of soil fungal communities using Illumina MiSeq sequencing revealed that SoilGard exerted a significant, albeit temporary, effect on the fungal community structure. It negatively impacted co-occurrence network complexity and alpha diversity in carrot-cultivated soil, whereas bare soil communities remained largely unaffected, thus explaining why preplant applications may yield better results. Our study showed that carrot cultivation without SoilGard enhanced fungal diversity, which was more pronounced late in the season, possibly due to carrot root-associated exudates. Our study sheds light on how complex interactions within soil fungal communities can be impacted by the application of beneficial/pathogenic microbes.