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bioRxiv2025

Inducible volatile chemical signalling drives antifungal activity of Trichoderma hamatum GD12 during confrontation with the pathogen Sclerotinia sclerotiorum

BACKGROUNDThe use of beneficial soil fungi or their natural products offers a more sustainable alternative to synthetic fungicides for pathogen management in crops. Volatile organic compounds (VOCs) produced by such fungi act as semiochemicals that inhibit pathogens, with VOC production influenced by physical interactions between competing fungi. This study explores the interaction between the beneficial soil fungus Trichoderma hamatum GD12 strain (GD12), previously shown to antagonize crop pathogens such as Sclerotinia sclerotiorum, to test the hypothesis that its antagonistic effect is mediated by volatile chemical signalling. A GD12 mutant deficient in the chitinolytic enzyme N-acetyl-{beta}-glucosaminidase ({Delta}Thnag : : hph), which shows reduced biocontrol activity, was also examined. RESULTSIn dual-culture confrontation assays, co-inoculation of GD12 and S. sclerotiorum led to fungistatic interactions after 7 days, whereas{Delta} Thnag : : hph showed no antagonism, indicating a loss of antagonistic function. VOCs collected from individual and co-cultures were analysed by gas chromatography - flame ionization detector (GC-FID) analysis and coupled GC-mass spectrometry (GC-MS), revealing significant differences in VOC production between treatments, with VOC production notably upregulated in the GD12 + S. sclerotiorum co-culture. Peak production of 6-pentyl-2H-pyran-2-one occurred 17 days post-inoculation. This upregulation was absent in the{Delta} Thnag : : hph co-culture, suggesting VOCs may drive antagonism. Synthetic VOC assays revealed several compounds inhibitory to S. sclerotiorum, including 1-octen-3-one, which also arrested the growth of key fungal pathogens (Botrytis cinerea, Pyrenopeziza brassicae, and Gaeumannomyces tritici). Structural insights into 1-octen-3-ones antifungal activity against S. sclerotiorum are also presented. CONCLUSIONSThese findings support the hypothesis that the antagonistic properties of T. hamatum GD12 against crop fungal pathogens can, in part, be attributed to VOC production. Further research is needed to assess the potential of these semiochemicals as tools for pathogen management in agriculture.

microbiology↗

bioRxiv2025

Integrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage

We built and characterised a mass spectrometer capable of performing CID (both beam type and resonant type), UVPD, EID and ECD in an automated fashion during an LCMS type experiment. We exploited this ability to generate large datasets through multienzyme deep proteomics experiments for characterisation of these activation techniques. As a further step, motivated by the complexity generated by these dissociation techniques, we developed a single Prosit deep learning model for fragment ion intensity prediction covering all of these techniques. The generated model has been made publicly available and has been utilised in FragPipe within its MSBooster module. Rescoring allowed both data-dependent acquisition (DDA) and data-independent acquisition (DIA) to achieve on average more than 10% increase in protein identifications across all dissociation techniques and enzymatic digestions. We demonstrate that these alternative fragmentation approaches can now be used within standard data analysis pipelines and can produce data competitive to CID in terms of eficiency, but in the cases of EID and UVPD with far richer and more comprehensive spectra.

systems biology↗