Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil

The free-living soil fungus Trichoderma hamatum GD12 is notable amongst other Trichoderma strains in exhibiting both biocontrol and plant growth promotion (PGP) activities, which are coincident with a markedly expanded genome when compared to other characterised biocontrol and PGP isolates. Here, we make direct comparisons of T. hamatum GD12 transcription during PGP, and during antagonism of the root-infecting pathogen Sclerotinia sclerotiorum, in peat-based microcosms. An extensive mRNA-seq analysis sampling six time-points, 1, 2, 4, 7, 10 and 15 days after microcosm establishment revealed dynamic and biphasic signatures in the transcriptional responses of T. hamatum GD12 during Sclerotinia biocontrol and lettuce growth promotion. Functional analysis of differentially expressed genes demonstrated up-regulation of transportation and oxidation-reduction genes during both processes. Sclerotinia biocontrol is most likely mediated by the synthesis and secretion of antifungal compounds. Notably, the biphasic response during biocontrol was further characterised by the expression of a number of uncharacterised GD12 genes, small-secreted cysteine rich proteins and secondary metabolite producing gene clusters. This work demonstrates that T. hamatum GD12 harnesses a reservoir of uncharacterised genes that are actively engaged during effective biological control of a plurivorous plant pathogen.

Overall design RNA extracted directly from soil containing lettuce seedlings with either Trichoderma hamatum GD12 alone, T.hamatum GD12 and Sclerotinia sclerotiorum, or S. sclerotiorum alone. RNA was extracted in triplicate at days one, two, four, seven, ten and fifteen and then sequenced using an Illumina HiSeq2500. Two samples were taken in duplicate due to issues with RNA extraction.