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

ABSTRACT: 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.

OTHER RELATED OMICS DATASETS IN: PRJNA281244

ORGANISM(S): Trichoderma hamatum GD12 Sclerotinia sclerotiorum

PROVIDER: GSE67909 | GEO | 2016/05/16

SECONDARY ACCESSION(S): PRJNA281244

REPOSITORIES: GEO

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Project description:Combating the action of plant pathogenic microorganisms by antagonistic or mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since more than 20 years, and gains additional importance in current trends to environmentally friendly agriculture. Taxa of the fungal genus Hypocrea/Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) contain prominent examples of such biocontrol agents, because they not only antagonize plant-pathogenic fungi, but are also often rhizosphere competent and can enhance plant growth. Identification of the primary factors that regulate the mycoparasitic behaviour and metabolic activities related to it will therefore allow the full ecological significance of this trait to be explored. We performed the analysis of the genome sequence from two mycoparasitic and rhizosphere competent Trichoderma spp. – T. atroviride and T. virens – and compare it to that of the saprophyte T. reesei. The predicted gene inventory of the T. atroviride and T.virens genome, therefore, points to previously unknown mechanisms operating during biocontrol of plant pathogens. The availability of these genomes provides a unique opportunity to develop a deeper understanding of the processes fundamental to mycoparasitism and its application for the breeding of improved biocontrol strains for plant protection. To investigate the potential role in mycoparasitism, microarrays were used to examine T. virens transcript levels when confronted with a potential prey (the plant pathogen Rhizoctonia solani) before contact, during first physical contact and during overgrowth of the host. The study presented here is the result of this analysis. Two biological pools by condition against a common reference control each sample hybridized in dye switch. On the two biological replicates we apply on the pretreated results the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes from the limma R package (Smyth 2004). For mycoparasitism confrontation assays T. virens was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were ca. 5 mm apart (before contact), at contact of the mycelia and after T. virens had overgrown the host fungus Rhizoctonia solani by ca. 5 mm (after contact). As control T. virens was confronted with itself and harvested at contact. Peripheral hyphal zones from each confrontation stage were harvested and shock frozen in liquid nitrogen. Mycelia were ground to a fine powder under liquid nitrogen and total RNA was isolated using the guanidinium thiocyanate method (Sambrook, 2001).

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

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