title: 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 strain GD12 is notable amongst Trichoderma strains in both controlling plant diseases and stimulating plant growth, a property enhanced during its antagonistic interactions with pathogens in soil. These attributes, alongside its markedly expanded genome and proteome compared with other biocontrol and plant growth-promoting Trichoderma strains, imply a rich potential for sustainable alternatives to synthetic pesticides and fertilizers for the control of plant disease and for increasing yields. The purpose of this study was to investigate the transcriptional responses of GD12 underpinning its biocontrol and plant growth promotion capabilities during antagonistic interactions with the pathogen Sclerotinia sclerotiorum in soil. Using an extensive mRNA-seq study capturing different time points during the pathogen-antagonist interaction in soil, we show that dynamic and biphasic signatures in the GD12 transcriptome underpin its biocontrol and plant (lettuce) growth-promoting activities. Functional predictions of differentially expressed genes demonstrate the enrichment of transcripts encoding proteins involved in transportation and oxidation-reduction reactions during both processes and an over-representation of siderophores. We identify a biphasic response during biocontrol characterized by a significant induction of transcripts encoding small-secreted cysteine-rich proteins, secondary metabolite-producing gene clusters and genes unique to GD12. These data support the hypothesis that Sclerotinia biocontrol is mediated by the synthesis and secretion of antifungal compounds and that GD12's unique reservoir of uncharacterized genes is actively recruited during the effective biological control of a plurivorous plant pathogen.
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.|Centre for Genome Enabled Biology and Medicine, University of Aberdeen, 23 St. Machar Drive, Old Aberdeen, AB24 3RY, UK.
authors.forename: Sophie
authors.initials: S
authors.lastname: Shaw
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.|Sustainable Soils and Grassland Systems Department, Rothamsted Research, North Wyke, Okehampton, EX20 2SB, UK.
authors.forename: Kate
authors.initials: K
authors.lastname: Le Cocq
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
authors.forename: Konrad
authors.initials: K
authors.lastname: Paszkiewicz
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
authors.forename: Karen
authors.initials: K
authors.lastname: Moore
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.|Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Winsbury
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
authors.forename: Marta
authors.initials: M
authors.lastname: de Torres Zabala
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Studholme
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
authors.forename: Deborah
authors.initials: D
authors.lastname: Salmon
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Thornton
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.|School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Murray R
authors.initials: MR
authors.lastname: Grant
mesh_terms: D001203:Ascomycota / Q000502:physiology*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D018545:Lactuca / Q000254:growth & development* / Q000382:microbiology*; D010572:Pest Control, Biological; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D064210:Secondary Metabolism / Q000235:genetics; D017423:Sequence Analysis, RNA; D012987:Soil; D012988:Soil Microbiology; D013045:Species Specificity; D013997:Time Factors; D014158:Transcription, Genetic; D014242:Trichoderma / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D012987:Soil
keywords: RNA-seq; Sclerotinia sclerotiorum; Trichoderma hamatum; biocontrol; plant growth promotion