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

Abstract

SUMMARYThe 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.

Trichoderma erinaceum Bio-Priming Modulates the WRKYs Defense Programming in Tomato Against the Fusarium oxysporum f. sp. lycopersici (Fol) Challenged Condition

“…The rhizospheric microbiome (beneficial) are known to play an indispensable role in the transcriptional reprogramming required for plant defense against pathogens (Spence et al, 2014) and requires complex signaling cascades, involving multiple Tfs that primarily function as transcriptional regulators. At the molecular level, the biocontrol mechanism induced by Trichoderma is mediated through the adaptive recruitment and reprogramming of defense-related transcripts (Shaw et al, 2016). The transcriptional regulation of stress-inducible genes and the activation of an adaptive response (microbial symbiosis) are mediated and modulated through an immediate early expression of the WRKY genes (Chen et al, 2012).…”

Molecular Tools for Monitoring Trichoderma in Agricultural Environments

“…With the availability of field-portable microarray analysis systems (Chandler et al, 2010 ), this approach not only enables the monitoring of active Trichoderma populations, but may also provide information about the structure and dynamics of the entire microbial community, as well as about the physiological status of Trichoderma populations in the soil environment. For the selection of target genes appropriate for monitoring by microarrays, the results deriving from transcriptomic studies and comparative transcriptome analyses performed in vitro or in soil microcosm systems for Trichoderma -fungus (Atanasova et al, 2013 ; Steindorff et al, 2014 ; Morán-Diez et al, 2015 ; Perazzolli et al, 2016 ; Shaw et al, 2016 ) and Trichoderma -plant (Chacón et al, 2007 ; Samolski et al, 2009 ; Rubio et al, 2012 ; Shaw et al, 2016 ) interactions are highly valuable. Metatranscriptome analysis of agricultural habitats after the introduction of Trichoderma as a biocontrol agent has further potential to reveal important information about the changes of the entire, active microbiome, however, similarly to the sequencing of full metagenome, this approach is also expensive and time-consuming due to the necessity of appropriate, high-throughput sequencing and computational platforms, furthermore, the choice of an appropriate RNA isolation method is crucial due to the RNA's high susceptibility to degradation by RNase enzymes.…”

Soil Type Affects Organic Acid Production and Phosphorus Solubilization Efficiency Mediated by Several Native Fungal Strains from Mexico

“…Faced with this situation, the idea arises to implement low technological cost alternatives to improve the acquisition of P by plants; these include the use of rhizosphere and endophytic microorganisms that promote the solubilization of P from chemically unavailable forms such as RP [5,11]. The beneficial effects of these organisms have been widely reported but frequently yield inconsistent results [12,13], possibly because the sole inoculation of microorganisms into the soil-plant system alters the relationship among the microorganisms inhabiting the microhabitat of the rhizosphere ecosystem [14,15]. It is also assumed that the differential response depends on the plant species [16], on the mineralogical composition of the soil [17,18], on the interactions between distinct groups of soils, and the different populations of microbes, their competition and their metabolism in response to these factors [19,20].…”