Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We further characterize the lettuce-T. hamatum interaction to show that bran extracts from GD12 and an N-acetyl-β-D-glucosamindase-deficient mutant differentially promote growth in a concentration dependent manner, and these differences correlate with differences in the small molecule secretome. We show that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12. To understand the genetic potential encoded by T. hamatum GD12 and to facilitate its use as a model beneficial organism to study plant growth promotion, induced systemic resistance and mycoparasitism we present de novo genome sequence data. We compare GD12 with other published Trichoderma genomes and show that T. hamatum GD12 contains unique genomic regions with the potential to encode novel bioactive metabolites that may contribute to GD12's agrochemically important traits.

Trichoderma species are ubiquitous soil fungi that hold enormous potential for the development of credible alternatives to agrochemicals and synthetic fertilizers in sustainable crop production. In this paper, we show that substantial improvements in plant productivity can be met by genetic modification of a plant-growth-promoting and biocontrol strain of Trichoderma hamatum, but that these improvements are obtained in the absence of disease pressure only. Using a quantitative monoclonal antibody-based ELISA, we show that an N-acetyl-b-D-glucosaminidase-deficient mutant of T. hamatum, generated by insertional mutagenesis of the corresponding gene, has impaired saprotrophic competitiveness during antagonistic interactions with Rhizoctonia solani in soil. Furthermore, its fitness as a biocontrol agent of the pre-emergence damping-off pathogen Sclerotinia sclerotiorum is significantly reduced, and its ability to promote plant growth is constrained by the presence of both pathogens. This work shows that while gains in T. hamatummediated plant-growth-promotion can be met through genetic manipulation of a single beneficial trait, such a modification has negative impacts on other aspects of its biology and ecology that contribute to its success as a saprotrophic competitor and antagonist of soil-borne pathogens. The work has important implications for fungal morphogenesis, demonstrating a clear link between hyphal architecture and secretory potential. Furthermore, it highlights the need for a holistic approach to the development of genetically modified Trichoderma strains for use as crop stimulants and biocontrol agents in plant agriculture. INTRODUCTIONTrichoderma species are ubiquitous soil saprotrophs that have attracted sustained scientific interest as biological control agents of plant disease. In addition to their biocontrol properties, certain strains have been shown to enhance crop productivity by stimulating plant growth (Contreras-Cornejo et al., 2009;Harman et al., 2004;Ortíz-Castro et al., 2009;Vinale et al., 2008Vinale et al., , 2009. While genetic modification of Trichoderma strains by constitutive overexpression of chitinase, b-glucanase and proteinase genes has allowed the development of strains with improved biocontrol capabilities (Flores et al., 1997;Baek et al., 1999;Limó n et al., 1999;Viterbo et al., 2001;Djonović et al., 2007), less attention has been paid to enhancing the plantgrowth-promoting (P-G-P) activities of these fungi via genetic modification, and the impact that any such modification might have on their saprotrophic competence and fitness as biocontrol agents.In a previous study, we showed that a naturally occurring strain of Trichoderma hamatum was able to promote plant growth in low pH, nutrient-poor peat soils (Thornton, 2008). These soils contain a significant pool of nitrogen sequestered in chitin of insect and fungal origin (Kerley & Read, 1998), and fungal N-acetyl-b-D-glucosaminidase has been shown to be a key chitinolytic enzyme releasing sequestered nitrogen for assimilation ...