Exploiting the growth promotion and induced resistance properties of Trichoderma hamatum for improved crop productivity.

With the human population projected to reach 9 billion by the year 2050, unsustainable demands will be placed on global agriculture to meet future food requirements. Improvements in crops yields that have traditionally relied on plant breeding and energy intensive agriculture are unlikely to meet these needs and therefore marginal land, previously considered unsuitable for agriculture, will need to be brought into cultivation. Much of this land will have sub-optimal fertility and nutrient-poor soils requiring substantial inputs of synthetic fertilizers to support sustainable crop production. However, significant increases in the price of fertilizers mean many farmers, particularly in developing countries, cannot afford such management practises. The spiraling financial burden of fertilizers, combined with growing public anxiety of the environmental and health impacts of synthetic chemical additives, means that alternative strategies for sustainable crop production need to be examined urgently. Trichoderma strains produce a diverse array of secondary metabolites and secreted proteins. Trichoderma isolates have been shown to activate broad spectrum immunity, ameliorate a wide range of abiotic stresses such as salinity and drought, improve photosynthetic efficiency, enhance nutrient uptake, and significantly increase nitrogen use efficiency in crops. These important attributes can all contribute to the enhanced plant growth characteristics often evident upon inoculation. The positive agronomic traits of growth promotion, enhanced tolerance to abiotic stress and broad spectrum enhanced systemic immunity afforded by many Trichoderma strains are striking and unique. The ability to exploit the signaling networks activated by Trichoderma to establish these agriculturally beneficial traits requires an understanding of both the bioactive inducing molecules and the signaling networks targeted by these activators. The rapid developments in genomic and analytical technologies means this is an opportune time to exploit the amazing chemical diversity of soil micro-organisms such as Trichoderma, with the objective of improving PGP and ISR on a range of agronomically important plant species. Research conducted at Exeter has identified a novel strain of the naturally occurring rhizosphere fungus Trichoderma hamatum (strain GD12) that improves crop productivity and imparts broad spectrum enhanced immunity to pathogens in the absence of costly fertilizers and environmentally damaging agrochemicals. At present, the mechanism underlying the plant-growth-promotion and enhanced systemic resistance phenomena are unknown and this proposal lays the foundations to address the molecular basis of the inducing bioactives and the plant response pathways targeted by these bioactives. This combined knowledge is important, and necessary to contemplate translating Trichoderma PGP and ISR into the agricultural arena. This multidisciplinary research programme will use a combination of genetics, genomics and metabolomics to unravel Trichoderma PGP/ISR bioactives, capture the plant transcriptional reprogramming induced by the bioactives and identify key components of the PGP, ISR signaling networks. We will use comparative transcriptomics to characterize signaling pathways in Arabidopsis and rice activated by Trichoderma inoculation. In combination with mutant Trichoderma and Arabidopsis lines compromised in phytohormone signaling we will identify candidate signaling components/pathways that contribute to PGP and ISR. We will undertake comparative metabolic profiling using liquid chromatography mass spectrometry to characterize the bioactives and test their efficacy on different plants with the objective of developing novel natural agrochemicals.

Trichoderma strains produce a diverse array of secondary metabolites and secreted proteins meaning there is enormous agrochemical potential to exploit these key agronomic traits. Work at Exeter has disrupted hexosaminidase activity in T. hamatum, an enzyme involved in chitin de-polymerisation and release of sequestered nitrogen for plant growth, and an enzyme thought to be key to plant growth promotion (PGP) activity of a strain of the fungus (strain GD12). Contrary to our expectations, disruption of enzyme production dramatically enhanced PGP by the fungus leading to a further significant increase in plant growth. Strikingly, this mutant strain caused different PGP responses compared to GD12 on Arabidopsis mutants compromised in phytohormone signaling. What is clear from our preliminary studies, is that both transcriptional and genetic data indicate that T. hamatum responses differ from conventional JA/ET dependencies reported in the literature. Therefore, understanding the mechanistic basis of T. hamatum PGP/ISR is clearly of both fundamental and strategic interest. The aim of this proposal is to unravel the host signaling networks activated in systemic foliar tissue following T. hamatum infection. These pathways are expected to provide a mechanistic insight into both PGP potential and systemic enhanced resistance. In parallel we will undertake a detailed comparative metabolic profiling of the T. hamatum secretome to identify bioactive compounds responsible for PGP and ISR. We outline a multidisciplinary proposal that exploits the rapid developments in genomic and analytical technologies to (i) examine the nature of the bioactive inducers in the mutant and GD12 Trichoderma lines, (ii) identify the plant signaling networks activated by these bioactive compounds through comparative transcriptomics in Arabidopsis mutant lines, and between Arabidopsis and rice undergoing PGP/ISR responses and (iii) characterise key plant regulatory component of this pathway.

There is a clear need to accelerate the translation of fundamental research into practice, the proposed project addresses the overarching BBSRC aim of delivering excellence with impact, and concentrates on an area of research under-developed in the current UK efforts towards improved food security via crop genetic improvement. A major positive benefit in pursuing natural elicitors and understanding their mode of action is that they should have generic inducing properties and subsequent developments are not dependent on major investment in a genomic research platform for each crop. The major aim of this research is to determine the contributory factors underpinning growth promotion and broad spectrum induced resistance activated by the rhizosphere fungus Trichoderma hamatum on a range of crop and experimental plants. Trichoderma strains have been shown to ameliorate a wide range of abiotic stresses such as salinity and drought, improve photosynthetic efficiency, enhance nutrient uptake, and significantly increase nitrogen use efficiency in crops. Recent research conducted in the co-I's research group has identified a novel strain of the naturally occurring rhizosphere fungus T. hamatum (strain GD12) that improves crop productivity in the absence of costly fertilizers and environmentally damaging agrochemicals. We wish to investigate how strain GD12 induces such benefits by focussing our study on the molecular and biochemical pathways (both the bioactive inducing molecules and the signalling networks targeted by these activators within the host plant) responsible for this phenomenon. Our goal is to provide the molecular foundations for exploiting this extraordinary capacity to improve crop growth and resistance to a broad spectrum of pathogens. We see this work as having a high probability of translational success and complementary to ongoing investment in genomic and breeding programmes for crop improvement within the UK. The approach is novel and quite different from other agricultural driven research in the UK. The long-term objective of the work is to exploit the growth promotion and induced resistance properties of T. hamatum in order to provide innovative approaches for improved crop productivity, leading to the development of sustainable agricultural practices. The work may lead to the generation of novel mechanisms of disease control in integrated pest management systems and the identification and exploitation of beneficial traits during plant breeding programmes. Emerging knowledge is expected to have tremendous biotechnological potential leading to increased crop productivity, improved sustainable resource management and the reduced environmental impact of agricultural practises (e.g. reduced use of synthetic fertilizer and pesticides). We therefore identify the agrochemical industry, plant breeders and the composting industry as key beneficiaries of this work.