Horticulture: Seeking new tools to manipulate soil and root microbiology for biocontrol of soft fruit Phytophthora diseases

Worldwide figures estimate that up to 40% of crop yields are lost to pest and diseases each year. Phytophthora root rot of Raspberry is caused by the soilborne pathogen Phytophthora rubi. Primary infection is initiated when motile water-borne zoospores of P. rubi are attracted to growing root tips, which they infect and spread through the whole root system destroying tissue and preventing nutrient and water uptake, killing the plant. Each infection releases zoospores which then spread to other plants. Phytophthora rubi may already be present on planting sites, as spores may persist for many years, being resistant to environmental extremes and many pesticides. Alternatively new infections can arrive on infected plants, or via irrigation water which has passed through contaminated soil. The initial motile spreading phase (zoospores) are reliant on free soil water.

The UK soft fruit industry has been devastated by root rot disease that forced growers to produce 80% of UK raspberries using pot-based systems in substrate to avoid contact with contaminated field soil. However, root rot is still a huge problem as the Phytophthora pathogen responsible for the disease is present in propagation stocks and can spread locally in irrigation water. To protect the raspberry industry, it is imperative that new, more sustainable methods of durable and effective pathogen control are identified. Indeed, improvements in sustainability, resilience and resource-use efficiency are required to meet the UK Government's Net Zero Strategy, that intends to halve UK net emissions in around a decade and eliminate them by 2050. The potential for new sustainable substrates that manage water more efficiently in combination with novel IPM tools to control disease are part of this strategy and are currently under development and there is great potential for these to manage root diseases

Disease suppressive cultural practices such as the use of organic mulches including sawdust, compost or bark can help to suppress soil pathogen populations. The microbial activity found in some organic mulches have been shown to cause breakdown of cell walls of Phytophthora hyphae. Trichoderma is an important free-living fungal genus comprising many strains that can interact directly with roots, promote plant growth, boost resistance to diseases, and increase tolerance to abiotic stresses. Many Trichoderma strains are known for their direct antagonistic activity against fungal pathogens and potential to reduce disease symptoms caused by pathogens by a range of mechanisms such as competition for resources, antibiosis, mycoparasitism, hyphal interactions, and secreted enzymes. Here we will investigate these potential benefits to raspberry as a model woody species with potential to help control a plethora of other economically and environmentally significant Phytophthora diseases. We have established a complimentary team to screen several Trichoderma fungal species for their suitability as an additive to soil and substrates in a range of Raspberry cultivars. Their direct impact on oomycete colony growth will be performed and a pot-based study will provide an assessment of health and resilience of the woody model host raspberry in presence of Trichoderma in sustainable substrate on the development of disease caused by pathogenic Phytophthora.

Non-chemical approaches for suppression of Phytophthora root rots target different phases of the life cycle of the pathogen. New substrates have been developed which limited the availability of free-water and hence reduce the ability of the motile zoospores to spread preventing new infections. Biocontrol of Phytophthora root rot involves the addition of organisms which are antagonistic to Phytophthora, either indirectly via competition for nutrients, production of suppressive compounds, or directly via parasitism. Combined effective control may be possible.

We propose a novel biocontrol approach against Phytophthora rubi, a soil borne pathogen which causes Raspberry root rot, a devastating disease of the raspberry industry in the UK and elsewhere. Here we aim to build on previous work showing that newly available sustainable substrates suppress Raspberry root rot by controlling water availability, by determining the combined impact on Phytophthora infection of the substrate and potentially antagonistic free-living fungi.

The first phase of the project will be an intensive literature review of current approaches to biocontrol of Phytophthora root rots. In particular, the fungal/microbial species involved will be collated to determine which species exhibit the greatest potential against Oomycete root pathogens - to which Phytophthora rubi belongs. Special attention will be giving to methodological considerations of production and incorporation of the antagonist into cultivation systems, and systems most closely related to those in use in the UK. Potential mechanisms of antagonism and life cycle phases affected will provide essential information for further development of this new approach against Phytophthora rubi.

The second phase will utilise isolates of free-living fungi identified in the literature review to determine their efficacy against Phytophthora both in vitro and in vivo. Initial screening of isolates will determine growth capabilities in the new substrate with unique water holding capacity. Isolations onto agar media will be used to determine growth, with microscopic identification of the distinctive asexual structures of Trichoderma. Confirmation on isolates will be done using sequencing of the ITS region. Direct antagonism by the fungal isolates on Phytophthora rubi will be carried out in vitro on media suitable for both organisms. In vivo analyses of the separate and combined impacts of the disease suppressive substrate and potential antagonists will be conducted under greenhouse conditions.