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Pathogen-informed Resistance to Oomycete diseases in Ecosystems, Agriculture and Aquaculture

Periodic Reporting for period 1 - PROTECTA (Pathogen-informed Resistance to Oomycete diseases in Ecosystems, Agriculture and Aquaculture)

Reporting period: 2018-08-01 to 2020-07-31

The oomycetes are a distinct lineage of Eukaryotic microbes that resemble fungi, but are genetically related to the heterokont (brown) algae. Oomycetes have a worldwide distribution and are destructive and highly adaptable pathogens, infecting vascular plants, fish, insects fungi and occasionally humans. Notorious crop damaging pathogens such as the potato late blight pathogen Phytophthora infestans, vegetable root rots and (re)-emerging diseases such as fish saprolegniosis and Sudden Oak Death are global threats to food security and our natural ecosystems.
Comparative genomics in the oomycetes reveals major classes of effector proteins used by pathogens to manipulate hosts that can also be recognised by host immune systems. The major challenges in oomycete research are to identify the precise biochemical functions of major pathogenicity determinants (such as effector proteins) and host immune responses (such as plant resistance genes) and translate this research into durable disease control in agriculture, ecosystems and aquaculture.

We are studying the biology, genetics, biochemistry, ecology and management of oomycete diseases and their interactions with their hosts and with other organisms within the ecosystems that they inhabit.
The overall objective of PROTECTA is to use our basic knowledge of oomycete effector biology to train the next generation of European scientific leaders to develop and exploit such data for the advancement of our understanding of host-oomycete interactions and the development of sustainable disease control measures.
Specific Objectives of the PROTECTA Training Programme:
1) The training of future European research leaders in cutting-edge inter-sectoral scientific and transferable skills to prepare them for future careers as research leaders and innovators, by:
i. Recruiting young scientists (ESRs) with an excellent potential to become leaders in their chosen fields, and providing multidisciplinary inter-sectoral scientific training through individual PhD projects;
ii. The development of a comprehensive four-step training programme, utilizing the experience and expertise of the partner laboratories in genomics, quantitative proteomics, computational biology, molecular biology, biochemistry, genetics, breeding, microbiology, cell biology, ecology, plant pathology, disease control, technology transfer, entrepreneurial skills, product development and management, with the direct involvement of both academic and industrial partners;
2) Advances in our understanding of the diversity, environmental impact, genetics, biochemistry and molecular and cellular biology of oomycete effectors, pathogenicity and host resistance;
3) The exploitation of our data for the development of new, environmentally sustainable and durable control measures against oomycete diseases in ecosystems, agriculture, horticulture and aquaculture.
We have recruited 15 ESRs, and begun the implementation of a four-phase training program, giving them experience and knowledge in transferable skills such as scientific communication and subject specific training courses linked to our research program. After two ESRs left the project, we have recruited one replacement with the second replacement recruitment ongoing. Towards the research objectives we have identified new effectors expressed by oomycetes in oomycete-plant and oomycete-oomycete interactions and functional characterisation of some of these effectors, their host targets and/or new immune responses is underway. Much of this data comes from a collection of transcriptomic and genomic data generated in the first part of the project. We have also developed new and efficient assays for the assessment of pathogenicity and/or effector function in several of our study systems, including Saprolegnia parasitica, Aphanomyces cochliodies, and Pythium oligandrum and optimised gene silencing or gene editing tools for use in some of our understudied oomycetes, such as Phytophthora cactorum.
In the Aphanomyces euteiches- Medigago truncatula pathosystem, we have identified an effector secreted by A. euteiches that interfers with an RNA helicase within the host to facilitate infection. In the Phytophthora infestans-Solanum pathosystem, we have identified receptor(s) that bind to members of a new, fastly evolving effector family, and we have also discovered that the host plant activates immune proteases through a proteolytic cascade, which P. infestans inhibits by secreting EPI1. We have new lines of potato that may carry more durable resistance to late blight, and our climate change experiments will evaluate how well different plants perform for traits including resistance to oomycete diseases under various possible future climates. We have identified that the activation of Carbohydrate Active Enzymes (CAZy) is important for pathogenicity of the mycoparasite Pythium oligandrum. We have also performed a pilot study to test if effector-assisted breeding, a method that members of the constortium have previously developed in potato, can be transferred to strawberry. We have discovered a species of Gluconobacter that can protect Pine trees from Phytophthora-induced root rot, and we have collected a large number of oomycete samples from production and natural forest ecosystems to assess species diversity in this landscape. Our ongoing experiments to assess the survival of Phytophthora species in simulated nursery conditions will help to design scientifically sound management recommendations in the plants-for-planting pathway, and allow us to test if biological control solutions will be effective strategies in these settings.
Our vision is to develop an integrated European research and training platform that advances our basic scientific understanding of oomycete-host interactions and innovates sustainable new methods to manage and control these devastating diseases across multiple sectors (agriculture, horticulture, aquaculture and silviculture). Scientific deliverables from PROTECTA will contribute to a sustainable future society, increased food security and sustainable management of our natural resources. We will provide new genetic resources to the crop production industry, and support the maintenance of biodiversity within agricultural, horticultural and forest systems. The results generated by the ESRs will directly contribute to a reduction in the use of chemicals across these sectors.

PROTECTA is based on a strong collaboration across multiple business and academic sectors. Such a strong intersectoral element means results will be exploited within the PROTECTA project and beyond, by European companies such as Solynta, Syngeta, De Sangosse, Fish Vet Group, Graminor and Vivai Michelini. We aim to provide, innovative new natural products for crop protection, new methodologies and tools for plant breeding and disease control which will be utilised by Maribohilleshog and Solynta and strengthen collaborations between European laboratories working at the forefront of host-microbe interactions and disease control.

Our Scientific results are published in open access journals and as reprints on the PROTECTA website, in order to encourage European innovation based on our research. The results from PROTECTA are expected to strengthen economic competitiveness across multiple sectors and provide the next generation of scientific leaders in Europe.
The logos of the Beneficiaries within PROTECTA
Our Project Logo
A graphical view of how ESRs work together within PROTECTA
The PROTECTA consortium meeting in Malmö 2019, with REA officer Luisa Marconi