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

Periodic Reporting for period 2 - PROTECTA (Pathogen-informed Resistance to Oomycete diseases in Ecosystems, Agriculture and Aquaculture)

Reporting period: 2020-08-01 to 2023-01-31

The oomycetes are a distinct lineage of Eukaryotic microbes that resemble fungi, but are genetically related to the brown algae. Oomycetes have a worldwide distribution and are destructive and highly adaptable pathogens, infecting 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. To tackle these diseases, the objective of the PROTECTA project was to elucidate how these oomycetes interact with their hosts e.g. via the use of effector proteins and how these interact with host resistance. PROTECTA has made scientific advances in our understanding of oomycetes and their host interactions. We have identified new effectors expressed by oomycetes in oomycete-plant and oomycete-oomycete interactions and functionally characterised of some of these effectors, their host targets and/or new immune responses, thus contributing towards a better understanding of the fundamental biology of oomycetes. Very importantly, we have trained the next scientific generation in cutting-edge inter-sectoral scientific and transferable skills preparing them to become the next generation of European scientific innovators and leaders.
We recruited 15 ESRs and implemented 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, which was adapted due to the covid19 pandemic. As part of the adapted training program the ESRs worked together in online teams to write and produce a series of review articles published in the journal Fungal Biology Reviews, (special issue, volume 40, June 2022), on topics related to the PROTECTA research objectives.Our project has identified new effectors in phytopathogens such as Phytophthora infestans, Phytophthora cactorum, Aphanomyces euteiches, Aphanomyces cochlioides, animal pathogens including Saprolegnia parasitica and the mycoparasites Pythium oligandrum and Pythium periplocum. These findings have greatly advanced our understanding of how the hosts of these species defend themselves, identifying new components of plant immunity and investigating if activation of such immune responses comes with fitness costs. We tested mycoparasitic oomycetes as biostimulators and biocontrol agents for crops including legumes, potatoes and wheat. By studying the host-range and longevity of tree pathogenic oomycetes and modeling what will happen under a changing climate, combined with a systematic review of the literature, published as 5 reviews, we are now better equipped to determine and manage the future risks posed by oomycetes across our different sectors.
In Aphanomyces euteiches we identified a new secreted effector that facilitates 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. We have identified determinants of mycoparasitism in Pythium oligandrum. We performed a pilot study to test if effector-assisted breeding, can be transferred to strawberry. We discovered a species of Gluconobacter that can protect Pine trees from root rot, and collected oomycete samples from production and natural forest ecosystems to assess species diversity in this landscape. We have also developed diploid, near-isogenic potato lines carrying different combinations of Resistance (R) genes, which are currently being exploited in the breeding programs at Solynta. 21 scientific papers have so far been published, and several more are in the pipeline. The ESRs have also attended scientific conferences, met with stakeholders and communicated their research widely. Popular science articles for policy makers and other stakeholders have also been published.
Our vision was to develop an integrated European research and training platform that advanced our basic scientific understanding of oomycete-host interactions and innovated sustainable new methods to manage and control these devastating diseases across multiple sectors (agriculture, horticulture, aquaculture and silviculture). Scientific deliverables from PROTECTA have contributed to a sustainable future society, increased food security and sustainable management of our natural resources. We have provided new genetic resources to the crop production industry, (e.g. new potato breeding lines, new information on the genetics of sugar beet breeding lines) and our data can be used to support the maintenance of biodiversity within agricultural, horticultural and forest systems through a better understanding of the relationship between soil health and the microbiome. The results generated by the ESRs will therefore contribute to a reduction in the use of chemicals across these sectors as we have identified new bacterial strains that are effective biocontrols in woody plants, and we have a better understanding of how to deploy Pythium oligandrum for biocontrol in agriculture or horticulture.
Although extensively modified due to covid19, our doctoral training program, provided a supportive, open environment designed to improve the working conditions and career perspectives of the ESRs. PROTECTA had a strong collaboration across multiple business and academic sectors, ensuring that results will continue to be exploited beyond the project, by European companies such as Solynta, DLF, De Sangosse, Fish Vet Group, Graminor and Vivai Michelini. The very early impact of the project is seen by the employment of the ESRs that have already defended their theses successfully. ESR3 is employed as a bioinformatician at Biomillenia in France, ESR14 is employed as phenotyping manager at Innolea SAS, France. ESR7 is employed as a mass spectrometry data analyst at Mnemo Theraputics, France and ESR15 is post-doctoral researcher looking at “Emerging water futures” at the James Hutton Institute, UK. This demonstrates our impact, in terms of career potential of our ESRs and shows that, as hoped, trans-sectoral students with an international mindset, and the key transferable and research skills gained during PROTECTA make our graduates highly sought after by employers. The non-academic sector had a meaningful contribution to the research training program. The ESRs thus gained a deeper understanding of non-academic research and developed creative and innovative mindsets. See the researcher blog on our website https://protectaitn.wordpress.com/blog/ for thoughts from the ESRs on innovation after the training courses within PROTECTA. We have strengthened European innovation capacity, by providing innovative new natural products for crop protection. For example, new bacteria that can control oomycete diseases; new methods, and new genes, for breeding better host resistance in crops including potato and sugar beet new potato breeding lines and assessments of the impact of plant resistance inducers and biocontrol agents on plant fitness and soil health.
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