POMATO Project: Fighting Bacterial Diseases in European Tomato and Potato Crops

Co-authors: Saul Vallejos,^b Christian Ghidelli^c

^b Project Scientific Coordinator, Lab Head of the Polymers Research Group at the Chemistry Department, Science Faculty, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain

^c Agrifood Principal Researcher of the Agrifood Department, Fundación Tecnológica Advantx (FUNDITEC), Calle Faraday 7, 28049 Madrid, Spain

A pressing concern for agriculture in Europe and beyond

Tomatoes and potatoes are two of the most essential crops in global agriculture, not only for their economic value but also for their role in nutrition and food security, especially in the context of climate change and emerging plant diseases. In the European Union alone, over 48 million tonnes of potatoes and more than 16 million tonnes of tomatoes were harvested in 2023. These crops also represent a rich cultural heritage and a vital income source for farmers across the continent and beyond, particularly in Latin America, which is the centre of origin and domestication for both potatoes and tomatoes, and home to an extraordinary diversity of native and wild varieties.

Yet these crops are under serious threat, with estimated annual losses from plant pests ranging from €2.4–3.1 billion for potatoes and €1.5–2.3 billion for tomatoes, corresponding to up to 25% of total production. These figures highlight the vulnerability of these essential crops to a wide range of biotic stressors, especially in the context of increased global trade, climate change, and the introduction of new crops. Among the many pathogens affecting these crops, the POMATO project focuses on two particularly harmful quarantine bacteria: Clavibacter sepedonicus (Cs), responsible for ring rot in potatoes, and Ralstonia solanacearum (Rs), which causes bacterial wilt in both potatoes and tomatoes. Outbreaks of Cs and Rs can devastate yields, damage market access, and lead to significant economic and environmental losses. Due to their high financial and environmental impact, particularly on seed production, these quarantine pests are classified as A2 pests by the European and Mediterranean Plant Protection Organization (EPPO) — meaning they are present but not widely distributed — and are subject to strict EU regulatory measures.

Key challenges for farmers facing Cs and Rs

Managing these pathogens is no easy task for farmers. The bacteria are highly persistent in the environment and can spread silently before any symptoms appear. Once established, they are extremely difficult to eradicate, often requiring the destruction of entire crops and long fallow periods. Their resilience, combined with strict regulatory measures, poses both a biological and an economic challenge for small—and large-scale producers.

Rs can survive for extended periods in contaminated soil, surface water, and crop residues, even in the absence of a host plant. It can also infect plants latently, meaning that it can spread silently without visible symptoms, especially through planting material. Cs, though more host-specific, can also survive in infected tubers, plant debris, and agricultural machinery. In both cases, symptoms may only become apparent once the disease is well established, making early detection extremely difficult.

This silent spread increases the risk of crop loss and threatens seed production systems, where the use of asymptomatic yet infected material can trigger widespread outbreaks. Moreover, the current lack of fast, field-deployable diagnostic tools forces many growers to rely on laboratory-based tests, which are costly, time-consuming, and often impractical during critical decision-making periods.

Traditional methods of control rely heavily on fossil-based pesticides and sanitary measures, including crop rotation, the use of certified seed, and strict field hygiene. While necessary, these approaches are not always sufficient — especially in light of increased global trade, the introduction of new crops, and the effects of climate change, which reshape pest distribution and behaviour. These challenges highlight the urgent need for innovative, science-based solutions—something the POMATO project is actively addressing through its integrated approach.

POMATO: A science-based, practical, and sustainable approach

In response to these growing challenges, the European-funded project POMATO has launched a four-year initiative to protect tomato and potato crops against Cs and Rs. POMATO is built around four main pillars:

1. Resistance gene identification: Researchers are isolating and characterizing resistance genes from cultivated and wild varieties of potatoes and tomatoes. These natural resistances offer a promising alternative to chemical control and could be introduced into future breeding programs.
2. Early detection and monitoring tools: POMATO is developing advanced but farmer-friendly detection technologies. These include:
   • Artificial intelligence (AI) predictive models trained on climate and soil data.
   • A multiparametric sensing device capable of detecting plant disease markers.
   • Easy-to-use polymer sensors that allow for portable and low-cost pathogen detection.
3. Natural biocontrol solutions: The project is designing bio-based treatments to reduce the bacterial load in seeds, plants, and soil. This includes plant-derived compounds, biocontrol coatings, chemoperception disruptive products, and growth-promoting microorganisms (PGPMs) that can boost plant resistance.
4. Field validation and integrated pest management (IPM): All innovations will be tested at pilot scale in four real-world case studies across Europe and Latin America. The goal is to produce a validated IPM strategy that can reduce Cs and Rs incidence by 40–60%, with clear benefits for crop health and farm economics.

Early detection: empowering farmers with smart tools

For farmers, one of the most exciting aspects of POMATO is the promise of early and accessible disease detection. Instead of relying solely on laboratory-based diagnostics, POMATO offers simpler, in-field tools to help farmers make real-time decisions.

The polymeric sensors being developed, for instance, use peptide-based fluorogenic compounds that respond to specific enzymes secreted by pathogens. These sensors are designed as thin films that glow under certain conditions, with no need for extra reagents or complex instruments. Farmers could visualize infections in under 30 minutes using only a smartphone and a portable light source.

Likewise, AI-powered prediction platforms can alert farmers about high-risk periods for disease outbreaks, enabling them to plan preventive actions in advance. Combined with data collected via drones or handheld devices, these technologies aim to support farmers, not replace them — making precision agriculture more inclusive and practical.

Biocontrol and sustainability: moving beyond chemical dependency

In line with the EU Green Deal and Farm to Fork Strategy, the POMATO project is committed to reducing reliance on synthetic pesticides. The project is exploring plant-based compounds and beneficial microbes that can naturally suppress Cs and Rs. When integrated into existing practices, these alternatives could help prevent resistance build-up in pathogens, protect soil biodiversity, and reduce residues in food and water.

One promising approach is the use of biopolymer coatings for seeds and seedlings. These coatings act as physical barriers and slow-release reservoirs for bioactive substances. Other solutions include chemoperception disruptors that interfere with bacterial communication and limit their spread.

What farmers can expect from POMATO

At the end of the project, POMATO aims to deliver a comprehensive IPM toolbox adapted to different farming contexts. Farmers participating in the field trials will help validate the proposed solutions' effectiveness, usability, and cost-efficiency.

The project is committed to ensuring the results reach the targeted end users. Training materials, videos, and field guides will be produced, and extension events will be organized in collaboration with farmers' associations and agricultural advisors.

In practical terms, farmers can expect:

• Faster, cheaper, and more accessible diagnosis methods;
• Science-based decision-making tools tailored to their local conditions;
• Natural and eco-friendly alternatives to conventional pesticides;
• Opportunities to diversify crop protection strategies and improve yields;
• Enhanced farm competitiveness and resilience.

A collaborative, international effort

What sets POMATO apart is its multi-actor, interdisciplinary, and cross-continental structure. The project brings together 16 partners from academia, industry, and the farming community, including key stakeholders from Spain, Portugal, Poland, Colombia, and Ecuador. Latin American partners play a crucial role in accessing diverse genetic material and validating strategies under different agroclimatic conditions.

This collaborative structure ensures that the project addresses real challenges on the ground, not just in theory. It also allows for the exchange of good practices and the development of scalable and transferable solutions to other crops or pathogens.

Looking ahead: building resilience for tomorrow's agriculture

The threats posed by Cs and Rs are not isolated cases — they are symptoms of a broader need to reconsider how we protect crops in a changing world. By combining cutting-edge science with field-tested practicality, POMATO aims to lead the way towards a new generation of pest control strategies that are smarter, greener, and more farmer-friendly.

Acknowledgement information:

This project is funded by the European Union. Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them. Grant Agreement Nº 101181658 (POMATO).

References:

• Key Figures of the EU Food Chain (2024). Eurostat. Link.
• Regulation (EU) 2019/2072 protective measures against pests of plants. Link.
• Regulation (EU) 2022/1194 on Clavibacter sepedonicus (Spieckermann & Kotthoff 1914) Nouioui et al. 2018. Link.
• Regulation (EU) 2022/1193 on Ralstonia solanacearum (Smith 1896) Yabuuchi et al. 1996 emend. Safni et al. 2014. Link.