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VIROME NGS ANALYSIS OF PESTS AND PATHOGENS FOR PLANT PROTECTION

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Applying viruses to limit crop disease

Turning viruses into biocontrol agents to combat the bacteria, fungi and insects that attack crops could reduce our dependence on chemicals and open the door to next generation pesticides.

Food and Natural Resources

Viruses are seen by most people as an outright danger and a threat. After all, they cause disease and, as we have seen with COVID-19, pandemics. The reality however is that the vast majority of viral species are completely harmless; in fact, some can be beneficial, and play an essential role in many ecosystems. One virus for example acts against chestnut blight, a fungal disease that attacks chestnut trees. This virus, which is harmless to the tree, acts as a kind of natural biocontrol, making the fungus less able to cause disease. “I’m a plant virologist by training, and I was interested to see if there were possibilities to use viruses in agriculture,” explains VIROPLANT project coordinator Massimo Turina from the National Research Council in Italy. “Using chemicals in agriculture is unsustainable, especially in more urbanised areas, and antibiotics against bacteria cannot be used due to antimicrobial resistance. The EU also wants to phase out the use of copper. It is therefore important that we find new approaches to protecting crops.”

Analysing ecological niches

The aim of the VIROPLANT project therefore was to examine the potential of new biocontrol agents based on viruses that attack bacteria, fungi and insect pests. Turina points out that there are currently only five virus-based biocontrol products on the EU market to control insects. “A lot of work has already been done on the ecological role of viruses in the marine environment, with the help of new high-throughput sequencing techniques,” says Turina. “We wanted to translate this approach to other ecological niches.” To do this, Turina and his team identified lesions on leaves, where plants were being attacked. Bacterial diseases attacking kiwis, beans, tomatoes and cucumbers were some of the case studies in the project. Insect pests that also vector viruses and phytoplasma to important crops such as grapevines, peppers and onions were also included. The team also collected downy and powdery fungal mildew. These samples were taken back to the lab and analysed using gene sequencing technology. This enabled the team to characterise the genetic make-up of a specific ecological niche, and to look for viruses that could be turned into biocontrol agents. Promising candidates were then used in trials.

New era in biocontrol

“We were able to describe in detail the genome of thousands of new viruses from looking at bacteria, fungi and insects,” adds Turina. “We found a lot of candidates that could be used against specific diseases and could one day be transformed into products.” The findings could also influence human medicine. There is growing interest in these bacteriophages – the viruses that attack bacteria – as a viable alternative to antibiotics. “Moving forward, addressing social acceptance of virus-based biocontrol agents will be critical,” he notes. “We also need to look at the commercial potential, and work towards a more simplified regulatory framework.” Turina points out that biocontrol agents face the same regulatory burdens as chemical pesticides. This is something that needs to be examined, he believes. Finally, Turina and his team were able to identify previously undiscovered virus types. “We found what could be missing links in viral evolution,” he says. “This is very interesting from a fundamental science point of view. With further research, these could help scientists to better understand the origin and evolution of viruses.”

Keywords

VIROPLANT, bacteria, biocontrol, fungal, virus, disease, antimicrobial, ecosystems

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