Viruses pose an important threat to many agricultural crops worldwide, causing great financial losses and a decrease in the quantity and quality of the products. Besides their role as plant pathogens, there is little information about the other roles of plant viruses in ecosystems.

Although most studies in plant virology have focused on pathogens, a broader look reveals more intricate and stable interactions, especially in wild plant communities, which are often latently infected with viruses without any clear symptoms, thus representing a potential viral reservoir. Although seemingly non-harmful, these viruses pose a threat because they can be transmitted to crops, cause disease and emerge as new pathogens of crops. Of particular interest are interactions between viruses and long-lived perennial plants, which are underrepresented in agricultural systems, but dominant in nature and can serve as infection sources or overwintering hosts of different plant viruses.

Until recently, there was a lack of appropriate analytical tools, which could help decipher the complex relationships between viruses, plants, and the environment. The advent of high-throughput sequencing (HTS) technologies has led to a revolution in plant virus detection and now enables fast identification of all viruses present in a sample simultaneously. Using shotgun metagenomics HTS approaches, complete viromes of plants or various environmental samples can now be obtained. A few metagenomic studies have shown that viruses are abundant in wild plants from different climates as well as in aquatic environments, such as freshwater, wastewater, reclaimed water, and animal feces.

The majority of the plant pathogenic viruses so far recovered from environmental waters are very stable and their dissemination in streams and rivers can enable their long-distance spread. The release of infective plant virions from urban environment (human) to the wider environment has also been proposed and demonstrated recently for environmentally persistent viruses. This could be especially problematic in light of increased irrigation and the use of hydroponic systems in agriculture. Very little is known about virus infections in aquatic plants and even less about the possible water-mediated transmission of plant viruses to aquatic plants.

The aim of this project is to address and answer some of the most pressing questions regarding the gaps in knowledge described above.

• Can plant viruses released from wastewater persist in the river and possibly infect aquatic plants and river bank vegetation?
• Is the virome observed in river water influenced by the virome of plants growing in or near the water?
• Is there any exchange of (or overlap in) plant virus species between river water, proximal aquatic and terrestrial wild plants, and crops?

 

The outcomes of this project will help to elucidate the flux of plant viruses between different parts of a fragmented anthropogenic ecosystem. Analysis of samples from different constituent parts of the ecosystem, including urban wastewater, recipient river, submerged, bank and surrounding wild vegetation, and selected crops, will give an overview of the viromes present in the environment. Very likely new virus species or new associations of known virus species with different hosts will be revealed. Network inference and network analyses will expose possible overlapping virus species in viromes from different environments. Finally, the experimental system for viral infections of crop and aquatic plants will give insights into the biological relevance of the plant viruses found in the environment.