Researchers have discovered that a group of viruses known to infect an agriculturally important plant pathogen has remained genetically stable for an astonishing four decades. The discovery of a disease-fighting virus that doesn't mutate at a rapid rate points the way toward new tools for fighting crop disease – and highlights how little is known about viruses that infect bacteria in agricultural settings.
"Bacteriophages are viruses that specifically infect bacteria, and they hold tremendous potential as tools that can help us manage plant diseases," says Alejandra Huerta, corresponding author of two papers on the work and an associate professor of entomology and plant pathology at North Carolina State University. "However, viruses tend to evolve very rapidly, and there was a widespread belief that this limits the utility of bacteriaphages in disease management. Our findings show that some bacteriophages are not evolving rapidly, at least in agricultural ecosystems.
"This work is a concrete example of how much remains undiscovered with regard to bacteriophages. We need to better understand the biology, ecology, evolution, and diversity of phages in agricultural systems in order to develop robust and reliable phage-based disease management strategies."
The findings stem from work the researchers did to analyze viruses associated with Xanthomonas arboricola pv. pruni, a bacterium that infects peaches and other stone fruits worldwide. Specifically, the researchers examined samples collected in North Carolina peach orchards over approximately 40 years, and analyzed 15 phages they were able to isolate from those samples. The researchers were surprised to find that the phage genomes remained remarkably similar over time.
"We expected to find a more substantial DNA sequence variation across the phages given the variation in phenotypical characteristics over the 40-year period," says Katherine D'Amico-Willman, co-author of the papers and a postdoctoral researcher at NC State.
The work also led to the classification and naming of this group of phages as Duraznoxanthovirus arenicola, which is known to infect the Xanthomonas peach pathogen.
"It revealed an entirely new branch of the phage family tree," says Huerta. "Two new genera, a proposed new subfamily – all of which are viruses that infect bacterial plant pathogens. These findings provide one of the first evolutionary frameworks for understanding phages that infect plant-associated bacteria."
The researchers note that these findings – while exciting – are important primarily because they provide a clear path forward for bacteriophage research that can help us address agricultural pathogens in a meaningful way.
"Our results highlight how little we know about the vast viral communities associated with crops," says Prasanna Joglekar, co-author of the papers and a postdoctoral researcher at NC State. "The discovery of entirely new taxonomic groups in a well-studied crop system underscores the need to explore phage diversity, ecology, and evolution across agricultural landscapes."
"Plant-associated phages represent a largely unexplored frontier in biology," Huerta explains. "We know they are there, but we still lack a basic understanding of who they are, how they function, and how they influence microbial communities in crops.
"What phages are present in agricultural landscapes? How do they evolve? How do they interact with bacterial populations over different timescales and ecosystems? What role do they play in shaping agricultural microbiomes? Can growers use them to reliably manage bacterial plant diseases? These are fundamental questions we need to answer, and our two papers lay the foundation for how we can address these questions moving forward."
"Furthermore, this research illustrates the importance of teamwork and the value of irreplaceable biological historical collections," says David Ritchie, co-author of the papers and a professor of entomology and plant pathology at NC State. "This research could not have been done without both."
A paper outlining the path forward for agricultural bacteriophage research is published in Philosophical Transactions of the Royal Society B: Biological Sciences. Noah Totsline, a Ph.D. student at NC State, is a co-author on this paper.
A paper on the newly characterized bacteriophages attacking Xanthonomas of peach is published in Frontiers in Microbiology. Co-authors on this paper include Meaghan Flaherty, an undergraduate researcher at NC State; and Dann Turner of the University of the West of England.
This work was done with support from the Foundation for Food & Agriculture Research New Innovator in Food & Agriculture Research Award [grant number 22-000116]; the Extension Capacity Fund (Smith-Lever 3(b)and 3(c)) [project award number 7007436]; the USDA NIFA EWD 606 Postdoctoral Fellowship [grant number 2021-08360]; the USDA NIFA SCRI [grant number 607 2019-51181-30019]; the USDA-NIFA Equipment Grant 2022-06352; the Genetics and Genomics Institute at North Carolina State University; and the North Carolina Agricultural Research Service.
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