(left to right) Graduate student team members Glorimar Marrero and Kevin Schneider with Drs. Anne Alvarez and Gernot Presting. (Photo: Joy Hakoda, UH Creative Services)
Ding-dong! Please sign here for your package of plant pathogens. With all the ag inspection protocols at the airport, it’s surprising to think of deliberately sending pathogenic material in and out of Hawai‘i. But researchers wanting to identify unknown strains of bacterial plant pathogens have had to do just that—until now.
Plant-associated bacterial pathogens cause billions of dollars in crop losses annually, so rapid and accurate identification is essential for agriculture. For example, the genus Xanthomonas contains many important plant pathogenic species, which altogether infect over 392 plant hosts. Quick identification of closely related strains helps agricultural workers make informed decisions about control methods, including quarantining and destroying infected plant material.
Using computational analysis to compare six sequenced genomes of Xanthomonas, Kevin Schneider, a graduate student in Gernot Presting’s (MBBE) lab, discovered a DNA marker that distinguishes closely related strains of Xanthomonas as well as or better than the widely used marker based on the ribosomal intergenic spacer region (ITS). This new marker, named RIF, can distinguish plant-associated bacteria below the species level and is also inherited more faithfully than the ITS marker. Kevin went on to genotype about 800 strains of phytopathogenic bacteria from Anne Alvarez’s (PEPS) collection, and the system should be transferable to most other bacterial genera in the future.
The other good news: The team created an online database to make these “reference” sequences available to the public. This will allow comparison of specimens from all over the world without having to ship the organisms into or out of Hawai‘i. This is important, both because accidental shipping of infected plant material has already led to global distribution of certain strains, and because the risk inherent in maintaining and shipping live pathogens into and out of our state makes side-by-side strain comparisons increasingly impractical. The database will continue expanding the more other scientists use it to identify and add other strains, or cross-reference it with other collections, which in turn will help with the classification of even more unknowns. And we can go back to shipping less potentially dangerous items, like snacks from Trader Joe’s.