A team of researchers led by Oregon State University has found a way to potentially stop the spread of a disease-causing bacterium that can harm more than 100 plant species worldwide. The discovery could save the nursery industry billions of dollars a year.
The research has implications for commercial plant growers because the work aims to stop spread of Agrobacterium, which causes crown gall. The disease is indiscriminate, hitting fruit trees, roses, grape vine, nursery plants and shade trees. Those species have a combined value of more than $16 billion annually in the United States alone, according to USDA.
The methods researchers developed for the study can also potentially be applied to track diseases in humans and animals, and even foodborne disease outbreaks. The OSU scientists worked with researchers at USDA’s Agricultural Research Service on the study, and the findings were published recently in the journal Science.
Understanding disease spread
Jeff Chang, a professor in OSU’s College of Agricultural Sciences and one of the authors of the study, explains that understanding the genetic basis of how pathogens emerge and diversify in agricultural ecosystems is foundational for determining their spread and assessing risks. “These are critical to informing policies for improving plant health and preparing against disease outbreaks to increase global food security,” he adds.
The paper centers on plasmids, which are self-replicating DNA molecules found in Agrobacterium. Their spread amplifies the spread of disease. The plasmids of Agrobacterium have genes that give the bacteria the unique ability to transfer a portion of the plasmid into plant cells and genetically reprogram the host to cause crown gall or hairy root disease.
These plasmids also have genes that allow Agrobacterium to transfer the entire plasmid horizontally from one bacterium to another rather than through vertical, or parent to child, inheritance. Upon acquiring a harmful plasmid, a previously benign strain of Agrobacterium can become a novel pathogen line. This ability makes control of the pathogen and tracking an outbreak difficult. To develop their tracing system, the researchers had to understand the evolution and classification of the plasmids.
Before this research, the accepted scientific view was that the frequent transfer of genetic information among plasmids, and the large amount of genetic variation among Agrobacterium species, made drawing evolutionary relationships between the two practically impossible. Without that information, it’s not possible to accurately track disease outbreaks.
The researchers focused on two classes of plasmids, tumor-inducing and root-inducing, both of which provide Agrobacterium the ability to transfer a portion of the plasmid into plants and cause disease.
The work involved working with hundreds of strains with plasmids. Those came with the help of Melodie Putnam, director of the Oregon State Plant Clinic, and others at OSU and USDA ARS. Those groups have a well-curated collection of plasmids, and they helped analyze the large datasets.
The work involved genetic sequencing on the plasmids. That work was done by Alexandra Weisberg, who is lead author of the study and a postdoctoral researcher who is co-mentored by Chang and Niklaus Grunwald, of the USDA ARS Horticultural Crops Research Unit in Corvallis, Ore. Weisberg sequenced 140 strains with plasmids and found a surprise: The plasmids all descended from just nine lineages.
Weisberg notes that with that extensive genetic sequencing information showing how to classify plasmids and Agrobacterium, “We could infer both how bacteria move among nurseries and how the plasmids move among bacteria.”
The data have power. Weisberg explains that with the whole genome sequences of Agrobacterium, it became possible to link nurseries in different ways. For example, nurseries with the strains with the same genome and plasmid sequences, or the same genome sequence but different plasmid sequences, or different genome sequences but the same plasmid sequences. Sounds complicated — but it’s tracking information that can be easily analyzed.
With that information, the researchers were able to track at least seven cases where global distribution of plants contributed to the widespread transmission of a single Agrobacterium strain-plasmid combination. One of these cases included a nursery that produces plants for wholesalers and may have served as a kind of “patient zero” source for many outbreaks. Strains of the same genotype-plasmid combination were later identified in two other nurseries in another part of the world.
With the ability to separately analyze the bacteria from the plasmid, the researchers found many cases in which plasmid transmission perpetuated disease spread. For example, they found one strain-plasmid combination that was collected in 1964. Plasmids with the same sequences were identified in strains collected 30 to 40 years later in different parts of the world.
The ability to track a disease is a first step to understanding spread and creating new control methods.
Other authors of the paper are: Edward Davis, Javier Tabima, Michael Belcher, Joyce Loper and Marilyn Miller, all of OSU; and Chih-Horng Kuo of the Institute of Plant and Microbial Biology, Academia Sinica, in Taiwan. This work was funded by the Specialty Crop Research Initiative supported by USDA National Institute of Food and Agriculture.