What a century-old grapevine reveals about a disease that plagues wine country

A century-old grapevine cutting is providing new clues into the history of a deadly plant pathogen that is decimating crops across the globe.

First reported in Anaheim, California in the 1880s, Pierce’s disease of the grapevine has since been found in much of California, as well as in other parts of the U.S. and, more recently, Europe. Triggered by the bacterium Xylella fastidiosa, the disease clogs the tiny tubes called xylem that transport water and nutrients throughout the plant. Starved of nourishment, the vine’s grapes shrivel, its leaves turn brown and drop, and eventually the plant dies. A recent study estimates that the disease costs California growers and taxpayers more than $100 million a year in lost revenue and prevention efforts.

In a new study, researchers at the University of California, Berkeley, and the French agricultural research organization CIRAD identified a 120-year old grapevine cutting in the UC Davis Center for Plant Diversity that still contained traces of X. fastidiosa DNA from the early 1900s.

By comparing the genome of this century-old X. fastidiosa strain with the genomes of more than 330 contemporary strains, the team was able to reconstruct the history of how the pathogen first arrived in California and later spread throughout the state. 

“Having a better estimate of what happened historically is vital for understanding the very complex, pathogen-riddled world around us right now,” said study co-first author Alexandra Kahn, a postdoctoral scholar at UC Berkeley. The study was published online today (Dec. 16) in the journal Current Biology. 

Scientists had long assumed that X. fastidiosa was first introduced to California in the 1880s or slightly before, when many species of grapes were brought to the state from the east to establish vineyards. At the time, local newspapers such as the Pacific Rural Press started reporting a mysterious new disease that was affecting “a large number of vineyards” in Anaheim and the Santa Ana Valley. 

However, the genomic data suggests that the pathogen actually arrived in the U.S. nearly 150 years earlier, around the year 1740, and came from Central America. The data further suggests that the disease in California arose from not one but at least three separate introductions of the pathogen. 

“Even though this occurred over 250 years ago, it's still relevant to understanding the global spread of plant pathogens today,” said Monica Donegan, a graduate student at UC Berkeley and co-first author of the study. “We found that the simplest assumptions about the routes and timing of pathogen introduction may be deceiving, which can impact things like international trade policies and quarantines for plant pathogens.”

The fact that there were likely three separate introductions of X. fastidiosa also suggests that multiple, genetically distinct pathogen populations of the pathogen may exist in California. Like different variants of SARS-CoV-2, these populations may all cause similar symptoms, but respond differently to stressors like climate change. 

“These biological differences, even if they're small, can be meaningful when it comes to disease management,” said study senior author Rodrigo Almeida, the Professor and Hildebrand-Laumeister Chair in Plant Pathology at UC Berkeley. 

The grapevine cutting was collected by an individual named Alfred Tournier on Aug. 2, 1906, in Modesto, California. The cuttings are bereft of leaves, but still cling to a few barren or “matchstick” petioles, the scientific term used for the stalks that connect leaves to the stem of a plant.

Tournier’s cuttings were labeled Anaheim disease, the original name given to Pierce’s disease. They are now among approximately 1100 historic grapevine specimens in the UC Davis herbarium’s collection. Working with herbarium curator Alison Colwell, the researchers tested 10 sickly-looking grapevine specimens from the collection, but only found one that was positive for X. fastidiosa bacteria. They also tested grapevine specimens from the University and Jepson Herbaria, but did not find any that tested positive. 

“A grapevine with a lot of X. fastidiosa is not necessarily a prime candidate for an herbarium collection, so we were very lucky to find even one infected sample,” said Donegan.

Study co-authors Nathalie Becker and Adrien Rieux led the painstaking work of isolating the old and degraded X. fastidiosa DNA from the specimen. With the genome sequence in hand, the researchers then used bioinformatics software to compare the genes from the century-old X. fastidiosa to contemporary strains. This analysis provided an estimate of how quickly the pathogen’s DNA mutates over time, which, in turn, allowed them to estimate the timing of key moments in the bacteria’s evolutionary tree. 

“The sample allowed us to calibrate the mutation rate of the pathogen as it evolved in California over the last hundred years,” Kahn said. “Once we had established this relationship between evolutionary time and absolute time, we could reconstruct the chronological history of the disease outbreak.”

In recent decades, X. fastidiosa has spread from the U.S. and Latin America to other countries, including Portugal, Spain, Italy, Israel and Taiwan. Knowing the evolutionary rate of the pathogen can also help researchers estimate the timing of these introductions and prevent further spread.

“It was only recently that people realized they could use these historic herbarium specimens to study plant pathogens,” Almeida said. “I think this highlights the value of herbarium collections for research. There's a lot of pressure on these collections because we can't support them adequately, but they provide a huge value, and you never know how we may benefit from them in the future.” 

Additional authors include Andreina Castillo Siri of UC Berkeley; Paola Campos of the French National Center for Scientific Research (CNRS); Karine Boyer of CIRAD; and Martial Briand of the French National Institute for Agriculture, Food, and the Environment (INRAE). This work was supported by the Agence Nationale de la Recherche, the Thomas Jefferson Fund, the European Regional Development Fund, the Conseil Régional de La Réunion, CIRAD, and the BeXyl Project.