Rows of meticulously tended grapevines sprawled across large vineyards, with a sweet, fruity aroma wafting through the air are classic features of America’s thriving wine industry. However, in the 1800s, these lands painted a different picture as Pierce’s disease (PD) ravaged grapevines, causing leaves to wilt and fruits to shrivel.1
Caused by the bacterium Xylella fastidiosa, PD was first reported in California in 1884.2 Since then, the disease has been found around the globe, ruining grapevines and causing financial losses. Researchers estimate that the disease causes more than $100 million in losses in California alone.3 The widespread damage wrought by PD has driven the research community to pinpoint the pathogen’s origin and determine how it spread across continents.
Herbaria serve as invaluable repositories of ancient plant samples, offering preserved specimens that provide a unique window into historical ecosystems, plant evolution, and the spread of pathogens over time.
UC Davis Center for Plant Diversity Herbarium
Now, after isolating the bacterium from a 120-year-old grapevine cutting, scientists have reconstructed the history of PD, including its arrival in California and its patterns of transmission.4 Their findings, published in Current Biology, also shed light on key moments in the bacterium’s evolutionary history.
“The biogeography of this pathogen specifically is really important because there keep being new outbreaks which have led to epidemic situations all over the world,” said study coauthor Alexandra Kahn, an evolutionary geneticist in plant pathologist Rodrigo Almeida’s lab at the University of California, Berkeley. Understanding the pathogen’s history can help researchers contextualize outbreaks and uncover the evolutionary adaptations driving them, she said.
To delve into the pathogen’s history, the researchers obtained historic grapevine specimens from the herbarium at the University of California, Davis. Of the 10 diseased cuttings they found, one was infected with X. fastidiosa.
In order to isolate DNA from this specimen, the researchers had to work in ultra-clean conditions to avoid cross-contamination from modern samples, recalled Monica Donegan, a study coauthor and graduate student in Almeida’s lab. After filtering through sequencing reads and extracting those that were mapped onto modern X. fastidiosa genomes, the team was left with a pile of short fragments that are typical of ancient DNA, confirming no cross-contamination from modern samples.
Next, the team stitched together these fragments and carried out de novo assembly of the ancient X. fastidiosa genome. Using computational phylogenetic tools, the researchers compared the historical genome of X. fastidiosa with 330 more recent strains collected from plants in the US, Costa Rica, Spain, Taiwan, and Mexico. This helped the team construct a detailed phylogenetic tree mapping the pathogen’s evolutionary descent.
Phylogenetic analyses revealed that the herbarium strain and more recent strains from California and eastern regions of the US were closely related, suggesting common ancestral origins. However, not all X. fastidiosa strains found in California grapevines share this common ancestor as some showed more similarity to strains hailing from east and central US and Spain. These findings suggest that, in California, the disease arose from multiple introductions of the pathogen.
On establishing that there were multiple entries of X. fastidiosa into plants in the US, the researchers set out to determine when the pathogen’s first entry into the country occurred. By measuring the mutation rate of the pathogen’s DNA over time, the researchers estimated that all X. fastidiosa strains in the US share a common ancestor dating back to approximately 1741—35 years before the Declaration of Independence was written and 150 years before PD was first documented in California.
In search for clues about the evolution of X. fastidiosa, Alexandra Kahn (left) and Monica Donegan (right) sampled ancient DNA from plants preserved in herbaria.
Mathew Burciaga, UC Berkeley
“It was actually a little surprising to us because we thought that the sample that we had, because it was from 1906, would be the ancestor of everything in California,” said Donegan. “Even just adding one herbarium sample from 1906 shifted the introduction date back. This underscores the power of adding these herbarium and ancient samples to these studies.”
“This is a nice study,” said Michael Martin, an evolutionary genomics researcher at the Norwegian University of Science and Technology, who was not involved with the study. Although researchers have sequenced ancient plant pathogens before, this study is notable because the team carried out a complete de novo assembly of X. fastidiosa, he noted.
However, he was not surprised that including the 1906 sample shifted the estimated introduction date of the pathogen further back. “Predictions of introduction time are all based on these phylogenetic trees, and the dates that you get for different parts of the tree directly depend on which samples you include,” he said.
The team hoped to include more samples to obtain a clearer picture of the pathogen’s entry and eventual transmission. Since most of their plant samples are from California, the researchers aim to diversify and carry out sampling in other parts of the country. “We can try to really [fill] the gaps in our data collection,” said Kahn.
