WALNUT CREEK, Oct. 16, 2002 - With Pacific coastal forests under assault, the federal government today launches a project to decode the genome of the fungus-like pathogen that swarms amid underbrush and triggers sudden oak death in centuries-old trees.
Cracking the bug's genetic code won't deliver a silver bullet anytime soon. But scientists say the DNA sequence -- to be performed at the Joint Genome Institute here -- will provide genetic markers for tracking the pathogen inside the forest and around the globe.
That's valuable, because the scientists who discovered Phytophthora ramorum don't know where their bug came from, although they suspect it's a foreign invader, some exotic from overseas, or possibly a dangerous hybrid of two fairly benign pathogens.
"The only way we're going to be 100 percent positive is to find it someplace else," said UC Davis plant pathologist David Rizzo, who co-discovered the microbe with UC-Berkeley forest pathologist Matteo Garbelotto.
Nor do scientists understand how the microbe coexists with young shrubs but spreads death so easily among mature trees. Along the way, the bug spawns several dozen strains. The DNA sequence would provide genetic markers for tracing those strains. Details of how those strains emerge and move could be critical to breaking the chain of infection and saving 17 species in West Coast forests, including California's state tree, the redwood, plus varieties of oaks spanning the United States.
"The range of susceptible species is just gigantic," said Brett M. Tyler, an expert in plant-disease genetics at Virginia Polytechnic Institute in Blacksburg, Va. The same bug cropped up in Germany but curiously has killed fewer trees. Elsewhere, the pathogen probably lives in relative harmony with a forest that has evolved to resist its attacks.
"There's probably some place in the world where it has escaped and started getting into nurseries in Europe and the United States," Tyler said.
As a former researcher at UC-Davis, Tyler was a moving force behind a $4 million project to sequence P. ramorum and a cousin, P. sojae, the pathogen that causes $1 billion a year in losses due to soybean rot. The National Science Foundation and the U.S. Department of Agriculture are funding the soybean project; the U.S. Department of Energy's Office of Science is funding the sudden oak death project. The agencies are expected to announce the research today in Washington and in Walnut Creek, at the DOE's Joint Genome Institute, where the sequencing will be performed.
The microbes under study are a bit of an oddity: They're often labeled fungi but are more closely related to golden brown algae and the white fuzzy stuff that grows on aquarium fish. Several tens of millions of years ago, they left the rivers and oceans for larger hunting grounds on land in wet climates, Tyler said.
The most valuable insights are likely to come from comparing the two genomes to each other and to the human genome. Within six months, scientists will put the two Phytophthora side by side and see what portions of the sequences are common to both. There's an excellent chance that those portions will be genes or critical regulatory elements. By identifying the genes, scientists then will be able to finger the microbes' likeliest vulnerabilities, for example, genes that can be triggered to cause cell death.
Then harder work begins to make sure the chemicals that trigger or kill off a target gene perhaps in all Phytophthora species won't otherwise cause harm in the environment.
The stakes are enormous: Phytophthora ramorum is freezing trade in affected wood products from California to Canada and parts of the Pacific Rim, while the remaining Phytophthora species -- all pathogens -- are blamed for more than $20 billion in crop losses a year, affecting potatoes, cocoa, cinnamon and other products.
"We're hoping we'll find ways to prevent or treat all of them," Jeff Boore, leader of the evolutionary genomics group at the Joint Genome Institute.
Garbelotto suggests the rewards could be a long time coming, however.
"I'm not as optimistic as other people are that things are going to happen in a short time," he said. "All this doesn't matter unless it's actually matched up by someone who actually finds it in soil or in the trees. And that means we'll still need a lot of people getting their hands dirty to understand the organism in the real world."
October 15, 2002