Whether you are a plant pathologist, horticulture greenhouse operator, forest manager or backyard gardener, Nick Grunwald foresees a possible future data source to keep plants healthy and safe.
“In 10 years, I foresee a future where we could ask Siri or Alexa, tell me about this pathogen. Where is it found?”
Part of the prognostication by this Agriculture Department plant pathologist in Oregon stems from work he and colleagues are conducting now. That comes in the form of an automated data pipeline or platform called pathogen surveillance.
“A bioinformatics pipeline that can analyze genomes of pathogens, basically with minimal intervention from a scientist. So, one command-line statement and it just runs, analyzes the data and tells you what you have.”
This platform, over a decade in the making, addresses a significant challenge when it comes to identifying pests and diseases that threaten plants and, in turn, developing real-time prevention responses.
“It has become very cheap to sequence a pathogen of any strain of pathogens, fungi or my seeds, bacteria, you name it, even nematodes. But what is really excruciatingly slow is analysis of the data.”
Or, put another way, in the realm of pathogen genomic sequencing and determining identification of existing or new variants, Grunwald says what currently takes a graduate student one to three years to analyze now takes hours. You may have heard him say earlier, command-line-statement computer-programming talk makes sense, as the pathogen surveillance platform relies on open-source software.
“So, anybody in the world can use this for the intended purpose of identifying pathogens or pests, using whole-genome sequences.”
To serve as an open data source to get a better idea of how the pathogen surveillance platform works in real time, Grunwald provides this example.
“We were contacted by the California Department of Food and Agriculture that they had a new fungus on a new host, and now they had several samples from other hosts, and they had never seen this before. Soon afterwards, the plant clinic at Oregon State University and the Oregon Department of Forestry identified similar samples here in Oregon, so we sequenced all those, roughly 30 isolates, and found that they’re all the same species. Basically, we sequenced those and put them into our pipeline, and overnight it ran, and by the next morning, we had a phylogenetic tree with all 30 samples identified to species,”
As well as data such as genetic, regional and host diversity for pathogens.