(Agricultural Research Service, USDA)
26 February 2018. A university plant science lab developed techniques with readily-available components and materials that make detecting destructive microbes in farm soil faster and easier. A team from Washington State University in Pullman describes its methods in the 23 February issue of the Journal of Visualized Experiments, a publication that includes a 15-minute video accompanying the text.
Researchers from the Molecular Plant Pathology Laboratory headed by Kiwamu Tanaka are seeking more effective techniques for potato growers, a major crop in Washington State, to detect pathogens in their soil. A particular scourge for potato farmers, and a key focus of the lab is potato powdery scab disease, a continuing problem that reduces nutrient and water uptake by developing potatoes and significant cosmetic damage on their skins. In addition, diseases like potato powdery scab can occur in potato plants with few, if any, symptoms, because of long latency periods, thus early detection of pathogens in the soil before planting is vital for growers.
Potato powdery scab disease results from the fungus Spongospora subterranea, which can be detected accurately and reliably in soil samples with the help of polymerase chain reaction, or PCR, a DNA analysis technique. PCR testing, however, is up to now largely a lab-based technique requiring specialized and expensive equipment, as well as trained staff. PCR amplifies segments of DNA, by making many copies of the target DNA segments allowing for subsequent detection and identification. The researchers led by first author and graduate student Joseph DeShields say portable DNA testing systems such as lateral flow devices can be used in the field, but they often lack the reliability and accuracy of PCR.
DeShields and colleagues then designed a system that tests for Spongospora in soil that aims to perform with the accuracy and reliability of PCR in the lab, but also feasible for on-the-spot tests in the field. Their system uses off-the-shelf components, starting with DNA extraction kits using magnetic beads to separate and purify DNA from soil samples. The team’s system then runs the extracted DNA through a portable PCR device, with the analysis performed on software loaded on a laptop computer linked to the PCR device. DeShields credits the magnetic beads method of producing purified DNA as a key step in the process.
Tests of the portable system at potato farms in Washington State show it can detect potato pathogens with almost the same accuracy as samples analyzed by traditional lab-based systems. One advantage of the portable system is its ability to use smaller soil samples than the lab systems, which require as much as 1 kilogram (2.2 lbs) of soil. In addition to detecting Spongospora fungi in the soil tests, the system finds a pathogenic virus in the soil transmitted by Spongospora fungi, also destructive pest to potatoes.
Tanaka notes the team’s focus on potatoes should not obscure the potential for this method of testing for soil pathogens affecting other crops. “It’s a really versatile method,” says Tanaka in a university statement. “You could use it for nationwide pathogen mapping or look at the distribution of pathogens around the country. We started small, but this could have huge implications for testing soil health and disease.”
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