DNA Reveals Imported Pests
Photo: Siri Elise Dybdal
At NIBIO, researchers have used DNA analysis in the fight against unwanted organisms that hide in the soil of imported plants. Environmental DNA makes it possible to find all the organisms hiding in the soil.
Plants with roots and lumps of soil that are transported in the plant trade can contain many different microscopic organisms that can cause plant disease. Among these are oomycetes, which are closely related to algae. These organisms can lead to disease outbreaks and pose a threat to ecosystems, biodiversity and food security. Species from the Phytophthora family have killed forests along rivers in several parts of Norway and are examples of organisms that are carried in soil.
However, the tools that make it possible to discover such oomycetes are not yet widely included in international plant hygiene testing protocols.
NIBIO is carrying out a soil monitoring program on behalf of the Norwegian Food Safety Authority, but the current methods are time-consuming with relatively limited findings. Now, researchers are testing out Environmental DNA metabarcoding to identify and gain a greater and better understanding of what is hiding in the soil of imported plants.
With environmental DNA metabarcoding all the DNA from the soil samples is isolated and sequenced specifically from oomycetes.
The researchers found approximately 1800 different oomycetes in 64 soil samples, while traditional methods led to the identification of barely 20 different species in the same samples, researcher Simeon Rossmann explains. He was responsible for the project’s data analysis.
“We believe this method of analysis will provide us with a far greater insight into what importing plants actually means for Norway’s nature and agriculture. Now we are able to see how much slips through undetected, despite the plants coming with a certificate of health,” comments senior researcher May Bente Brurberg.
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Abstract
Plants with roots and soil clumps transported over long distances in plant trading can harbor plant pathogenic oomycetes, facilitating disease outbreaks that threaten ecosystems, biodiversity, and food security. Tools to detect the presence of such oomycetes with a sufficiently high throughput and broad scope are currently not part of international phytosanitary testing regimes. In this work, DNA metabarcoding targeting the internal transcribed spacer (ITS) region was employed to broadly detect and identify oomycetes present in soil from internationally shipped plants. This method was compared to traditional isolation-based detection and identification after an enrichment step. DNA metabarcoding showed widespread presence of potentially plant pathogenic Phytophthora and Pythium species in internationally transported rhizospheric soil with Pythium being the overall most abundant genus observed. Baiting, a commonly employed enrichment method for Phytophthora species, led to an increase of golden-brown algae in the soil samples, but did not increase the relative or absolute abundance of potentially plant pathogenic oomycetes. Metabarcoding of rhizospheric soil yielded DNA sequences corresponding to oomycete isolates obtained after enrichment and identified them correctly but did not always detect the isolated oomycetes in the same samples. This work provides a proof of concept and outlines necessary improvements for the use of environmental DNA (eDNA) and metabarcoding as a standalone phytosanitary assessment tool for broad detection and identification of plant pathogenic oomycetes.