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The Use of eDNA Metabarcoding to Detect and Identify Phytophthora in Water Samples.

Eva Randall¹, Beatrix Keillor¹, David E L Cooke²

¹The James Hutton Institute, Dundee, UK.

Methods in Molecular Biology (Clifton, N.J.)

|December 27, 2024

Summary

This study presents a DNA amplification protocol for identifying known and unknown plant pathogenic oomycetes, like Phytophthora, in various environments. The method efficiently captures and preserves pathogen DNA from water samples for later analysis.

Keywords:

Environmental DNA Filtration ITS rDNA Sampling

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Area of Science:

Environmental microbiology
Plant pathology
Molecular biology

Background:

Phytophthora and related oomycetes are significant plant pathogens.
Accurate identification of these pathogens is crucial for disease management.
Existing methods for pathogen detection can be limited in scope or efficiency.

Purpose of the Study:

To develop a robust protocol for amplifying DNA barcodes of Phytophthora and related oomycetes.
To enable the detection of both known and previously unknown taxa.
To facilitate pathogen identification from diverse environmental samples, particularly water.

Main Methods:

A protocol for DNA barcode amplification was developed.
Methods focused on sampling pathogen propagules directly from water.
In situ sampling, filtration, and specialized buffers were employed for efficient DNA preservation and extraction.

Main Results:

The protocol allows for the amplification of DNA barcodes from target oomycetes.
It is applicable to samples from various environmental sources.
The method supports the identification of both known and unknown taxa.

Conclusions:

The described protocol provides an effective means for detecting and identifying Phytophthora and related plant pathogenic oomycetes.
This method enhances the ability to monitor and manage plant diseases caused by these important pathogens.
The protocol is suitable for diverse environmental monitoring applications.