Screening for Exotic Forest Pathogens to Increase Survey Capacity Using Metagenomics

Area of Science:

• Plant pathology
• Environmental science
• Genomics

Background:

• Anthropogenic activities and global trade facilitate the introduction and spread of invasive fungal pathogens.
• These pathogens pose a significant threat to Canada's natural resources, leading to extensive forest decline.
• Early detection and prevention are crucial for mitigating the damage caused by invasive species.

Purpose of the Study:

• To evaluate a nationwide sample collection strategy combined with next-generation sequencing (NGS) for rapid and comprehensive screening of exotic invasive fungal species.
• To provide guidance for phytopathology stakeholders, including regulatory agencies, in managing invasive species.
• To assess the potential of NGS to increase survey capacity, detection sensitivity, and reduce costs.

Main Methods:

• A nationwide sample collection strategy was implemented over three years (2013-2015) near high-risk areas in Canada.
• Field samples were processed using high-throughput screening with customized fungi-specific and Phytophthora-specific barcoded primers.
• Next-generation sequencing (NGS) on the Ion Torrent platform generated 45 million reads from 398 samples, followed by validation with species-specific quantitative polymerase chain reaction (qPCR) assays.

Main Results:

• NGS successfully detected several Phytophthora species, which were confirmed by qPCR.
• The invasive fungus Heterobasidion annosum sensu stricto was uniquely identified using metagenomics.
• The study demonstrated that NGS, validated by qPCR, enhances detection sensitivity and survey capacity.

Conclusions:

• The integrated approach of sampling techniques and NGS, validated by qPCR, significantly improves the ability to detect invasive fungal species.
• This methodology offers a cost-effective and time-efficient solution for regulatory agencies to identify potential ports of entry for invasive species.
• The developed method is a valuable tool for plant pathology management, emphasizing early detection and prevention strategies to protect natural resources.