Development of genomic-based tools for detecting, tracking, and monitoring invasive pathogens introduced in U.S. tree nurseries and restoration sites

Tree nurseries serve as reservoirs for a diverse suite of native and invasive pathogens of trees. These forest pathogens can move undetected through asymptomatic, infected nursery stock, and subsequently can kill field-planted seedlings and/or introduce pathogens into novel landscapes (e.g., post-fire restoration areas). Once introduced, these forest pathogens can persist in landscapes and cause irreparable harm to native plants and forest ecosystems.

Conifer seedlings at a nursery. Photo by Mee-Sook Kim, USDA Forest Service.

For example, white pine blister rust is caused by an invasive fungal pathogen (Cronartium ribicola) that is native to Asia. This pathogen was introduced to both the east and west coasts of the United States in the early 1900s on infected nursery stock of eastern white pine (Pinus strobus) and western white pine (P. monticola) imported from Europe. In interior northwestern North America, the coverage of western white pine has been reduced by 90 percent compared with its distribution 80 years ago. This reduction is primarily attributed to white pine blister rust.

Establishing biosurveillance protocols for early detection of potentially invasive forest pathogens in U.S. tree-nursery systems. These protocols are critical for preventing further spread of these pathogens to other area where postfire restoration or other vegetative rehabilitation efforts are underway. We are developing biosurveillance protocols for detecting introductions of potentially invasive pathogens into the United States by using existing databases and data acquired from this project.

Objectives

1. Identify potentially invasive pathogens using multiple available sources.
2. Collect publicly available genomic data for these potentially invasive pathogens.
3. Characterize existing microbial communities within selected tree nurseries that represent likely points of entry in the United States with the use of metagenomic approaches to generate microbial (e.g., fungi, bacteria) genomic sequencing data from diverse samples of plants, soil, water, and air.
4. Conduct bioinformatic analyses of existing and newly obtained genomic data for identifying, predicting, and prioritizing potentially invasive forest pathogens in tree nursery systems of the United States.

Expected Products

• Biosurveillance protocols and databases, including any newly acquired genomic sequence data from nurseries of interest for comparisons with other available genomic databases for detecting and identifying potentially invasive pathogen species in U.S. tree-nursery systems. These databases can also be used for regulatory and quarantine purposes.
• Bioinformatic pipelines and protocols for the identification and detection of potential invasive pathogens. Workshops and technology transfer will provide demonstrations of the availability and use of genomic tools for identifying specific invasive forest pathogens.
• Scientific and technology-transfer publications will provide the protocols, surveys, invasive species information, and other results.

Expected Outcomes

We will identify potentially invasive pathogens that threaten tree hosts grown in U.S. nurseries by developing genomic-based tools for rapid diagnostics. The protocols we develop will help to prevent further spread of these forest pathogens to other regions, including post-fire restoration/rehabilitation areas and other reforestation areas. Once we establish the bioinformatic pipelines, any newly acquired genomic sequencing data from any nursery of interest can be compared to the genomic databases for detecting and identifying potentially invasive forest pathogens.

Metrics of Success

Ultimately, success will be determined by the implementation of the genomic detection tools and the resulting detection of invasive (and native) forest pathogens in U.S. nurseries that will help prevent pathogen spread into forest landscapes.

Geographies: Nationwide United States.