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Niklaus Grunwald (Nik)

Research Plant Pathologist


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3420 NW Orchard Ave
Corvallis, OR 97330
(541) 738-4049

Our research group combines basic tools from genomics, epidemiology and bioinformatics, with translational research approaches to strategically address some of the fundamental challenges posed by plant diseases caused by emerging pathogens with a focus on the genus Phytophthora.

 

Emergence of plant pathogens

Specifically, our team is interested in the epidemiology, genetics and evolution of exotic and reemerging plant pathogens. The genus Phytophthora contains most destructive plant pathogens affecting agricultural and forest crops. Important examples include P. ramorum, a devastating exotic pathogen causing sudden oak death, and P. infestans, known as the cause of the Irish potato famine. Much of our work is conducted with a focus on translational applications towards improving disease management in agriculture.

 

One focus of our work is the sudden oak death pathogen Phytophthora ramorum:

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Emergence of Phytophthora ramorum

 

The recently emerged plant pathogen Phytophthora ramorum is responsible for causing the sudden oak death epidemic. We have documented the emergence of P. ramorum based on evolutionary and population genetic analyses. Currently infection by P. ramorum occurs only in Europe and North America and three clonal lineages are distinguished: EU1, NA1 and NA2. We are currently studying newly discovered Asian populations of the SOD pathogen. We also demonstrated that at least 3 introductions occurred into Oregon forests. This recent work sheds new light on pathways of pathogen emergence and provides regulatory agencies with insights into how to manage emerging pathogens.

 

Development of computational tools

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Heat-trees produced with our metacoder R package

 

Our lab has developed several open-source, computational tools in R including poppr, popprxl, vcfR, metacoder, taxa, and effectr. These tools are useful for characterizing emergence of plant pathogens using approaches including population genetics, genomics, and community ecology of microbiomes. These tools are provided with extensive educational resources.

 

Diagnostic tools

We have developed a range of open source tools for rapid diagnosis of oomycete microbiomes (http://oomycetedb.cgrb.oregonstate.edu/), Phytophthora species and genotypes of P. infestans and P. ramorum (http://phytophthora-id.org/).

 

For more information, please visit our lab site.