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Ned B. Klopfenstein

Research Plant Pathologist

Research Plant Pathologist

1221 South Main Street
Moscow, ID 83843
Contact Ned B. Klopfenstein

Current Research

My current research studies include molecular diagnostics (root pathogens, foliar pathogens, fungal endophytes, fungal decomposers) and evolutionary relationships among forest hosts and pathogens. My research also explores population genetics of forest hosts and pathogens, genetic relationships among forest hosts and pathogens in the northern hemisphere, the role of soil microflora in forest health, gene expression of forest pathogens causing disease, predicting potentially invasive pathogens, and influences of climate, disturbances, and other environmental factors on forest hosts, pathogens, and beneficial microbes.

Research Interests

My research interests are numerous, but include forest pathology, molecular diagnostics of forest microbes, population genetics of forest hosts and pathogens, phylogenetics of forest pathogens, predicting invasive forest pathogens, predicting climate-change impact on forest disease, environmental influences on genetic structure of forest hosts and pathogens, woody plant defense systems, host/parasite interactions, expression of pathogen genes related to disease, the role of soil microbes in forest health, and woody plant endophytes and symbioses.

Past Research

My earlier research included molecular genetics of Populus spp., especially related to plant defense.

Why This Research is Important

Forest pathogens (the cause of forest disease) and other beneficial forest microbes are key regulators of the growth, sustainability, productivity, and carbon sequestration of forests. Forest disease causes more long-term damage to forest productivity than any other natural disturbance, but this damage is frequently attributed to other factors. Furthermore, severe threats from invasive pathogens and diseases related to climate change continue to rise, and information is needed to address these threats. Precise DNA-based identification of forest pathogens and beneficial microbes is essential to determine their distribution, ecological role, and predictions of future behavior (including invasiveness), so that appropriate management practices can be developed and/or applied. Further understanding the genetic-based interactions of pathogens, host trees, and the abiotic and biotic environment is critical to managing forest diseases and maintaining healthy, sustainable, and resilient forests in a changing environment.


  • Iowa State University, Ph.D., Plant Pathology, 1985
  • Iowa State University, Ames, IA, B.S., Biology, with a minor in Chemistry, 1976
  • Awards

    Certificate of Merit, 2012
    for contributions to the Civil Rights Committee as a lab representative
    Award, 2012
    Co-recipient of RMRS Science You Can Use Bulletin Award for Range-wide Diversity of Western White Pine Populations (with Bryce Richardson and Marcus Warwell)
    Certificate of Merit, 2011
    for contributions to the Civil Rights Committee as a lab representative
    Certificate of Merit from the RMRS Civil Rights Committee, 2003
    for active leadership in Helping Orient Indian Students and Teachers to Science and Mathematics
    Award from the RMRS Civil Rights Committee, 2000
    In appreciation for your outreach to Native American youth through the HOIST program
    Spot award and certificate of appreciation, 1999
    participation in the Hantavirus cleanup, above and beyond the call of duty at the USDA Forest Service, Forestry Sciences Laboratory, Moscow, ID
    Spot award, 1999
    contributions to an outreach program directed toward Native American high school students. The HOIST (Helping Orient Indian Students & Teachers to Science and Mathematics) program was sponsored by the University of Idaho
    Cerificate of Appreciation from Tennessee State University, 1999
    for discussions with students and associated presentation on Genetic studies in forest pathology and approaches toward understanding forest ecosystem processes"

    Featured Publications


    Ashiglar, Sara M.; Cannon, Phil G.; Klopfenstein, Ned B., 2015. Aggressive root pathogen Phellinus noxius and implications for western Pacific Islands
    Blodgett, James T.; Hanna, John W.; Pitman, Eric W. I.; Ashiglar, Sara M.; Lundquist, John E.; Kim, Mee-Sook; Ross-Davis, Amy; Klopfenstein, Ned B., 2015. Bioclimatic models estimate areas with suitable climate for Armillaria spp
    Ashiglar, Sara M.; Cannon, Phil G.; Schlub, Robert L.; Kim, Mee-Sook; Ota, Yuko; Sahashi, Norio; Klopfenstein, Ned B., 2015. DNA-based characterization of wood-, butt- and root-rot fungi from the western Pacific Islands
    Ashiglar, S. M.; Brooks, F.; Cannon, Phil G.; Klopfenstein, Ned B., 2015. Preliminary survey of wood-associated fungi in southeast O'ahu of Hawai'i using DNA-based identification
    Ross-Davis, Amy; Settles, Matt; Hanna, John W.; Shaw, John D.; Hudak, Andrew T.; Page-Dumroese, Deborah S.; Klopfenstein, Ned B., 2015. Using a metagenomic approach to improve our understanding of Armillaria root disease
    Cannon, Phil; Klopfenstein, Ned B.; Schlub, Robert L.; Kim, Mee-Sook; Ota, Yuko; Sahashi, Norio; Quitugua, Roland J.; Hanna, John W.; Ross-Davis, Amy; Sweeney, J. D., 2014. Characterizing butt-rot fungi on USA-affiliated islands in the western Pacific
    Hanna, John W.; Blodgett, James T.; Pitman, Eric W. I.; Ashiglar, Sarah M.; Lundquist, John E.; Kim, Mee-Sook; Ross-Davis, Amy; Klopfenstein, Ned B., 2014. Climate-based species distribution models for Armillaria solidipes in Wyoming: A preliminary assessment
    Klopfenstein, Ned B.; Hanna, John W.; Cannon, P. G.; Medel-Ortiz, R.; Alvarado-Rosales, D.; Lorea-Hernandez, F.; Elias-Roman, R. D.; Kim, M. -S., 2014. First report of the Armillaria root-disease pathogen, Armillaria gallica, associated with several woody hosts in three states of Mexico
    Ross-Davis, Amy; Stewart, Jane E.; Hanna, John W.; Shaw, John D.; Hudak, Andrew T.; Jain, Terrie B.; Denner, Robert J.; Graham, Russell T.; Page-Dumroese, Deborah S.; Tirocke, Joanne M.; Kim, Mee-Sook; Klopfenstein, Ned B., 2014. Forest soil microbial communities: Using metagenomic approaches to survey permanent plots
    Keca, N.; Klopfenstein, Ned B.; Kim, M.-S.; Solheim, H.; Woodward, S., 2014. Initial characterization of unidentified Armillaria isolate from Serbia using LSU-IGS1 and TEF-1a genes
    Hoffman, Christ W.; Mathiasen, Robert L.; Hofstetter, Richard W.; Fairweather, Mary Lou; Shaw, John D.; Hanna, John W.; Klopfenstein, Ned B., 2014. Survey for Armillaria by plant associations in northern Arizona
    Ross-Davis, Amy; Graca, Rodrigo N.; Alfenas, Acelino C.; Peever, Tobin L.; Hanna, John W.; Uchida, Janice Y.; Hauff, Rob D.; Kadooka, Chris Y.; Kim, Mee-Sook; Cannon, Phil G.; Namba, Shigetou; Minato, Nami; Simeto, Sofia; Perez, Carlos A.; Rayamajhi, Min B.; Moran, Mauricio; Lodge, D. Jean; Arguedas, Marcela; Medel-Ortiz, Rosario; Lopez-Ramirez, M. Armando; Tennant, Paula; Glen, Morag; Klopfenstein, Ned B., 2014. Tracking the distribution of Puccinia psidii genotypes that cause rust disease on diverse myrtaceous trees and shrubs
    Klopfenstein, Ned B.; Hanna, John W.; Ross-Davis, Amy; Stewart, Jane E.; Ota, Yuko; Medel-Ortiz, Rosario; Lopez-Ramirez, Miguel Armando; Elias-Roman, Ruben Damian; Alvarado-Rosales, Dionicio; Kim, Mee-Sook, 2013. Armillaria phylogeny based on tef-1α sequences suggests ongoing divergent speciation within the boreal floristic kingdom
    Case, Anna E.; Ashiglar, Sara M.; Cannon, Phil G.; Militante, Ernesto P.; Tadiosa, Edwin R.; Quintos-Manalo, Mutya; Pampolina, Nelson M.; Hanna, John W.; Brooks, Fred E.; Ross-Davis, Amy; Kim, Mee-Sook; Klopfenstein, Ned B., 2013. DNA-based approaches to identify forest fungi in Pacific Islands: A pilot study
    Elias-Roman, Ruben D.; Klopfenstein, Ned B.; Kim, Mee-Sook; Alvarado-Rosales, Dionicio; Hanna, John W.; Ross-Davis, Amy; Guzman-Plazola, Remigio Anastacio; Calderon-Zavala, Guillermo; Mora-Aguilera, Antonio, 2013. DNA-based identification of Armillaria isolates from peach [Prunus persica (l.) batsch] orchards in méxico state, Mexico
    Rayamajhi, M. B.; Pratt, P. D.; Klopfenstein, Ned B.; Ross-Davis, A. L.; Rodgers, L., 2013. First report of Puccinia psidii caused rust disease epiphytotic on the invasive shrub Rhodomyrtus tomentosa in Florida
    Ross-Davis, Amy; Kim, Mee-Sook; Stewart, Jane E.; Hanna, John W.; Shaw, John D.; Klopfenstein, Ned B., 2013. From diagnostics to metagenomics: Applications of DNA-based tools in forest pathology
    Elias-Roman, R. D.; Guzman-Plazola, R. A.; Klopfenstein, Ned B.; Alvarado-Rosales, D.; Calderon-Zavala, G.; Mora-Aguilera, J. A.; Kim, M.-S.; Garcia-Espinosa, R., 2013. Incidence and phylogenetic analyses of Armillaria spp. associated with root disease in peach orchards in the State of Mexico, Mexico
    Cook, R. James; Edmonds, Robert L.; Klopfenstein, Ned B.; Littke, Willis; McDonald, Geral; Omdahl, Daniel; Ripley, Karen; Shaw, Charles G.; Sturrock, Rona; Zambino, Paul, 2013. Opportunities for addressing laminated root rot caused by Phellinus sulphuracens in Washington's forests: A Report from the Washington State Academy of Sciences in cooperation with the Washington State Department of Natural Resources
    ; Klopfenstein, Ned B.; Richardson, Bryce A.; Warwell, Marcus V.; Kim, Mee-Sook, 2013. Return of the king: Western white pine conservation and restoration in a changing climate
    Graca, Rodrigo N.; Ross-Davis, Amy; Klopfenstein, Ned B.; Kim, Mee-Sook; Peever, Tobin L.; Cannon, Phil G.; Aun, Cristina P.; Mizubuti, Eduardo G.; Alfenas, Acelino C., 2013. Rust disease of eucalypts, caused by Puccinia psidii, did not originate via host jump from guava in Brazil
    Ross-Davis, Amy; Stewart, J. E.; Hanna, John W.; Kim, M.-S.; Knaus, B. J.; Cronn, R.; Rai, H.; Richardson, Bryce A.; McDonald, G. I.; Klopfenstein, Ned B., 2013. Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host-pathogen interface
    Hanna, John W.; Graca, R. N.; Kim, M. -S.; Ross-Davis, A. L.; Hauff, R. D.; Uchida, J. W.; Kadooka, C. Y.; Rayamajhi, M. B.; Arguedas Gamboa, M.; Lodge, D. J.; Medel-Ortiz, R. Medel; Lopez Ramirez, A.; Cannon, P. G.; Alfenas, A. C.; Klopfenstein, Ned B., 2012. A bioclimatic approach to predict global regions with suitable climate space for Puccina psidii
    Kim, Mee-Sook; Hanna, John W.; Ross-Davis, Amy; Klopfenstein, Ned B., 2012. Application of molecular genetic tools for forest pathology
    Hanna, John W.; Ashiglar, Sara; Case, Anna; Fairweather, Mary Lou; Hoffman, Chris; Kim, Mee-Sook; Maffei, Helen; Mathiasen, Robert; McDonald, Geral; Nelson, Erik; Ross-Davis, Amy; Shaw, John D.; Klopfenstein, Ned B., 2012. Armillaria root disease in the western USA
    Roman, Ruben Damian Elias; Klopfenstein, Ned B.; Rosales, Dionicio Alvarado; Kim, Mee-Sook; Case, Anna E.; Ashiglar, Sara M.; Hanna, John W.; Ross-Davis, Amy L.; Guzman Plazola, Remigio A., 2012. DNA-based identification of Armillaria isolates from peach orchards in Mexico state
    Ross-Davis, Amy L.; Stewart, Jane E.; Hanna, John W.; Kim, Mee-Sook; Cronn, Rich C.; Rai, Hardeep S.; Richardson, Bryce A.; McDonald, Geral I.; Klopfenstein, Ned B., 2012. De novo assembly and transcriptome characterization of an Armillaria solidipes mycelial fan
    Klopfenstein, Ned B.; Hanna, John W.; Fairweather, M. L.; Shaw, J. D.; Mathiasen, R.; Hoffman, C.; Nelson, E.; Kim, M. -S.; Ross-Davis, A. L., 2012. Developing a prediction model for Armillaria solidipes in Arizona
    Hanna, John W.; Klopfenstein, Ned B.; Kim, M. -S.; Ashiglar, S. M.; Ross-Davis, A. L.; McDonald, G. I., 2012. Discovery of cryptic Armillaria solidipes genotypes within the Colorado Plateau
    Kim, Mee-Sook; Stewart, Jane E.; Dumroese, Kasten; Klopfenstein, Ned B., 2012. Occurrence of the root-rot pathogen, Fusarium commune, in forest nurseries of the midwestern and western United States
    Stewart, J. E.; Dumroese, Kasten; Klopfenstein, Ned B.; Kim, M. -S., 2012. Occurrence of the root-rot pathogen, Fusarium commune, in midwestern and western United States
    Stewart, J. E.; Abdo, Z.; Dumroese, Kasten; Klopfenstein, Ned B.; Kim, M. -S., 2012. Virulence of Fusarium oxysporum and F. commune to Douglas-fir (Pseudotsuga menziesii) seedlings
    Klopfenstein, Ned B.; Hanna, John W.; Graca, R. N.; Ross-Davis, A. L.; Cannon, P. G.; Alfenas, A. C.; Kim, M. -S., 2011. Approaches to predicting current and future distributions of Puccinia psidii in South America under climate change scenarios
    Klopfenstein, Ned B.; Kim, Mee-Sook; Hanna, John W.; Richardson, Bryce A.; Lundquist, John E., 2011. Approaches to predicting potential impacts of climate change on forest disease: An example with Armillaria root disease
    Ross-Davis, Amy L.; Hanna, John W.; Klopfenstein, Ned B., 2011. DNA-based identification and phylogeny of North American Armillaria species
    Klopfenstein, Ned B.; Geils, Brian W., 2011. II. Pathogens
    Graca, R. N.; Alfenas, A. C.; Ross-Davis, A. L.; Klopfenstein, Ned B.; Kim, M. -S.; Peever, T. L.; Cannon, P. G.; Uchida, J. Y.; Kadooka, C. Y.; Hauff, R. D., 2011. Multilocus genotypes indicate differentiation among Puccinia psidii populations from South America and Hawaii
    McDonald, Geral I.; Hanna, John W.; Smith, Aaron L.; Maffei, Helen M.; Kim, Mee-Sook; Ross-Davis, Amy L.; Klopfenstein, Ned B., 2011. Preliminary report on the ecology of Armillaria in the East Cascades of Oregon
    Graca, Rodrigo Neves; Ross-Davis, Amy; Klopfenstein, Ned B.; Kim, Mee Sook; Peever, Tobin; Cannon, Phil; Uchida, Janice; Alfenas, Acelino Couto, 2011. Tracking down worldwide Puccinia psidii dispersal
    Richardson, Bryce A.; Ekramoddoulah, A. K. M.; Liu, J.-J.; Kim, M.-S.; Klopfenstein, Ned B., 2010. Current and future molecular approaches to investigate the white pine blister rust pathosystem
    Cannon, Philip G.; Alfenas, Acelino Couto; Graca, Rodrigo Neves; Kim, Mee-Sook; Peever, Tobin L.; Klopfenstein, Ned B., 2010. Determining if there are lines of guava rust (Puccinia psidii) that could seriously impact ohia (Metrosideros polymorpha), in Hawaii
    Kim, Mee-Sook; Klopfenstein, Ned B.; McDonald, Geral I., 2010. Effects of forest management practices and environment on occurrence of Armillaria species
    Kim, M.-S.; Klopfenstein, Ned B.; Hanna, John W.; Cannon, P.; Medel, R.; Lopez, A., 2010. First report of Armillaria root disease caused by Armillaria tabescens on Araucaria araucana in Veracruz, Mexico
    Richardson, Bryce A.; Warwell, Marcus V.; Kim, Mee-Sook; Klopfenstein, Ned B.; McDonald, Geral I., 2010. Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats
    Klopfenstein, Ned B.; Geils, Brian W., 2010. Invasive Species Science Update (No. 4)
    Geils, Brian W.; Klopfenstein, Ned B.; Kim, Mee-Sook; Spaine, Pauline; Richardson, Bryce A.; Zambino, Paul J.; Shaw, Charles G.; Walla, James; Bulluck, Russ; Redmond, Laura; Smith, Kent., 2009. Recovery plan for Scots pine blister rust caused by Cronartium flaccidum (Alb. & Schwein.) G. Winter and Peridermium pini (Pers.) Lév. [syn. C. asclepiadeum (Willd.) Fr., Endocronartium pini (Pers.) Y. Hiratsuka]
    Klopfenstein, Ned B.; Geils, Brian, 2009. Summary of taxa-specific research: 2. pathogens
    Richardson, Bryce A.; Kim, Mee-Sook; Klopfenstein, Ned B.; Ota, Yuko; Woo, Kwan Soo; Hamelin, Richard C., 2009. Tracking the footsteps of an invasive plant pathogen: Intercontinental phylogeographic structure of the white-pine-blister-rust fungus, Cronartium ribicola
    Hanna, John W.; Kim, Mee-Sook; Klopfenstein, Ned B.; Smith, Aaron L.; Maffei, Helen M., 2008. Determination of suitable climate space for Armillaria ostoyae in the Oregon East Cascades
    Richardson, Bryce A.; Klopfenstein, Ned B.; Zambino, P. J.; McDonald, G. I.; Geils, B. W.; Carris, L. M., 2008. Influence of host resistance on the genetic structure of the white pine blister rust fungus in the western United States
    Hanna, John W.; Smith, A. L.; Maffei, H. M.; Kim, M.-S.; Klopfenstein, Ned B., 2008. Survey of Armillaria spp. in the Oregon East Cascades: Baseline data for predicting climatic influences on Armillaria root disease
    Kim, Mee-Sook; Richardson, Bryce A.; Klopfenstein, Ned B., 2008. Western forest diseases and climate relations: Root diseases and climate change
    Zambino, Paul J.; Richardson, Bryce A.; McDonald, Geral I.; Klopfenstein, Ned B.; Kim, Mee-Sook., 2007. A paradigm shift for white pine blister rust: Non-Ribes alternate hosts for Cronartium ribicola in North America
    Richardson, Bryce A.; Zambino, Paul J.; Klopfenstein, Ned B.; McDonald, Geral I.; Carris, Lori M., 2007. Assessing host specialization among aecial and telial hosts of the white pine blister rust fungus, Cronartium ribicola
    Hanna, John W.; Klopfenstein, Ned B.; Kim, M. -S., 2007. First report of the root-rot pathogen, Armillaria nabsnona, from Hawaii
    Hanna, John W.; Klopfenstein, Ned B.; Kim, M. -S.; McDonald, G. I.; Moore, J. A., 2007. Phylogeographic patterns of Armillaria ostoyae in the western United States
    Stewart, Jane E.; Kim, Mee-Sook; James, Robert L.; Dumroese, Kasten; Klopfenstein, Ned B., 2006. Molecular characterization of Fusarium oxysporum and fusarium commune isolates from a conifer nursery
    Zambino, Paul J.; Richardson, Bryce A.; McDonald, Geral I.; Klopfenstein, Ned B.; Kim, Mee-Sook., 2006. Non-Ribes alternate hosts of white pine blister rust: What this discovery means to whitebark pine
    McDonald, Geral I.; Richardson, Bryce A.; Zambino, Paul J.; Klopfenstein, Ned B.; Kim, Mee-Sook, 2006. Pedicularis and Castilleja are natural hosts of Cronartium ribicola in North America: A first report
    Hudgins, J. W.; McDonald, G. I .; Zambino, P. J.; Klopfenstein, Ned B.; Franceschi, V. R., 2005. Anatomical and cellular responses of Pinus monticola stem tissues to invasion by Cronartium ribicola
    Kim, Mee-Sook; Klopfenstein, Ned B.; Hamelin, Richard C., 2005. Application of molecular genetic tools to studies of forest pathosystems [Chapter 2]
    Richardson, Bryce A.; Klopfenstein, Ned B.; Peever, Tobin L., 2005. Assessing forest-pathogen interactions at the population level [Chapter 3]
    McDonald, Geral I.; Tanimoto, Philip D.; Rice, Thomas M.; Hall, David E.; Stewart, Jane E.; Zambino, Paul J.; Tonn, Jonalea R.; Klopfenstein, Ned B.; Kim, Mee-Sook, 2005. Fuels planning: science synthesis and integration; environmental consequences fact sheet 13: Root Disease Analyzer-Armillaria Response Tool (ART)
    McDonald, Geral I.; Zambino, Paul J.; Klopfenstein, Ned B., 2005. Naturalization of host-dependent microbes after introduction into terrestrial ecosystems [Chapter 5]
    Rippy, Raini C.; Stewart, Jane E.; Zambino, Paul J.; Klopfenstein, Ned B.; Tirocke, Joanne M.; Kim, Mee-Sook; Thies, Walter G., 2005. Root diseases in coniferous forests of the Inland West: potential implications of fuels treatments
    Hoff, J. A.; Klopfenstein, Ned B.; McDonald, Geral I.; Tonn, Jonalea R.; Kim, Mee-Sook; Zambino, Paul J.; Hessburg, Paul F.; Rodgers, J. D.; Peever, T. L.; Carris, L. M., 2004. Fungal endophytes in woody roots of Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa)
    Hoff, Jill A.; Klopfenstein, Ned B.; Tonn, Jonalea R.; McDonald, Geral I.; Zambino, Paul J.; Rogers, Jack D.; Peever, Tobin L.; Carris, Lori M., 2004. Roles of Woody Root-Associated Fungi in Forest Ecosystem Processes: Recent Advances in Fungal Identification
    Kim, Mee-Sook; Klopfenstein, Ned B.; McDonald, Geral I.; Arumuganathan, Kathiravetpillai, 2001. Use of flow cytometry, fluorescence microscopy, and PCR-based techniques to assess intraspecific and interspecific matings of Armillaria species
    Tabor, G. M.; Kubisiak, Thomas L.; Klopfenstein, Ned B.; Hall, R. B.; McNabb, Henry S. Jr., 2000. Bulked segregant analysis identifies molecular markers linked to Melampsora medusae resistance in Populus deltoides
    Klopfenstein, Ned B.; Chun, Y. W.; Kim, M. -S.; Ahuja, M. A.; Dillon, M. C.; Carman, R. C.; Eskew, L. G., 1997. Micropropagation, genetic engineering, and molecular biology of Populus
    Currently, an invasive myrtle rust disease pathogen is spreading around the globe, which threatens native and planted trees/shrubs in the Myrtaceae family, such as eucalypt, guava, and allspice. The established belief was that this rust disease originated on guava in Brazil, then the rust pathogen shifted its host to eucalypt after non-native eucalypts were planted in Brazil, and subsequently has shifted to other hosts around the world. DNA-based studies provided new insights into the emergent myrtle rust disease.
    Invasive root pathogens are a major threat to forest health worldwide, and the fungal pathogens that cause Armillaria root disease (Armillaria species) impact diverse tree species and are distributed globally. Studies to document the distribution of Armillaria species are essential for assessing potential invasive threats and potential impacts of climate change.
    Puccinia psidii is the cause of rust disease of many host species in the Myrtaceae, including guava, eucalypts, rose apple, and ‘ōhi’a. Our ongoing project indicates a single biotype is present in the United States (as well as Costa Rica, Mexico, and Jamaica) that is capable of infecting multiple host species. Data from South America indicate multiple genotypes are present, each associated with a particular host. Furthermore, our analyses revealed that the biotype in the United States is quite distinct from genotypes found in South America.
    This project will predict the potential distribution of Armillaria solidipes (A. ostoyae) under present and future climate scenarios across the interior Western United States. The three proposed elements of the project include: