NSF DEB 1554181.   Evolutionary genomics of plant-fungal symbiosis: coevolution of Pinaceae and their ectomycorrhizal fungi in the genus Suillus.  (with Peter Kennedy, Nu Nguyen, Sunny Liao and members of the International Suillus consortium). The genus Suillus is one of the most iconic genera of symbiotic ectomycorrhizal fungi and play critical roles in the functioning of forest ecosystems. Outcomes from this project include (1) the first global-scale phylogenomic reconstruction of a single ectomycorrhizal fungal genus using full genome sequences of over 35 strains from North America, Europe and Asia; (2) Experimental testing of coevolutionary hypotheses, mycorrhizal compatibility, and functional relationships of Suillus species; (3) Ecogenomics of Suilloid fungi including their roles in facilitating global forestry, phytorestoration and biological invasions; (4) Functional genomic studies of fungi and plant genes involved in ectomycorrhizal symbiosis; (5) Two population-genomics studies of S. luteus from its native and introduced ranges across 5 continents. Broader impacts: (1) the development of germplasm and genomics resources of Suilloid fungi for use in forestry research, (2) outreach activities with amateur mycology societies (NAMA), (3) training for 4 postdoctoral scientists (3 from Duke) and 3 graduate students (2 from Duke).  Broader Impacts: The application of cutting-edge technologies for genome-enabled study of Suillus-Pine interactions has benefited meta-functional studies of the plant mycobiome. This project has catalyzed numerous collaborations among a growing international network of fungal biologists who study symbiotic EMF involving Suilloid fungi.  The study has provided training for at least 5 postdoctoral scholars and 3 graduate students, and has also fostered greater interaction with the citizen scientist community through partnerships with nationally affiliated mushroom clubs including lectures, workshops, and field sampling.

NSF-DBI-10-46052: “Dimensions of Biodiversity: Deconstructing diversity and ecosystem function at multiple spatial and genetic scales in a keystone plant-microbe symbiosis” PIs: Tom Bruns, John W Taylor, and Kabir Peay).   This collaborative project between 5 labs (Berkeley, Stanford, Boston Univ. and Duke) utilizes next-generation sequencing techniques to investigate diversity of mycorrhizal fungi associated with pines (Pinus spp.).  Aims of the project include  (1)  the first continental scale perspective of ectomycorrhizal communities associated with pines,  (2) establish patterns of gene flow and selection for several key fungal taxa across North America, (3) measure variation in functional enzyme production, and  (4) use RNA based metagenomics to measure the full spectrum of  functional trait expression on individual mycorrhizal root tips.  By doing so, this project aims to synthesize links among taxonomic, genetic and functional diversity of fungi across dominant pinaceous ecosystems in North America.  Web site:

JGI/EMSL Collaborative Science Project (proposal 48480) Integrated genomic/transcriptomic/secretomic study of plant-fungal interactions between pines and their symbiotic ectomycorrhizal fungi in the mushroom genus Suillus. PIs: Rytas Vilgalys, Duke University (with H.L. Liao, Jennfer Talbot, Tom Bruns, Sara Branco, John Taylor and Kabir Peay). This follow-up to our DOB project above will support an ‘omics’ approach to study of symbiotic interactions between pines (Pinus spp.) and their ectomycorrhizal fungi (EMF) in the genus Suillus. We are developing the Pine-Suillus symbiosis as a model for understanding EME function across diverse pine-dominated forests of North America, including how symbiotic fungi utilize and sequester plant-derived carbon. As the dominant community of symbiotic microbes in forest soils, EMF atransfer nutrients to tree roots and receive plant carbon in exchange. Suillus species are keystone members of the EMF community that exhibit strong hostspecific associations with different Pinus spp. This project will combine study of the fungal genome (by JGI), the mycorrhizal transcriptome (by JGI) and proteome/metabolome (by EMSL) of symbiotic fungal/plant pairs to identify genes/transcripts/proteins/metabolites associated with fungal-plant interaction, nutrient acquisition strategies of Suillus, and host-specificity between species of Suillus and Pinus. By simultaneously exploring the biochemistry of the plant-fungal interface and the fungal-soil interface, results from this study will address the full capacity of Pinus and Suillus species to influence carbon cycling and energy flow in ecosystems.   (

PMI: Plant Microbe Interfaces. This project is a Foundational Genomics Scientific Focus Area supported by the U.S. Department of Energy.  The project examines tghe dynamic interface  between plants, microbes and their environment, with a focus on defining the genetic bases of molecular communication between Populus and its microbial consortia. The project  is based at the Oak Ridge National Laboratory, with collaborators at the University of Washington, Duke University, and INRA – Nancy (France).   The Vilgalys lab is using both culture-based and culture-independent methods (nextgen sequencing) to identify the dominant species of symbiotic fungi within the Populus rhizosphere. To date, we have isolated over 2000 strains representing about 100 fungal taxa that serve many different ecological roles as saprobes, endophytes, pathogens, and mutualistic symbionts. Many of the fungi isolated by our project have been found to have a growth-promotion effect on Populus and other plant hosts, though its molecular basis is still not fully understood (a patent disclosure has been filed). Representative strains of over 20 fungal species have been submitted for genome sequencing by the JGI, providing a genome-based assessment of their metabolic functioning.   We we currently investigating function of different root-associated fungi with Populus i metagenomics (RNAseq, metabolomics, and proteomics).
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ZyGoLife.  Zygomycete Genealogy of Life (ZyGoLife).  PI’s: Jason Stajich (UC Riverside), Joseph Spatafora (OSU), Timothy James (Mich.), Robert Roberson (ASU), Mary Berbee (UBC), Tom Taylor (KU), Merlin While (Boise St.), Rytas Vilgalys (Duke), Matt Smith and Gerry Benny (UF), Nicolas Corradi (UO) and Kerry O’Donnell (USDA).  Zygomycetes comprise ancient lineages of Kingdom Fungi that include plant symbionts, animal and human pathogens, and decomposers of a wide variety of organic compounds. Zygomycetes are thought to be among some of the first terrestrial organisms and facilitated the origin of land plants.  They represent one of the earliest origins of multicellularity and the filamentous body plan and polar cell growth that characterize most species of fungi.  They are also used in numerous industrial processes (e.g., organic acid production) and fermentation of foods (e.g., tempeh, soy sauce).  Despite these critical ecological roles and morphological innovations, and importance to human civilization, little is understood about their evolutionary relationships.  ZyGoLife will resolve the evolutionary relationships through integration of numerous types of data including genome sequencing and analyses, discovery and description of zygomycete fossils, development of enhanced tools for detecting zygomycetes in the environment, and elucidation of novel morphological characteristics through state-of-the-art bioimaging.  In addition, the project will develop educational resources for the general public for this important but poorly known group of Kingdom Fungi.  Web site:

NSF-DEB-0955904: “Pathogen mediated diversity and response to climate change” PI’s: James Clark, Rytas Vilgalys, and Michelle Hersh.  This project is a collaboration between  Clark and Vilgalys labs (Duke Univ) to investigate the role of fungal pathogen communities on plant diversity in temperate forests .  Field sites include experimental plots in both Duke Forest and Harvard Forest.
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NSF Digital Biological Collections: “The Macrofungi Collection Consortium: Unlocking a Biodiversity Resource for Understanding Biotic Interactions, Nutrient Cycling and Human Affairs” (Barbara Thiers, PI, New York Botanical Garden).  This is a subcontract to Duke University for databasing of fungal herbarium and establishing a single database for North American mushroom collections.
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NSF DEB-0641297   “Phylogenetic and Revisionary Systematics of North American Truffles (Tuber, Ascomycota)”.   This project is a collaboration between American and Mexican truffle-experts to catalogue the diversity of the genus Tuber across North America.  Web site:

NSF DEB 0918730  “Ectomycorrhizal fungal diversity of the central Guiana Shield”.  This is a collaborative project to survey mycorrhizal fungi of Guyana with Terry Henkel (UC-Humboldt).  The Vilgalys lab is responsible for conducting DNA sequencing for this project.  Web sites:

NSF DEB0228668  AFTOL – Assembling the Fungal Tree of Life
(PIs: J. Spatafora, D. Hibbett, M. Berbee, C. Aime, D. Maclaughlin, F. Lutzoni).  This is a multi-investigator effort to identify all major lines of descent in Fungi using multi-gene phylogenies. The Vilgalys lab is responsible for assembling molecular data from chytrid and zygomycete fungi which comprise the most basal portions of the fungal tree of life.  Web Site:

conserved PCR  primers for fungal amplification

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