Plant Pathology Faculty

Matthew E. Smith

Matthew E. Smith - UF Plant Pathology

As an Assistant Professor in the Department of Plant Pathology and the curator of the UF Fungal Herbarium (FLAS) I have duties in three main areas: research (60%), teaching (20%) and extension (20%). I teach the UF mycology course and am responsible for identifying unknown fungi for a variety of Florida stakeholders, including the UF Plant Disease Clinic, UF-IFAS Extension Service, and the UF Veterinary School. I am broadly interested in fungal ecology, evolution, and systematics. I have worked extensively on the biology and systematics of hypogeous fungi (“truffles”) and the ecology of plant-symbiotic ectomycorrhizal (ECM) fungi. However, I have also studied a variety of other fungal groups, including plant pathogens Armillaria mellea ("oak root fungus") and Claviceps purpurea (Ergot disease of grasses) as well as the nematode-destroying fungi (Orbiliales and other Ascomycota). My work combines the synergistic use of molecular, morphological, and culture-based methods in both laboratory and field settings. Below is a synopsis of some of my long-standing interests and ongoing projects.

Global Systematics, Ecology, and Biogeography of Ectomycorrhizal Fungi

Ectomycorrhizal fungi are mutualistic symbionts that associate with a wide diversity of plants, including ecologically important pines, oaks, and eucalypts as well as economically important orchard crop trees such as pecans, hazelnuts, and chestnuts. These plant symbiotic fungi are important because they enhance plant nutrient uptake, mitigate drought stress, and aid in plant establishment. ECM fungi are hyperdiverse but because they live most of their lives hidden in forest soils they can be challenging to study. We use molecular tools to examine their diversity, distribution, and ecological interactions at both local and global scales. Studies in my lab have focused on the ECM communities associated with individual plant lineages (e.g. the south Asian endemic Keteleeria – Ge et al. 2012) and have explored the biology, molecular ecology, and morphology of particular fungal lineages (e.g. cryptic diversity in Membranomyces, a resupinate group within the Clavulina lineage – Uehling et al., 2013). Several ongoing projects in the lab are broadly focused on the biology of ECM fungi.

Neotropical Ectomycorrhizal Fungi in the Guiana Shield of South America

Ectomycorrhizal fungi were once thought to be absent from the tropics, but recent research has shown that this guild of mutualistic fungi is diverse and abundant in tropical hotspots with several lineages of unrelated host plants. From 2009-2011, I worked as a postdoctoral researcher with Rytas Vilgalys (Duke University) and Terry Henkel (Humboldt State University) on a collaborative, NSF-funded project to study the ecology, diversity, and systematics of ectomycorrhizal fungi from the neotropical Guiana Shield region of South America (DEB-0918591 to TWH, DEB-3331108 to RV). This ongoing project has resulted in more than 16 publications, 20 new species, and a new genus (Guyanagaster, a wood-inhabiting truffle-like fungus that is closely related to the mushroom genus Armillaria). In addition to the novel fungi documented by this project, we have also shown that the ECM symbiosis has evolved independently in at least 4 distinct lineages of leguminous trees and we have found evidence to suggest that tropical South America is a putative center of origin for the Clavulina ECM lineage (Cantharellales). Lastly, our data confirms earlier reports that the Guiana Shield is a unique neotropical hotspot loaded with endemic diversity of ECM fungi. More details about this ongoing project can be found at

Global Systematics of Truffles and Truffle-like Fungi

Truffles are the hypogeous (subterranean) fruiting bodies of fungi. Instead of shooting their spores out into the air like many macrofungi (ballistospory), truffles retain their spores inside the fruiting body (statismospory). Since they cannot rely on the wind to disperse their spores, many truffles employ animal mycophagy for dispersal (e.g. animals eat their fruiting bodies and disperse their spores to new habitats via nutrient rich fecal pellets). In the past mycologists believed that truffles evolved once or perhaps a few times throughout the course of evolutionary history. However, molecular phylogenetic studies of macrofungi have shown that truffles have evolved hundreds of different times in many various fungal lineages. Many of the truffle fungi belong to well-studied groups (such as the genera Tuber and Rhizopogon) but for other obscure truffles there are no formal descriptions, no sequence data, and no credible ideas about the closest macrofungal relatives. Work in my lab is focused on documenting the diversity of truffles across the many different fungal lineages, learning about the ecology of truffle fungi in different phylogenetic groups, and understanding the broad biogeographic patterns that govern the distributions of these enigmatic fungi.

The Biology and Ecology of the Pecan Truffle (Tuber lyonii) in Pecan Orchards of the Southeastern USA.

The Pecan Truffle (Tuber lyonii) is a large, native truffle and is considered a choice edible. This truffle species is harvested and consumed locally throughout parts of the southeastern U.S. where trufflers sell it for $10-$20 per ounce ($160-$320 per pound) or more. Herbarium records indicate that this species is distributed across eastern and southern North America, from northern Mexico to Quebec and as far west as the Rocky Mountains. The pecan truffle has been reported in 16 U.S. states, two states of Mexico, and two Canadian provinces. This truffle is most frequently found in symbiotic association with pecan trees in orchards but has also been found in native forests and woodlands dominated by Carya (hickory) and Quercus (oak). It also fruits in U.S. truffle orchards that were originally established to grow the European Black Truffle (Tuber melanosporum). Tuber lyonii usually fruits during late summer and early fall (August-October), although in Florida the fruiting bodies have also been found during winter and spring. A second named truffle species, Tuber texense, has been treated recently as a synonym but probably represents a different species. Preliminary studies based on ITS rDNA sequences from fruiting bodies suggest that there may be several additional cryptic species in the Tuber lyonii complex, but further studies are needed. Although the pecan truffle was first recognized in 1903, its biology remains mysterious and poorly understood. Studies suggest that it is common across much of the pecan-growing region of the U.S. Like all truffles, Tuber lyonii fruits below the ground and is therefore likely to be more widespread than the scattered records suggest. At the same time, the pecan truffle can be extremely abundant at some locations; we have found several pounds of truffles in only a few hours at several sites in Georgia pecan orchards. Currently, we are working with Tim Brenneman (University of Georgia) and Greg Bonito (Duke University) to document the distribution and understand the fruiting patterns of Tuber lyonii in Florida and Georgia. We are surveying ECM root tips in an effort to understand edaphic factors, management considerations, and habitat requirements that may influence the distribution of this fungus. We are also using trained truffle dogs to find fresh Tuber lyonii specimens ( in order to study the population biology and species boundaries in this group of fungi. If you find collections of this fungus, we welcome your contributions! To learn more about the biology of the pecan truffle, check out this informational article recently published in Georgia Pecan magazine (PDF).


  • Henkel TW, Husbands D*, Bonito GM, Vilgalys R, Smith ME. (2013) New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence. Mycologia. In Press.
  • Gryganski AP, Humber RA, Smith ME, Hodge K, Huang B, Voigt K, Vilgalys R. (2013) Phylogenetic lineages inEntomophthoromycotaPersoonia. In Press.
  • Uehling JK*, Henkel TW, Vilgalys R, Smith ME. (2013) Membranomyces species are common ectomycorrhizal symbionts on a wide range of hosts in Northern Hemisphere forests. Mycorrhiza. doi:10.1007/s00572-012-0457-8
  • Takamichi O, Smith ME, Ge Z-W. (2013) Rossbeevera yunnanensis (Boletaceae, Boletales), a new sequestrate species from southern China. Mycotaxon. In Press.
  • Gryganski AP, Humber RA, Smith ME, Miadlikovska J, Wu S, Voigt K, Walter G, Anishchenko IM, Vilgalys R. (2013) Molecular Phylogeny of the EntomophthoromycotaMolecular Phylogenetics and Evolution. doi: 10.1016/j.ympev.2012.07.026. 
  • Ge Z-W, Smith ME. (2013) Phylogenetic analysis of rDNA sequences indicates that the sequestrate Amogaster viridiglebus is derived from within the agaricoid genus Lepiota (Agaricaceae). Mycological Progress. doi:10.1007/s11557-012-0841-y
  • Matheny PB, Aime MC, Smith ME, Henkel TW (2012) New species and reports of Inocybe (Agaricales) from Guyana. Kurtziana. 37: 23-39.
  • Smith ME, Bonito GM, Sharma J, Long J, Davis-Long B, Brenneman T (2012) Pecan truffles (Tuber
    lyonii) – what we know and what we need to know. For publication in Georgia Pecan Magazine (trade
    publication for Southeastern pecan growers). PDF
  • Kennedy PG, Matheny PB, Henkel TW, Uehling JK*, Smith ME, Ryberg M. (2012) Scaling up: examining the macroecology of ectomycorrhizal fungi. Molecular Ecology. 21: 4151–4154.
  • Tedersoo L, Bahram M, Toots M, Diédhiou AG, Henkel TW, Kjøller R, Morris MH, Nara K, Nouhra E, Peay KG, Põlme S, Ryberg M,Smith ME, Kõljalg U. (2012) Global patterns in the diversity and community structure of a keystone microbial symbiont. Molecular Ecology. 21: 4160-4170 doi: 10.1111/j.1365-294X.2012.05602.x
  • Castellano MA, Henkel TW, Miller SL, Smith ME, Aime MC. (2012) New Elaphomyces species (Elaphomycetaceae, Eurotiales, Ascomycota) from Guyana. Mycologia. doi:10.3852/12-061
  • Takamichi O, Smith ME, Shimomura N, Iwase K, Maekawa N. (2012) Diversity and systematics of the sequestrate genus Octavianiain Japan: two new subgenera and eleven new species. Persoonia. 28: 85–112.
  • Bonito GM, Smith ME, Brenneman T, Vilgalys R. (2012)Assessing ectomycorrhizal fungal spore banks of truffle producing soils with pecan seedling trap-plants. Plant and Soil. 356: 357–366. DOI: 10.1007/s11104-012-1127-5
  • Hodkinson BP, Uehling JK, Smith ME (2012) Lepidostroma vilgalysii, a new basidiolichen from the New World. Mycological Progress.11: 827-833. doi:10.1007/s11557-011-0800-z
  • Travadon R, Smith ME, Fujiyoshi P, Douhan GW, Rizzo DM, Baumgartner K (2012) Inferring dispersal patterns of the generalist root fungus Armillaria melleaNew Phytologist. 193: 959–969doi: 10.1111/j.1469-8137.2011.04015.x
  • Ge Z-W, Smith ME, Zhang Q, Yang ZL (2012) Two species of the Asian endemic genus Keteleeria form ectomycorrhizas with diverse fungal symbionts in southwestern China. Mycorrhiza. 22:403–408. DOI 10.1007/s00572-011-0411-1
  • Henkel TW, Aime MC, Chin MML, Miller SL, Vilgalys R, Smith ME (2012) Ectomycorrhizal fungal sporocarp diversity and discovery of new taxa in Dicymbe monodominant forests of the Guiana Shield. Biodiversity and Conservation. 21: 2195–2220.  DOI 10.1007/s10531-011-0166-1
  • Uehling JK, Henkel TW, Aime MC, Vilgalys R, Smith ME. (2012) New species of Clavulina (CantharellalesBasidiomycota) with resupinate and effused basidiomata from the Guiana Shield. Mycologia. 103: 883–94.