Dr. Matthew E. Smith - Interests & 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 focus on the biogeography and diversity of ECM fungal communities associated with particular plant lineages and we have also explored the biology, ecology, morphology, systematics and evolution of particular fungal lineages. Several ongoing projects in the lab are broadly focused on the biology of ECM fungi (see below).

Symbiotic ectomycorrhizal fungi in southern South America – macroecology and evolutionary history from community to landscape scale

In summer 2014 we initiated a new project in the lab that is focused on the ecology, evolutionary history, biodiversity, and biogeography of ectomycorrhizal fungi that are associated with Nothofagus (southern beech) in southern South America (NSF grant DEB-1354802). The biodiversity patterns of plants and animals are well studied, but most microbial groups remain poorly known. The flora and fauna of South America have been strongly influenced by historical continental movements (e.g. the “Gondwanan breakup” and “Great American Interchange”), but effects from these events have not been comprehensively studied from a microbial perspective. Plant-symbiotic ectomycorrhizal (ECM) fungi are critical for normal plant growth and are keystone species in global nutrient cycles. This guild of essential plant-mutualists exhibit biogeographic patterns at the regional to continental scale, but there has only been one preliminary molecular study of ECM fungal communities in southern South America (SSA). As a consequence, the diversity and evolutionary history of ECM fungi in this biome remain mostly unexplored. Our project is partnering with local mycologists and ecologists (Dr. Eduardo Nouhra from the University of Cordoba in Argentina; Dr. Götz Palfner from the University of Concepcion in Chile; Giuliana Furci from Foundacion Fungi in Chile) to launch several field campaigns that are documenting the diversity, distribution, and evolutionary history of ECM fungi in southern South America and elucidating the natural history of the “Gondwanan breakup” and the “Great American Interchange” from a microbial perspective.

The Zygomycetes Genealogy of Life (ZyGoLife)- the conundrum of Kingdom Fungi

In January 2015 we launched a new project on zygomycete fungi (ZygoLife – NSF grant DEB 1441677) with a consortium of mycologists from across the USA, including the foremost zygomycete expert Dr. Gerald Benny. Zygomycete fungi are an ancient group in which most of the morphological and ecological traits associated with Kingdom Fungi first arose, but their evolutionary history and ecological associations have not yet been well resolved. An initial analysis of zygomycete genomes support the hypothesis that the group is a pivotal transition point between certain flagellated Fungi and their specific life histories, and what became the dominant eukaryotic terrestrial clade of Fungi (the fleshy fungi, e.g., mushrooms). Because the zygomycetes are the first terrestrial fungi that exhibit fruiting bodies, understanding how these structures evolved will provide a basis for understanding the origins of multicellularity in the Fungi, as well as the evolution of complex life histories. Zygomycetes also display a diversity of ecological relationships with plants (mycorrhizae), animals (pathogens) and bacteria (endosymbionts). Resolving the phylogenetic origins of these interactions will provide an evolutionary framework for elucidating molecular and biochemical mechanisms that govern these interactions will have direct impacts on research into natural and managed ecosystems and human welfare. This project will reconstruct the genealogical relationships of this earliest branch in fungal evolutionary history, resolve the origins of symbiotic relationships between plants and zygomycetes, reveal how complex body plans evolved in the group, elucidate mechanisms of mating genetics between organisms with complex and differing life cycles, and develop genomic barcodes to facilitate identification of unknown fungi. Expanding and maintaining expertise on these fungi is critical for the field of biology, human health and productivity, and safe food production. To learn more about the ZygoLife project, check out the website ( and also see

Neotropical Ectomycorrhizal Fungi in the Guiana Shield of South America

From 2008-2011, I worked as a postdoc with Rytas Vilgalys (Duke) and Terry Henkel (Humboldt State) on an NSF-funded project to study the ecology, diversity, and systematics of ectomycorrhizal fungi in the Guiana Shield region of South America (DEB-0918591 to TWH, DEB-3331108 to RV). This project resulted in >16 publications, >20 new species, and a new genus (Guyanagaster)For more details see:

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. This species is distributed across eastern and southern North America, from northern Mexico to Quebec and west to the Rocky Mountains. The pecan truffle is 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 with Carya (hickory) and Quercus (oak). It also fruits in U.S. truffle orchards originally established to grow the European Black Truffle (Tuber melanosporum). Tuber lyonii fruits in late summer and early fall (August-October), although fruiting can extend into winter when conditions are favorable. A second named truffle species, Tuber texense, has been recently as a synonym but probably represents a different species. Preliminary studies based on ITS rDNA sequences suggest that there may be several additional cryptic species in the Tuber lyonii complex. Although the pecan truffle was first recognized in 1903, its biology remains poorly understood. Studies suggest that this truffle is common across much of the pecan-growing region of the U.S. Like all truffles, T. lyonii fruits belowground and is likely to be more widespread than the records suggest. At the same time, the pecan truffle can be extremely abundant at some sites; we have found several pounds of truffles in only a few hours at several sites in Georgia. Currently, we are working with Tim Brenneman (University of Georgia) and Greg Bonito (Michigan State University) to document the distribution and to understand the fruiting patterns of T. lyonii. 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 T. lyonii ( If you find collections of this fungus, we welcome your contributions! To learn more about the biology of the pecan truffle, check out this article (PDF).