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Dr. Matthew Smith's 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

Since 2015 we have conducted research on the ecology, evolutionary history, biodiversity, and biogeography of ectomycorrhizal fungi associated with Nothofagaceae (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. These essential plant-mutualists exhibit biogeographic patterns at the regional to continental scale, but there is still limited information on the ECM fungi of southern South America. We have partnered with fungal biologists in Argentina (Dr. Eduardo Nouhra & Francisco Kuhar, University of Cordoba, Chile (Foundacion Fungi director Giuliana Furci, independent researcher Pablo Sandoval Leiva), and Australia (Camille Truong, Royal Botanic Gardens Victoria) to document the diversity, distribution, and evolutionary history of ECM fungi in southern South America. This ongoing work has resulted in >20 peer reviewed papers and yielded >25 newly described fungi species. We have also collected and archived >2700 publicly accessioned fungal specimens and >2000 ITS rDNA sequences, many of which are highlighted by Truong et al. (2017, New Phytologist). A 2019 National Geographic Explorer grant (obtained in collaboration with Smith Lab Ph.D. student Marcos Caiafa and postdoc Michelle Jusino) documented the ecological importance and widespread occurrence of bird dispersal of fungi in Chilean Nothofagaceae forests (Caiafa et al. 2021, Current Biology). An overview of the bird dispersal work can be found at Popular Science and at Audubon.

Global Systematics of Truffles and Truffle-Like Fungi

Truffles are the subterranean fruiting bodies of fungi. Instead of shooting their spores into the air, they retain their spores inside their fruiting bodies. They cannot rely on wind dispersal, so many truffles employ animal mycophagy for spore dispersal (e.g. animals eat truffles and disperse spores in their scat). Truffles were thought to have evolved only once or a few times, but molecular studies indicate they have evolved hundreds of times via convergent evolution. The majority of truffles are also ECM symbionts of plants. The Smith Lab is focused on: 1) documenting truffle diversity across different phylogenetic lineages, 2) understanding truffle ecology, 3) determining broad biogeographic patterns that govern the distribution of truffles, and 4) exploring ecological interactions between truffle fungi and animals that disperse the spores. Basic systematics research by Smith et al. has also resulted in 8 new genera, >50 new species, and two new families (Densosporaceae, Geomoriaceae). Recent works have shown that truffles evolved even more frequently among ectomycorrhizal fungi than previously suspected (e.g. Caiafa et al. 2021 Mycologia, Truong et al. 2017 Fungal Biology, Nouhra et al. 2021 Mycologia) and have also highlighted that a wide diversity of vertebrates consume truffles and disperse their spores, such as ground-dwelling birds (Caiafa et al. 2021 Current Biology) and bonobos (Elliott et al. 2020 Mycologia).

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

The Pecan Truffle (Tuber lyonii) is a tasty edible native truffle. This truffle is harvested and consumed locally throughout parts of the southeastern USA. This species is distributed across eastern and southern North America, from northern Mexico to Quebec and west to the Rocky Mountains. This truffle is frequently found in symbiotic association with pecans in orchards but is also found in native forests and woodlands with Carya (hickory) and Quercus (oak). It has also been found in truffle orchards originally established to grow European Black Truffles (T. melanosporum). Tuber lyonii fruits in late summer and early fall (August-October), although fruiting can extend into winter when conditions are favorable. Although the pecan truffle was first recognized in 1903, its biology remains poorly understood. Extensive surveys of ECM roots in Georgia and Florida pecan orchards have confirmed that T. lyonii is widespread and have also shown that elevated soil pH is a critical factor tied to the prevalence of Tuber species in pecan orchards (Ge et al. 2017, Plant and Soil). We have also identified and named two additional Tuber species (T. floridana and T. brennemanii) that are putative competitors of T. lyonii in pecan orchards (Grupe et al. 2018, Mycologia). More recently, our research showed that T. lyonii can be established and propagated on seedlings in a nursery environment under certain conditions (Grupe et al. 2021, Frontiers in Microbiology) – although  more work is needed to scale up the process so that truffles can be produced in the future. Our lab continues to explore the biology and systematics of Pecan Truffles and to understand how future management may expand the cultivation and consumption of these fungi. For more information, please see our EDIS outreach document (https://edis.ifas.ufl.edu/publication/PP330) and learn about how truffle dogs have potential to help locate truffles in pecan orchards (www.youtube.com/watch?v=h514cjmJD84&feature=youtu.be).

The Evolution of Truffles, Morels, and Relatives (Pezizales)

Pezizales are a monophyletic lineage of Ascomycota that include morels and truffles. This diverse group of fungi is undersampled, understudied, and unresolved in terms of genus and family-level relationships. The objective of this NSF-funded research (DEB-1946445). The main goal of this work is to generate a phylogenomic framework to resolve higher level evolutionary relationships and generate and test hypotheses on fungal genomic traits related to fruiting body form, nutritional ecology and plant-animal-bacterial symbioses. This international collaboration with Greg Bonito (Michigan State), Rosanne Healy (Assistant Scientist in the Smith Lab) and Segula Masaphy (Galilee Research Institute, Israel). This work will work to document the biodiversity of Pezizales fungi in the United States and the Middle East, facilitate student training and international exchange, improve our understanding of the microbiomes of Pezizales fungi, and reconstruct a genome-based phylogeny of the Pezizales that will improve understanding of this group and stabilize higher-level taxonomic relationships. For more information, see the project website at: https://sites.google.com/view/trufflemb/home

The Zygomycetes Genealogy of Life (Zygolife)

Zygolife is an NSF-funded project (ZygoLife – NSF grant DEB 1441677) with a consortium of mycologists from across the USA (including the foremost zygomycete expert Dr. Gerald Benny, based in the Smith Lab) to renew interest and study of zygomycete fungi. 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 were only recently studied using modern genomic approaches. An initial analysis of zygomycete genomes support the hypothesis that the group is a pivotal transition point between the flagellated Fungi (and their specific life histories) and what became the dominant eukaryotic terrestrial clade of Fungi (the fleshy fungi, Dikarya). Because the zygomycetes are the first terrestrial fungi that exhibit fruiting bodies, understanding how these structures evolved will be critical for future understanding of the origins of multicellularity in the Fungi, as well as the evolution of complex life histories. Although studies of zygomycetes are ongoing in the Smith Lab, efforts from this research collaboration have already yielded important research products. These include pioneering phylogenomic analyses of zygomycete fungi (e.g. Spatafora et al. 2016, Chang et al. 2022), explorations of the evolution and trophic ecology of Endogonales (Chang et al. 2019), studies that have used single-cell genomic techniques to study the evolution of early diverging fungi (e.g. Ahrendt et al. 2018), studies that have explored environmental detection of early diverging fungi (Reynolds et al. 2021) and phylogenetic analyses of fastidious groups of obligate symbiont Zoopagomycotina fungi (e.g. Syncephalis, Piptocephalis, and other Zoopagales – Lazarus et al. 2017, Davis et al. 2019, Reynolds et al. 2019). 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 (http://zygolife.org/) and also see zygomycetes.org.

Neotropical Ectomycorrhizal Fungi of the Guiana Shield

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 with updates that include new data by Henkel et al. from Africa, please see: www.tropicalfungi.org.