Our research centers on the ecology, evolution, systematics, and -omics of symbiotic fungi, and on the diversity and roles of their secondary metabolites. As a group, we are inspired by the astonishing diversity of the organisms we study. Here’s a tour of a few of our recently supported research topics.

• Taxonomic, genetic, and functional diversity of endophytes in boreal forests

Boreal forests represent earth's largest terrestrial biome and some of our planet's most threatened and important drivers of global carbon- and hydrologic cycles. Through a five-year NSF award, we are working with collaborators at Duke University, NC State University, and the University of Minnesota to characterizing the diversity of culturable and unculturable fungi associated with iconic species of boreal lichens and plants at seven sites around the circumboreal belt. Fungi obtained in our surveys will be used for genomic and transcriptomic analyses of function, coupled with infection trials and assessments of secondary metabolite production. Data obtained from our work will be used to enhance current methods to delimit and identify fungal species from environmental samples. Coupled with rich population-level studies, deep phylogenetics, and bioinformatics development, our field- and lab studies will provide an unprecedented perspective on the ecological roles, taxonomic diversity, and functional traits of important and diverse endophytes in critically imperiled forests on three continents.

Funding: NSF (Dimensions of Biodiversity) and Huron Wildlife Foundation.
For more information: www.endobiodiversity.org


Photo: Betsy Arnold

• Diversity and demographic effects of seed-infecting fungi in tropical forests: understanding seed defense syndromes

Fungal pathogens are increasingly recognized as an important source of adult-plant and seedling mortality in tropical forests, influencing tree demography, distributions, and diversity. However, very little is known regarding the cryptic effects of tropical seed-infecting fungi, including endophytes, pathogens, and saprotrophs that decay seed tissues in soil. Seed-infecting fungi are likely to be especially important for tree species depending upon seed survival in soil (seed banks) for successful recruitment, including pioneer species - the trees that rapidly exploit treefall gaps and comprise the first steps in tropical forest succession. We are working with Drs. Jim Dalling (University of Illinois) and Adam Davis (USDA) to characterize seed fate in soil through a large-scale common garden experiment at Barro Colorado Island, Panana.  Our work synthesizes field studies of seed demography with molecular analysis of fungal communities, providing a first glimpse at the diversity, spatial structure, and ecological roles of these little-known fungal assemblages.

Funding: NSF (Ecology), with RET and REU supplements.
For more:


Photo: Betsy Arnold

• Diversity and phenotypic effects of bacterial endosymbionts of fungal endophytes

Fungal endophytes live within healthy plant tissues without causing disease. These fungi represent apparently avirulent symbionts that are closely related to pathogenic species, and recent analyses have shown that endophytism and pathogenicity are intimately linked over the evolution of the Ascomycota. These observations raise the question: what factors influence the virulence of fungi associated with living plant tissues? Several other labs have shown that endosymbiotic bacteria inhabiting fungi can influence the virulence of their hosts. Work by Michele Hoffman in our lab showed that apparently pure genomic DNA from fungal endophyte cultures often contains bacterial DNA. We are testing the hypothesis that bacterial endosymbionts influence the fungal phenotype and ultimately, the outcome of plant-fungus interactions. Under leadship by Dr. Dave Baltrus (UA) we're part of a team to examine the genomic architecture and phenotypic effects of these intriguing symbionts.

Funding: NSF (IOS starter grant, Microbial Interactions/Processes, Ecology);
JGI/DOE (genome sequencing).


Photo: Michele Hoffman

• Diversity and pharmaceutical importance of secondary metabolites of endophytic fungi

Endophytes are increasingly recognized as a trove of biochemical richness, often yielding novel compounds and pharmaceutically or industrially important metabolites. We are working with collaborators on four projects that focus on natural product chemistry, with team members based at the University of Arizona, Mississippi State, Zagaya/Berkeley, the Smithsonian Tropical Research Institute, and the Universidad de Panama, with the goal of identifying bioactive fungin in deserts, diverse temperate and boreal  environments, and tropical forests. Our targets include breast cancer, prostate cancer, antibiotic-resistant bacteria, and the causal agents of malaria, leishmaniasis, and Chagas' disease. Through this work we are evaluating ecological distributions of endophytes and other fungi associated with plant parts such as cactus spines and tree thorns, often through citizen-scientist workshops and outreach to high school students.

Funding: National Institutes of Health (R01 and P41); US Army; consultantship on ICBG  award in Panama (NSF/NIH/USDA); Western National Parks Association


Photo: Mariana del Olmo Ruiz

• Beta diversity of tropical fungal endophytes

Fungal endophytes are highly abundant and diverse in leaves of tropical trees, but the scale of their diversity is unclear: disparate studies are generally not comparable due to differences in endophyte isolation methods and fungal species concepts. Accordingly, beta diversity of tropical endophytes remains unknown, and the degree to which different ecological or geographic factors shape endophyte communities has not been examined. With the development of the network of Forest Dynamics plots through the Center for Tropical Forest Science, we have a critical tool for coherent studies of alpha diversity at multiple sites; for explicit examination of beta diversity among sites; and for hypothesis testing with regard to the importance of forest diversity, host plant frequency, and abiotic factors such as precipitation in shaping host-endophyte associations. We are conducting a three-year study to assess the endophytic flora of three tropical forests (Mudumalai Forest Reserve, India; Korup, Cameroon; Barro Colorado Island, Panama). Our study asks: what factors shape fungal symbiont communities in tropical forests?

Funding: Center for Tropical Forest Science and Indo-US Technology Forum


Photo: Betsy Arnold

• Cryptic biodiversity of Diné Bikéyah: Fungal endophytes of the Navajo Nation

Fungal endophytes are ubiquitous among terrestrial plants, can confer significant ecological benefits on their hosts, are closely related to pathogens, and move across borders during plant introductions. However, little is known regarding their diversity and species composition in most host plants, and their cryptic roles in facilitating invasion by the plants that harbor them have not been explored. We are conducting an 18-month study to examine the ecological roles of fungal endophytes in the context of one of the most dramatic landscapes in the arid west: the Colorado Plateau, with a special focus on Diné Bikéyah (the Navajo Nation). The goals of this project are (1) to provide a first understanding of the morphological and molecular diversity of fungal communities associated with native and non-native plants of Diné Bikéyah; (2) to examine diverse symbiont communities for taxa with potential use in biological control of tamarisk (salt-cedar), one of the most devastating invaders in western waterways; and (3) to provide a unique, on-Nation research experience for Navajo undergraduates through Diné College, Tsaile, Arizona.

Funding: USDA and NSF