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. For more information on our collaborative activities, please see these sites:

NSF Genealogy of Life: evolution and diversity of Pezizomycotina (w/ colleagues at Duke, UConn, Ole Miss, NCSU): www.mycophygolife.org
NSF DEB, leaf functional traits and endophytes in tropical forests (w/ Sunshine Van Bael at Tulane) (TBA)
NSF Dimensions of Biodiversity: boreal endophytes (w/ François Lutzoni, Duke; Georgiana May, UMinn; Ignazio Carbone, NCSU: www.enDoBiodiversity.org
NSF IOS, endohyphal bacteria (w/ Dave Baltrus and Rachel Gallery, UA): www.endohyphalbacteria.com
NSF DEB, seed-associated fungi (w/ Jim Dalling, UIUC, and Adam Davis, USDA): https://publish.illinois.edu/tropicalseeds/

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Jana U'Ren in the field in central Alaska • Photo: B. Arnold
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 water cycles. Through a five-year NSF award, we are working with collaborators at Duke University, NC State University, and the University of Minnesota to characterize the diversity of culturable and unculturable fungi associated with iconic lichens and plants at seven sites around the circumboreal belt. Fungi obtained in our surveys are used for genomic and transcriptomic analyses of function, taxonomic analysis, infection trials, and assessments of secondary metabolite production. Data are used to enhance current methods to delimit and identify fungal species from environmental samples. Coupled with population-level studies, deep phylogenetics, and bioinformatics development, work led by postdoc Dr. Jana U'Ren is contributing a new perspective on the ecological, taxonomic, and functional traits of diverse endophytes in critically imperiled forests on three continents.

Funding: NSF (Dimensions of Biodiversity) and Huron Wildlife Foundation. For more information: www.endobiodiversity.org
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Tropical forest canopy with Cecropia • Photo: B. Arnold
Diversity and demographic effects of seed-infecting fungi in tropical forests

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, little known regarding the cryptic effects of tropical seed-infecting fungi, which 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 work 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, Panama. PhD student Justin Shaffer is contributing to our efforts to link 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 information: publish.illinois.edu/tropicalseeds
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Endohyphal bacteria • Photo: M Hoffman
Diversity and phenotypic effects of bacterial endosymbionts of fungi

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? Work by Michele Hoffman 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. With Drs. Dave Baltrus and Rachel Gallery (UA) we're part of a team to examine the genomic architecture, phenotypic effects, and ecological impacts of these intriguing symbionts. Work in this area is currently led by PhD students Justin Shaffer and Sarah Araldi.

Funding: NSF (IOS, with Dave Baltrus and Rachel Gallery; IOS starter grant, Microbial Interactions/Processes, and Ecology); JGI/DOE (genome sequencing). For more information: http://www.endohyphalbacteria.com/
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Populus trichocarpa for greenhouse experiments.
Genetic mechanisms shaping interactions between foliar fungi and plants

Plants and fungi share an ancient coexistence that dates to the earliest colonization of land. While it is well known that plant-fungal interactions range from mutualism to pathogenicity, it is less widely recognized that these interactions can be labile, and that the life history strategies of plant-associated fungi can change over ecologically relevant timescales. We are using fungal endophytes as models to explore these transitions.

This research, led by postdoc Dr. Naupaka Zimmerman, examines how environmental factors shift fungal/host interactions from beneficial to pathogenic modes, and assesses the evolutionary context of such transitions. Using pathogenic and endophytic Mycosphaerella that affect the model tree Populus trichocarpa, this work combines greenhouse experiments and metatranscriptomics with the conceptual tools of functional and comparative genomics. Understanding the dynamic relationship between plants and their associated microbiomes represents an emerging frontier in ecological science—with important implications for shaping our understanding and management of plants in both natural and agricultural systems.

Funding: Gordon and Betty Moore Foundation (through a fellowship from the Life Sciences Research Foundation), the College of Agriculture and Life Sciences/Hatch, JGI/DOE (genome sequencing and RNA-Seq), and NSF Dimensions of Biodiversity.
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Chiricahuas after 2011 Horseshoe II Fire • Photo: YL Huang
Plant-fungal associations in a changing world

We are interested in how a changing environment effects the fungal communities that are integrally linked with their hosts. One project, led by MS student and NSF GRFP Fellow Liz Bowman, investigates how foliar fungal endophytes and ectomycorrhizal fungi associated with Pinus ponderosa are affected by climate change: how is each partner, and their interaction, affected by abiotic stresses? A related project led by PhD student Yu-Ling Huang focuses on the effects of wildfire on endophyte communities in two economically and ecologically important tree species (Quercus hypoleucoides and Juniperus deppeana) in southern Arizona. A third project focuses on discovering and translating the microbiome of arid-land plants. Many wild plants in the desert southwest are closely related to crop species, and flourish in marginal and degraded landscapes. With collaborators we are evaluating the diversity and potential applications of these arid-land microbiomes. Through this initiative, our focus on invaded plant communities is led by MS student Gavin Lehr, who engages high school students in his study of fungal symbionts of Lehmann's lovegrass in the Santa Rita Experimental Range.

Funding: NSF, private partnerships, and the College of Agriculture and Life Sciences/Hatch
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Endophyte-pathogen interactions • Photo: M del Olmo Ruiz
Secondary metabolites of endophytic and endolichenic fungi

Endophytes are increasingly recognized as a trove of biochemical richness, often yielding novel compounds and pharmaceutically or industrially important metabolites. We are collaborating 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 Panamá, with the goal of identifying bioactive fungi 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
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One of the Big Trees on BCI, 2005 • Photo: B Arnold
Beta diversity of tropical fungal endophytes

Fungal endophytes are 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.

Funding: Center for Tropical Forest Science and Indo-US Technology Forum
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dine_all_sm_resized.jpgCryptic biodiversity of Diné Bikéyah (Navajo Nation)
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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. In partnership with Dine College, the college of the Navajo Nation, we work in one of the most dramatic landscapes in the arid west: the Colorado Plateau, with a special focus on plants and lichens -- and training in microbiology -- within Diné Bikéyah (the Navajo homeland).

Funding: USDA and NSF