We are interested in a diversity of topics at the intersection of ecology and evolution, with a special focus on fungal biology. Our work in mycology reaches across boundaries with respect to microbiology, plant pathology, genomics, functional traits analysis, and phylogenetics. Here are some of our active projects and ongoing interests.
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Phylogenetic diversity and the origins of plant-fungal symbioses in the Ascomycota
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Why are plant-fungal associations ubiquitous in all terrestrial ecosystems? How did the fungal component of leaf microbiomes arise and diversify? How can endophytic fungi fill gaps in the fungal tree of life, thus informing our perspective on evolutionary dynamics in the most diverse fungal lineages? These questions frame our collaboration with researchers at Duke University (François Lutzoni and Jolanta Miadlikowska), UConn (Louise Lewis), Ole Miss (Erik Hom), and NC State University (Ignazio Carbone). Fieldwork in diverse ecosystems located in global biodiversity hotspots is the centerpiece of a multi-level study that ranges from the associations of fungi with cyanobacteria and algae to phylogenomics of the major lineages of fungi. Team members at the UA include experts in the Nagoya Protocol and botany (Dr. Alicia Ibáñez), fungal genomics (Drs. Jana U'Ren), and leaf traits (Shuzo Oita). We are grateful to be collaborating with researchers in each of our major field sites, including areas of Panama, Chile, Borneo, and South Africa, and with experts in lichenology, algal biology, soil fungi, and bioinformatics worldwide. www.mycophygolife.org
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Taxonomic, genetic, and functional diversity of endophytes in boreal forests
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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. We work with collaborators at the UA (Jana U'Ren), Duke University (François Lutzoni and Jolanta Miadlikowska), NC State University (Ignazio Carbone), and the University of Minnesota (Georgiana May), to characterize the diversity of culturable and unculturable fungi associated with iconic lichens (endolichenic fungi) and plants (endophytic fungi) 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. www.endobiodiversity.org
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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), Adam Davis (USDA), and Camilo Zalamea (Simons Foundation Fellow, Smithsonian Tropical Research Institute), and with scientist Carolina Sarmiento (STRI), to characterize seed fate in soil through large-scale common garden experiment at Barro Colorado Island, Panama. https://publish.illinois.edu/tropicalseeds/
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 PhD student 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. www.endohyphalbacteria.com
Genetic and functional mechanisms shaping interactions of foliar fungi and plants
Plants and fungi share an ancient coexistence that dates to the earliest colonization of land. Plant-fungal interactions can labile, and life history strategies of plant-associated fungi can change over ecologically relevant timescales. (1) With Drs. Naupaka Zimmerman (University of San Francisco) and Posy Busby (Oregon State University), we are using fungal endophytes as models to explore these 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. (2) We are collaborating with Drs. Jana U'Ren (UA) and Jen Wisecaver (Purdue) to study the phylogenomics and genetic underpinnings of the saprotroph-endophyte continuum, with a focus on Xylaria and related fungi. (3) With Drs. Sunshine Van Bael (Tulane University) and Joe Wright and Kaoru Kitajima (STRI) we are examining how functional traits of leaves and fungi define endophyte community structure and plant ecology in tropical forests. Contact us for more information.
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. (1) One project, led by 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? (2) 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. (3) 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. (4) With collaborators, graduate students Emma Woytenko, Aasiya Hamzazai, and Ashton Leo are evaluating the diversity and potential applications of these arid-land microbiomes. (5) Through this initiative, our focus on invaded plant communities is led by MS student and high school teacher Gavin Lehr, who engages students in his study of fungal symbionts of Lehmann's lovegrass in the Santa Rita Experimental Range. Contact us for more information.
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 UA, 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, agricultural pests, 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. In our lab we are fortunate to host Dr. Joe Spraker, a postdoc studying interkingdom communication and fungal secondary metabolites.
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.
Cryptic biodiversity of Diné Bikéyah (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. 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).
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New collaboration: Drs. Stacey Weiss & Mark Martin, Univ. of Puget Sound
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In collaboration with Dr. Stacey Weiss and her students at the University of Puget Sound, we are investigating the microbial ecology of lizards. In a multi-year project based largely at the Southwestern Research Station in Portal, Arizona, Stacey and her team are testing the hypothesis that beneficial cloacal microbes are passively transferred to eggshells and provide eggs with protection from fungal pathogens. Our focal species is the striped plateau lizard, Sceloporus virgatus, which lay eggs in soil burrows at the beginning of the summer monsoon season, and provide no parental care during the two month incubation period. We are delighted to be embarking on this new collaboration (Apr 2018!).