Using collections data to infer biogeographic, environmental, and host structure in communities of endophytic fungi

ABSTRACT

Biodiversity collections contain a wealth of information encapsulated both in specimens and in their metadata, providing the foundation for diverse studies in fields such as ecology. Yet biodiversity repositories can present a challenge for ecological inferences because collections rarely are structured with ecological questions in mind: collections may be opportunistic in space or time, may focus on particular taxonomic groups, may reflect different collection strategies in different places or times, or may not be exhaustive in terms of retaining every specimen or having similar metadata for each record. In addition to its primary holdings, the Robert L. Gilbertson Mycological Herbarium at the University of Arizona holds a collection of living specimens of fungi isolated from the interior of healthy plants and lichens (i.e., endophytic and endolichenic fungi). Over the past decade, more than 7000 isolates from the southwestern United States were accessioned, including strains from diverse hosts in more than 50 localities across the biotically rich state of Arizona. This collection is distinctive in that metadata and barcode sequences are available for each specimen, many localities have been sampled with consistent methods, and all isolates obtained in surveys have been retained. Here, we use this herbarium collection to examine endophyte community structure in an ecological and evolutionary context. We then artificially restructure the collection to resemble collections more typical of biodiversity repositories, providing a case study for ecological insights that can be gleaned from collections that were not structured explicitly to address ecological questions. Overall, our analyses highlight the relevance of biogeography, climate, hosts, and geographic separation in endophyte community composition. This study showcases the importance of extensive metadata in collections and highlights the utility of biodiversity collections that can yield emergent insights from many surveys to answer ecological questions in mycology, ultimately providing information for understanding and conserving fungal biodiversity.

KEYWORDS:

• Ascomycota
• biodiversity
• biogeography
• fungaria
• herbaria
• metadata
• symbiosis

ACKNOWLEDGMENTS

We thank the many students and colleagues who contributed endophyte collections to the Robert L. Gilbertson Mycological Herbarium at the University of Arizona. We especially thank Barbara Klein, Mary Shimabukuro, François Lutzoni, Jolanta Miadlikowska, Matthew Lau, Gavin Lehr, Michele Hoffman, and numerous student-collaborators for contributing to the collections housed in the endophyte collection at ARIZ. We remember with great fondness Dr. Robert L. Gilbertson (Gil) and his immense contributions to mycology, fungal herbaria, and studies of biodiversity, systematics, and ecology. We are honored to thank Dr. Meredith Blackwell for her exceptional contributions to the field and landscape of mycology as a discipline, many of which are interwoven thematically throughout this issue and this paper.

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Funding

The Robert L. Gilbertson Mycological Herbarium is supported by the University of Arizona (UA) College of Agriculture and Life Sciences (CALS), with additional support from the National Science Foundation (NSF). We thank NSF for financial support of E.A.B. (Graduate Research Fellowship) and for funding some of the collections included in the analyses presented here. Y.L.H. was supported by the UA School of Plant Sciences and CALS in completing this work, which constitutes a portion of her doctoral dissertation research in plant sciences at the UA.