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.

The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here?

“…If coevolution or codivergence has occurred between hosts and their endophytes, then unusual endophytic taxa could occur in hosts from remote portions of the plant phylogeny (Hassani et al ., ). Non‐vascular plants, in particular, deserve more attention, as these plants have different evolutionary histories, physiology, growth habits and preferred habitats than vascular plants (Huang et al ., ).…”

“…To best share information among vouchers, standardized protocols (such as drying time and temperature) could be helpful to adopt, though we acknowledge the challenge of implementing such standards during field collection. Deposited cultures could provide many of the same benefits as host vouchers, but would also allow researchers to grow endophytes of interest to meet various experimental goals (Huang et al ., ; Suryanarayanan, ). Finally, the plant taxonomy is ever‐changing, thus as future researchers interpret published work, they may wish to examine accessions to determine the most current taxonomic placement of the focal host or endophyte.…”

An In Vitro Pipeline for Screening and Selection of Citrus-Associated Microbiota with Potential Anti-“ Candidatus Liberibacter asiaticus” Properties

“…Reductionist experiments facilitate mechanistic studies to elucidate the underlying biology of a system, rendering culture collections an important translational research tool to bridge big HTS data sets with biologically relevant activities. These resources enable critical inquiries into specific microbial interactions, such as linking functional phenotypes like pathogen suppression to specific microbiome constituents and their respective bioactive chemistries (53). For this study, we designed a pipeline that allowed us to assign taxonomy to bulk cultures obtained from citrus tissues.…”

Drivers of grass endophyte communities in prairies of the Pacific Northwest, USA

“…However, examination of the literature revealed that a wide range of fungi often occur as endophytes, including lichenicolous fungi (Huang et al 2018, Moler and Aho 2018, Voglmayr et al 2019) and insect pathogens (Razinger et al 2018, Rondot andReineke 2018). We expect that the kinds of fungi known to occur as endophytes will only increase as more NGS studies are published.…”