Site-specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales

Candice Y. Lumibao, Elizabeth T. Borer, Bradford Condon, Linda Kinkel, Georgiana May, Eric W. Seabloom

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13 Scopus citations


The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within-host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.

Original languageEnglish (US)
Pages (from-to)12231-12244
Number of pages14
JournalEcology and Evolution
Issue number21
StatePublished - Nov 1 2019

Bibliographical note

Funding Information:
This project was funded by National Science Foundation (NSF) grant EF 12- 41895 (DEB-1556649) to EB, ES, GM and LK. This work was generated using data from the Nutrient Network ( experiment, funded at the site scale by individual researchers. Coordination and data management have been supported by funding to E. Borer and E. Seabloom from the National Science Foundation Research Coordination Network (NSF-DEB-1042132) and Long Term Ecological Research (NSF-DEB-1234162 to Cedar Creek LTER) programs, and the Institute on the Environment (DG-0001-13). We also thank the Minnesota Supercomputer Institute for hosting project data and the Institute on the Environment for hosting Network meetings. We are also grateful to Nhu Nguyen, Zewei Song, Joseph Deal and Hannah Hoekstra for help in sample collection, processing and insights into bioinformatics pipeline.

Publisher Copyright:
© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.


  • Andropogon gerardii
  • Nutrient Network
  • nitrogen, phosphorus, potassium
  • phylogenetic diversity
  • plant fungal endophytes
  • spatial variation


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