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Community Analysis Reveals Close Affinities Between Endophytic and Endolichenic Fungi in Mosses and Lichens

  • Plant Microbe Interactions
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Abstract

Endolichenic fungi live in close association with algal photobionts inside asymptomatic lichen thalli and resemble fungal endophytes of plants in terms of taxonomy, diversity, transmission mode, and evolutionary history. This similarity has led to uncertainty regarding the distinctiveness of endolichenic fungi compared with endophytes. Here, we evaluate whether these fungi represent distinct ecological guilds or a single guild of flexible symbiotrophs capable of colonizing plants or lichens indiscriminately. Culturable fungi were sampled exhaustively from replicate sets of phylogenetically diverse plants and lichens in three microsites in a montane forest in southeastern Arizona (USA). Intensive sampling combined with a small spatial scale permitted us to decouple spatial heterogeneity from host association and to sample communities from living leaves, dead leaves, and lichen thalli to statistical completion. Characterization using data from the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS-LSU rDNA) provided a first estimation of host and substrate use for 960 isolates representing five classes and approximately 16 orders, 32 families, and 65 genera of Pezizomycotina. We found that fungal communities differ at a broad taxonomic level as a function of the phylogenetic placement of their plant or lichen hosts. Endolichenic fungal assemblages differed as a function of lichen taxonomy, rather than substrate, growth form, or photobiont. In plants, fungal communities were structured more by plant lineage than by the living vs. senescent status of the leaf. We found no evidence that endolichenic fungi are saprotrophic fungi that have been “entrapped” by lichen thalli. Instead, our study reveals the distinctiveness of endolichenic communities relative to those in living and dead plant tissues, with one notable exception: we identify, for the first time, an ecologically flexible group of symbionts that occurs both as endolichenic fungi and as endophytes of mosses.

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Acknowledgements

We gratefully acknowledge the National Science Foundation for supporting this research (DEB-0640996 to AEA, DEB-0640956 to FL, and an NSF-supported IGERT Fellowship in Genomics to JMU) and for fostering discussion that informed this work through the Fungal Environmental Sampling and Informatics Network (FESIN; DEB-0639048 to T. Bruns, K. Hughes, and AEA). We thank E. Gaya, A. Laetsch, F. Santos, M. Gunatilaka, M. Hoffman and M. del Olmo R. for technical assistance, D. R. Maddison for sharing pre-release versions of Mesquite and ChromaSeq, T. Wheeler and J. Stajich for computational assistance, R. J. Steidl for helpful discussion, R. Harris, B. Hodkinson, E. Gaya and S. Heidmarsson for assistance with lichen identifications, and J. Bronstein for helpful comments on the manuscript.

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Authors and Affiliations

  1. Division of Plant Pathology and Microbiology, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA

    Jana M. U’Ren & A. Elizabeth Arnold

  2. Department of Biology, Duke University, Durham, NC, 27708, USA

    François Lutzoni & Jolanta Miadlikowska

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  1. Jana M. U’Ren
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Correspondence to A. Elizabeth Arnold.

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Fig. S1

Excerpts from majority rule-consensus trees with posterior probability values generated from 10,000 post burn-in trees sampled during a Bayesian analysis of ITS-LSU rDNA data with GTR model of evolution demonstrating the congruence of ITS-LSU rDNA genotype groups based on Sequencher analyses of 95% and 100% sequence similarity. Name, host species, substrate, and OTU at both 95% and 100% sequence similarity are listed for each isolate. Nine isolates (a) and 23 isolates (b) from both plants and lichens were aligned in MUSCLE (default parameters) and the appropriate model of evolution was determined for each alignment using the Akaike Information Criterion (AIC) in ModelTest. Phylogenetic estimations were conducted for each alignment using the appropriate model of evolution using MrBayes 3.1.2 for 1 million generations each, using two independent runs (each with four chains) and sampling every 100th generation. To determine the burn-in for each analysis, the average standard deviation of the split frequencies was evaluated, as well as plots of –lnL values. Posterior probability values are shown on trees. Genotype groups based on 95% ITS-LSU rDNA similarity as calculated in Sequencher are conservative, in that individual genotype groups often contain within them more than one strongly supported phylogenetic group (DOC 6352 kb)

Fig. S2

Host-based accumulation curves (Sobs Mao Tau), 95% confidence intervals, and bootstrap estimates of richness, based on ITS-LSU rDNA OTU (95% sequence similarity) for a 36 OTU of endophytic fungi from living photosynthetic tissues of 33 individual plants; b 53 OTU of endolichenic fungi from living thalli of 30 lichens; c 32 OTU of fungi from dead leaves in canopies of 16 trees (dead leaf fungi (DLF)); and d 33 OTU of fungi from leaf litter beneath 16 trees (leaf litter fungi (LLF)) (DOC 3633 kb)

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U’Ren, J.M., Lutzoni, F., Miadlikowska, J. et al. Community Analysis Reveals Close Affinities Between Endophytic and Endolichenic Fungi in Mosses and Lichens. Microb Ecol 60, 340–353 (2010). https://doi.org/10.1007/s00248-010-9698-2

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