Dimensions of Host Specificity in Foliar Fungal Endophytes

  • Austen ApigoEmail author
  • Ryoko Oono
Part of the Forestry Sciences book series (FOSC, volume 86)


Foliar fungal endophytes (FFE) colonized the phyllosphere at least 400 million years ago and have since diversified across every terrestrial ecosystem that supports plant life. Understanding how these complex symbiotic associations are generated, distributed and maintained is a challenging task that requires an understanding of host specificity. We propose a conceptual framework that outlines four ‘dimensions’ of host specificity that account for the geographic, phylogenetic or sampling scale under consideration. These ‘dimensions’ quantify FFE abundance and evenness (structural specificity), interaction strength (network specificity), evolutionary relationships (phylogenetic specificity) and the spatial or temporal consistency of the interaction (beta-specificity). We present one case study that quantifies and compares structural, network and phylogenetic specificity across FFE communities partitioned by taxonomy (Ascomycota vs. Basidiomycota). We focus on the effects of rare FFE species, approximated as Operational Taxonomic Units (OTUs), as a key methodological consideration for communities surveyed with next-generation sequencing (NGS) because the statistical nature of rarity confounds the quantification of host specificity. The exclusion of rare FFE OTUs consistently changed ecological inference by decreasing host specificity averages and increasing variances within FFE phyla. To evaluate the degree to which rare FFE OTUs affect statistical power, we compared our empirical community to that of randomized communities. Excluding rare FFE OTUs (>10% of total sequences in the case community removed) may lead to spurious host specificity metrics that are not statistically significant from that of randomized communities. Therefore, rare FFE OTU removal should be done with explicit rationale. We propose conceptualizing FFE host specificity with a multidimensional framework that will allow future studies to use quantitative, comparable and theory-driven metrics that can scale towards more meaningful estimates of global fungal biodiversity.



Foliar fungal endophytes


Next-generation sequencing


Operational taxonomic unit



We thank Cindy Quach and Kevin Feller for their assistance in the field at the University of California, James San Jacinto Reserve. We thank Kiana Lee, Vanessa Greenman, Angelina Hyunh and Theodore Kwan for their assistance in the lab. We thank Professor Holly Moeller for reviewing previous drafts and helpful advice that improved the quality of this chapter.


  1. Ahlholm JU, Helander M, Henriksson J, Metzler M, Saikkonen K (2002) Environmental conditions and host genotype direct genetic diversity of Venturia ditricha, a fungal endophyte of birch trees. Evolution 56:1566–1573CrossRefPubMedGoogle Scholar
  2. Arnold AE (2007) Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev 21:51–66CrossRefGoogle Scholar
  3. Arnold AE, Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541–549CrossRefGoogle Scholar
  4. Arnold AE, Maynard Z, Gilbert GS, Coley PD, Kursar TA (2000) Are tropical fungal endophytes hyperdiverse? Ecol Lett 3:267–274CrossRefGoogle Scholar
  5. Bacon CW, White J (2000) Microbial endophytes. CRC Press, Boca RatonGoogle Scholar
  6. Bascompte J (2010) Structure and dynamics of ecological networks. Science 329:765–766CrossRefPubMedGoogle Scholar
  7. Blüthgen N, Menzel F, Blüthgen N (2006) Measuring specialization in species interaction networks. BMC Ecol 6:9CrossRefPubMedPubMedCentralGoogle Scholar
  8. Branco S, Gladieux P, Ellison CE, Kuo A, LaButti K, Lipzen A et al (2015) Genetic isolation between two recently diverged populations of a symbiotic fungus. Mol Ecol 24:2747–2758CrossRefPubMedGoogle Scholar
  9. Brooks AW, Kohl KD, Brucker RM, van Opstal EJ, Bordenstein SR (2016) Phylosymbiosis: relationships and functional effects of microbial communities across host evolutionary history. PLoS Biol 14:e2000225CrossRefPubMedPubMedCentralGoogle Scholar
  10. Brown SP, Veach AM, Rigdon-Huss AR, Grond K, Lickteig SK, Lothamer K et al (2015) Scraping the bottom of the barrel: are rare high throughput sequences artifacts? Fungal Ecol 13:221–225CrossRefGoogle Scholar
  11. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinform 10:421CrossRefGoogle Scholar
  12. Cannon PF, Simmons CM (2002) Diversity and host preference of leaf endophytic fungi in the Iwokrama Forest Reserve, Guyana. Mycologia 94:210–220CrossRefPubMedGoogle Scholar
  13. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973CrossRefPubMedPubMedCentralGoogle Scholar
  14. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336CrossRefPubMedPubMedCentralGoogle Scholar
  15. Carroll GC, Carroll FE (1978) Studies on the incidence of coniferous needle endophytes in the Pacific Northwest. Can J Bot 56:3034–3043CrossRefGoogle Scholar
  16. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW (2009) The merging of community ecology and phylogenetic biology. Ecol Lett 12:693–715CrossRefGoogle Scholar
  17. Chagnon P-L, U’Ren JM, Miadlikowska J, Lutzoni F, Arnold AE (2016) Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale. Oecologia 180:181–191CrossRefGoogle Scholar
  18. Davey ML, Heimdal R, Ohlson M, Kauserud H (2013) Host- and tissue-specificity of moss-associated Galerina and Mycena determined from amplicon pyrosequencing data. Fungal Ecol 6:179–186CrossRefGoogle Scholar
  19. Davis EC, Shaw AJ (2008) Biogeographic and phylogenetic patterns in diversity of liverwort-associated endophytes. Am J Bot 95:914–924CrossRefPubMedGoogle Scholar
  20. Devictor V, Clavel J, Julliard R, Lavergne S, Mouillot D, Thuiller W et al (2010) Defining and measuring ecological specialization. J Appl Ecol 47:15–25CrossRefGoogle Scholar
  21. Diserud OH, Odegaard F (2007) A multiple-site similarity measure. Biol Lett 3:20–22CrossRefPubMedGoogle Scholar
  22. Dormann CF (2011) How to be a specialist? Quantifying specialisation in pollination networks. Netw Biol 1:1–20Google Scholar
  23. Dormann CF, Gruber B, Fruend J (2008) Introducing the bipartite package: analysing ecological networks. R News 8:8–11Google Scholar
  24. Dormann CF, Fründ J, Blüthgen N, Gruber B (2009) Indices, graphs and null models: analyzing bipartite ecological networks. Open Ecol J 2:7–24CrossRefGoogle Scholar
  25. Dreyfuss MM, Chapela IH (1994) Potential of fungi in the discovery of novel, low-molecular weight pharmaceuticals. Biotechnology 26:49–80PubMedGoogle Scholar
  26. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461CrossRefGoogle Scholar
  27. Edgar RC (2016) UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing [Internet].
  28. Efron B (1987) Better bootstrap confidence intervals. J Am Stat Assoc 82(397):171–185CrossRefGoogle Scholar
  29. Faeth SH, Fagan W (2002) Fungal endophytes: common host plant symbionts but uncommon mutualists. Integr and Comp Biol 42:360–368CrossRefGoogle Scholar
  30. Fröhlich J, Hyde KD (1999) Biodiversity of palm fungi in the tropics: are global fungal diversity estimates realistic? Biodiv and Conserv 8:977–1004CrossRefGoogle Scholar
  31. Futuyma DJ, Moreno G (1988) The evolution of ecological specialization. Annu Rev Ecol Syst 19:207–233CrossRefGoogle Scholar
  32. Gilbert GS, Reynolds DR, Bethancourt A (2007) The patchiness of epifoliar fungi in tropical forests: host range, host abundance, and environment. Ecology 88:575–581CrossRefPubMedGoogle Scholar
  33. Gobet A, Quince C, Ramette A (2010) Multivariate cutoff level analysis (MultiCoLA) of large community data sets. Nucleic Acids Res 38:e155CrossRefPubMedPubMedCentralGoogle Scholar
  34. Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422–1432CrossRefGoogle Scholar
  35. Higgins KL, Arnold AE, Miadlikowska J, Sarvate SD, Lutzoni F (2007) Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Mol Phylogenet Evol 42:543–555CrossRefPubMedGoogle Scholar
  36. Hubbell SP (2001) The unified neutral theory of biodiversity and biogeography (MPB-32). Princeton University Press, PrincetonGoogle Scholar
  37. Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386CrossRefPubMedPubMedCentralGoogle Scholar
  38. Katoh K, Misawa K, Kuma K-I, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066CrossRefPubMedPubMedCentralGoogle Scholar
  39. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD et al (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–1464CrossRefGoogle Scholar
  40. Kerkhoff AJ, Moriarty PE, Weiser MD (2014) The latitudinal species richness gradient in New World woody angiosperms is consistent with the tropical conservatism hypothesis. Proc Natl Acad Sci USA 111:8125–8130CrossRefPubMedGoogle Scholar
  41. Kraft NJB, Adler PB, Godoy O, James EC, Fuller S, Levine JM (2014) Community assembly, coexistence and the environmental filtering metaphor. Funct Ecol 29:592–599CrossRefGoogle Scholar
  42. Krasnov BR, Mouillot D, Shenbrot GI, Khokhlova IS, Poulin R (2011) Beta-specificity: the turnover of host species in space and another way to measure host specificity. Int J Parasitol 41:33–41CrossRefPubMedGoogle Scholar
  43. Levin SA (1992) The problem of pattern and scale in ecology. Ecological Time SeriesCrossRefGoogle Scholar
  44. Liu L, Yang J, Yu Z, Wilkinson DM (2015) The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China. ISME J 9:2068–2077CrossRefPubMedPubMedCentralGoogle Scholar
  45. McMurdie PJ, Holmes S (2014) Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol 10:e1003531CrossRefPubMedPubMedCentralGoogle Scholar
  46. Minchin PR (1987) An evaluation of the relative robustness of techniques for ecological ordination. Vegetatio 69:89–107CrossRefGoogle Scholar
  47. Mittelbach GG, Schemske DW, Cornell HV, Allen AP, Brown JM, Bush MB et al (2007) Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol Lett 10:315–331CrossRefPubMedGoogle Scholar
  48. Moran VC, Southwood TRE (1982) The guild composition of arthropod communities in trees. J Animal Ecol 51:289–306CrossRefGoogle Scholar
  49. Nguyen NH, Smith D, Peay K, Kennedy P (2014) Parsing ecological signal from noise in next generation amplicon sequencing. New Phytol 205:1389–1393CrossRefPubMedGoogle Scholar
  50. Oksanen JF, Blanchet FG, Friendly M, Kindt R, Legendre P, et al (2017) Vegan: community ecologyGoogle Scholar
  51. Olesen JM, Bascompte J, Dupont YL, Jordano P (2007) The modularity of pollination networks. Proc Natl Acad Sci USA 104:19891–19896CrossRefPubMedGoogle Scholar
  52. Oono R, Lefèvre E, Simha A, Lutzoni F (2015) A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda). Fungal Biol 119:917–928CrossRefPubMedPubMedCentralGoogle Scholar
  53. Ortiz-García S, Gernandt DS, Stone JK, Johnston PR, Chapela IH, Salas-Lizana R et al (2003) Phylogenetics of Lophodermium from pine. Mycologia 95:846–859CrossRefPubMedGoogle Scholar
  54. Package. R package version 2.4-4.
  55. Pandey AK, Reddy MS, Suryanarayanan TS (2003) ITS-RFLP and ITS sequence analysis of a foliar endophytic Phyllosticta from different tropical trees. Mycol Res 107:439–444CrossRefPubMedGoogle Scholar
  56. Patin NV, Kunin V, Lidström U, Ashby MN (2013) Effects of OTU clustering and PCR artifacts on microbial diversity estimates. Microb Ecol 65:709–719CrossRefPubMedGoogle Scholar
  57. Pearse WD, Purvis A (2013) phyloGenerator: an automated phylogeny generation tool for ecologists. Methods Ecol Evol 4:692–698CrossRefGoogle Scholar
  58. Poisot T, Bever JD, Nemri A, Thrall PH, Hochberg ME (2011) A conceptual framework for the evolution of ecological specialisation. Ecol Lett 14:841–851CrossRefPubMedPubMedCentralGoogle Scholar
  59. Poisot T, Canard E, Mouquet N, Hochberg ME (2012) A comparative study of ecological specialization estimators. Methods Ecol Evol 3:537–544CrossRefGoogle Scholar
  60. Poulin R, Krasnov BR, Mouillot D (2011) Host specificity in phylogenetic and geographic space. Trends Parasitol 27:355–361CrossRefPubMedGoogle Scholar
  61. Ricotta C, Pavoine S (2015) A multiple-site dissimilarity measure for species presence/absence data and its relationship with nestedness and turnover. Ecol Indic 54:203–206CrossRefGoogle Scholar
  62. Rodriguez RJ, White JF Jr, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. New Phytol 182:314–330CrossRefGoogle Scholar
  63. Saavedra S, Stouffer DB, Uzzi B, Bascompte J (2011) Strong contributors to network persistence are the most vulnerable to extinction. Nature 478:233–235CrossRefPubMedGoogle Scholar
  64. Saikkonen K, Faeth SH, Helander M, Sullivan TJ (1998) Fungal endophytes: a continuum of interactions with host plants. Ann Rev Ecol Syst 29:319–343CrossRefGoogle Scholar
  65. Schleuning M, Fründ J, Klein A-M, Abrahamczyk S, Alarcón R, Albrecht M et al (2012) Specialization of mutualistic interaction networks decreases toward tropical latitudes. Curr Biol 22:1925–1931CrossRefPubMedGoogle Scholar
  66. Schoener TW (1989) Food webs from the small to the large: The Robert H. MacArthur award lecture. Ecology 70:1559–1589CrossRefGoogle Scholar
  67. Shannon CE, Weaver W (1948) The mathematical theory of communication. University of Illinois Press, UrbanaGoogle Scholar
  68. Sieber TN (2007) Endophytic fungi in forest trees: are they mutualists? Fungal Biol Rev 21:75–89CrossRefGoogle Scholar
  69. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313CrossRefPubMedPubMedCentralGoogle Scholar
  70. Stone J, Petrini O (1997) Endophytes of forest trees: a model for fungus-plant interactions. In Plant Relationships Part B. Springer, Berlin, HeidelbergGoogle Scholar
  71. Sun X, Ding Q, Hyde KD, Guo LD (2012) Community structure and preference of endophytic fungi of three woody plants in a mixed forest. Fungal Ecol 5:624–632CrossRefGoogle Scholar
  72. Suryanarayanan TS (2011) Diversity of fungal endophytes in tropical trees. For SciCrossRefGoogle Scholar
  73. Swenson NG (2014) Functional and phylogenetic ecology in R. Springer, New York, NYCrossRefGoogle Scholar
  74. Thébault E, Fontaine C (2010) Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329:853–856CrossRefPubMedGoogle Scholar
  75. Toju H, Tanabe AS, Yamamoto S, Sato H (2012) High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS ONE 7:e40863CrossRefPubMedPubMedCentralGoogle Scholar
  76. U’Ren JM, Lutzoni F, Miadlikowska J, Laetsch AD, Arnold AE (2012) Host and geographic structure of endophytic and endolichenic fungi at a continental scale. Am J Bot 99:898–914CrossRefPubMedGoogle Scholar
  77. Vega FE (2008) Insect pathology and fungal endophytes. J Invertebr Pathol 98:277–279CrossRefPubMedGoogle Scholar
  78. Vega FE, Simpkins A, Catherine Aime M, Posada F, Peterson SW, Rehner SA et al (2010) Fungal endophyte diversity in coffee plants from Colombia, Hawai’i, Mexico and Puerto Rico. Fungal Ecol 3:122–138CrossRefGoogle Scholar
  79. Vincent JB, Weiblen GD, May G (2016) Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees. Mol Ecol 25:825–841CrossRefPubMedGoogle Scholar
  80. Walker DM, Castlebury LA, Rossman AY, Struwe L (2013) Host conservatism or host specialization? Patterns of fungal diversification are influenced by host plant specificity in Ophiognomonia (Gnomoniaceae: Diaporthales). Biol J Linn Soc Lond 111:1–16CrossRefGoogle Scholar
  81. Walter GH (1991) What is resource partitioning? J Theor Biol 150:137–143CrossRefPubMedGoogle Scholar
  82. Wardhaugh CW, Edwards W, Stork NE (2015) The specialization and structure of antagonistic and mutualist networks of beetles on rainforest canopy trees. Biol J Linn Soc 114:287–295CrossRefGoogle Scholar
  83. Webb CO (2000) Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am Nat 156:145–155CrossRefGoogle Scholar
  84. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ (2002) Phylogenies and community ecology. Ann Rev Ecol Syst 33:475–505CrossRefGoogle Scholar
  85. Webb CO, Ackerly DD, Kembel SW (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24:2098–2100CrossRefPubMedGoogle Scholar
  86. Weiss NA (2016) wBoot: bootstrap methods. R package version 1.0.3.
  87. Whittaker RH (1972) Evolution and measurement of species diversity. Taxon 21:213CrossRefGoogle Scholar
  88. Zhang T, Yao Y-F (2015) Endophytic fungal communities associated with vascular plants in the high arctic zone are highly diverse and host-plant specific. PLoS ONE 10:e0130051CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Ecology, Evolution and Marine BiologyUniversity of California Santa BarbaraSanta BarbaraUSA

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