Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation


All plants form symbioses with endophytic fungi, which affect host plant health and function. Most endophytic fungi are horizontally transmitted, and consequently, local environment and geographic location greatly influence endophyte community composition. Growing evidence also suggests that identity of the plant host (e.g., species, genotype) can be important in shaping endophyte communities. However, little is known about how disturbances to plants affect their fungal symbiont communities. The goal of this study was to test if disturbances, from both natural and anthropogenic sources, can alter endophyte communities independent of geographic location or plant host identity. Using the plant species white snakeroot (Ageratina altissima; Asteraceae), we conducted two experiments that tested the effect of perturbation on endophyte communities. First, we examined endophyte response to leaf mining insect activity, a natural perturbation, in three replicate populations. Second, for one population, we applied fungicide to plant leaves to test endophyte community response to an anthropogenic perturbation. Using culture-based methods and Sanger sequencing of fungal isolates, we then examined abundance, diversity, and community structure of endophytic fungi in leaves subjected to perturbations by leaf mining and fungicide application. Our results show that plant host individual and geographic location are the major determinants of endophyte community composition even in the face of perturbations. Unexpectedly, we found that leaf mining did not impact endophyte communities in white snakeroot, but fungicide treatment resulted in small but significant changes in endophyte community structure. Together, our results suggest that endophyte communities are highly resistant to biotic and anthropogenic disturbances.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7


  1. 1.

    Lepage P, Leclerc MC, Joossens M et al (2013) A metagenomic insight into our gut’s microbiome. Gut 62:146–158

    Article  PubMed  Google Scholar 

  2. 2.

    Russell JA, Dubilier N, Rudgers JA (2014) Nature’s microbiome: introduction. Mol Ecol 23:1225–1237

    Article  PubMed  Google Scholar 

  3. 3.

    Francino MP (2016) Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances. Front Microbiol 6:1–11

    Article  Google Scholar 

  4. 4.

    Röthig T, Ochsenkühn MA, Roik A et al (2016) Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome. Mol Ecol 25:1308–1323

    Article  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Christian N, Whitaker BK, Clay K (2015) Microbiomes: unifying animal and plant systems through the lens of community ecology theory. Front Microbiol 6:1–15

    Article  Google Scholar 

  6. 6.

    Humphrey PT, Nguyen TT, Villalobos MM, Whiteman NK (2014) Diversity and abundance of phyllosphere bacteria are linked to insect herbivory. Mol Ecol 23:1497–1515

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Kandalepas D, Blum MJ, Van Bael SA (2015) Shifts in symbiotic endophyte communities of a foundational salt marsh grass following oil exposure from the deepwater horizon oil spill. PLoS ONE 10:1–18. doi:10.1371/journal.pone.0122378

    Article  Google Scholar 

  8. 8.

    Nettles R, Watkins J, Ricks K et al (2016) Influence of pesticide seed treatments on rhizosphere fungal and bacterial communities and leaf fungal endophyte communities in maize and soybean. Appl Soil Ecol 102:61–69

    Article  Google Scholar 

  9. 9.

    Pedraza RO, Bellone CH, Carrizo de Bellone S et al (2009) Azospirillum inoculation and nitrogen fertilization effect on grain yield and on the diversity of endophytic bacteria in the phyllosphere of rice rainfed crop. Eur J Soil Biol 45:36–43

    CAS  Article  Google Scholar 

  10. 10.

    U’Ren JM, Lutzoni F, Miadlikowska J et al (2012) Host and geographic structure of endophytic and endolichenic fungi at a continental scale. Am J Bot 99:898–914

    Article  PubMed  Google Scholar 

  11. 11.

    Rodriguez RJ, White JF, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. New Phytol 182:314–330

    CAS  Article  PubMed  Google Scholar 

  12. 12.

    Ernst M, Mendgen KW, Wirsel SGR (2003) Endophytic fungal mutualists: seed-borne Stagonospora spp. enhance reed biomass production in axenic microcosms. Mol Plant Microbe Interact 16:580–587

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Arnold A, Mejía L, Kyllo D et al (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci 100:15649–15654

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Bae H, Sicher RC, Kim MS et al (2009) The beneficial endophyte Trichoderma hamatum isolate DIS 219b promotes growth and delays the onset of the drought response in Theobroma cacao. J Exp Bot 60:3279–3295

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Clay K, Hardy T, Hammond A Jr (1985) Fungal endophytes of grasses and their effects on an insect herbivore. Oecologia 66:1–5

    Article  Google Scholar 

  16. 16.

    Herre EA, Mejía LC, Kyllo DA et al (2007) Ecological implications of anti-pathogen effects of tropical fungal endophytes and mycorrhizae. Ecology 88:550–558

    Article  PubMed  Google Scholar 

  17. 17.

    Panaccione DG, Beaulieu WT, Cook D (2014) Bioactive alkaloids in vertically transmitted fungal endophytes. Funct Ecol 28:299–314

    Article  Google Scholar 

  18. 18.

    Christian N, Whitaker BK, Clay K (2016, in press) A novel framework for decoding fungal endophyte diversity. In: Dighton J and White JF (ed) The Fungal Community: its Organization and Role in the Ecosystem, 4th edn. CRC Taylor & Francis, Boca Raton.

  19. 19.

    Kaneko R, Kaneko S (2004) The effect of bagging branches on levels of endophytic fungal infection in Japanese beech leaves. For Pathol 34:65–78

    Google Scholar 

  20. 20.

    Herrera CM, De Vega C, Canto A, Pozo MI (2009) Yeasts in floral nectar: a quantitative survey. Ann Bot 103:1415–1423

    Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Arnold AE, Maynard Z, Gilbert GS et al (2000) Are tropical fungal endophytes hyperdiverse? Ecol Lett 3:267–274

    Article  Google Scholar 

  22. 22.

    Zimmerman NB, Vitousek PM (2012) Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. Proc Natl Acad Sci 109:13022–13027

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Mei L, Zhu M, Zhang DZ et al (2014) Geographical and temporal changes of foliar fungal endophytes associated with the invasive plant Ageratina adenophora. Microb Ecol 67:402–409

    Article  PubMed  Google Scholar 

  24. 24.

    David AS, Seabloom EW, May G (2015) Plant host species and geographic distance affect the structure of aboveground fungal symbiont communities, and environmental filtering affects belowground communities in a coastal dune ecosystem. Microb Ecol 71:912–926

    Article  PubMed  Google Scholar 

  25. 25.

    Pan JJ, May G (2009) Fungal-fungal associations affect the assembly of endophyte communities in maize (Zea mays). Microb Ecol 58:668–678

    Article  PubMed  Google Scholar 

  26. 26.

    Bálint M, Bartha L, O’Hara R et al (2015) Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars. Mol Ecol 24:235–248

    Article  PubMed  Google Scholar 

  27. 27.

    Estrada C, Wcislo WT, Van Bael SA (2013) Symbiotic fungi alter plant chemistry that discourages leaf-cutting ants. New Phytol 198:241–251

    Article  PubMed  Google Scholar 

  28. 28.

    Estrada C, Degner EC, Rojas EI et al (2015) The role of endophyte diversity in protecting plants from defoliation by leaf-cutting ants. Curr Sci 109:19–25

    Google Scholar 

  29. 29.

    Ahlholm J, Helander M, Elamo P et al (2002) Micro-fungi and invertebrate herbivores on birch trees: fungal mediated plant-herbivore interactions or responses to host quality? Ecol Lett 5:648–655

    Article  Google Scholar 

  30. 30.

    Weis AE (1982) Use of symbiotic fungus by the gall maker Asteromyia carbonifera to inhibit attack by the parasitoid Torymus capite. Ecology 63:1602–1605

    Article  Google Scholar 

  31. 31.

    Lawson SP, Christian N, Abbot P (2014) Comparative analysis of the biodiversity of fungal endophytes in insect-induced galls and surrounding foliar tissue. Fungal Divers 66:89–97

    Article  Google Scholar 

  32. 32.

    Yamazaki K (2010) Leaf mines as visual defensive signals to herbivores. Oikos 119:796–801

    Article  Google Scholar 

  33. 33.

    Wilson D, Carroll G (1997) Avoidance of high-endophyte space by gall-forming insects. Ecology 78:2153–2163

    Article  Google Scholar 

  34. 34.

    Faeth SH, Hammon KE (1997) Fungal endophytes in oak trees: long-term patterns of abundance and associations with leafminers. Ecology 78:810–819

    Article  Google Scholar 

  35. 35.

    Wilson D, Faeth SH (2001) Do fungal endophytes result in selection for leafminer ovipositional preference? Ecology 82:1097–1111

    Article  Google Scholar 

  36. 36.

    Gange AC, Dey S, Currie AF, Sutton BC (2007) Site- and species-specific differences in endophyte occurrence in two herbaceous plants. J Ecol 95:614–622

    Article  Google Scholar 

  37. 37.

    Fuentes-Ramírez LE, Caballero-Mellado J, Sepúlveda J, Martínez-Romero E (1999) Colonization of sugarcane by Acetobacter diazotrophicus is inhibited by high N-fertilization. FEMS Microbiol Ecol 29:117–128

    Article  Google Scholar 

  38. 38.

    Seghers D, Wittebolle L, Top EM et al (2004) Impact of agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol 70:1475–1482

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Helander ML, Neuvonen S, Sieber T, Petrini O (1993) Simulated acid rain affects birch leaf endophyte populations. Microb Ecol 26:227–234

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Huang YL, Devan MMN, U’Ren JM et al (2015) Pervasive effects of wildfire on foliar endophyte communities in montane forest trees. Microb Ecol 71:452–468

    Article  PubMed  Google Scholar 

  41. 41.

    Fischer MS, Rodriguez RJ (2013) Fungal endophytes of invasive Phagramites australis populations vary in species composition and fungicide susceptibility. Symbiosis 61:55–62

    CAS  Article  Google Scholar 

  42. 42.

    Clewell AF, Wooten JW (1971) A Revision of Ageratina (Compositae: Eupatorieae) from Eastern North America. Brittonia 23:123–143

    Article  Google Scholar 

  43. 43.

    Davis TZ, Lee ST, Collett MG et al (2015) Toxicity of white snakeroot (Ageratina altissima) and chemical extracts of white snakeroot in goats. J Agric Food Chem 63:2092–2097

    CAS  Article  PubMed  Google Scholar 

  44. 44.

    Spencer KA, Steyskal GC (1986) Manual of the Agromyzidae (Diptera) of the United States.

  45. 45.

    Mejía L, Rojas EI, Maynard Z et al (2008) Endophytic fungi as biocontrol agents of Theobroma cacao pathogens. Biol Control 46:4–14

    Article  Google Scholar 

  46. 46.

    White TJ, Bruns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protoc. A Guid. to Methods Appl. Academic Press, Inc., New York, pp 315–322

    Google Scholar 

  47. 47.

    Del Olmo-Ruiz M, Arnold AE (2014) Interannual variation and host affiliations of endophytic fungi associated with ferns at La Selva, Costa Rica. Mycologia 106:8–21

    Article  PubMed  Google Scholar 

  48. 48.

    Deshpande V, Wang Q, Greenfield P et al (2016) Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences. Mycologia 108:1–5

    Article  PubMed  Google Scholar 

  49. 49.

    Hassall KA (1990) The biochemistry and uses of pesticides: structure, metabolism, mode of action and uses in crop protection, 2nd edn. VCH Publishers, New York

    Google Scholar 

  50. 50.

    Colwell RK (2013) EstimateS: statistical estimation of species richness and shared species from samples. Version 9. User’s Guide and application at <>.

  51. 51.

    Gotelli NJ, Colwell RK (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol Lett 4:379–391

    Article  Google Scholar 

  52. 52.

    R Development Core Team (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL R Found. Stat. Comput. Vienna, Austria

  53. 53.

    Oksanen J, Blanchet FG, Kindt R et al (2013) Package “vegan”. R Packag ver 20–8:254

    Google Scholar 

  54. 54.

    Legendre P, Legendre L (1998) Numerical ecology, 2nd edn. Elsevier Science BV, Amsterdam

    Google Scholar 

  55. 55.

    Aschehoug ET, Callaway RM, Newcombe G et al (2014) Fungal endophyte increases the allelopathic effects of an invasive forb. Oecologia 175:285–291

    Article  PubMed  Google Scholar 

  56. 56.

    Rojas EI, Rehner SA, Samuels GJ et al (2010) Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes. Mycologia 102:1318–1338

    Article  PubMed  Google Scholar 

  57. 57.

    Serdani M, Rooney-Latham S, Wallis KM, Blomquist CL (2013) First report of Colletotrichum phormii causing anthracnose on New Zealand flax the United States. Plant Dis 97:1115

    Article  Google Scholar 

  58. 58.

    Lima NB, Marcus MV, De Morais MA et al (2013) Five Colletotrichum species are responsible for mango anthracnose in northeastern Brazil. Fungal Divers 61:75–88

    Article  Google Scholar 

  59. 59.

    Berner D, Cavin C (2011) Leaf anthracnose, a new disease of swallow-worts caused by Colletotrichum lineola from Russia. Plant Dis 95:1586

    Article  Google Scholar 

  60. 60.

    Helander M, Ahlholm J, Sieber TN et al (2007) Fragmented environment affects birch leaf endophytes. New Phytol 175:547–553

    CAS  Article  PubMed  Google Scholar 

  61. 61.

    Preszler RW, Gaylord ES, Boecklen WJ et al (1996) Reduced parasitism of a leaf-mining moth on trees with high infection frequencies of an endophytic fungus. Oecologia 108:159–166

    Article  Google Scholar 

  62. 62.

    Sempere F, Santamarina MP (2008) Biological control of one species belonging to the dominant mycobiota of rice of Valencia. Ann Microbiol 58:7–14

    Article  Google Scholar 

  63. 63.

    Carvalho CR, Gonçalves VN, Pereira CB et al (2012) The diversity, antimicrobial and anticancer activity of endophytic fungi associated with the medicinal plant Stryphnodendron adstringens (Mart.) Coville (Fabaceae) from the Brazilian savannah. Symbiosis 57:95–107

    Article  Google Scholar 

  64. 64.

    Gond SK, Mishra A, Sharma VK et al (2012) Diversity and antimicrobial activity of endophytic fungi isolated from Nyctanthes arbor-tristis, a well-known medicinal plant of India. Mycoscience 53:113–121

    Article  Google Scholar 

  65. 65.

    Lawrie A (2011) Using the fungus Nigrospora oryzae for the biological control of giant parramatta grass. Rural Industries Research and Development Corporation, Bundoora, Victoria, Australia

    Google Scholar 

  66. 66.

    Li YC, Yang Y (2015) On the paradox of pesticides. Commun Nonlinear Sci Numer Simul 29:179–187

    Article  Google Scholar 

  67. 67.

    Wilson C, Tisdell C (2001) Why farmers continue to use pesticides despite environmental, health and sustainability costs. Ecol Econ 39:449–462

    Article  Google Scholar 

  68. 68.

    Busby PE, Ridout M, Newcombe G (2016) Fungal endophytes: modifiers of plant disease. Plant Mol Biol 90(6):645–655

    CAS  Article  PubMed  Google Scholar 

  69. 69.

    Rodriguez Estrada AE, Hegeman A, Kistler HC, May G (2011) In vitro interactions between Fusarium verticillioides and Ustilago maydis through real-time PCR and metabolic profiling. Fungal Genet Biol 48:874–885

    CAS  Article  PubMed  Google Scholar 

  70. 70.

    Hartley SE, Eschen R, Horwood JM et al (2015) Infection by a foliar endophyte elicits novel arabidopside-based plant defence reactions in its host, Cirsium arvense. New Phytol 205:816–827

    Article  PubMed  Google Scholar 

Download references


We gratefully acknowledge financial support from Sigma Xi (NC), the Indiana Academy of Science (NC and NDV), the Indiana University Research and Teaching Preserve (NC) and the Indiana University Hutton Honors College (CS). NC was supported by the NSF Graduate Research Fellowship program. We thank M. Abolins-Abols, Q. Chai, L. Durden, L. Henry, Z. Shearin, A. Snyder, B. Whitaker, Y. Zhao, and an anonymous reviewer for their feedback on the manuscript, the Indiana University Research and Teaching Preserve for use of sampling sites, and the Indiana Molecular Biology Institute for sequencing assistance.

Author information



Corresponding author

Correspondence to Natalie Christian.

Ethics declarations

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of Interest

The authors declare that they have no conflict of interest.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Christian, N., Sullivan, C., Visser, N.D. et al. Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation. Microb Ecol 72, 621–632 (2016).

Download citation


  • Microbiome
  • Fungi
  • Disturbance
  • Herbivory
  • Fungicide
  • Ageratina altissima