Skip to main content
Log in

Fungal Endophytes of Aquatic Macrophytes: Diverse Host-Generalists Characterized by Tissue Preferences and Geographic Structure

  • Microbiology of Aquatic Systems
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Most studies of endophytic symbionts have focused on terrestrial plants, neglecting the ecologically and economically important plants present in aquatic ecosystems. We evaluated the diversity, composition, host and tissue affiliations, and geographic structure of fungal endophytes associated with common aquatic plants in lentic waters in northern Arizona, USA. Endophytes were isolated in culture from roots and photosynthetic tissues during two growing seasons. A total of 226 isolates representing 60 putative species was recovered from 9,600 plant tissue segments. Although isolation frequency was low, endophytes were phylogenetically diverse and species-rich. Comparisons among the most thoroughly sampled species and reservoirs revealed that isolation frequency and diversity did not differ significantly between collection periods, among species, among reservoirs, or as a function of depth. However, community structure differed significantly among reservoirs and tissue types. Phylogenetic analyses of a focal genus (Penicillium) corroborated estimates of species boundaries and informed community analyses, highlighting clade- and genotype-level affiliations of aquatic endophytes with both sediment- and waterborne fungi, and endophytes of proximate terrestrial plants. Together these analyses provide a first quantitative examination of endophytic associations in roots and foliage of aquatic plants and can be used to optimize survey strategies for efficiently capturing fungal biodiversity at local and regional scales.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  2. Arenal F, Platas G, Pelaez F (2007) A new endophytic species of Preussia (Sporormiaceae) inferred from morphological observations and molecular phylogenetic analysis. Fungal Divers 25:1–17

    Google Scholar 

  3. Anonymous. Arizona Department of Environmental Quality (2010) Lake Mary regional TMDL for mercury in fish tissue. Arizona Department of Environmental Quality open file report. Available from http://www.azdeq.gov/environ/water/assessment/download/Lake_Mary_Region_Draft-6-16-2010.pdf

  4. Anonymous, U.S. Fish and Wildlife Service (2011) Biological assessment of the Arizona Game and Fish Department's Statewide and Urban Fisheries Stocking Program for the years 2011–2012. Wildlife and Sport Fish Restoration Program, U.S. Fish and Wildlife Service, Albuquerque, NM

  5. Arnold AE, Maynard Z, Gilbert GS, Coley PD, Kursar TA (2000) Are tropical fungal endophytes hyperdiverse? Ecol Lett 3:267–274

    Article  Google Scholar 

  6. Arnold AE, Maynard Z, Gilbert G (2001) Fungal endophytes in dicotyledonous neotropical trees: patterns of abundance and diversity. Mycol Res 105:1502–1507

    Article  Google Scholar 

  7. Arnold AE (2007) Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev 21:51–66

    Article  Google Scholar 

  8. Arnold AE, Henk DA, Eells R, Lutzoni F, Vilgalys R (2007) Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99:185–206

    Article  CAS  PubMed  Google Scholar 

  9. Arnold AE, Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541–549

    Article  PubMed  Google Scholar 

  10. Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F (2009) A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst Biol 58:283–297

    Article  PubMed  Google Scholar 

  11. Arya P, Sati SC (2011) Evaluation of endophytic aquatic hyphomycetes for their antagonistic activity against pathogenic bacteria. Int Res J Microbiol 2:343–347

    Google Scholar 

  12. Beck-Nielsen D, Madsen TV (2001) Occurrence of vesicular arbuscular mycorrhiza in aquatic macrophytes from lakes and streams. Aquat Bot 71:141–148

    Article  Google Scholar 

  13. Blackwell M (2011) The fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–438

    Article  PubMed  Google Scholar 

  14. Borman S, Korth R, Temte J, Watkins C (1997) Through the looking glass: a field guide to aquatic plants. Wisconsin Lakes Partnership, Stevens Point

    Google Scholar 

  15. Brix H, Schierup HH (1989) The use of aquatic macrophytes in water-pollution control. Ambio 18:100–107

    Google Scholar 

  16. Brönmark C, Hansson LA (2005) The biology of lakes and ponds. Oxford University Press, Oxford

    Google Scholar 

  17. Carroll GC, Carroll FE (1978) Studies on the incidence of coniferous needle endophytes in the Pacific Northwest. Can J Bot 56:3034–3043

    Article  Google Scholar 

  18. Carroll G (1988) Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69:2–9

    Article  Google Scholar 

  19. Clarke KR (1993) Non-parametric multivariate analysis of changes in community structure. Austral J Ecol 18:117–143

    Article  Google Scholar 

  20. de Marins JF, Carrenho R, Thomaz SM (2009) Occurrence and coexistence of arbuscular mycorrhizal fungi and dark septate fungi in aquatic macrophytes in a tropical river flood plain system. Aquat Bot 91:13–19

    Article  Google Scholar 

  21. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194

    Article  CAS  PubMed  Google Scholar 

  22. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185

    Article  CAS  PubMed  Google Scholar 

  23. Faeth SH, Hammon KE (1997) Fungal endophytes in oak trees: experimental analyses of interactions with leafminers. Ecology 78:820–827

    Article  Google Scholar 

  24. Ferrer A, Miller AN, Sarmiento C, Shearer CA (2012) Three new genera representing novel lineages of Sordariomycetidae (Sordariomycetes, Ascomycota) from tropical freshwater habitats in Costa Rica. Mycologia 104:865–879

    Article  PubMed  Google Scholar 

  25. Fisher PJ, Anson AE, Petrini DO (1986) Fungal endophytes in Ulex europaeus and Ulex gallii. T Brit Mycol Soc 86:153–156

    Article  Google Scholar 

  26. Fisher PJ (1996) Survival and spread of the endophyte Stagonospora pteridiicola in Pteridium aquilinum, other ferns and some flowering plants. New Phytol 132:119–122

    Article  Google Scholar 

  27. Fulmer JE, Robinson AT (2008) Aquatic plant species distributions and associations in Arizona's reservoirs. J Aquat Plant Manage 46:100–106

    Google Scholar 

  28. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118

    Article  CAS  PubMed  Google Scholar 

  29. Gauch HGJR (1982) Multivariate analysis in community structure. Cambridge University Press, Cambridge

    Book  Google Scholar 

  30. Gunatilaka AAL (2006) Natural products from plant-associated microorganisms: distribution, structural diversity, bioactivity, and implications of their occurrence. J Nat Prod 69:509–526

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9

    Google Scholar 

  32. Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422–1432

    Article  Google Scholar 

  33. 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 42:543–555

    Article  CAS  PubMed  Google Scholar 

  34. Higgins KL, Coley PD, Kursar TA, Arnold AE (2011) Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses. Mycologia 103:247–260

    Article  PubMed  Google Scholar 

  35. Hoffman M, Arnold AE (2008) Geography and host identity interact to shape communities of endophytic fungi in cupressaceous trees. Mycol Res 112:331–344

    Article  CAS  PubMed  Google Scholar 

  36. Hoffman M, Arnold AE (2010) Diverse bacteria inhabit living hyphae of phylogenetically diverse fungal endophytes. Apple Environ Microb 76:4063–4075

    Article  CAS  Google Scholar 

  37. Houbraken J, Samson RA (2011) Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud Mycol 70:1–51

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755

    Article  CAS  PubMed  Google Scholar 

  39. Janos DP (1980) Mycorrhizae influence tropical succession. Biotropica 12:56–64

    Article  Google Scholar 

  40. Jayachandran K, Shetty KG (2003) Growth response and phosphorus uptake by arbuscular mycorrhizae of wet prairie sawgrass. Aquat Bot 76:281–290

    Article  CAS  Google Scholar 

  41. Kandalepas D, Stevens KJ, Shaffer GP, Platt WJ (2010) How abundant are root-colonizing fungi in southeastern Louisiana's degraded marshes? Wetlands 30:189–199

    Article  Google Scholar 

  42. Kandalepas D (2012) Effects of coastal dynamics on colonization of Louisiana wetland plants by fungal endophytes. Dissertation, Louisiana State University

  43. Kohout P, Sýkorová Z, Ctvrtlíková M, Rydlová J, Suda J, Vohník M, Sudová R (2012) Surprising spectra of root-associated fungi in submerged aquatic plants. FEMS Microbiol Ecol 80:216–235

    Article  CAS  PubMed  Google Scholar 

  44. Krauss G-J, Sole M, Krauss G, Schlosser D, Wesenberg D, Baerlocher F (2011) Fungi in freshwaters: ecology, physiology and biochemical potential. FEMS Microbiol Rev 35:620–651

    Article  CAS  PubMed  Google Scholar 

  45. Lau MK, Arnold AE, Johnson NC (2013) Factors influencing communities of foliar fungal endophytes in riparian woody plants. Fungal Ecol 6:365–378

    Article  Google Scholar 

  46. Le Calvez T, Burgaud G, Mahe S, Barbier G, Vandenkoornhuyse P (2009) Fungal diversity in deep-sea hydrothermal ecosystems. Apple Environ Microb 75:6415–6421

    Article  Google Scholar 

  47. Les DH, Garvin DH, Wimpee CF (1991) Molecular evolutionary history of ancient aquatic angiosperms. Proc Natl Acad Sci U S A 88:10119–11023

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. Li HY, Zhao CA, Liu CJ, Xu XF (2010) Endophytic fungi diversity of aquatic/riparian plants and their antifungal activity in vitro. J Microbiol 48:1–6

    Article  PubMed  Google Scholar 

  49. Lodge DJ, Fisher PJ, Sutton BC (1996) Endophytic fungi of Manilkara bidentata leaves in Puerto Rico. Mycologia 88:733–738

    Article  Google Scholar 

  50. Maddison DR, Maddison WP (2005) ChromaSeq module. Mesquite: a modular system for evolutionary analysis. Version 1.06. Available from http://mesquiteproject.org/

  51. Maddison WP, Maddison DR (2009) Mesquite: a modular system for evolutionary analysis. Version 2.6. Available from http://mesquiteproject.org/

  52. Maier RM, Pepper IL, Gerba CP (2009) Environmental microbiology. Academic, Burlington

    Google Scholar 

  53. Malcolm Pirnie and Arizona Department of Environmental Quality (2000) Stoneman Lake TMDL. Arizona Department of Environmental Quality open file report. Available from http://www.epa.gov/waters/tmdldocs/11720_stonemanlaketmdl.pdf

  54. Neubert K, Mendgen K, Brinkmann H, Wirsel SGR (2006) Only a few fungal species dominate highly diverse mycofloras associated with the common reed. Appl Environ Microb 72:1118–1128

    Article  CAS  Google Scholar 

  55. Niereg WA, National Audubon Society (1985) Wetlands. Knopf, New York

    Google Scholar 

  56. Petrini O (1991) Fungal endophytes of tree leaves. In: Andrews JH, Hirano SS (eds) Microbial ecology of leaves. Springer, New York

    Google Scholar 

  57. Polunin N (2008) Aquatic ecosystems: trends and global prospects. Cambridge University Press, Cambridge

    Book  Google Scholar 

  58. Posada D (2008) jModelTest: phylogenetic model averaging. Molec Biol Evol 25:1253–1256

    Article  CAS  PubMed  Google Scholar 

  59. Raja HA, Hirayama K, Tanaka K, Miller AN, Shearer CA (2011) Freshwater Ascomycetes: two new species of Lindgomyces (Lindgomycetaceae, Pleosporales, Dothideomycetes) from Japan and USA. Mycologia 103:1421–1432

    Article  PubMed  Google Scholar 

  60. Robinson AT, Fulmer JE, Avenetti LD (2007) Aquatic plant surveys and evaluation of aquatic plant harvesting in Arizona reservoirs. Arizona Game and Fish Department, Research Branch, Technical Guidance Bulletin No. 9, Phoenix. 39 pp

  61. Rodriguez R, White J, Arnold AE, Redman R (2009) Fungal endophytes: diversity and ecological roles. New Phytol 182:314–330

    Article  CAS  PubMed  Google Scholar 

  62. Rosling A, Cox F, Cruz-Martinez K, Ihrmark K, Grelet G-A, Lindahl BD, Menkis A, James TY (2011) Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi. Science 333:876–879

    Article  CAS  PubMed  Google Scholar 

  63. Sandberg DC (2013) Host affiliations and geographic distributions of fungal endophytes inhabiting aquatic plants in northern Arizona, USA. MS thesis, University of Arizona

  64. Sati SC, Belwal M (2005) Aquatic hyphomycetes as endophytes of riparian plant roots. Mycologia 97:45–49

    Article  CAS  PubMed  Google Scholar 

  65. Schulthess FM, Faeth SH (1998) Distribution, abundances, and associations of the endophytic fungal community of Arizona fescue (Festuca arizonica). Mycologia 90:569–578

    Article  Google Scholar 

  66. Schulz B, Wanke U, Draeger S, Aust HJ (1993) Endophytes from herbaceous plants and shrubs—effectiveness of surface sterilization methods. Mycol Res 97:1447–1450

    Article  Google Scholar 

  67. Schulz B, Boyle C, Draeger S, Römmert A-K, Krohn K (2002) Endophytic fungi: a source of novel biological active secondary metabolites. Mycol Res 106:996–1004

    Article  CAS  Google Scholar 

  68. Shearer JF (2001) Recovery of endophytic fungi from Myriophyllum spicatum. APCRP Technical Notes Collection. ERDC TN-APCRP-BC-03. U.S. Army Engineer Research and Development Center, Vicksburg, MS

  69. Shearer CA, Descals E, Kohlmeyer B, Kohlmeyer J, Marvanova L, Padgett D, Porter D, Raja HA, Schmit JP, Thorton HA, Voglymayr H (2007) Fungal biodiversity in aquatic habitats. Biodiv Conserv 16:49–67

    Article  Google Scholar 

  70. Shearer JF (2010) Relationship between Eurasian watermilfoil phenology and endophyte presence. APCRP Technical Notes Collection. ERDC/TN APCRP-BC-20. U.S. Army Engineer Research and Development Center, Vicksburg, MS

  71. Sridhar KR, Bärlocher F (1992) Endophytic aquatic hyphomycetes of roots from spruce, birch and maple. Mycol Res 96:305–308

    Article  Google Scholar 

  72. Strobel G, Daisey B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol Molec Biol Rev 67:491–502

    Article  CAS  Google Scholar 

  73. Suryanarayanan TS, Kumaresan V (2000) Endophytic fungi of some halophytes from an estuarine mangrove forest. Mycol Res 104:1465–1467

    Article  Google Scholar 

  74. Suryanarayanan TS, Murali TS, Venkatesan G (2002) Occurrence and distribution of fungal endophytes in tropical forests across a rainfall gradient. Can J Bot 80:818–826

    Article  Google Scholar 

  75. Suryanarayanan TS, Wittlinger SK, Faeth SH (2005) Endophytic fungi associated with cacti in Arizona. Mycol Res 109:635–639

    Article  PubMed  Google Scholar 

  76. Suryanarayanan TS, Murali TS, Thirunavukkarasu N, Rajulu MBG, Venkatesan G, Sukumar R (2011) Endophytic fungal communities in woody perennials of three tropical forest types of the Western Ghats, southern India. Biodiv Conserv 20:913–928

    Article  Google Scholar 

  77. Tan RX, Zou WX (2001) Endophytes: a rich source of functional metabolites. Nat Prod Rep 18:448–459

    Article  CAS  PubMed  Google Scholar 

  78. Upper Granite Creek Watershed Management Plan (2011) Improvement plan for the Upper Granite Creek Watershed, Arizona, Version 1.0. Prescott Creeks and the Granite Creek Watershed Improvement Council open report. Available from http://www.prescottcreeks.org/sites/prescottcreeks.org/files/.wysiwyg/WIP-full_wm.pdf

  79. U'Ren JM, Dalling JW, Gallery RE, Maddison DR, Davis EC, Gibson CM, Arnold AE (2009) Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analyzing fungal environmental samples. Mycol Res 113:432–449

    Article  PubMed  Google Scholar 

  80. U'Ren JM, Lutzoni F, Miadlikowska J, Arnold AE (2010) Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microb Ecol 60:340–353

    Article  PubMed  Google Scholar 

  81. 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 99:898–914

    Article  PubMed  Google Scholar 

  82. Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246

    PubMed Central  CAS  PubMed  Google Scholar 

  83. Warwick RM, Clarke KR, Suharsono (1990) A statistical analysis of coral community responses to the 1982–83 El Niño in the Thousand Islands, Indonesia. Coral Reefs 8:171–179

    Article  Google Scholar 

  84. Wetzel RG (2001) Limnology: lake and river ecosystems, 3rd edn. Academic, San Diego

  85. White TJ, Bruns T, Lee SB, 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 protocols: a guide to methods and applications. Academic, San Diego

    Google Scholar 

  86. Willoughby LG (1977) Freshwater biology. Pica Press, New York

    Google Scholar 

  87. Wurzbacher C, Barlöcher M, Grossart HP (2010) Fungi in lake ecosystems. Aquat Microb Ecol 59:125–149

    Article  Google Scholar 

  88. Wurzbacher C, Williams J, Grossart HP (2011) Aquatic fungi. In: Grillo O (ed) Biodiversity, Book 2. Intech. doi:10.5772/23029

  89. Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comp Biol 7:203–214

    Article  CAS  Google Scholar 

  90. Zhang HW, Song YC, Tan RX (2006) Biology and chemistry of endophytes. Nat Prod Rep 23:753–771

    Article  CAS  PubMed  Google Scholar 

  91. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Dissertation, The University of Texas

Download references

Acknowledgments

The authors thank the School of Plant Sciences and the College of Agriculture and Life Sciences at The University of Arizona for supporting this work. DCS was supported in part by a Pierson Fellowship through the Plant Pathology graduate major at The University of Arizona. Additional support was provided by the National Institutes of Health (R01 to A.A.L. Gunatilaka and AEA) and the National Science Foundation (NSF DEB-1045766 to AEA). The authors also thank Kayla Arendt, Mariana del Olmo-Ruiz, Nicholas Massimo, Jakob Riddle, Justin Shaffer, and especially Jana U'Ren for lab assistance and helpful discussion; and Lauren Dominick, Chan Jung, Thaddeus Metz, Jamie Moy, Brittany Peña, Ethan Posey, Adrian Ramirez, Cole Steen, and Brittany Wohl for assistance in the field. The authors are especially grateful to Anthony Robinson and the Arizona Game and Fish Department, Jacob Butler, Kevin Fitzsimmons, and William Matter for helpful discussion and sharing their knowledge regarding limnology and aquatic biology, Marc J. Orbach and Barry M. Pryor for helpful guidance, and two anonymous reviewers for improving the manuscript. This paper represents a portion of the MS research of DCS in the Plant Pathology major within the School of Plant Sciences at The University of Arizona.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to A. Elizabeth Arnold.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Table S1

(DOCX 129 kb)

Table S2

(XLS 32 kb)

Table S3

(DOC 436 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sandberg, D.C., Battista, L.J. & Arnold, A.E. Fungal Endophytes of Aquatic Macrophytes: Diverse Host-Generalists Characterized by Tissue Preferences and Geographic Structure. Microb Ecol 67, 735–747 (2014). https://doi.org/10.1007/s00248-013-0324-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-013-0324-y

Keywords

Navigation