Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.

Biodiversity Unit University of Turku 20014 Turku Finland

Department of Biology University of Turku 20014 Turku Finland

Laboratory of Hormonal Regulations in Plants Institute of Experimental Botany of the Czech Academy of Sciences Rozvojova 263 16502 Prague Czech Republic

Zobrazit více v PubMed

Kowalchuk G.A., Jones S.E., Blackall L.L. Microbes Orchestrate Life on Earth. ISME J. 2008;2:795–796. doi: 10.1038/ismej.2008.61. PubMed DOI

Gilbert J.A., Neufeld J.D. Life in a World without Microbes. PLoS Biol. 2014;12:e1002020. doi: 10.1371/journal.pbio.1002020. PubMed DOI PMC

Kemen A.C., Agler M.T., Kemen E. Host–Microbe and Microbe–Microbe Interactions in the Evolution of Obligate Plant Parasitism. New Phytol. 2015;206:1207–1228. doi: 10.1111/nph.13284. PubMed DOI

Hassani M.A., Durán P., Hacquard S. Microbial Interactions within the Plant Holobiont. Microbiome. 2018;6:58. doi: 10.1186/s40168-018-0445-0. PubMed DOI PMC

Berg G. Plant-Microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture. Appl. Microbiol. Biotechnol. 2009;84:11–18. doi: 10.1007/s00253-009-2092-7. PubMed DOI

Elmer G.W., Mcfarland L.V., Mcfarland M., Russo E.B. The Power of Probiotics: Improving Your Health with Beneficial Microbes. Routledge; Abingdon, UK: 2013.

Trivedi P., Batista B.D., Bazany K.E., Singh B.K. Plant–Microbiome Interactions under a Changing World: Responses, Consequences and Perspectives. New Phytol. 2022;234:1951–1959. doi: 10.1111/nph.18016. PubMed DOI

Saikkonen K., Nissinen R., Helander M. Toward Comprehensive Plant Microbiome Research. Front. Ecol. Evol. 2020;8:61. doi: 10.3389/fevo.2020.00061. DOI

Vandenkoornhuyse P., Quaiser A., Duhamel M., Le Van A., Dufresne A. The Importance of the Microbiome of the Plant Holobiont. New Phytol. 2015;206:1196–1206. doi: 10.1111/nph.13312. PubMed DOI

Carvalhais L.C., Schenk P.M., Dennis P.G. Jasmonic Acid Signalling and the Plant Holobiont. Curr. Opin. Microbiol. 2017;37:42–47. doi: 10.1016/j.mib.2017.03.009. PubMed DOI

Dini-Andreote F., Raaijmakers J.M. Embracing Community Ecology in Plant Microbiome Research. Trends Plant Sci. 2018;23:467–469. doi: 10.1016/j.tplants.2018.03.013. PubMed DOI

Sánchez Márquez S., Bills G.F., Herrero N., Zabalgogeazcoa Í. Non-Systemic Fungal Endophytes of Grasses. Fungal Ecol. 2012;5:289–297. doi: 10.1016/j.funeco.2010.12.001. DOI

Trivedi P., Leach J.E., Tringe S.G., Sa T., Singh B.K. Plant–Microbiome Interactions: From Community Assembly to Plant Health. Nat. Rev. Microbiol. 2020;18:607–621. doi: 10.1038/s41579-020-0412-1. PubMed DOI

Saikkonen K., Faeth S.H., Helander M., Sullivan T.J. Fungal Endophytes: A Continuum of Interactions with Host Plants. Annu. Rev. Ecol. Syst. 1998;29:319–343. doi: 10.1146/annurev.ecolsys.29.1.319. DOI

Van Wees S.C.M., Van der Ent S., Pieterse C.M.J. Plant Immune Responses Triggered by Beneficial Microbes. Curr. Opin. Plant Biol. 2008;11:443–448. doi: 10.1016/j.pbi.2008.05.005. PubMed DOI

Yu Y., Gui Y., Li Z., Jiang C., Guo J., Niu D. Induced Systemic Resistance for Improving Plant Immunity by Beneficial Microbes. Plants. 2022;11:386. doi: 10.3390/plants11030386. PubMed DOI PMC

Ngou B.P.M., Jones J.D.G., Ding P. Plant Immune Networks. Trends Plant Sci. 2022;27:255–273. doi: 10.1016/j.tplants.2021.08.012. PubMed DOI

Hamilton C.E., Gundel P.E., Helander M., Saikkonen K. Endophytic Mediation of Reactive Oxygen Species and Antioxidant Activity in Plants: A Review. Fungal Divers. 2012;54:1–10. doi: 10.1007/s13225-012-0158-9. DOI

Eichmann R., Richards L., Schäfer P. Hormones as Go-Betweens in Plant Microbiome Assembly. Plant J. 2021;105:518–541. doi: 10.1111/tpj.15135. PubMed DOI PMC

Xu G., Yang S., Meng L., Wang B.-G. The Plant Hormone Abscisic Acid Regulates the Growth and Metabolism of Endophytic Fungus Aspergillus nidulans. Sci. Rep. 2018;8:6504. doi: 10.1038/s41598-018-24770-9. PubMed DOI PMC

Robert-Seilaniantz A., Grant M., Jones J.D.G. Hormone Crosstalk in Plant Disease and Defense: More than Just Jasmonate-Salicylate Antagonism. Annu. Rev. Phytopathol. 2011;49:317–343. doi: 10.1146/annurev-phyto-073009-114447. PubMed DOI

Foo E., Plett J.M., Lopez-Raez J.A., Reid D. Editorial: The Role of Plant Hormones in Plant-Microbe Symbioses. Front. Plant Sci. 2019;10:1391. doi: 10.3389/fpls.2019.01391. PubMed DOI PMC

Carvalhais L.C., Dennis P.G., Badri D.V., Tyson G.W., Vivanco J.M., Schenk P.M. Activation of the Jasmonic Acid Plant Defence Pathway Alters the Composition of Rhizosphere Bacterial Communities. PLoS ONE. 2013;8:e56457. doi: 10.1371/journal.pone.0056457. PubMed DOI PMC

Bürger M., Chory J. Stressed out about hormones: How plants orchestrate immunity. Cell Host Microbe. 2019;26:163–172. doi: 10.1016/j.chom.2019.07.006. PubMed DOI PMC

Fitzpatrick C.R., Salas-González I., Conway J.M., Finkel O.M., Gilbert S., Russ D., Teixeira P.J.P.L., Dangl J.L. The plant microbiome: From ecology to reductionism and beyond. Annu. Rev. Microbiol. 2020;74:81–100. doi: 10.1146/annurev-micro-022620-014327. PubMed DOI

Gupta R., Elkabetz D., Leibman-Markus M., Sayas T., Schneider A., Jami E., Kleiman M., Bar M. Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues. ISME J. 2022;16:122–137. doi: 10.1038/s41396-021-01060-3. PubMed DOI PMC

Saikkonen K., Lehtonen P., Helander M., Koricheva J., Faeth S.H. Model Systems in Ecology: Dissecting the Endophyte–Grass Literature. Trends Plant Sci. 2006;11:428–433. doi: 10.1016/j.tplants.2006.07.001. PubMed DOI

Müller C.B., Krauss J. Symbiosis between Grasses and Asexual Fungal Endophytes. Curr. Opin. Plant. Biol. 2005;8:450–456. doi: 10.1016/j.pbi.2005.05.007. PubMed DOI

Schardl C.L., Leuchtmann A., Spiering M.J. Symbioses of Grasses with Seedborne Fungal Endophytes. Annu. Rev. Plant Biol. 2004;55:315–340. doi: 10.1146/annurev.arplant.55.031903.141735. PubMed DOI

Saikkonen K., Saari S., Helander M. Defensive Mutualism between Plants and Endophytic Fungi? Fungal Divers. 2010;41:101–113. doi: 10.1007/s13225-010-0023-7. DOI

Saikkonen K., Gundel P.E., Helander M. Chemical Ecology Mediated by Fungal Endophytes in Grasses. J. Chem. Ecol. 2013;39:962–968. doi: 10.1007/s10886-013-0310-3. PubMed DOI

Bastías D.A., Alejandra Martínez-Ghersa M., Newman J.A., Card S.D., Mace W.J., Gundel P.E. The Plant Hormone Salicylic Acid Interacts with the Mechanism of Anti-Herbivory Conferred by Fungal Endophytes in Grasses. Plant Cell Environ. 2018;41:395–405. doi: 10.1111/pce.13102. PubMed DOI

Fuchs B., Krischke M., Mueller M.J., Krauss J. Herbivore-Specific Induction of Defence Metabolites in a Grass–Endophyte Association. Funct. Ecol. 2017;31:318–324. doi: 10.1111/1365-2435.12755. DOI

Laihonen M., Saikkonen K., Helander M., Vázquez de Aldana B.R., Zabalgogeazcoa I., Fuchs B. Epichloë Endophyte-Promoted Seed Pathogen Increases Host Grass Resistance Against Insect Herbivory. Front. Microbiol. 2022;12:786619. doi: 10.3389/fmicb.2021.786619. PubMed DOI PMC

Pérez L.I., Gundel P.E., Ghersa C.M., Omacini M. Family Issues: Fungal Endophyte Protects Host Grass from the Closely Related Pathogen Claviceps purpurea. Fungal Ecol. 2013;6:379–386. doi: 10.1016/j.funeco.2013.06.006. DOI

Bastías D.A., Bustos L.B., Jáuregui R., Barrera A., Acuña-Rodríguez I.S., Molina-Montenegro M.A., Gundel P.E. Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities. Front. Microbiol. 2022;12:795354. doi: 10.3389/fmicb.2021.795354. PubMed DOI PMC

König J., Guerreiro M.A., Peršoh D., Begerow D., Krauss J. Knowing Your Neighbourhood—The Effects of Epichloë Endophytes on Foliar Fungal Assemblages in Perennial Ryegrass in Dependence of Season and Land-Use Intensity. PeerJ. 2018;6:e4660. doi: 10.7717/peerj.4660. PubMed DOI PMC

Nissinen R., Helander M., Kumar M., Saikkonen K. Heritable Epichloë Symbiosis Shapes Fungal but Not Bacterial Communities of Plant Leaves. Sci. Rep. 2019;9:5253. doi: 10.1038/s41598-019-41603-5. PubMed DOI PMC

Dale J.C.M., Newman J.A. A First Draft of the Core Fungal Microbiome of Schedonorus arundinaceus with and without Its Fungal Mutualist Epichloë coenophiala. J. Fungi. 2022;8:1026. doi: 10.3390/jof8101026. PubMed DOI PMC

Zabalgogeazcoa I., Gundel P.E., Helander M., Saikkonen K. Non-Systemic Fungal Endophytes in Festuca rubra Plants Infected by Epichloë festucae in Subarctic Habitats. Fungal Divers. 2013;60:25–32. doi: 10.1007/s13225-013-0233-x. DOI

Ju Y., Zhong R., Christensen M.J., Zhang X. Effects of Epichloë gansuensis Endophyte on the Root and Rhizosphere Soil Bacteria of Achnatherum inebrians Under Different Moisture Conditions. Front. Microbiol. 2020;11:747. doi: 10.3389/fmicb.2020.00747. PubMed DOI PMC

Liu B., Ju Y., Xia C., Zhong R., Christensen M.J., Zhang X., Nan Z. The Effect of Epichloë Endophyte on Phyllosphere Microbes and Leaf Metabolites in Achnatherum inebrians. iScience. 2022;25:104144. doi: 10.1016/j.isci.2022.104144. PubMed DOI PMC

Saha D.C., Jackson M.A., Johnson-Cicalese J.M. A Rapid Staining Method for Detection of Endophytic Fungi in Turf and Forage Grasses. Phytopathology. 1988;78:237–239. doi: 10.1094/Phyto-78-237. DOI

Chelius M.K., Triplett E.W. The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L. Microb Ecol. 2001;41:252–263. doi: 10.1007/s002480000087. PubMed DOI

Lane D.J. 16S/23S rRNA sequencing. In: Stackebrandt E., Goodfellow M., editors. Nucleic Acid Techniques in Bacterial Systematics. Wiley; New York, NY, USA: 1991. pp. 115–175.

Ghyselinck J., Pfeiffer S., Heylen K., Sessitsch A., De Vos P. The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies (J Ravel, Ed.) PLoS ONE. 2013;8:e71360. doi: 10.1371/journal.pone.0071360. PubMed DOI PMC

Mäki A., Rissanen A.J., Tiirola M. A practical method for barcoding and size-trimming PCR templates for amplicon sequencing. BioTechniques. 2016;60:88–90. doi: 10.2144/000114380. PubMed DOI

Zheng D., Alm E.W., Stahl D.A., Raskin L. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 1996;62:4504–4513. doi: 10.1128/aem.62.12.4504-4513.1996. PubMed DOI PMC

Ihrmark K., Bödeker I.T.M., Cruz-Martinez K., Friberg H., Kubartova A., Schenck J., Strid Y., Stenlid J., Brandström-Durling M., Clemmensen K.E., et al. New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol. Ecol. 2012;82:666–677. doi: 10.1111/j.1574-6941.2012.01437.x. PubMed DOI

Dobrev P.I., Vankova R. Quantification of Abscisic Acid, Cytokinin, and Auxin Content in Salt-Stressed Plant Tissues. In: Shabala S., Cuin T.A., editors. Plant Salt Tolerance: Methods and Protocols. Humana Press; Totowa, NJ, USA: 2012. pp. 251–261. Methods in Molecular Biology. PubMed

Fuchs B., Laihonen M., Muola A., Saikkonen K., Dobrev P.I., Vankova R., Helander M. A Glyphosate-Based Herbicide in Soil Differentially Affects Hormonal Homeostasis and Performance of Non-Target Crop Plants. Front. Plant Sci. 2022;12:787958. doi: 10.3389/fpls.2021.787958. PubMed DOI PMC

Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl. Environ. Microbiol. 2007;73:5261–5267. doi: 10.1128/AEM.00062-07. PubMed DOI PMC

Rodriguez R.J., White J.F., Jr., Arnold A.E., Redman R.S. Fungal Endophytes: Diversity and Functional Roles. New Phytol. 2009;182:314–330. doi: 10.1111/j.1469-8137.2009.02773.x. PubMed DOI

Fuchs B., Kuhnert E., Krauss J. Contrasting Effects of Grass–Endophyte Chemotypes on a Tri-Trophic Cascade. J. Chem. Ecol. 2020;46:422–429. doi: 10.1007/s10886-020-01163-9. PubMed DOI PMC

Saikkonen K., Young C.A., Helander M., Schardl C.L. Endophytic Epichloë Species and Their Grass Hosts: From Evolution to Applications. Plant Mol. Biol. 2016;90:665–675. doi: 10.1007/s11103-015-0399-6. PubMed DOI PMC

König J., Fuchs B., Krischke M., Mueller M.J., Krauss J. Hide and Seek—Infection Rates and Alkaloid Concentrations of Epichloë festucae var. lolii in Lolium perenne along a Land-Use Gradient in Germany. Grass Forage Sci. 2018;73:510–516. doi: 10.1111/gfs.12330. DOI

Fuchs B., Krischke M., Mueller M.J., Krauss J. Plant Age and Seasonal Timing Determine Endophyte Growth and Alkaloid Biosynthesis. Fungal Ecol. 2017;29:52–58. doi: 10.1016/j.funeco.2017.06.003. DOI

Vikuk V., Fuchs B., Krischke M., Mueller M.J., Rueb S., Krauss J. Alkaloid Concentrations of Lolium perenne Infected with Epichloë festucae var. J. Fungi. 2020;6:177. doi: 10.3390/jof6030177. PubMed DOI PMC

Saari S., Lehtonen P., Helander M., Saikkonen K. High Variation in Frequency of Infection by Endophytes in Cultivars of Meadow Fescue in Finland. Grass Forage Sci. 2009;64:169–176. doi: 10.1111/j.1365-2494.2009.00680.x. DOI

Wahdan S.F.M., Buscot F., Purahong W. Future Climate Alters Pathogens-Microbiome Co-Occurrence Networks in Wheat Straw Residues during Decomposition. Proceedings. 2021;66:22. doi: 10.3390/proceedings2020066022. DOI

McGorum B.C., Chen Z., Glendinning L., Gweon H.S., Hunt L., Ivens A., Keen J.A., Pirie R.S., Taylor J., Wilkinson T., et al. Equine Grass Sickness (a Multiple Systems Neuropathy) Is Associated with Alterations in the Gastrointestinal Mycobiome. Anim. Microbiome. 2021;3:70. doi: 10.1186/s42523-021-00131-2. PubMed DOI PMC

Pérez L.I., Gundel P.E., Zabalgogeazcoa I., Omacini M. An Ecological Framework for Understanding the Roles of Epichloë Endophytes on Plant Defenses against Fungal Diseases. Fungal Biol. Rev. 2020;34:115–125. doi: 10.1016/j.fbr.2020.06.001. DOI

Card S.D., Bastías D.A., Caradus J.R. Antagonism to Plant Pathogens by Epichloë Fungal Endophytes—A Review. Plants. 2021;10:1997. doi: 10.3390/plants10101997. PubMed DOI PMC

Xia C., Li N., Zhang Y., Li C., Zhang X., Nan Z. Role of Epichloë Endophytes in Defense Responses of Cool-Season Grasses to Pathogens: A Review. Plant Dis. 2018;102:2061–2073. doi: 10.1094/PDIS-05-18-0762-FE. PubMed DOI

Vujanovic V. Tremellomycetes Yeasts in Kernel Ecological Niche: Early Indicators of Enhanced Competitiveness of Endophytic and Mycoparasitic Symbionts against Wheat Pathobiota. Plants. 2021;10:905. doi: 10.3390/plants10050905. PubMed DOI PMC

Torres M.S., White J.F., Zhang X., Hinton D.M., Bacon C.W. Endophyte-Mediated Adjustments in Host Morphology and Physiology and Effects on Host Fitness Traits in Grasses. Fungal Ecol. 2012;5:322–330. doi: 10.1016/j.funeco.2011.05.006. DOI

Kou M.-Z., Bastías D.A., Christensen M.J., Zhong R., Nan Z.-B., Zhang X.-X. The Plant Salicylic Acid Signalling Pathway Regulates the Infection of a Biotrophic Pathogen in Grasses Associated with an Epichloë Endophyte. J. Fungi. 2021;7:633. doi: 10.3390/jof7080633. PubMed DOI PMC

Benjamin G., Pandharikar G., Frendo P. Salicylic Acid in Plant Symbioses: Beyond Plant Pathogen Interactions. Biology. 2022;11:861. doi: 10.3390/biology11060861. PubMed DOI PMC