Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups


Eukaryote-associated microbiomes vary across host taxa and environments but the key factors underlying their diversity and structure in fungi are still poorly understood. Here we determined the structure of bacterial communities in fungal fruitbodies in relation to the main chemical characteristics in ectomycorrhizal (EcM) and saprotrophic (SAP) mushrooms as well as in the surrounding soil. Our analyses revealed significant differences in the structure of endofungal bacterial communities across fungal phylogenetic groups and to a lesser extent across fungal guilds. These variations could be partly ascribed to differences in fruitbody chemistry, particularly the carbon-to-nitrogen ratio and pH. Fungal fruitbodies appear to represent nutrient-rich islands that derive their microbiome largely from the underlying continuous soil environment, with a larger overlap of operational taxonomic units observed between SAP fruitbodies and the surrounding soil, compared with EcM fungi. In addition, bacterial taxa involved in the decomposition of organic material were relatively more abundant in SAP fruitbodies, whereas those involved in release of minerals were relatively more enriched in EcM fruitbodies. Such contrasts in patterns and underlying processes of the microbiome structure between SAP and EcM fungi provide further evidence that bacteria can support the functional roles of these fungi in terrestrial ecosystems.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: The relative abundance of bacterial taxa across fungal phylogenetic groups and functional guilds.
Fig. 2: Nonmetric multidimensional scaling (NMDS) ordination illustrating compositional differences in bacterial communities associated with different host taxa and functional guilds as well as their surrounding soils and different sample types.
Fig. 3: Patterns of bacterial diversity across fungal orders and functional guilds.
Fig. 4: The relationship between the chemical properties of soil and fungal fruitbodies.


  1. 1.

    de Boer W, Folman LB, Summerbell RC, Boddy L. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev. 2005;29:795–811.

  2. 2.

    Kobayashi DY, Crouch JA. Bacterial-fungal interactions: from pathogens to mutualistic endosymbionts. Annu Rev Phytopathol. 2009;47:63–82.

  3. 3.

    Li Q, Chen CH, Penttinen P, Xiong CH, Zheng L, Huang W. Microbial diversity associated with Tricholoma matsutake fruiting bodies. Microbiology 2016a;85:531–9.

  4. 4.

    Oh SY, Kim M, Eimes JA, Lim YW. Effect of fruiting body bacteria on the growth of Tricholoma matsutake and its related molds. PLoS One 2018;13:e0190948.

  5. 5.

    Frey-Klett P, Garbaye J, Tarkka M. The mycorrhiza helper bacteria revisited. N Phytologist. 2007;176:22–36.

  6. 6.

    Tarkka MT, Drigo B, Deveau A. Mycorrhizal microbiomes. Mycorrhiza. 2018;28:403–9.

  7. 7.

    Schulz-Bohm K, Tyc O, de Boer W, Peereboom N, Debets F, Zaagman N, et al. Fungus-associated bacteriome in charge of their host behavior. Fungal Genet Biol. 2017;102:38–48.

  8. 8.

    Cho YS, Kim JS, Crowley DE, Cho BG. Growth promotion of the edible fungus Pleurotus ostreatus by fuorescent pseudomonads. FEMS Microbiol Lett. 2003;218:271–6.

  9. 9.

    Noble R, Dobrovin-Pennington A, Hobbs PJ, Pederby J, Rodger A. Volatile C8 compounds and pseudomonads influence primordium formation of Agaricus bisporus. Mycologia 2009;101:583–91.

  10. 10.

    Riedlinger J, Schrey SD, Tarkka MT, Hampp R, Kapur M, Fiedler HP. Auxofuran, a novel metabolite that stimulates the growth of fly agaric, is produced by the mycorrhiza helper Bacterium Streptomyces strain AcH 505. Appl Environ Microbiol. 2006;72:3550–7.

  11. 11.

    Tauber JP, Gallegos-Monterrosa R, Kovács ÁT, Shelest E, Hoffmeister D. Dissimilar pigment regulation in Serpula lacrymans and Paxillus involutus during inter-kingdom interactions. Microbiology 2018;164:65–77.

  12. 12.

    Zhou J, Bai X, Zhao R. Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing. Sci Rep. 2017;7:15719.

  13. 13.

    Kalač P. Chemical composition and nutritional value of European species of wild growing mushrooms: a review. Food Chem. 2009;113:9–16.

  14. 14.

    Rangel-Castro JI, Danell E, Pfeffer PE. A 13 C-NMR study of exudation and storage of carbohydrates and amino acids in the ectomycorrhizal edible mushroom Cantharellus cibarius. Mycologia. 2002;94:190–9.

  15. 15.

    Warmink JA, Nazir R, van Elsas JD. Universal and species-specific bacterial ‘fungiphiles’ in the mycospheres of different basidiomycetous fungi. Environ Microbiol. 2009;11:300–12.

  16. 16.

    Guhr A, Borken W, Spohn M, Matzner E. Redistribution of soil water by a saprotrophic fungus enhances carbon mineralization. Proc Natl Acad Sci USA. 2015;112:14647–51.

  17. 17.

    Li Q, Li X, Chen C, Li S, Huang W, Xiong C, et al. Analysis of bacterial diversity and communities associated with tricholoma matsutake fruiting bodies by barcoded pyrosequencing in Sichuan Province, Southwest China. J Microbiol Biotechnol. 2016b;26:89–98.

  18. 18.

    Pent M, Hiltunen M, Põldmaa K, Furneaux B, Hildebrand F, Johannesson H, et al. Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies. Environ Microbiol. 2018;20:1641–50.

  19. 19.

    Pent M, Põldmaa K, Bahram M. Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity. Front Microbiol. 2017;8:836.

  20. 20.

    Rinta-Kanto JM, Pehkonen K, Sinkko H, Tamminen MV, Timonen S. Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms. Can J Microbiol. 2018;64:716–26.

  21. 21.

    Benucci GMN, Bonito GM. The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales. Microb Ecol. 2016;72:4–8.

  22. 22.

    Eilers KG, Lauber CL, Knight R, Fierer N. Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol Biochem. 2010;42:896–903.

  23. 23.

    Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA. 2006;103:626–31.

  24. 24.

    Ge Y, Chen C, Xu Z, Eldridge SM, Chan KY, He Y, et al. Carbon/nitrogen ratio as a major factor for predicting the effects of organic wastes on soil bacterial communities assessed by DNA-based molecular techniques. Environ Sci Pollut Res Int. 2010;17:807–15.

  25. 25.

    Alves M, Ferreira I, Dias J, Teixeira V, Martins A, Pintado M. A review on antimicrobial activity of mushroom (Basidiomycetes) extracts and isolated compounds. Planta Med. 2012;78:1707–18.

  26. 26.

    Olagbemide PT, Ogunnusi TA. Proximate analysis and chemical composition of Cortinarius species. Eur J Adv Res Biol Life Sci. 2015;3:1–9.

  27. 27.

    Sanmee R, Dell B, Lumyong P, Izumori K, Lumyong S. Nutritive value of popular wild edible mushrooms from northern Thailand. Food Chem. 2003;82:527–32.

  28. 28.

    Vieira V, Barros L, Martins A, Ferreira I. Expanding current knowledge on the chemical composition and antioxidant activity of the Genus Lactarius. Molecules. 2014;19:20650–63.

  29. 29.

    Taylor AFS, Hogbom L, Hogberg M, Lyon AJE, Nasholm T, Hogberg P. Natural 15N abundance in fruit bodies of ectomycorrhizal fungi from boreal forests. N Phytologist. 1997;136:713–20.

  30. 30.

    Trocha LK, Rudy E, Chen W, Dabert M, Eissenstat DM. Linking the respiration of fungal sporocarps with their nitrogen concentration: variation among species, tissues and guilds. Funct Ecol. 2016;30:1756–68.

  31. 31.

    Kranabetter JM, Harman-Denhoed R, Hawkins BJ. Saprotrophic and ectomycorrhizal fungal sporocarp stoichiometry (C: N: P) across temperate rainforests as evidence of shared nutrient constraints among symbionts. N Phytologist. 2019;221:482–92.

  32. 32.

    Alam N, Amin R, Khan A, Ara I, Shim MJ, Lee MW, et al. Nutritional analysis of cultivated mushrooms in Bangladesh—Pleurotus ostreatus, Pleurotus sajor-caju, Pleurotus florida and Calocybe indica. Mycobiology. 2008;36:228–32.

  33. 33.

    Rudawska M, Leski T. Macro- and microelement contents in fruiting bodies of wild mushrooms from the Notecka forest in west-central Poland. Food Chem. 2005;92:499–506.

  34. 34.

    Hobbie EA, Weber NS, Trappe JM. Mycorrhizal vs saprotrophic status of fungi: the isotopic evidence. N Phytologist. 2001;150:601–10.

  35. 35.

    Vogt KA, Edmonds RL, Grier CC. Biomass and nutrient concentrations of sporocarps produced by mycorrhizal and decomposer fungi in Abies amabilis stands. Oecologia. 1981;50:170–5.

  36. 36.

    Landeweert R, Hoffland E, Finlay RD, Kuyper TW, van Breemen N. Linking plants to rocks: ectomycorrhizal fungi mobilize nutrients from minerals. TRENDS Ecol Evolution. 2001;16:248–54.

  37. 37.

    Liu Y, Sun Q, Li J, Lian B. Bacterial diversity among the fruit bodies of ectomycorrhizal and saprophytic fungi and their corresponding hyphosphere soils. Sci Rep. 2018;8:11672.

  38. 38.

    Konuk M, Afyon A, Yağiz D. Chemical composition of some naturally growing and edible mushrooms. Pak J Bot. 2006;38:799–804.

  39. 39.

    Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560:233–7.

  40. 40.

    Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010;4:1340–51.

  41. 41.

    Antony-Babu S, Deveau A, Van Nostrand JD, Zhou J, Le Tacon F, Robin C, et al. Black truffle - associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles: tuber melanosporum-associated bacterial communities. Environ Microbiol. 2014;16:2831–47.

  42. 42.

    Hildebrand F, Tadeo R, Voigt A, Bork P, Raes J. LotuS: an efficient and user- friendly OTU processing pipeline. Microbiome. 2014;2:30.

  43. 43.

    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

  44. 44.

    Tedersoo L, Sánchez-Ramírez S, Kõljalg U, Bahram M, Döring M, Schigel D, et al. High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Diversity. 2018;90:135–59.

  45. 45.

    Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L. Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environ Microbiol Rep. 2019;11:487–94.

  46. 46.

    Põldmaa K, Jürgenstein S, Bahram M, Teder T, Kurina O. Host diversity and trophic status as determinants of species richness and community composition of fungus gnats. Basic Appl Ecol. 2015;16:46–53.

  47. 47.

    Hoppe B, Krüger D, Kahl T, Arnstadt T, Buscot F, Bauhus J, et al. A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies. Sci Rep. 2015;5:9456.

  48. 48.

    Zhang X, Xu S, Li C, Zhao L, Feng H, Yue G, et al. The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau. Res Microbiol. 2014;165:128–39.

  49. 49.

    Johnston SR, Boddy L, Weightman AJ. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol. 2016;92:fiw179.

  50. 50.

    Ruthes AC, Smiderle FR, Iacomini M. Mushroom heteropolysaccharides: a review on their sources, structure and biological effects. Carbohydr Polym 2016;136:358–75.

  51. 51.

    Boersma FGH, Warmink JA, Andreote FA, van Elsas JD. Selection of sphingomonadaceae at the base of laccaria proxima and russula exalbicans fruiting bodies. Appl Environ Microbiol. 2009;75:1979–89.

  52. 52.

    de Carvalho MP, Türck P, Abraham WR. Secondary metabolites control the associated bacterial communities of saprophytic basidiomycotina fungi. Microbes Environ. 2015;30:196–8.

  53. 53.

    Boersma FGH, Otten R, Warmink JA, Nazir R, van Elsas JD. Selection of Variovorax paradoxus-like bacteria in the mycosphere and the role of fungal-released compounds. Soil Biol Biochem. 2010;42:2137–45.

  54. 54.

    Taylor AFS, Fransson PM, Högberg P, Högberg MN, Plamboeck AH. Species level patterns in 13C and 15N abundance of ectomycorrhizal and saprotrophic fungal sporocarps. N Phytologist. 2003;159:757–74.

  55. 55.

    Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, et al. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev. 2020;95:409–33.

  56. 56.

    Danell E, Alström S, Ternström A. Pseudomonas fluorescens in association with fruit bodies of the ectomycorrhizal mushroom Cantharellus cibarius. Mycological Res. 1993;97:1148–52.

  57. 57.

    Xing R, Yan H, Gao Q, Zhang F, Wang J, Chen S. Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria. J Basic Microbiol. 2018;58:554–63.

  58. 58.

    Nazir R, Warmink JA, Boersma H, van Elsas JD. Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats. FEMS Microbiol Ecol. 2010b;71:169–85.

  59. 59.

    Ingelög T, Nohrstedt HÖ. Ammonia formation and soil pH increase caused by decomposing fruitbodies of macrofungi. Oecologia. 1993;93:449–51.

  60. 60.

    Nazir R, Tazetdinova DI, van Elsas JD. Burkholderia terrae BS001 migrates proficiently with diverse fungal hosts through soil and provides protection from antifungal agents. Front Microbiol. 2014;5:598.

  61. 61.

    Warmink JA, Nazir R, Corten B, van Elsas JD. Hitchhikers on the fungal highway: The helper effect for bacterial migration via fungal hyphae. Soil Biol Biochem. 2011;43:760–5.

  62. 62.

    Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.

  63. 63.

    Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 2011;43:1450–5.

  64. 64.

    Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, et al. Rapid transfer of plant photosynthates to soil bacteria via ectomycorrhizal hyphae and its interaction with nitrogen availability. Front Microbiol. 2019;10:168.

  65. 65.

    Ghodsalavi B, Svenningsen NB, Hao X, Olsson S, Nicolaisen MH, Al-Soud WA, et al. A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil. PLoS One. 2017;12:e0187116.

  66. 66.

    Haq IU, Calixto RO, da R, Yang P, dos Santos GMP, Barreto-Bergter E, et al. Chemotaxis and adherence to fungal surfaces are key components of the behavioral response of Burkholderia terrae BS001 to two selected soil fungi. FEMS Microbiol Ecol. 2016;92:fiw164.

  67. 67.

    Shin D, Lee Y, Park J, Moon HS, Hyun SP. Soil microbial community responses to acid exposure and neutralization treatment. J Environ Manag. 2017;204:383–93.

  68. 68.

    Nazir R, Boersma FGH, Warmink JA, van Elsas JD. Lyophyllum sp. strain Karsten alleviates pH pressure in acid soil and enhances the survival of Variovorax paradoxus HB44 and other bacteria in the mycosphere. Soil Biol Biochem. 2010a;42:2146–52.

  69. 69.

    Izumi H, Anderson IC, Alexander IJ, Killham K, Moore ERB. Diversity and expression of nitrogenase genes (nifH) from ectomycorrhizas of Corsican pine (Pinus nigra). Environ Microbiol. 2006;8:2224–30.

  70. 70.

    Jayasinghearachchi HS, Seneviratne G. Can mushrooms fix atmospheric nitrogen? J Biosci. 2004;29:293–6.

  71. 71.

    Barbieri E, Ceccaroli P, Saltarelli R, Guidi C, Potenza L, Basaglia M, et al. New evidence for nitrogen fixation within the Italian white truffle Tuber magnatum. Fungal Biology. 2010;114:936–42.

  72. 72.

    Hoppe B, Kahl T, Karasch P, Wubet T, Bauhaus J, Buscot F, et al. Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi. PLos One. 2014;9:e88141.

  73. 73.

    Pavić A, Stanković S, Saljnikov E, Krüger D, Buscot F, Tarkka M, et al. Actinobacteria may influence white truffle (Tuber magnatum Pico) nutrition, ascocarp degradation and interactions with other soil fungi. Fungal Ecol. 2013;6:527–38.

  74. 74.

    Calvaruso C, Turpault MP, Leclerc E, Frey-Klett P. Impact of ectomycorrhizosphere on the functional diversity of soil bacterial and fungal communities from a forest stand in relation to nutrient mobilization processes. Microb Ecol. 2007;54:567–77.

  75. 75.

    Fontaine L, Thiffault N, Paré D, Fortin JA, Piché Y. Phosphate-solubilizing bacteria isolated from ectomycorrhizal mycelium of Picea glauca are highly efficient at fluorapatite weathering. Botany. 2016;94:1183–93.

  76. 76.

    Rodríguez H, Fraga R. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv. 1999;17:319–39.

  77. 77.

    Hervé V, Le Roux X, Uroz S, Gelhaye E, Frey-Klett P. Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay. Environ Microbiol. 2014;16:2238–52.

  78. 78.

    Sun H, Terhonen E, Kasanen R, Asiegbu FO. Diversity and community structure of primary wood-inhabiting bacteria in boreal forest. Geomicrobiol J. 2014;31:315–24.

  79. 79.

    López-Mondéjar R, Brabcová V, Štursová M, Davidová A, Jansa J, Cajthaml T, et al. Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling. ISME J. 2018;12:1768–78.

  80. 80.

    Stopnisek N, Zühlke D, Carlier A, Barberán A, Fierer N, Becher D, et al. Molecular mechanisms underlying the close association between soil Burkholderia and fungi. ISME J. 2016;10:253–64.

  81. 81.

    Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol. 2013;64:807–38.

  82. 82.

    Timonen S, Hurek T. Characterization of culturable bacterial populations associating with Pinus sylvestris —Suillus bovinus mycorrhizospheres. Can J Microbiol. 2006;52:769–78.

  83. 83.

    Uroz S, Oger P, Morin E, Frey-Klett P. Distinct ectomycorrhizospheres share similar bacterial communities as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol. 2012;78:3020–4.

Download references


We thank Leho Tedersoo and three anonymous reviewers for constructive comments on the paper. We also thank Rasmus Puusepp for laboratory assistance. Funding was provided by Estonian Research Council grants (PUT1317 and IUT20-30), Swedish Research Council (Vetenskapsrådet, grant no: 2017‐05019) and the European Union through the European Regional Development Fund (the Center of Excellence EcolChange).

Author information




MP, MB, and KP contributed to study design and writing; MP performed molecular and data analysis.

Corresponding authors

Correspondence to Mari Pent or Mohammad Bahram.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pent, M., Bahram, M. & Põldmaa, K. Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups. ISME J (2020).

Download citation