, Volume 28, Issue 5–6, pp 451–463 | Cite as

Plant host habitat and root exudates shape fungal diversity

  • Mylène Hugoni
  • Patricia Luis
  • Julien Guyonnet
  • Feth el Zahar HaicharEmail author
Original Article


The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.


Plant nutrient-use strategies Rhizosphere Root exudates Active fungal communities Microbiota Stable-isotope probing 



We thank CNRS EC2CO research programs for providing funding to the project “RhizoDen” and “CaIMan.” We thank the “Serre et chambres climatiques” platform (Université Lyon1, FR41) for plant growing and Elise Lacroix for her help. We thank M. Guegan and A. Dubost for their help on statistical and bioinformatic analyses.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Mylène Hugoni
    • 1
  • Patricia Luis
    • 1
  • Julien Guyonnet
    • 1
  • Feth el Zahar Haichar
    • 1
    Email author
  1. 1.CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418Université Lyon 1Villeurbanne CedexFrance

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