Biodiversity 3 min

Differentiating friends from foes in the fungal root microbiome

PRESS RELEASE - A collaborative project between researchers from the Max Planck Institute for Plant Breeding Research (MPIPZ), the French National Institute for Agriculture, Food and Environment (INRAE) and the Joint Genome Institute (JGI) has shed light on the fungal genetic determinants that explain why some fungi from the root microbiome can colonize roots and cause disease more efficiently than others.

Published on 14 December 2021

illustration Differentiating friends from foes in the fungal root microbiome
© S. Hacquard / MPIPZ

Complex microbial communities inhabit plants and modulate their development. Roots especially, host a wide diversity of micro-organisms – including bacteria and fungi – that directly influence plant health. Researchers from the MPIPZ previously discovered that these fungi are important members of the root microbiome that can promote plant growth, but only when they are kept in check by the combined action of the host innate immune system and root-inhabiting bacteria.

In a new study published in Nature Communications, The authors provide novel insights into how these fungi colonize roots, why many of them are potentially harmful and what differentiates beneficial from pathogenic fungi in the root mycobiome (i.e. the fungal component of the root microbiota). 


To address these questions, the researchers focused on the model plant Arabidopsis thaliana (Thale Cress), which cannot rely on beneficial mycorrhizal fungi to acquire nutrients since it does not harbour the genetic network needed to establish a functional symbiosis with these fungi. A. thaliana likely relies on other fungi to compensate the loss of mycorrhizal partners and to survive in nature. To better characterize these root-colonizing fungi in their broad diversity, researchers have isolated a variety of fungal strains from the roots of healthy plants across Europe and selected 41 that are representative of the root mycobiome of A.thaliana.


Photograph of 41 fungal isolates representative of the A. thaliana root mycobiome
© S. Hacquard / MPIPZ

In collaboration with INRAE Grand-Est Nancy research centre (France) and the Joint Genome Institute (USA), the genomes of these fungi were sequenced and compared to other fungi that were previously described as saprotrophic, pathogenic, endophytic or mycorrhizal. Surprisingly, the scientists found that most root mycobiota membersisolated from the roots of healthy plants derived from ancestors that were likely pathogenic, and have retained a battery of genes that were previously shown to be lost in genomes of beneficial mycorrhizal fungi. These genes encode effector-like small secreted proteins that could modulate the host immune system, and enzymes that can degrade a large number of plant cell-wall constituents including pectin, cellulose and hemicellulose. These findings raised the possibility that many of these fungi may have retained at least part of their ancestral pathogenic capabilities.


To test this hypothesis, A. thaliana plants were grown in a closed system in the absence of any microorganism, or re-colonized with each of the selected 41 fungal isolates. This experiment identified a wide diversity of fungal effects on plant growth, ranging from highly detrimental to beneficial. Notably, the authors observed that the strains most harmful to the plant were colonizing roots much more aggressively than those having beneficial effects. Furthermore, the fungi most often detected in the roots of A. thaliana in nature were also the ones showing harmful effects on their host in mono-association experiments. Previous work from the group of Stéphane Hacquard had suggested that the mycobiome of A. thaliana can become detrimental when the host immune system and the root-inhabiting bacteria do not tightly control the proliferation of these fungi. These new results show that in nature, fungi with a high root-colonizing potential have a high pathogenic potential, explaining the need to control their growth. 


Using a combination of association methods, including machine-learning models, the authors then associated the fungal effects on A. thaliana growth to genome compositions, and successfully identified a candidate gene family that could explain the detrimental effects and root colonization abilities. This family (pectate lyase PL1_7) encodes enzymes that degrade pectin, an essential constituent of plant cell walls, which is especially abundant in the roots of dicotyledonous plants such as A. thaliana. To validate its involvement in fungal detrimental activity, a gene from this family was introduced into the genome of a fungal species that naturally does not harbour it. The resulting mutant strain was able to colonize roots more aggressively than the original isolate and this increase in fungal load in roots was associated with a penalty on plant performance.

These results indicate that repertoires of plant cell-wall degrading enzymes in fungal genomes are key genetic determinants driving access to the root endosphere and explaining why robust root colonizers can potentially become harmful if they degrade roots too aggressively.

This study highlighted that the mycobiome of healthy plants in nature is composed of both friends and foes. This finding offers a new perspective on the effects of fungi on plant health, and possibly opens the door to new exciting considerations and developments for agriculture. Taking advantage of these results could potentially provide a rationale on how to design and optimize synthetic fungal communities to obtain beneficial outcomes on plant performance.



Mesny, F., Miyauchi, S., Thiergart, T. et al. Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun 12, 7227 (2021).

INRAE press office

Scientific contact

Francis Martin Tree-Microorganism Interactions Joint Research Unit (INRAE / Université de Lorraine)



Learn more


Symbioses between plants, fungi and bacteria: a new look at these ancestral alliances

PRESS RELEASE - A review appearing in the online edition of Science (26th May 2017), authored by three INRA researchers (associated with the Universities of Lorraine and Toulouse and the CNRS), starts with an overview of the rich evolutionary history of the principal mycorrhizal and nitrogen-fixing plant symbioses. This is followed by a discussion of key conserved features which characterize these mutually beneficial plant-microbe associations, including the molecular and cellular mechanisms which are involved in the successful colonization of plant roots by the respective fungal and bacterial symbionts. A deeper understanding of these mechanisms and their modulation by different factors (plant genotype, soil type etc) will be essential for facilitating the future use of the entire plant microbiota in developing sustainable agriculture practices.

19 March 2020


Large-scale genomics sheds light on the evolutionary history of mutualistic forest-dwelling fungi

PRESS RELEASE - Mutualistic fungi, known as mycorrhizae, play a major role in terrestrial ecosystems because they help plants acquire nutrients. However, how these fungi became symbionts was a mystery until now. Answers to this question have been provided by an international research consortium coordinated by INRAE and the Joint Genome Institute (US Department of Energy) to which the University of Lorraine and CNRS also contributed. The group analysed the genomes of 135 species of forest-dwelling fungi. The study's results clarify how fungi living as decomposers became plant symbionts over the course of evolution. These findings were published on October 12 in Nature Communications.

12 October 2020


A plant-fungi partnership at the origin of terrestrial vegetation

PRESS RELEASE - 450 million years ago, the first plants left aquatic life. Researchers from the CNRS and the Université de Toulouse III - Paul Sabatier, in collaboration with INRAE, have succeeded in demonstrating that this colonisation of land by plants was made possible by a partnership between plants and fungi. Validating this 40-year-old hypothesis allows us to understand a stage that was crucial to the development of life on Earth. The study is published in Science on 21 May 2021.

20 May 2021