The language of fungi

Soil is an environment that is inhabited by many organisms such as plants, fungi and bacteria. Plants interact with soil microorganisms primarily through their roots. Within soil microorganisms, fungi play a dual role, being either pathogenic or beneficial to the plant. Pathogenic fungi lead to plant diseases, causing annual reductions in crop yields. Conversely, beneficial fungi can protect the plant from other pathogenic microorganisms, but also enhance plant resistance to environmental stresses such as drought and high temperatures, and can promote plant growth.

Plant-microbe interactions are complex mechanisms that are regulated by many factors. Pathogenic and beneficial fungi produce molecules called effectors that modulate the interaction between microbes and their hosts. Effectors are required to establish both pathogenic and beneficial interactions. To produce effector molecules, fungi activate effector genes (ON switch): the portion of DNA that encodes effectors is transcribed into a messenger RNA that is translated into proteins. When the gene is repressed, the effector proteins is not produced (OFF switch). 


So far, most of research has focused on the study of effectors produced by pathogenic fungi during the colonization of their plant host. However, our understanding of how beneficial fungi regulate effector gene expression during the colonization of different plant hosts and in response to other microbes remains limited.

In my research project, I study the beneficial fungi, Serendipita indica and Serendipita vermifera, that colonize roots of different plants. In particular I am interested in studying how they regulate the expression of effector genes that help the fungus to colonize different plant species and to interact with other microbes. To study the “ON/OFF” switches of effector genes I use bioinformatics. This allows me to look at all effector genes predicted in the fungal genome at once instead of individually studying each effector gene. In particular we check which fungal effector genes are activated during plant colonization and during the interaction with other microbes. We compare the expression of fungal effector genes during the interaction with plants and microbes versus the fungus grown alone to identify genes and molecular pathways involved in the interaction. This study will allow us to identify some key genes that are important for the production of effector proteins and so for the fungal beneficial colonization of different plants and for microbe-microbe interactions.

Understanding the molecular pathway involved in plant-microbe interaction is crucial to develop more sustainable agriculture practices and fungal disease control.

Planter’s Punch

Under the heading Planter’s Punch we present each month one special aspect of the CEPLAS research programme. All contributions are prepared by our early career researchers.

About the author

Concetta De Quattro is a postdoctoral researcher in the group of Prof. Alga Zuccaro at the Institute for Plant Sciences (University of Cologne). Her research focuses on studying the host-specific regulation of effector gene expression in mutualistic root endophytic fungi.

She completed her PhD in Agrobiosciences at the Scuola Superiore Sant’Anna in Pisa in Italy studying the epigenetic regulation of leaf development under drought stress in Brachypodium distachyon young leaves. Before joining CEPLAS, she worked in the group of Prof. Massimo Delledonne at the University of Verona in Italy where she was responsible for the bioinformatic section focusing on RNA-seq data analysis.

Further Reading

Mahdi, L.K., Miyauchi, S., Uhlmann, C. et al. The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. ISME J 16, 876–889 (2022)

Sarkar D, Rovenich H, Jeena G, Nizam S, Tissier A, Balcke GU, Mahdi LK, Bonkowski M, Langen G, Zuccaro A. The inconspicuous gatekeeper: endophytic Serendipita vermifera acts as extended plant protection barrier in the rhizosphere

Weiß, M., Waller, F., Zuccaro, A. and Selosse, M.-A. (2016), Sebacinales – one thousand and one interactions with land plants. New Phytol, 211: 20-40