The impact of fungal genotypes and species on the transcriptomic landscape of ectomycorrhizal symbioses

Annegret Kohler annegret.kohler@inra.fr ¹ Joske Ruytinx ^1,2 Maira de Freitas Pereira ^1,3 Laure Fauchery ¹ Shingo Miyauchi ¹ Frederic Guinet ¹ Sebastian Wittulsky ¹ Feng Zhang ¹ Alan Kuo ⁴ Vasanth R. Singan ⁴ Kerrie W. Barry ⁴ Emmanuelle Morin ¹ Claire Veneault-Fourrey ¹ Martina Peter ³ Igor Grigoriev ⁴ Francis Martin ¹

¹UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d’Excellence ARBRE, Institut National de la Recherche Agronomique, Champenoux, France
²Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
³Forest Dynamics, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
⁴Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California, USA

Ectomycorrhizal (ECM) fungi are essential for forest ecosystems. In exchange for carbohydrates, ECM fungi offer an improved mineral supply to trees. Proper functioning of ECM implies differentiation of specific tissues and communication between partners. Fungal hyphae surround root tips of host trees and penetrate between cells to form a symbiotic interface dedicated to nutrient exchange. Hyphae extending from mycorrhizal roots, the extraradicular mycelium, explore the soil for essential elements such as N and P and transfer them to the host.

The aim of this study is to understand how ECM fungi regulate the expression of their gene repertoire to communicate with their host tree, to develop specialized morphological structures and to exchange nutrients. Is the “symbiosis toolbox“ expressed by colonising ECM fungi the same within a species? How different is the set of symbiosis-related transcripts used by two phylogenetically- and ecologically-distant species, i.e. the basidomycete Laccaria bicolor and the ascomycete Cenococcum geophilum? And are the transcriptome alterations taking place in their host tree, Populus, similar?

To tackle these questions, we performed a series of RNA-seq analyses on different developmental stages of Laccaria bicolor S238N – Populus tremula x alba ECM and associated extraradicular mycelium, fruiting body and free-living mycelium grown on increasing levels of NH₄⁺, Pi or glucose. Further, changes in gene expression triggered by C. geophilum and seven L.bicolor geographical accessions during the interaction with Populus roots were compared.

We identify symbiosis-upregulated genes with a putative role in plant-fungal interaction, but we also show that ectomycorrhiza development recruits gene networks involved in hyphal aggregation and in N-P-C homeostasis. We highlight the effect of genetic variability on the regulation of symbiosis-related gene expression. These genome-wide transcript profiling allowed us to identify candidate genes for further functional analyses aiming to better understand how ECM fungi fulfill their important role in forest ecosystems.