Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities

Lara Danielsen (1) , Andrea Thürmer (2) , Peter Meinicke (3) , Marc Buée (4) , Emmanuelle Morin (4) , Francis Martin (4) , Gilles Pilate (5) , Rolf Daniel (2) , Andrea Polle (1) , Marlis Reich (1, 6)

1 Department of Forest Botany and Tree Physiology, Büsgen-Institute
2 Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory
3 Department of Bioinformatics
4 IAM - Interactions Arbres-Microorganismes
5 AGPF - Unité de recherche Amélioration, Génétique et Physiologie Forestières
6 NW2/Plant Physiology

Fungal communities play a key role in ecosystem functioning. However, only little is known about their composition in plant roots and the soil of biomass plantations. The goal of this study was to analyze fungal biodiversity in their belowground habitats and to gain information on the strategies by which ectomycorrhizal (ECM) fungi form colonies. In a 2-year-old plantation, fungal communities in the soil and roots of three different poplar genotypes (Populus × canescens, wildtype and two transgenic lines with suppressed cinnamyl alcohol dehydrogenase activity) were analyzed by 454 pyrosequencing targeting the rDNA internal transcribed spacer 1 (ITS) region. The results were compared with the dynamics of the root-associated ECM community studied by morphotyping/Sanger sequencing in two subsequent years. Fungal species and family richness in the soil were surprisingly high in this simple plantation ecosystem, with 5944 operational taxonomic units (OTUs) and 186 described fungal families. These findings indicate the importance that fungal species are already available for colonization of plant roots (2399 OTUs and 115 families). The transgenic modification of poplar plants had no influence on fungal root or soil communities. Fungal families and OTUs were more evenly distributed in the soil than in roots, probably as a result of soil plowing before the establishment of the plantation. Saprophytic, pathogenic, and endophytic fungi were the dominating groups in soil, whereas ECMs were dominant in roots (87%). Arbuscular mycorrhizal diversity was higher in soil than in roots. Species richness of the root-associated ECM community, which was low compared with ECM fungi detected by 454 analyses, increased after 1 year. This increase was mainly caused by ECM fungal species already traced in the preceding year in roots. This result supports the priority concept that ECMs present on roots have a competitive advantage over soil-localized ECM fungi.

Mots clés: transgenic poplar; community ecology; environmental DNA; fungus; genetically modified organism; metagenomics; microbial biology; fungal community; fungal biodiversity; fungal biota

Domaines: Sciences du Vivant [q-bio]

Lara Danielsen, Andrea Thürmer, Peter Meinicke, Marc Buée, Emmanuelle Morin, et al.. Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities. Ecology and Evolution, 2012, 2 (8), pp.1935-1948. ⟨10.1002/ece3.305⟩. ⟨hal-01267977⟩