Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

• Published in: PeerJ (San Francisco, CA) Vol. 5; p. e3454
• Main Authors: Lê Van, Amandine, Quaiser, Achim, Duhamel, Marie, Michon-Coudouel, Sophie, Dufresne, Alexis, Vandenkoornhuyse, Philippe
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 08.06.2017; PeerJ, Inc; PeerJ; PeerJ Inc
• Subjects: Agrostis stolonifera; Analysis; Biodiversity; Biodiversity and Ecology; Biology; Biomes; Deoxyribonucleic acid; DNA; Ecology; Ecophylogeny; Endophytes; Environmental aspects; Environmental Sciences; Fungi; Genetic aspects; Host plants; Mean expression ratio; Microorganisms; Molecular Biology; Mycology; Phylogenetic signal; Phylogenetics; Phylogeny; Plant communities; Plant Science; Ribonucleic acid; RNA; Root fungal microbiome; Roots; SSU rRNA amplicons; Mean expression ratio; SSU rRNA amplicons; Ecophylogeny; Phylogenetic signal; Agrostis stolonifera; Plant microbiota; Phylogenetic structure; Root fungal microbiome
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.3454

Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce. We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an population. The normalized RNA/DNA ratio, designated the 'mean expression ratio', was used as a functional trait proxy. The link between this trait and phylogenetic relatedness was measured using the Blomberg's statistic. Fungal communities were highly diverse. Only ∼1.5% of the 635 OTUs detected were shared by all individuals, however these accounted for 33% of the sequence number. The endophytic fungal communities in plant roots exhibit phylogenetic clustering that can be explained by a plant host effect acting as environmental filter. The ' displayed significant but divergent phylogenetic signals between fungal phyla. These results suggest that environmental filtering by the host plant favours the co-existence of related and similar OTUs within the Basidiomycota community assembly, whereas the Ascomycota and Glomeromycota communities seem to be impacted by competitive interactions which promote the co-existence of phylogenetically related but ecologically dissimilar OTUs.