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

Abstract

BackgroundWithin 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.MethodsWe 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 Agrostis stolonifera 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 K statistic.ResultsFungal 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 ‘mean expression ratio’ displayed significant but divergent phylogenetic signals between fungal phyla.DiscussionThese 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.

Past spatial structure of plant communities determines arbuscular mycorrhizal fungal community assembly

“…The roots were separated from the rest of the plant, washed with a stringent detergent solution (Triton X100, 1% V/V), then rinsed with ultra‐pure water before storage at −80°C and subsequent analysis of the root endosphere compartment (e.g. Lê Van et al, ).…”

“…The sequence production and trimming strategy have been published previously (e.g. Ben Maamar et al, ; Ciobanu et al, ; Lê Van et al, ). Sequences shorter than 300 bp in length, with homopolymers longer than 8 bp or with ambiguous nucleotides, were removed from the dataset.…”

“…The technical replicates were sequenced to filter sequencing errors. Only full length 100% identical sequences found in both technical replicates were kept in the dataset (Ciobanu et al, ; Lê Van et al, ). In addition to this first stringent filtering process, each sample was subjected to a search for chimeric sequences with the chimera.uchime command in MOTHUR (Kozich, Westcott, Baxter, Highlander, & Schloss, ).…”

The influence of host‐plant connectivity on fungal assemblages in the root microbiota of Brachypodium pinnatum

“…Healthy root fragments were selected for being representative of the different parts of the rooting system. After this cleaning step, only root‐adhering epiphytic and endophytic microorganisms were still present with the roots (Lê Van et al ). Cleaned roots of each sample were ground to powder under liquid nitrogen using a pestle and mortar.…”

“…Understanding the assembly rules of plant microbiota is a central question of plant biology because of the tremendous ecological functions provided by symbiotic microorganisms to plants (Davison et al , Lekberg and Waller ). Next‐generation sequencing approaches have demonstrated that the microbiota of plants is composed of a large diversity of microorganisms, including bacteria (Lundberg et al , Bulgarelli et al ), archaea (Edwards et al , Vannier et al ), and fungi (Vandenkoornhuyse et al , Coleman‐Derr et al , Lê Van et al ). An increasing number of studies suggest that the identity of the host‐plant species (Vandenkoornhuyse et al , Martinez‐Garcia and Pugnaire , Yang et al ) and to some extent, its genotype (Bodenhausen et al , Edwards et al ) condition the associated microbiota through the preferential recruitment of particular fungi.…”