Evidence of Phylosymbiosis in the Microbiome of Conifer Roots

Phylosymbiosis describes an association between the phylogenetic relationships among host species and the composition of their microbiomes. Conifers have long evolutionary histories and extensive opportunity for coevolution to have occurred among these host plants and their microbiomes. We tested for phylosymbiosis in the root microbiomes of conifer seedlings as an indicator of coevolutionary plant–microbiome selection processes or concurrent ecological filtering. We grew 23 species of Pinaceae and Cupressaceae in a common soil for 52 weeks and assessed whether similarity in bacterial and fungal root microbiome composition was based on host phylogenetic distances using correlation and topology-based methods. Relationships among soil physicochemical properties, host traits, and microbial community composition were also assessed. Phylosymbiosis was significant in both bacterial and fungal root microbiomes. Host taxonomic relationships consistently explained more variance in microbiome composition than host traits or soil physicochemical properties. Indirect host effects on soil physicochemical properties, specifically sulfate sulfur, explained variation in microbiome composition in most models. We have evidence for phylosymbiosis in the root systems of conifer seedlings in both bacterial and fungal communities. This represents an important step toward uncovering patterns of coevolution in long-lived organisms and their associated microbes and indicates the fundamental role of phylosymbiosis in root microbiome assembly. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .