Affiliation:
1. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen 518120 , China
2. Department of Agricultural Biology, Colorado State University , Fort Collins, CO 80523 , USA
3. Kunpeng Institute of Modern Agriculture at Foshan , Foshan 528225 , China
Abstract
Abstract
Phylosymbiosis, the congruence of microbiome composition with host phylogeny, is a valuable framework for investigating plant–microbe associations and their evolutionary ecology. This review assesses the prevalence of phylosymbiosis across the plant kingdom, elucidates the fundamental ecological and evolutionary processes contributing to its occurrence based on previous research and explores commonly used methods for identifying phylosymbiosis. We find that the presence of phylosymbiosis may be influenced by both phylogenetic distance and the taxonomic level at which host plants are examined, with the strength of associations potentially decreasing as the taxonomic scale becomes finer. Notably, the endophytic microbiome exhibits a stronger phylosymbiosis signal compared with the epiphytic or rhizosphere-associated microbiomes. Microorganisms such as fungi and bacteria can yield highly variable evidence for phylosymbiosis due to differences in colonization, transmission or functional characteristics. We also outline how the four community assembly processes (dispersal, selection, diversification and drift) contribute to the establishment and maintenance of host–microbe phylosymbiosis. Furthermore, we highlight the diversity of methods employed to detect phylosymbiosis, which involves three key processes: constructing host phylogenies, assessing microbial data and statistically evaluating the correlation between host phylogeny and microbial composition. Remarkably different methodologies across studies make comparisons between findings challenging. To advance our understanding, future research is expected to explore phylosymbiosis at lower taxonomic levels and investigate different microbial communities coexisting synergistically within the same host. Understanding the relative importance of community assembly processes in driving phylosymbiosis will be critical for gaining deeper insights into the ecology and evolution of host–microbe interactions.
Funder
National Key Research and Development Program of China
National Natural Science Foundation of China
Shenzhen Fundamental Research Program
Shenzhen Science and Technology Program
Key Project at Central Government Level
Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District
China Postdoctoral Science Foundation
Basic and Applied Basic Research Fund of Guangdong
Science, Technology, and Innovation Commission of Shenzhen Municipality of China
Sichuan Science and Technology Program
Publisher
Oxford University Press (OUP)