Seasonality and longer-term development shape temporal patterns in the Populus microbiome

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet our knowledge of temporal dynamics in the microbiome of long-lived plants, such as trees, remains limited. We hypothesized temporal dynamics in tree microbiomes arise from seasonal fluctuations and longer-term changes that arise due to host development or microbial succession. To test this hypothesis, we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus species grown in a common garden over four seasons across two consecutive years. Microbial community composition differed among seasons, and seasonal patterns differed between years in all plant-associated habitats. Microbial community dissimilarity was also positively correlated with time, reflecting compositional shifts due to succession or host development. Temporal dynamics in rhizosphere communities were driven by ectomycorrhizal fungi and ammonia-oxidizing archaea, with potential implications for plant nutrient acquisition. Temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes tracking host development or due to succession, which together generate unique seasonal patterns each year. Future studies of tree microbiomes must account for these background temporal dynamics when assessing spatial patterns and temporal responses to environmental change.