Argiroff et al. 2024 mSystems

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

William A. ArgiroffAlyssa A. CarrellDawn M. KlingemanNicholas C. DoveWellington MucheroAllison M. VeachToni WahlSteven J. LebreuxAmber B. WebbKellie PeytonChristopher W. Schadt, and Melissa A. Cregger
February 29, 2024, mSystems; DOI: 10.1128/msystems.00886-23


Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.


Argiroff WA, Carrell AA, Klingeman DM, Dove NC, Muchero W, Veach AM, Wahl T, Lebreux SJ, Webb AB, Peyton K, Schadt CW, Cregger MA. 0. Seasonality and longer-term development generate temporal dynamics in the Populus microbiome. mSystems 0:e00886-23. DOI:10.1128/msystems.00886-23