Traversing the canopy: phenology-driven changes and within-canopy transport shape the phyllosphere microbiome in a temperate floodplain hardwood forest

Phyllosphere microbiomes are subject to microbial import from various sources and undergo substantial changes during phenological changes of plants. However, especially for forest canopies, these processes are still poorly understood. We disentangled the controls of phenology-driven changes versus tree species identity on the phyllosphere microbiome in a temperate floodplain forest and assessed the role of transport processes in shaping distribution patterns within the canopy. Leveraging the infrastructure of the Leipzig canopy crane (Central Germany), we followed bacterial community composition and rainwater-mediated bacterial transport for oak ( Quercus robur L.), ash ( Fraxinus excelsior L.) and linden ( Tilia cordata MILL) across early (May), mid (July) and late (October) phenological stages. These stages explained 23% of phyllosphere bacterial community variation, followed by tree species identity (13%) and canopy position (2%). Phyllosphere bacterial community assembly was mostly driven by dispersal limitation at the early phenological stage while communities became more homogeneous and functionally redundant during mid and late phenological stages, along with a strong decline of plant pathogens and increasing potential for microbially mediated biocontrol mechanisms. Throughfall-mediated transport of bacteria increased substantially from March to May, indicating the strong influence of wash-off effects from the emerging foliage. Our findings demonstrate that in temperate forests, phenology-driven effects on the phyllosphere microbiome exceed tree species’ specific effects. Extent and selectivity of throughfall-mediated mobilization of microbes adds another layer of complexity to the spatial heterogeneity of microbial communities in tree crowns.