Islands in a sea of stone: Distinct microbial soil communities in Tilia tree pits compared to paved soils

With ongoing population growth and large-scale urbanization, urban ecosystems are now the predominant habitats for humans. Yet, the biodiversity and dynamics of these ecosystems have been studied only sparsely, especially considering soil microbes. Soils in cities are disturbed and largely covered by (semi-)impervious covering, except in the highly fragmented urban greenspaces. Street trees are one of the smallest and often most confined greenspaces and can serve as a model system to better understand the urban soil microbiome. We used DNA metabarcoding to characterize bacterial and fungal communities in five urban typologies: 1) open soils around street trees (tree pits, Tilia spp.), soils underneath 2) sidewalks and 3) roadways, 4) with and 5) without these trees in five cities in the Netherlands. Bacterial alpha diversity was consistent in all typologies, while fungal richness was 91% higher with street trees nearby and was 304% higher in open tree pits, when compared to typologies without trees. Bacterial and fungal community structure were influenced by soil covering as well as presence of trees consistently throughout the cities. Trait annotation indicates that tree pits harbor more bacteria with putative nitrogen-cycling potential and nearly all putative fungal traits are overrepresented in the presence of trees, implying more functional redundancy. Inferred community assembly differed between typologies: bacterial communities were shaped by homogeneous selection which correlates with sensitivity to edaphic factors, whereas fungal assembly was dominated by dispersal limitation in covered areas, but not in the tree pits. Taken together, street trees have a distinct influence on soil microbial communities, even beneath paving.