Diversity and assembly of the microbiome of a leguminous plant along an urbanization gradient

Abstract

Interactions between plants and bacterial communities are essential for host physiology and broader ecosystem functioning, but plant-microbiome interactions can be disrupted by environmental change like urbanization. Here, we evaluated how urbanization affected the diversity and assembly of soil and white clover (Trifolium repens) microbiome communities. We sampled 35 populations of white clover and associated roots and soil along an urbanization gradient. Soil alpha diversity was greater at the urban and rural limits of the gradient and lower in suburban habitats, while root alpha diversity was not influenced by urbanization. Root and soil bacterial communities had distinct compositions, with greater beta diversity for root compared to soil microbiomes. We found that urbanization directly and indirectly affected soil microbiome assembly, particularly through soil carbon. In contrast, root microbiome assembly was not linked to urbanization, which suggested that the host plant acted as an additional filter on microbiome assembly independent of urbanization. We also found that key pathogenic bacteria like Legionella and Clostridium varied in abundance with urbanization, which has implications for human health. Together, our study underscores the importance of examining how urban-driven environmental change alters the ecology and function of soil and root microbiomes.