Population density is a selective driver of urban soil microbiomes: evidence from bacteria, fungi and protozoan communities in a regional city

Abstract

Urbanisation is widely recognised as a major driver of environmental change, yet its impacts on soil microbiomes remain poorly understood, particularly outside megacities and beyond bacterial taxa. Population density is frequently used as a proxy for urban intensity, but its relevance across different microbial kingdoms and urban contexts is unclear. Here, we investigated how soil microbial communities vary across population density bands in the regional, temperate city of Hobart, Australia. Using a multi-kingdom metabarcoding approach, we analysed bacterial, fungal, and protozoan communities from soils collected in urban green spaces along a population density gradient. Bacterial alpha-diversity differed significantly across population density bands, exhibiting an inverse U-shaped relationship, with the highest diversity at green spaces in intermediate population density areas. In contrast, fungal and protozoan alpha-diversity did not vary with population density. Community composition (beta-diversity) did not differ consistently across density bands for any microbial group, and variation in soil physicochemical properties explained more community variation than population density alone. These results indicate that population density is a selective, rather than universal, driver of urban soil microbiomes and that responses to urbanisation differ markedly among microbial kingdoms. Our findings highlight important limitations of using population density as a sole indicator of urban impact and challenge the generalisability of conclusions drawn from bacteria-focused studies in large cities. By demonstrating kingdom-specific and context-dependent responses in a regional city, this study underscores the need for multi-kingdom, multi-scale approaches to better understand how urbanisation shapes soil microbiomes and their potential implications for urban ecosystem functioning and human health.