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Heterogeneity of the urban soil microbiome and associations with physicochemical soil characteristics

W. Smets,Taline Bosiers,Nona De Groof,E. Diels,Jente Dubois,Fine Gilis,Agustina Santullo Latorre,K. Wuyts

Published 2026 in Web Ecology

ABSTRACT

Abstract. Urban soil plays a fundamental role in supporting a range of ecosystem services important for both human health and urban resilience. While many ecosystem services rely on soil microbial communities, studies on urban soil microbes have remained scarce. A major complexity in understanding urban soil bacteria is the heterogeneity of soil throughout the city. In this study, we investigated the urban soil bacterial communities of street tree areas in relation to soil characteristics. We sampled soils under London plane trees at 20 street sites throughout the city of Antwerp (Belgium) and looked into the horizontal and vertical spatial variation in soil bacterial communities. Using 16S  rRNA gene amplicon sequencing, we found great bacterial diversity (over 1800 bacterial genera) and heterogeneity in the urban soil of a single city. Our findings suggest that, first and foremost, urban soil community variation is determined by the sampling site, indicating that samples grouped together in space are more similar. Additionally, but to a smaller extent, the bacterial communities are affected by soil characteristics as is the case for non-urban soils. Significant relationships were observed between composition and soil pH, moisture, density, depth, air pollution, and land use class (all p values < 0.01). We found that soils, especially those with relatively low moisture content in the city under study, showed a decline in soil bacterial biodiversity with decreasing moisture content (p value = 0.047), indicating that soil moisture content may be an important aspect of sustainable urban soil management. Furthermore, soils under trees with a smaller circumference varied greatly in bacterial community composition relative to soils under trees with a bigger circumference, which were significantly more alike in bacterial composition. This indicates that, to better predict urban resilience, factors such as soil and vegetation development should be taken into account. In conclusion, we recommend including microbial soil diversity in urban sustainable soil management and focusing future urban soil research on understanding what the desired microbial functions and compositions for urban soils are.

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