Urbanization shapes ecological networks and energy flows in depth-stratified wetland soil micro-food web

• Urbanization decreased the abundance of soil biota in deep soils. • Urbanization changed the community composition of soil biota. • Urbanization decreased the complexity and stability of soil micro-food web ecological networks. • Deeper soils exhibited higher network complexity than surface soils. • Response of soil micro-food web to urbanization were depth-dependent. Urbanization greatly shapes wetland environment and affects its ecosystem functions. Soil micro-food web, through energy flows, plays a vital role in regulating wetland ecosystem processes and functions. However, little is known about how urbanization affects the composition and energetic structure of soil micro-food webs across different soil depths in wetlands. This knowledge gap limits our understanding of ecological processes throughout the soil profile and hinders the formulation of effective management policies for wetland conservation in urban areas. In this study, soil samples were collected from 46 wetlands along a rural-suburban-urban gradient at three soil depths (0–10, 10–20 and 20–30 cm). The abundances and community compositions of soil biota (i.e. bacteria, fungi and nematodes) were investigated using real-time quantitative PCR and Illumina Miseq sequencing, respectively. Results showed that the surface soils (0–10 cm) showed no significant changes in overall soil biota abundance, while the abundance of nematodes in subsurface layers (10–30 cm) decreased significantly along the urbanization gradient. In addition, the relative abundances of bacterivores and predators decreased, whereas fungivores and herbivores increased along the urbanization gradient. Notably, energy channel analysis showed that urbanization amplified the energy flux through the herbivorous and fungivorous pathways in surface soils but reduced it in deeper layers. Co-occurrence network analysis showed that urbanization reduced the number of network edges and nodes at each soil depth, indicating a decline in soil micro-food web complexity and stability. However, deeper soil (10–30 cm) networks exhibited unexpected higher complexity and potential resilience relative to surface soils. The main factors affecting ecological networks were plant diversity, soil structure, pH, organic carbon and ammonium nitrogen. These results indicate a distinct depth-dependent response of soil micro-food web to urbanization. Our findings highlight the essential role of deep soil biota in wetland resistance to urbanization. Future researches should employ depth-stratified approach and integrate deep soil micro-food web into biogeochemical models for accurate prediction of urban wetland ecosystem functions.