Seasonal forcing and substrate legacy shape the biogeochemical organization of rooftop vs. ground-level urban gardens

Abstract

Urban agriculture is expanding rapidly in densely populated cities, yet the ecological functioning of rooftop soils relative to ground-level gardens remains poorly understood. We evaluated soil carbon and nitrogen cycling, microbial activity, and broad microbial community structure in five urban gardens in Mexico City (three ground-level, GL, and two rooftop, RT), sampled in the dry and wet seasons, established either on ground-level soils or on rooftop substrates. We hypothesized that shared management would promote functional convergence across systems, while differences in substrate origin would maintain distinct microbial communities. Univariate analyses revealed few differences between garden types in microbial biomass, enzyme activities, and several soil chemical properties. However, multivariate analyses showed that seasonality and its interaction with establishment condition—rather than garden type per se—were the dominant factors structuring soil biogeochemical space. In design-aware PERMANOVA, season (R² = 0.13, p<0.001) and the condition × season interaction (R² = 0.07, p=0.007) were significant, whereas establishment condition tested at the garden level was not (R² = 0.16, p=0.70), indicating partial functional convergence rather than full equivalence. Seasonality strongly reorganized soil functioning: moisture, pH, ammonium, and enzyme activities exhibited pronounced seasonal shifts, and redundancy analysis (adjusted R² = 0.21, p=0.002) identified moisture (p=0.002) and pH (p=0.021) as the dominant drivers of microbial functional patterns. Microbial biomass pools were comparatively stable, whereas process-related traits and fungal guild composition were more responsive. Whole-cell fatty acid profiles obtained in the wet season showed similar total bacterial and fungal biomass across systems and no overall difference in guild composition (PERMANOVA p=0.50); nevertheless, the arbuscular mycorrhizal-to-saprotrophic fungi ratio was lower in rooftop gardens (p=0.026), a guild-specific signal consistent with persistent soil legacy effects. Overall, rooftop gardens sustained much of the microbial and biogeochemical functioning observed in ground-level soils, yet their functioning was reorganized seasonally and retained a guild-specific mycorrhizal legacy. These findings indicate that rooftop agriculture can support soil functioning broadly comparable to that of ground-level gardens, shaped by the interaction of design, management, legacy, and seasonal forcing, and highlight the need to evaluate both functional convergence and compositional differentiation when assessing the ecological potential of urban agriculture.