Stable cores and dynamic peripheries: spatial structuring dominates over temporal turnover in wastewater microbiomes across 16 Swedish cities

Background Wastewater microbial communities integrate biological inputs from human populations, the surrounding environment, and sewer infrastructure. Understanding how spatial and temporal factors shape these communities is essential for ecological interpretation and wastewater-based surveillance. However, the relative contributions of geography and short-term temporal change remain unclear at national scales. Results We analyzed influent wastewater from 16 Swedish wastewater treatment plants collected at two timepoints, in winter (Week 3) and late spring (Week 21) of 2024, using shotgun metagenomic sequencing and compositional data analysis. A median of 24.9 million reads per sample were classified to Bacteria, Viruses, or Archaea, with communities dominated by Bacteria (97.6 percent), followed by Viruses (1.97 percent) and Archaea (0.42 percent). Genus-level diversity increased significantly from winter to spring, with median within-city changes of +10 genera in richness and +0.21 in the Shannon index (p < 0.003). Community composition was strongly structured by geography: city explained 58.3 percent of total variance (p = 0.0003), while week accounted for 3.7 percent (p = 0.106). Within cities, temporal turnover was substantial (median Aitchison distance 37.5; p = 4.8 × 10⁻⁴) but largely confined to peripheral taxa, which accounted for approximately 93 percent of total change. A stable core of 88 genera persisted across both timepoints, decreasing slightly in relative abundance (median change −0.020; p = 0.0021). Geographic distance and population size showed no significant associations with microbial composition. Discussion Swedish wastewater microbiomes are characterized by strong spatial differentiation, stable core communities, and locally variable peripheral turnover. Spatial factors dominate over temporal variation, emphasizing the importance of location-specific baselines for ecological assessment and wastewater-based monitoring. These findings highlight the robustness yet dynamism of urban wastewater ecosystems and provide a foundation for future national surveillance efforts.