Establishing biotic baselines in urban freshwater ecosystems using eDNA

Urban catchments provide valuable habitat for threatened species and host unique biodiversity that supports critical ecosystem services. Persistent anthropogenic stressors threaten the integrity of urban freshwater streams, creeks, and ponds, causing ecological degradation that impacts this biodiversity. Several methods exist for monitoring biodiversity in urban catchments; however, these fail to capture the full biological community due to inherent biases and logistical constraints. Tree of Life (ToL) metabarcoding presents a new approach for addressing challenges associated with establishing biotic baselines in the most underrepresented urban catchments. In this study, we used ToL-metabarcoding of filtered water samples collected from urban streams, creeks, and ponds in the Eastern Suburbs of Sydney, Australia to characterise whole ecosystem biodiversity, test for fluctuations in taxonomic diversity, and explore the effectiveness of this approach for future monitoring of these marginal environments. We detected 1038 total taxa using this approach, and taxonomic richness and community structure appeared to fluctuate significantly in response to season, rainfall, and site condition. This variability was correlated with taxonomic subgroup, suggesting that micro-organisms, invertebrates, and photosynthetic organisms may be optimal indicators of ecosystem health given their much higher turnover rates. Based on these findings, we suggested adapting the site condition index used here to be more responsive to fluctuations in Australian (versus New Zealand) freshwater aquatic taxa typical of impacted environments. We also suggest that ToL-metabarcoding can provide a promising tool for rapidly establishing biotic baselines in urban freshwater catchments, particularly when targeted monitoring programs are limited or absent.