Establishing biotic baselines in urban catchments 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 lotic and lentic systems, 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 freshwater lotic and lentic systems 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 catchments. In total, we detected 1038 total taxa using this approach, and taxonomic richness as well as 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, photosynthetic organisms and invertebrates may be optimal indicators of urban ecosystem health given their shorter generation times and much higher turnover rates. Based on these findings, we suggest adapting the site condition index used here, developed in New Zealand freshwater environments, to be more responsive to fluctuations in aquatic taxa typical of, or unique to, Australian urban catchments. We also suggest that ToL-metabarcoding can provide a promising tool for rapidly establishing biotic baselines in urban catchments, particularly when targeted monitoring programs are limited or absent.