Conventional net tow versus environmental DNA for metabarcoding-based analysis of plankton-environment interactions in polluted aquatic ecosystems

Human societal development has caused rapid degradation of freshwater ecosystems, resulting in significant biodiversity decline globally. The conservation of aquatic ecosystems, particularly the management of biodiversity in urban areas, has become an increasingly significant issue for ensuring the sustainability of these ecosystems. The restoration of degraded aquatic ecosystems relies on a comprehensive understanding of the interactions between biological communities and multiple stressors derived from human activities. Environmental DNA (eDNA)-based methods have emerged as effective tools for dissecting complex community-environment interactions. Nevertheless, potential causes for technical disparities and conclusions drawn from conventional sampling versus eDNA-based methods remain inadequately evaluated. In this study, we conducted a comprehensive survey of plankton communities along the environmental gradient of the North Canal River in Northern China to assess causes and consequences for any disparities between conventional plankton net tow and eDNA sampling for metabarcoding-based analysis of plankton-environment interactions. Our findings demonstrated that eDNA-metabarcoding was effective for characterizing both biodiversity and geographical distribution. Both methods exhibited general consistency in elucidating community structure and identifying the key environmental factors influencing geographical distribution of both zooplankton and phytoplankton. As we explored lower taxonomic ranks, we found inconsistent patterns at certain levels (e.g., phylum or order) within some taxa (e.g., Bacillariophyta and Rotifera), even substantial variability for several taxonomic groups (e.g., Euglenozoa and Apicomplexa). The varied environmental prevalence and persistence of eDNA, biological and ecological characteristics of diverse taxa in plankton, and sampling efficiency of both methods likely contributed to the observed disparities. Given its higher biodiversity recovery capacity, efficiency, sampling convenience, and capability to identify influential factors driving the geographical distribution of biodiversity, eDNA-based metabarcoding is recommended for studying plankton-environment interactions, particularly in studies involving a large number of samples at extended geographical scales.