Environmental DNA analysis reveals diverse impacts of organic factors on community stability in aquatic ecosystems

Environmental factors increasingly influence species survival and the diversity of river systems worldwide. However, a thorough understanding of assembly mechanisms and the dominant environmental variables mediating community stability in aquatic environments remains limited. In this study, by analyzing environmental DNA (eDNA) datasets collected over two seasons, including 12 mesocosm systems with 8 years of stable operation and 3 natural systems, we investigated both the community assembly and the mechanisms underlying stability across multiple communities. Long-established aquatic mesocosm systems developed high taxonomic diversity across invertebrate, protozoa, algae, and bacteria under stable water conditions, with significant differences in relative abundances between mesocosm and natural systems. A positive correlation was observed between organic factors and diversity (Shannon-Wiener index, Simpson index, and Pielou index) of species and community in mesocosm systems, while in natural systems, no significant correlation was found between community-level diversity and organic factors, with a negative association between species-level diversity and organic factors. Species synchrony and average variation degree decreased as community stability increased with growing organic factors. The results showed that deterministic environmental filtering significantly contributed to community assembly and structure, with community stability being positively influenced by organic factors through the indirect pathway of species diversity in aquatic ecosystems. Overall, this study combines multidimensional indicators (responses of species, populations, and communities) and provides valuable insights for the restoration and sustainable management of aquatic environments by regulating environmental factors, particularly organic factors.