Evaluating the quantitative performance of environmental DNA metabarcoding for freshwater zooplankton community: a case study in Lake Biwa, Japan

• Published in: Environmental science and pollution research international 2024-10, Vol.31 (47), p.58069-58082
• Main Authors: Jo, Toshiaki S., Sasaki, Yoshiharu
• Format: Article
• Language: English
• Subjects: Abundance; Aquatic Pollution; Atmospheric Protection/Air Quality Control/Air Pollution; case studies; Cladocera; Copepoda; DNA barcoding; Earth and Environmental Science; Ecotoxicology; Environment; Environmental changes; Environmental Chemistry; Environmental DNA; Environmental Health; freshwater; Freshwater ecosystems; Japan; Lakes; Life history; microscopy; Nucleotide sequence; Performance evaluation; Performance prediction; Plankton; Population dynamics; Population studies; quantitative polymerase chain reaction; Real time; Research Article; Species composition; species diversity; uncertainty; Waste Water Technology; Water Management; Water Pollution Control; Zooplankton
• ISSN: 1614-7499; 0944-1344; 1614-7499
• DOI: 10.1007/s11356-024-35025-8

Zooplankton monitoring is important for understanding their population dynamics and life history, ecosystem health, and environmental changes. Compared with traditional morphological identification, environmental DNA (eDNA) analysis allows for more sensitive and efficient monitoring of zooplankton diversity. Previous eDNA studies have primarily used metabarcoding approaches to reveal their richness and composition, whereas its performance in predicting zooplankton abundance remains understudied. We conducted water and bulk sampling in Lake Biwa, Japan, showing that the number of sequence reads by metabarcoding moderately correlated with eDNA concentrations estimated by quantitative real-time PCR (qPCR). In addition, the eDNA read number was significantly related to cladoceran and copepod abundance estimated by microscopy sorting, although there remained too much uncertainty in the read-abundance relationship. Moreover, there was a significant difference in species composition between eDNA metabarcoding and sorting. Although our results indicated the potential applicability of eDNA metabarcoding for quantifying multiple zooplankton abundance, several methodological validations in eDNA metabarcoding would also be required to optimize its performance in the future.