Temporal and spatial dynamics of rotifer communities in the Pearl River Delta (China) with emphasis on DNA metabarcoding versus morphology to assess rotifer diversity

Rotifers are essential invertebrates in freshwater ecosystems. Rotifer community structure reflects the environmental changes. To assess the diversity of rotifers in the Pearl River Delta, we investigated the rotifer community structure in different water bodies types using morphology and DNA metabarcoding. A total of 101 species in 30 genera were recorded. 82 rotifer species were identified by morphology and 31 by OTUs based on DNA metabarcoding. Only 40% (2 orders), 42.9% (9 families), 29.7% (11 genera), and 4% (4 species) were shared by the two identification methods. Primers and imperfect rotifer databases might be responsible for the low annotation of rotifer OTU species. The community structure of rotifer morphospecies and OTUs in the Pearl River Delta changed with seasonal and spatial distribution. Heatmaps showed that different rotifer species responded differently to environmental factors. Our results show that DNA metabarcoding provides complementary rather than identical estimates compared to traditional approaches for rotifers. However, if widely validated and improved, this approach could be a useful alternative for practical applications of rotifers as bioindicators. In the future, environmental DNA metabarcoding is promising for the large-scale study and assessment of rotifer diversity.