Spatial and Seasonal Variations in Invertebrate Communities in the Chai River Based on eDNA Biomonitoring

As environmental indicators, invertebrate communities are closely related to changes in the water environment. Efficient and accurate monitoring of invertebrates is of great significance for providing references for water environment conservation. However, environmental DNA metabarcoding has rarely been used in invertebrate research at the Chai River in Kunming, Yunnan, China, and the current characteristics of invertebrate communities are unclear. Therefore, this study investigated the spatial and seasonal patterns of invertebrates and the environmental stressors of the Chai River. Based on eDNA metabarcoding, 873 ASVs of invertebrates belonging to Annelida, Arthropoda, Cnidaria, Gastrotricha, Mollusca, Nematoda, Platyhelminthes, Protozoa, and Rotifera were identified, with Arthropoda being the absolute dominant phylum. Distinct spatial and seasonal variations in the invertebrate communities (e.g., ASV number, dominant genera, relative abundances) were observed. Macrothrix and Acanthamoeba were the first and second most dominant genera, both in dry and wet periods. A spatial–seasonal heterogeneity of the relation between the invertebrate communities and environmental factors was observed in the Chai River. The water temperature (WT), chemical oxygen demand (COD), conductivity (C), and Chlorophyll-a (Chl-a) levels were deemed to be the crucial environmental factors influencing the distributions of invertebrate communities in the Chai River, which was consistent with the spatial and seasonal differences in pollution characteristics around the Chai River. This study provides insights into conserving the diversity of invertebrate communities and the management of the Chai River and similar agricultural rivers.