Fish are among the main target groups when conducting biomonitoring and ecological assessment of aquatic environments. Environmental DNA (eDNA) metabarcoding provides a unique opportunity to enhance biomonitoring throughput, precision, and standardization. However, few fish monitoring studies based on eDNA metabarcoding have been conducted at the basin scale. Taking Dianchi Lake and the three inflowing rivers (Panlong River, Baoxiang River, and Chai River) as research objects, this study monitored fish diversity via eDNA metabarcoding, and the Fish Index of Biological Integrity (F-IBI) was constructed and applied for the ecological assessment of the aquatic environment. Here, we detected 41 species belonging to 9 orders, 15 families, and 35 genera in the sampling areas, including 17 native fish species such as Hemiculter leucisculus, Cyprinus carpio, and Silurus soldatovi. Distinct diversity patterns were observed among Dianchi Lake and the three inflowing rivers. Particularly, the fish diversity of Panlong River was richer than that of Dianchi Lake, Baoxiang River, and Chai River. Water temperature (WT), chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) significantly influenced the distribution of fish communities in most sampling sites of the Dianchi Lake basin (p < 0.05). Moreover, according to the F-IBI assessment system, 25% of the sampling sites were defined as ‘fine’ or above, and 75% were ‘impaired’ or below. This study provided insights into the ecological restoration and precise management of the aquatic environment of the Dianchi Lake basin.

The survey of fish diversity is an important part of the protection of the ecological health of rivers and lakes. Environmental DNA technology is a new tool to improve the accuracy of traditional morphological surveys of biodiversity and to monitor the amount of diversity. At present, there are few studies on monitoring fish diversity in lake inlets using eDNA technology. In this study, we used various types of estuaries in the Dianchi basin as the research object, used environmental DNA technology to monitor the fish diversity in typical estuaries, and analyzed the temporal and spatial changes and the relationship between environmental factors and fish diversity. In the Dianchi basin, we identified a total of 63 fish species belonging to 8 different orders, 21 families, and 51 genera across two seasons. The Carpidae family had the highest number of species, with Carassius auratus being the most prevalent species. The Shannon index analysis yielded a p-value of 0.0018 (<0.05), suggesting significant seasonal variations in the fish community structure within the typical estuaries of the Dianchi basin. Furthermore, the β-diversity accounted for 59.6% and 57% of the variations in fish communities among the various estuary types in March and July, respectively. Fish species varied considerably between estuaries, with Carassius auratus, Cyprinus carpio, Rhodeus sinensis, Acheilognathus chankaensis, and Coilia nasus all occurring at various points. The agricultural estuary differed substantially from the urban, suburban, and lake areas. Redundancy analysis revealed that the fish community structure during the dry period was primarily influenced by total phosphorus, pH, total nitrogen (TN), and chlorophyll. Conversely, during the rich period, the fish community structure was mainly influenced by dissolved oxygen and TN. This study demonstrated the utilization of environmental DNA technology in assessing the ecological health of rivers and lakes, specifically highlighting its effectiveness in exposing the ecological condition of a representative Dianchi estuary.

The growth and reproduction of phytoplankton are closely associated with the changes of water environment; thus, phytoplankton have been taken as environmental indicator organisms and provided references for water environment protection. However, the phytoplankton community characteristics of Dianchi Lake (a seriously polluted lake in China) are unclear under the background of the cumulative effects of historical pollutants and current control measures, and environmental DNA (eDNA) metabarcoding monitoring has rarely been applied in phytoplankton research at Dianchi Lake. Therefore, this study investigated the temporal and spatial characteristics of phytoplankton community and the environmental stressors of Dianchi Lake via eDNA metabarcoding monitoring. A total of 10 phyla, 22 classes, 50 orders, 82 families, 108 genera and 108 species of phytoplankton were detected, and distinct temporal and spatial variations in the phytoplankton community (e.g., ASV number, dominant taxon, the relative abundance) were observed in Dianchi Lake. Microcystis dominated the prokaryotic phytoplankton community from the dry period to the wet period, but interestingly, the first dominant cyanobacteria genus was changed from Microcystis (dry period) to Planktothrix (wet period). Cryptophyta dominated in the eukaryotic phytoplankton community from the dry period to the wet period, and eukaryotic-phytoplankton-dominant genera included Cryptomonas, Aulacoseira, Plagioselmis and others. A temporal–spatial heterogeneity of the relationships between the phytoplankton community and environmental factors was shown in Dianchi Lake. Dissolved oxygen was the crucial environmental stressor influencing the phytoplankton community structure in Dianchi Lake during the dry period, while pH was the crucial one during the wet period. The impacts of total phosphorus and nitrogen also showed differences at different periods. This research provides an interesting perspective on phytoplankton diversity monitoring and the health assessment and restoration of Dianchi Lake.

This study investigated zooplankton distribution in Lake Dianchi, focusing on river mouths and their ecological conditions, using environmental DNA (eDNA) technology. It analyzed zooplankton diversity during the dry and rainy seasons, employing alpha diversity indices to assess community differences. A total of 24 species from 22 genera and 17 families across two phyla were identified, among Arthropoda (54%) and Rotifera (46%). Cyclopidae made up 29% of Arthropoda. β-diversity analysis showed a 37% difference between seasons and significant differences between estuaries: 61.4% in the dry season and 42.1% in the rainy season. Redundancy analysis identified total nitrogen (TN) as the main factor correlated with zooplankton diversity, with the highest TN levels in suburban estuaries. The findings provide insights for ecological restoration efforts in Lake Dianchi estuaries.

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.