Anthropogenic habitat alteration interferes the natural aquatic habitats and the system's hydrodynamics in the Yangtze River floodplain lakes, resulting in a serious decline in freshwater biodiversity. Zooplankton communities possess major position in freshwater ecosystems, which play essential parts in maintaining biological balance of freshwater habitats. Knowledge of processes and mechanisms for affecting variations in abundance, biomass, and diversity of zooplankton is important for maintaining biological balance of freshwater ecosystems. Here, we analyzed that the temporal and spatial changes in the structure of zooplankton community and their temporal and spatial variations respond to changes in environmental factors in the middle reach of Yangtze River floodplain lakes. The results showed that zooplankton samples were classified into 128 species, and Rotifera was the most common taxa. Significant seasonal differences were found among the abundance and diversity of zooplankton. Similarly, we also found significant seasonal differences among the biomass of zooplankton functional groups. The spatial turnover component was the main contributor to the β diversity pattern, which indicated that study areas should establish habitat restoration areas to restore regional biodiversity. The NMDS plot showed that the structure of zooplankton community exhibited significant seasonal changes, where the community structure was correlated with pH, water temperature, water depth, salinity, total nitrogen, chlorophyll‐a, and total phosphorus based on RDA. This study highlights that it is very important to ensure the floodplain ecosystem's original state of functionality for maintaining the regional diversity of the ecosystem as a whole.

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Freshwater ecosystems face multiple threats to their stability globally. Poyang Lake is the largest lake in China, but its habitat has been seriously degraded because of human activities and natural factors (e.g. climate change), resulting in a decline in freshwater biodiversity. Zooplankton are useful indicators of environmental stressors because they are sensitive to external perturbations. DNA metabarcoding is an approach that has gained significant traction by aiding ecosystem conservation and management. Here, the seasonal and spatial variability in the zooplankton diversity were analyzed in the Poyang Lake Basin using DNA metabarcoding. The results showed that the community structure of zooplankton exhibited significant seasonal and spatial variability using DNA metabarcoding, where the community structure was correlated with turbidity, water temperature, pH, total phosphorus, and chlorophyll‐a. These results indicated habitat variations affected by human activities and seasonal change could be the main driving factors for the variations of zooplankton community. This study also provides an important reference for the management of aquatic ecosystem health and conservation of aquatic biodiversity.

Background: The water level of Poyang Lake (China) fluctuates seasonally. Shahu Lake, a smaller body of water connected to Poyang Lake during the wet season, is separated in the dry season. Due to a special fishing method termed ‘lake enclosed in autumn’, the water level is lowered and reaches its lowest point in January, which is <0.5 m deep in the middle of the lake. Our research investigated the effect of water level changes on the zooplankton community composition in Shahu Lake. Methods: We used both DNA metabarcoding method (MBC) (18S rRNA gene V4 region) and morphological method (MOI) to track the zooplankton community structure over four seasons in Shahu Lake (China). Results: Totals of 90 and 98 species of zooplankton were detected by MOI and MBC, respectively, with rotifers being the main zooplankton component. The α-diversity index of both methods increased from spring to summer and decreased from summer to autumn, reaching the lowest value in winter. NMDS and a cluster analysis showed that all zooplankton communities detected by MOI and MBC were significantly separated by season. The zooplankton community in winter was separated from that of the other three seasons, but the summer and autumn communities were more similar. Conclusions: Changes in the water level had significant effects on the zooplankton community composition. We found that MBC was more able to detect the differences in the zooplankton composition than MOI. MBC also had more advantages in copepod recognition. In our study, 37 species of copepods were detected by MBC, but only 11 species were detected by MOI. We concluded that MBC should be used to research the seasonal variations of zooplankton.