Biodiversity of zooplankton in 0–3000 ​m waters from the eastern Indian Ocean in spring 2019 based on metabarcoding

To increase knowledge on zooplankton diversity in the deep sea, 42 zooplankton samples (depths of 0–3000 ​m) were taken across five stations throughout the northeastern Indian Ocean using a vertical multi-plankton sampler. According to metabarcoding results of the V4 region of the 18S rRNA gene, Copepoda, Hydrozoa and Malacostraca were present at all stations, while Polychaeta, Scyphozoa, and Thaliacea mainly appeared in the Bay of Bengal. A correlation heatmap showed that the abundance of surface species belonging to Copepoda, Gastropoda, Thaliacea, and Sagittoidea responded most closely to temperature, dissolved oxygen and chlorophyll-a, while the abundance of deep-water species belonging to Thecofilosea, Copepoda, Sagittoidea, and Polychaeta was negatively correlated with temperature, suggesting that temperature differences were driving depth-based variation in zooplankton community distributions in the tropical region. Furthermore, Copepods are important for differentiating depth assemblages in the Indian Ocean. Gaetanus minutus, Lucicutia ovalis, Heterostylites major and Metridia asymmetrica prefer the mesopelagic environment. The vertical distribution of zooplankton diversity showed a bimodal pattern. Generally, communities between 200 and 400 ​m at stations ZS1, ZS3 and ZS4 differed greatly from those of 0–200 ​m. However, at stations ZS2 and ZS5, communities between 200 and 400 ​m had high similarity with those of 0–200 ​m, possibly due to the influence of upwelling. Findings from this study significantly improve our understanding of zooplankton diversity and ecological functions in the deep sea. •Provide the depth profiles of zooplankton diversity from the pelagic ocean to the offshore basin based on 18S analysis.•Decipher the environmental adaption of typical zooplankton taxa in the tropical ocean.•Improve the understanding of the zooplankton diversity and their ecological functions in the deep sea.