Abstract: The zooplankton in coastal regions are of great significance and plays a major role in sustaining the health of marine ecosystems. However, comprehending the environmental factors that influence diversity and community assembly in marine ecosystems remains a challenge. This study utilized high-throughput sequencing (HTS) of the 18S rRNA gene (V4 region) to examine the impact of environmental variables on the diversity, co-occurrence networks, and assembly processes of zooplankton in a bay and estuarine area in Beibu Gulf, China. This study indicates that there are significant seasonal variations in alpha diversity, beta diversity, and co-occurrent network. The alpha diversity of zooplankton demonstrated intricate associations with environmental factors, and the adaptation to varying temperatures can account for the majority of the impacts of environmental factors on alpha diversity. The regional distance-decay had an impact on the beta diversity, with the exception of December. The deterministic processes were more pronounced in December (35%) compared to other seasons (3.3%-10%). At elevated temperatures in September or reduced temperatures in December, the zooplankton community exhibited increased susceptibility to fluctuations in seawater properties. This finding coincided with the partial least-squares path modeling (PLS-PM) analysis. The varied responses of zooplankton assemblages to environmental factors may be attributed to the presence of different dominant zooplankton in different seasons. The seasonal variation in the zooplankton community may be primarily influenced by the zooplankton’s adaptation to ambient temperatures, leading to distinct network characteristics throughout different seasons. The collective findings provide insights into the environmental characteristics and seasonal variability affecting the community assemblage of zooplankton in bays and estuaries.

Key words: zooplankton, 18S rRNA metabarcoding, high-throughput sequencing, temperature, deterministic processes