Microeukaryotic community dynamics and assembly mechanisms in shrimp aquaculture ponds

Microeukaryotes play a crucial role in maintaining microbial diversity and stability of aquaculture pond ecosystems. Despite their importance, our understanding of microeukaryotic community assembly and temporal dynamics throughout the aquaculture cycle remained limited. This study investigated microeukaryotic community dynamics in nine shrimp (Litopenaeus vannamei) farming ponds over 60 days using 18S rRNA gene sequencing. The results indicated that microeukaryotic community dynamics in the pond system can be divided into two stages: a fluctuating stage from day 0 to day 40 and a stable stage from day 40 to day 60. The alpha diversity of the microeukaryotic community in sediment increased in the first stage and decreased in the second stage, while it remained relatively stable in water. The community structure, network complexity, and stability of the microeukaryotic community in water were more stable in the second stage than in the first stage. Additive partitioning analysis indicated local diversity and within-habitat variation were the primary contributors to the total microeukaryotic metacommunity diversity of aquaculture pond system. Furthermore, the species pool in both water and sediment primarily originated from historical sources within the microeukaryotic metacommunity, and the dispersal route between habitats (water and sediment) was strengthened in the second stage compared to the first stage. Additionally, the assembly of microeukaryotic community was primarily governed by stochastic processes in the first stage and deterministic processes in the second stage. Specifically, increasing nitrogen loading influenced the relative abundance of dominant green algae and strengthened the homogeneous environmental selection of the microeukaryotic community. Overall, this study demonstrates the significant impact of historical species pool and nutrient loading in structuring the microeukaryotic metacommunity in the aquaculture pond system. •Microeukaryotic communities fluctuated early but stabilized in later stages.•Dispersal between habitats increased over time, but historical sources remained primary contributors to species pools.•Community assembly shifted from stochastic to deterministic with more nutrients.•Dominant green algae drove assembly patterns and were influenced by nitrogen compounds.