Bottom Grinding Increases the Phototrophic Bacteria While Reduces Bacterial Community Stability in Sea Cucumber Cultural Ponds

ABSTRACT Bottom grinding (BG), which suspends the anaerobic microorganisms deposited at the bottom of the pond through aeration, is a common practice in sea cucumber aquaculture for maintaining water quality. However, little is known about the effects of BG on the environmental microbiome. This study investigated differences in bacterial communities from three niches (surface water, bottom water and sediments) of culture ponds with and without BG operations. Only minor changes in sediment bacterial communities were observed between BG‐treated and control ponds. In contrast, the composition of the bacterial communities in the water was also significantly altered by the BG operation, with an increase in Cyanobacteria and a decrease in Proteobacteria. Additionally, functional prediction revealed increased phototrophy and decreased chemoheterotrophy in aquatic bacterial communities following BG treatment. Co‐occurrence network analysis revealed that bacterial communities in all three niches were more complex but unstable with BG treatment compared to without, indicating some remedial operations for farming practice. Analysis of community assembly mechanisms showed increased stochastic assembly of bacterial communities in all three niches induced by BG treatment. Overall, this study revealed the effects of BG operation on the bacterial communities in culture ponds, providing insights into the ongoing evolution of farming techniques.