Environmental Sources and Tissue-Specific Selection Jointly Shape the Bacterial Community of the Sea Cucumber (Apostichopus japonicus) in Artificial Reef Areas of Laizhou Bay, Bohai Sea

The sea cucumber Apostichopus japonicus is an important aquaculture species in artificial reef areas. Understanding the bacterial communities in its different tissues and their relationship with the environment is of great ecological significance for reef area management and healthy aquaculture. In this study, environmental samples, including seawater and sediment, as well as tissue samples of A. japonicus gut and respiratory tree, were collected from seven stations in the artificial reef area of Laizhou Bay, Bohai Sea. Total DNA was extracted from each sample, and the bacterial communities were characterized using PacBio full-length 16S rRNA amplicon sequencing technology. The results showed that bacterial diversity was highest in sediments, followed by the gut, whereas seawater and respiratory tree samples showed lower diversity. The gut bacterial community structure closely resembled that of the surrounding sediments, characterized by a substantial enrichment of taxa such as Cyanobacteriota and Planctomycetota. FAPROTAX analysis exhibited relatively high representation of putative functions related to complex organic matter degradation in gut samples. In contrast, the respiratory tree bacterial community structure was more similar to that of seawater, with Alphaproteobacteria as the dominant group. The respiratory tree samples showed relatively high predicted representation of methylotrophy and methanol oxidation, suggesting a putative functional association with one-carbon compound utilization. These results indicate that the bacterial community in A. japonicus tissues is shaped by a combination of environmental sources and tissue-specific selection, with the gut community being more closely associated with sediment and the respiratory tree community with seawater. These findings provide microecological insights into habitat optimization and sea cucumber stock enhancement management in artificial reef areas, specifically indicating that sediment- and seawater-derived microbial sources should be taken into account to support the tissue-specific bacterial communities of A. japonicus.