Objective In the process of studying the structural characteristics of the bacteria community in the breeding environment of Stichopus Japonicum in Dalian, we hope to use the diversity index and other parameters as ecological signals to provide real-time monitoring means for healthy breeding, provide data support for the regulation of the breeding environment, and help the green sustainable and healthy development of S. Japonicum breeding industry.

Methods DNA was extracted from water and sediment samples of sea cucumber culture ponds in different locations around Dalian, and high-throughput sequencing was completed by PCR amplification, product acquisition, mixing and purification, library construction and sequencing. The sequences obtained by data splitting, double-ended data splicing and filtering were compared with Silva species annotation database to detect chimera sequences. Following removal of chimeric sequences, high-quality reads were obtained for downstream bioinformatic analyses including: (1) OTU clustering and taxonomic annotation, (2) alpha diversity assessment of sample complexity, (3) beta diversity comparison across samples, (4) microbial community differential analysis, and (5) functional potential prediction. Subsequently, we conducted comprehensive analyses of microbial community structure and identified key influencing factors.

Results High-throughput sequencing yielded 3,059,097 seawater and 2,682,116 sediment 16S rDNA sequences after filtering low-quality/short sequences and removing chimeras, with an average read length of 373 bp. Alpha diversity analysis revealed that the PMW3 community exhibited the lowest uniformity and richness, while the POW6 community showed the highest. The PMS2 bacterial community in sediment samples displayed the highest diversity, with the PMS6 community demonstrating the greatest uniformity and abundance. Conversely, the POS5 bacterial community had the lowest diversity, uniformity, and abundance. Beta diversity analysis indicated that seawater microbial communities were primarily influenced by seasonal factors, whereas sediment bacterial community structures were more similar. Canonical correspondence analysis (CCA) examined the relationship between key environmental factors (major pollution indicators) and microbial community structure and dominant species. The results showed that microbial community structure and dominant species in most seawater and sediment samples were positively correlated with nitrogen concentration. However, the sediment community structure was more complex, with more potential influencing factors, resulting in less consistent CCA patterns compared to seawater samples. Nevertheless, it can be inferred that certain bacterial genera are associated with nitrogen biotransformation.

Conclusion The microbial community structure in the seawater of S. japonicum breeding pond is affected by both space and season, while the microbial community structure in the sediment is mainly affected by the function of the corresponding sea area. Under the influence of offshore aquaculture, more dominant species which can degrade nitrogen and organic pollutants are enriched in seawater and sediments.