The microbial community composition of substrate biofilm limits the growth of indoor-cultured sea urchins (Strongylocentrotus intermedius)

In benthic aquaculture, the use of substrates enhances farming efficiency and also induces microbial biofilm formation. The presence of biofilms is closely associated with the aquacultural environment and potentially influences the growth and development of aquatic animals. Strongylocentrotus intermedius is a highly valued species in aquaculture due to its commercially significant gonads. To date, however, few studies have investigated the associations between gut microbial community structures and functions in S. intermedius and substrate surface biofilms. In this study, we examined dynamic changes in the microbial communities on substrate biofilms in S. intermedius culture and assessed their potential effects on sea urchin health. Scanning electron microscopy, contact angle measurement, and quantitative analyses of biofilms revealed that biofilms on the surface of polyvinyl chloride (PVC) substrates gradually increased over time. Fourier-transform infrared spectrometry analysis indicated that PVC substrates gradually age with prolonged cultivation time. Microbial community analysis revealed a succession of dominant bacterial genera in PVC substrate biofilms, particularly those in genera with plastic-degradation ability, including Pseudomonas, Cladosporium, and Alternaria, which may promote PVC aging. Comparative microbial analyses revealed that Vibrio was highly abundant in S. intermedius grown in indoor and offshore culture environments, Cobetia and Debaryomyces were highly abundant in the intestine of offshore-cultured S. intermedius, and Pseudoalteromonas, Candidatus_Hepatoplasma, Cladosporium, and Aspergillus were highly abundant in the guts of indoor-cultured S. intermedius, among which only Candidatus_Hepatoplasma was not detected in PVC substrates. These differences are assumed to reflect the ecological interactions and nutritional requirements of S. intermedius in different habitats, as well as their adaptability to environmental change. Our research demonstrates that the relationship between the biofilms on sea urchin attachment bases and their gut microbiota must be better understood to optimise aquaculture. In particular, the role of beneficial microbes, notably fungi, within these attachment bases requires further investigation. Creating a beneficial bacterial biofilm can optimise the gut environment, improve the growth rate, and promote the overall health of sea urchins.