Microbial dynamics of wild and cultured Sinularia flexibilis: Implications for coral aquaculture

Cembrane-type diterpenes are among the most common natural marine substances in the soft coral Sinularia flexibilis. Cembranoids from the soft coral S. flexibilis exhibited interesting biological activities, especially the anti-inflammatory effect. To establish a stable source S. flexibilis and protect its natural habitat, we used aquaculture technology to farm the coral in large quantities since 2016 and isolated several bioactive natural products. However, by 2022, the bioactive compound content in cultured S. flexibilis had declined by over 50 % compared to wild-type levels, indicating a progressive loss associated with extended culture duration. We used high-performance liquid chromatography with tandem mass spectrometry (LC–MS/MS) to analyze the changes in the contents of cembranoids in the wild-type and cultured S. flexibilis. The results revealed the cultured S. flexibilis contained much fewer cembranoids than the wild-type soft coral. To investigate the relationship between S. flexibilis and its associated microorganisms and explore whether the composition of microorganisms affects the content of cembranoids in the soft coral, we used next-generation sequencing technology to analyze the 16S and 18S rRNA genes of prokaryotic and eukaryotic communities associated with wild-type and cultured S. flexibilis and elucidate the differences. Additionally, next-generation sequencing of the coral-associated microbiota revealed significant differences in the bacterial phyla composition between the wild and cultured S. flexibilis. Wild-type coral harbored at least 27 distinct bacterial phyla, while the cultured coral contained at least 23. Wild S. flexibilis exhibited higher proportions of Proteobacteria and Spirochaetota, while cultured coral showed higher abundance of Firmicutes and Bacteroidota. At the family level, we also observed notable differences between the wild and cultured corals. The dominant bacterial families in the wild coral included Spongiibacteraceae (33.50 %), Endozoicomonadaceae (23.22 %), Spirochaetaceae (11.94 %), Terasakiellaceae (4.30 %), Phycisphaeraceae (3.89 %), and Comamonadaceae (2.89 %). In contrast, the major families in the cultured corals were Bacillaceae (29.76 %), Chitinibacteraceae (10.60 %), Terasakiellaceae (6.27 %), SAR324 clade (5.84 %), Enterobacteriaceae (5.43 %), Lachnospiraceae (3.73 %), Flavobacteriaceae (3.11 %), and Helicobacteraceae (3.08 %). Except for Terasakiellaceae, the major bacterial families in the wild coral were almost entirely different from those in the cultured S. flexibilis. These findings suggested that changes in the coral-associated microbiota may be one of the key factors contributing to the observed decline in the production of bioactive natural products in cultured corals.