Which is more priority, substrate type or food quality? A case study on a tropical coral reef sea cucumber Stichopus chloronotus revealed by prokaryotic biomarker.

Background: Different species of sea cucumbers in various regions have diverse preferred habitats and feeding habits. However, detailed research on the correlation between food selection and habitat preference of sea cucumbers, as well as their adaptive adjustments to specific habitat types, is still lacking.

Methods: A field study was carried out to explore the relationship between food selection and habitat preference, as well as the adaptation process, of the tropical sea cucumber Stichopus chloronotus, which has specific food preferences. This was achieved using an in situ mesocosm method with three single habitat types: sandy, broken coral branches, and reef. Changes is the prokaryotic community structure of gut contents, revealed by high-throughput sequencing analysis of the 16S rRNA gene, were used as the biomarker. Tax4Fun assessed the metabolic pathways of samples, and FAPROTAX evaluated the biogeochemical cycling processes.

Results: Alpha diversity, PCoA, and UPGMA tree analyses consistently revealed that bacterial community structures in the gut contents of S. chloronotus in reef bottom cages (GRee) are closely related to those of wild S. chloronotus collected in September (GWS) and October (GWO) than those from the sandy bottom (GSan) and broken coral branches bottom (GBra) cages. The relative abundance of Ruegeria is one of the dominant genera in the control groups (GWS and GWO), while Synechococcus CC9902 is among the predominant genera in the treatment groups (GSan, GBra and GRee). Functional prediction outcomes from Tax4Fun and FAPROTAX also indicate that the metabolic pathways in the gut contents of the treatment groups are distinct from those of the control groups.

Conclusions: Compared with S. chloronotus in single habitat types, wild S. chloronotus showed stronger feeding selectivity and ingested actively larger proportion of Ruegeria sp. For this picky species, hard-substrate habitats that can keep it away from strong waves seem to be more important to than those with good sedimentary food. Inappropriate habitats without stable substrate for attachment may cause an unusual change in food preference of S. chloronotus. Tax4Fun and FAPROTAX functional annotation also confirmed that the adaptive adjustment of S. chloronotus can be completed within a month.