Design of novel primer sets for easy detection of Ruegeria species from seawater

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.

Specific Detection of Coral-Associated Ruegeria, a Potential Probiotic Bacterium, in Corals and Subtropical Seawater

Coral microbial flora has been attracting attention because of their potential to protect corals from environmental stresses or pathogens. Although coral-associated bacteria are considered to be acquired from seawater, little is known about the relationships between microbial composition in corals and its surrounding seawater. Here, we tested several methods to identify coral-associated bacteria in coral and its surrounding seawater to detect specific types of Ruegeria species, some of which exhibit growth inhibition activities against the coral pathogen Vibrio coralliilyticus. We first isolated coral-associated bacteria from the reef-building coral Galaxea fascicularis collected at Sesoko Island, Okinawa, Japan, via random colony picking, which showed the existence of varieties of bacteria including Ruegeria species. Using newly constructed primers for colony PCR, several Ruegeria species were successfully isolated from G. fascicularis and seawater. We further investigated the seawater microbiome in association with the distance from coral reefs. By seasonal sampling, it was suggested that the seawater microbiome is more affected by seasonality than the distance from coral reefs. These methods and results may contribute to investigating and understanding the relationships between the presence of corals and microbial diversity in seawater, in addition to the efficient isolation of specific bacterial species from coral or its surrounding seawater.

Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter

Environmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.