Microbiome of ascidian ‘Halocynthia roretzi’ and taxonomic study of strain RR4-40

Abstract

A Korean edible ascidian, ‘Halocynthia roretzi’, is one of most important economic invertebrates which has been mostly consumed in South Korea and Japan. Studies of H. roretzi are, however, focused mainly on farming systems of the ascidian and tunic-softness syndrome. In this thesis, microbial communities of three digestive parts, gill-slit, digestive gland, and intestine, from a Korean ascidian, H. roretzi were studied through high throughput parallel sequencing with tagged PCR. A total of 2,215 OTUs were grouped and taxonomically assigned to 23 phyla, 46 classes, 79 orders, 139 families and 203 genera. Comparison analysis showed that three digestive organs shared core-microbiome such as candidate phylum OD1 as a predominant phylum. Minor core-microbiome were genus of Gammaproteobacteria and Entomoplasmatales in three digestive organs. Different bacterial taxa were identified in different organ as predominant groups as follows: an unidentified genus of Gammaproteobacteria (17.85%) in the gill-slit, Hepatoplasma (14.73%) and Entomoplasmatales (26.15%) in the digestive gland, and Bacillus (15.29%) in the intestine. In beta diversity, intestine generally showed higher values of species richness and Shannon index than the other organs. Gill-slit, on the other hand, comprised the simplest microbial composition. H. roretzi absorbs planktonic organisms as food. We predicted limited foods of H. roretzi lead to simple microbial diversity. In contrast, intestine supports to remove residue from host through atrial siphon and is adjacent organs to atrial siphon. Therefore, functions and positions of three digestive organs affect to microbial composition. Analysis of microbial diversity will improve to comprehend the nutrition and physiology of H. roretzi.

A novel strain RR4-40T isolated from a recirculating aquaculture system was classified to member belonging to the Flavobacteriaceae family by using a polyphasic approach. Phylogenetic, genomic and biochemical characteristics of strain RR4-40T were analyzed and compared with six reference strains. Cells of RR4-40T were aerobic, gram-negative, non-motile and irregular short-rod. Strain RR4-40T was catalase and oxidase negative and growth occurred at 15–35°C (optimum: 25–30 °C), pH 5–9.5 (optimum: pH 8.5) and 0.5–6% NaCl (optimum: 3% NaCl; w/v). Phylogenetic features based on analysis of 16S rRNA gene sequences indicated that RR4-40T was most closely to Marinirhabdus gelatinilytica NH83T (94.16%). Whole genome sequences showed that novel bacterium, designated RR4-40T, have phylogenetic distance from its reference strains and we suggest that strain RR4-40T is novel genus within the Flavobacteriaceae through these results.