Comparative analysis of the symbiotic microbiota in Chinese mitten crab (Eriocheir sinensis): microbial structure, co-occurrence patterns, and predictive functions

Symbiotic microorganisms in the digestive and circulatory systems have been found in various crustaceans, and their essential roles in crustacean health, nutrition, and disease have drawn increasing attention. Although the intestinal microbiota of Chinese mitten crab (Eriocheir sinensis) has been extensively studied, information on the symbiotic microbiota at various sites of this aquatic economic species, particularly hepatopancreas and hemolymph, is lacking. This study aimed to comprehensively characterize the hemolymph, hepatopancreas, and intestinal microbiota of Chinese mitten crab by high-throughput sequencing of the 16S rRNA gene. Results showed no significant differences in microbial diversity between the hemolymph and hepatopancreas (Welch t-test; p > 0.05), but both were significantly higher than (p < 0.05) intestine. Distinct differences were found in the structure, composition, and predicted function of the symbiotic microbiota at these sites. At the phylum level, the hemolymph and hepatopancreas microbiota were dominated by Proteobacteria, Firmicutes, and Acidobacteriota, followed by Bacteroidota and Actinobacteriota, whereas the gut microbiota was mainly composed of Firmicutes, Proteobacteria, and Bacteroidota. At the genus level, Candidatus Hepatoplasma, Shewanella, and Aeromonas were dominated in the hepatopancreas; Candidatus Bacilloplasma, Roseimarinus, and Vibrio were dominated in the intestine; Enterobacter, norank_Vicinamibacterales, and Pseudomonas were relatively high abundance genera in the hemolymph. The composition and abundance of symbiotic microbiota in hemolymph and hepatopancreas were extremely similar (p > 0.05), and there were no significant differences in functional predictions (p > 0.05). Compared to the intestine and hepatopancreas, the hemolymph had less variation in bacterial composition among individuals, in terms of a more uniform abundance of major bacterial taxa, a smaller coefficient of variation, and the highest proportion of shared genera. Network complexity varied greatly across the three sites, among which the hepatopancreas microbiota was the most complex, followed by hemolymph microbiota, and the intestinal microbiota had the simplest network. The functional prediction revealed that xennobiotics biodegradation and metabolism, energy metabolism, and metabolism of terpenoids and polyketides were significantly enriched in the hemolymph compared with the intestine and hepatopancreas. Moreover, porphyrin and chlorophyll metabolism was significantly enriched in the intestine, whereas environmental information processing, glycan biosynthesis and metabolism, human disease, and bacterial infectious disease were significantly enriched in the hepatopancreas. This study revealed the taxonomic and functional characteristics of the hemolymph, hepatopancreas, and gut microbiota in Chinese mitten crab. The results expanded our understanding of the symbiotic microbiota in crustaceans, providing potential indicators for assessing the health status of Chinese mitten crab and new clues for exploring the potential role of the symbiotic microbes in maintaining host health and affecting disease occurrence.