Composition and potential functions of the dominant microbiota in deep-sea hagfish gut from the South China Sea

Abstract

Hagfishes, the most ancient jawless fishes, have a pivotal biological status. Gut bacterial communities are considered to be another organ that supports host survival and reproduction, while most gut microbiota cannot be cultured in vitro. In this study, four deep-sea hagfish individuals were collected from the South China Sea (>900 m). 16S rRNA and metagenomics approaches were used to analyze the gut microbiota assembly and the functions of the dominant microbes. The results revealed 16 phyla and 21 genera (relative abundance ≥ 0.5%) of microbes in total. Ureaplasma and Arcobacter were the dominant genera across all the gut samples, and the microbiota diversity showed no significant differences among the different gut regions. To investigate the potential functions of the dominant microbial taxa, the draft genomes of Ureaplasma (Hg1 and Hg2) and Arcobacter (LC1) from the midgut and hindgut were successfully recovered. The Hg1 and Hg2 genomes were enriched in genes encoding phosphoenolpyruvate-dependent phosphotransferase systems (PTSs) and sodium-driven symporters responsible for the uptake of sugars and other carbohydrates. The functional repertoire of Ureaplasma was likely to help the host in the metabolism of multiple carbohydrates, especially chitin degradation. The LC1 genome harbored genes encoding a restriction-methylation system, two CRISPR-Cas systems and multiple toxin-antitoxin systems. The enrichment of genes related to bacterial defense indicated that the functions of LC1 may involve protection against harmful or foreign microorganisms and balancing the host intestinal flora. These results hint that genetic and functional diversification might be present among Ureaplasma and Arcobacter. Though the exact functions of the dominant microbes remain to be further identified, our results allow us a glimpse into hagfish-microbe alliances in deep-sea ecosystems.