Previous studies of the symbiosis in siboglinids have primarily focused on the giant tubeworm R. Only eight endosymbiont genomes (from Escarpia spicata, Lamellibrachia luymesi, Galathealinum brachiosum, Ridgeia piscesae, Riftia pachyptila, Seepiophila jonesi, Tevnia jerichonana and Osedax frankpressi) have been sequenced. Among the 194 species in 34 genera of Siboglinidae, none has a published genome, although the genomes of several species are being sequenced by multiple groups. The genomes of both the host and the symbiont contain critical genetic information about the symbiosis. Substrates for chemosynthesis including sulfide and oxygen are obtained from ambient seawater through the branchial plume of the host or from the sediment through the posterior end of the host and delivered to the symbiont through the host’s circulation system which uses hemoglobin. In the adult stage, the symbiotic bacteria are housed in a specialized organ of their host called the trophosome and no longer in direct contact with the ambient environment. Larvae of the tubeworms obtain free-living γ-proteobacteria from the ambient environment through a symbiont-specific infection process. Symbiosis with γ-proteobacteria, a group of chemosynthetic bacteria, is a key adaptation allowing tubeworms to thrive in vent and seep ecosystems. They are mouthless and gutless yet can have high productivity. Siboglinid tubeworms are often conspicuous members of the benthic communities of deep-sea hydrothermal vents and cold seeps. Overall, our results reveal the interdependence of the tubeworm holobiont through mutual nutrient supply, a pathogen-type regulatory mechanism, and host-symbiont cooperation in energy utilization and nutrient production, which is a key adaptation allowing the tubeworm to thrive in deep-sea chemosynthetic environments. Moreover, the symbiont is speculated to have evolved strategies to mediate host protective immunity, resulting in weak expression of host innate immunity genes in the trophosome. There is close cooperation within the holobiont in production and supply of nutrients, and the symbiont may be able to obtain nutrients from host cells using virulence factors. Metatranscriptome and metaproteome analyses of the Paraescarpia holobiont reveal that the symbiont is highly versatile in its energy use and efficient in carbon fixation. Our comparative analyses indicate that seep-living siboglinid endosymbionts have more virulence traits for establishing infections and modulating host-bacterium interaction than the vent-dwelling species, and have a high potential to resist environmental hazards. We characterized the symbiont genome of the seep-living siboglinid Paraescarpia echinospica and compared seven siboglinid-symbiont genomes. Deep-sea hydrothermal vents and methane seeps are often densely populated by animals that host chemosynthetic symbiotic bacteria, but the molecular mechanisms of such host-symbiont relationship remain largely unclear.
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