A specific and widespread association between deep‐sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria

Abstract

Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfur-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world. These epsilonproteobacterial sequences were closely related, indicating that the association is highly specific. The Bathymodiolus-associated epsilonproteobacterial 16S rRNA sequences were at most 87.6% identical to the closest cultured relative, and 91.2% identical to the closest sequences in public databases. This clade therefore represents a novel family within the Epsilonproteobacteria. Fluorescence in situ hybridization and transmission electron microscopy showed that the bacteria are filamentous epibionts associated with the gill epithelia in two Bathymodiolus species. In animals that host highly specific symbioses with one or a few types of endosymbionts, other less-abundant members of the microbiota can be easily overlooked. Our work highlights how widespread and specific associations with less-abundant microbes can be. Possibly, these microbes play an important role in the survival and health of their animal hosts.

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

“…To better resolve the relationships of the mussel epibionts to other Campylobacterota we analyzed a set of 18 conserved marker genes from the two epibiont draft genomes and other publicly available Campylobacterota genomes (Figure S1). In contrast to the previous 16S rRNA based phylogeny 32 , our analysis placed the mussel epibionts on a long branch, basal to the main Campylobacterota families. The long-branch formation for the genomes presented in this study is likely related to low amino acid sequence identity (AAI) values between these and the Campylobacterota representative genomes.…”

“…According to the guidelines of Rodriguez and Konstantinidis 36 , organisms with AAI values higher than 30% and lower than 55-60% are likely to belong to the same division, but not the same genus. This is corroborated on the 16S rRNA level 37 , where our genomic data supports the previously published 16S rRNA based study 32 , indicating that the epibiont species belong to a novel family of Campylobacterota.…”

“…The Campylobacterota draft genome from “B.” childressi contained a partial 16S rRNA sequence (586 bp) that was 100% identical to the epibiont sequence previously published 32 . The 16S rRNA sequence identity and the ANI information allowed us to link the two draft genomes to the previously described epibiont 32 . To better resolve the relationships of the mussel epibionts to other Campylobacterota we analyzed a set of 18 conserved marker genes from the two epibiont draft genomes and other publicly available Campylobacterota genomes (Figure S1).…”

“…Previous 16S ribosomal RNA gene (16S rRNA) sequence analysis identified this group of epibionts as a novel family-level deep-branching sister group of the Sulfurovum clade within the Campylobacterota 32 . The Campylobacterota draft genome from “B.” childressi contained a partial 16S rRNA sequence (586 bp) that was 100% identical to the epibiont sequence previously published 32 . The 16S rRNA sequence identity and the ANI information allowed us to link the two draft genomes to the previously described epibiont 32 .…”

“…Many bathymodiolin species host both types in a ‘dual symbiosis’. Assié et al recently discovered a novel family of Campylobacterota, which colonizes bathymodiolin mussels from around the world 32 . In contrast to the gammaproteobacterial endosymbionts of these mussels that are harbored inside gill cells called bacteriocytes, these Campylobacterota are filamentous epibionts that colonize the surface of the gill epithelia in dense patches.…”