Exploring the genomic diversity of tubeworm endosymbionts

Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how nifty these creatures are, you could check out this educational video by Ed Yong published last November, and then read this recently published article by Reveillaud and colleagues.

In this study, the authors report the characterization of the endosymbionts from the giant tube worm genera Lamellibrachia and Escarpia from the Caribbean Sea. This study is the first to take a swing at characterizing the endosymbionts from tubeworms outside of the Pacific Ocean as well as from these two lesser studied genera.
Escarpia sp. tubeworms. Image credit: The Chemo III project, BOEM and NOAA OER

Giant tube worms, some reaching more than six feet in length, were first discovered at a hydrothermal vent in 1977, and while they’re amazing for multiple reasons, one of the most fascinating things about these critters is they are lacking both mouths and guts, instead relying on bacterial symbionts that use the oxygen, sulfide, and carbon dioxide produced by hydrothermal vents to survive. These

bacteria are housed in a specialized organ known as the trophosome, and even though there are plenty of bacteria in the ocean, only a very specific group (Gammaproteobacteria) inhabit this organ. Since these symbionts have never been obtained in pure culture, understanding them has been based largely on metagenomic studies. While some tubeworm endosymbionts (such as those of Riftia pachyptila) have been extensively studied, others are less well understood.
Figure 2. Static image from the Anvi’o interactive display for the Escarpiaand Lamellibrachia tubeworm datasets with two symbiont genome bins highlighted in red (MCR MAG 1) and purple (MCR MAG 2).
Overall, Reveillaud et al. found that most of the endosymbionts were more than 98% identical across all the individual tube worms sampled (from both species studied). However, there were two symbionts with short (60 bp) insertions found in the ITS region that indicated that there was some diversity among these unique microbes.

“However, with more than 5% divergence from both Rifta and Ridgeia endosymbionts at the 16S rRNA gene level, it is possible that the differences in symbionts between and within seep and vent tubeworm have been underestimated in past studies and that different species occur at seep and vent habitats.

Interestingly, the endosymbionts studied by Reveillaud and colleagues, were phylogenetically distinct from those in vestimentiferans at other locations, including the Pacific Ocean, the Gulfof Mexico, and the Mediterranean Sea. The authors took the next step in characterizing the endosymbionts of the two tubeworm species collected and found different Gammaproteobacteria metagenome assembled genomes (MAGs), (which are what they sound like, genomes recovered from metagenomic data sets). While there was one MAG recovered from both species of tubeworms, it looks like there are a diverse group of endosymbionts in each as well.

Figure 4. Distribution of protein  clusters (PC) in the seven metagenome-assembled genomes (MAGs) from Ridgeia piscesae, Tevnia jerichonana, Riftia pachyptila and from the MCR specimen studied.
The MAGs were enlightening. For example, the authors noted that at the site where the tubeworms were collected, high concentrations of hydrogen were measured, and they were able to find evidence of the Hox gene pathway, which is implicated in hydrogen oxidation, and not previously reported in tubeworm endosymbionts.
Overall, the study supports the theory that tubeworm endosymbionts are pretty darn amazing, and possibly able to switch between being autotrophic (making its own food) and heterotrophic (relying on other food sources), or maybe are mixotrophic (can do both!). Finally, the authors propose that they have potentially identified a new genera tubeworm endosymbiotic bacteria (Candidatus Vondammii) due to the high level of divergence at the whole genome level as well as the rRNA operon.
So, hopefully you’re convinced… Tubeworms are cool.
Cavanaugh, C.M., Gardiner, S.L., Jones, M.L., Jannasch, H.W. and Waterbury, J.B., 1981. Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts. Science, pp.340-342.
Reveillaud, J., Anderson, R., Reves-Sohn, S., Cavanaugh, C., and Huber, J.A. 2018. Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity. Microbiome, 6:19. https://doi.org/10.1186/s40168-018-0411-x

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