Metagenomics reveals again!

Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics
(Robidart et al 2008) Environmental Microbiology (2008) 10(3), 727–737

Most derived adapted animals in hydrothermal vents is the giant tubeworm Riftia pachyptila. Riftia has no mouth or digestive tract and maintains an obligate nutritional association with chemolithoautotrophic symbionts housed in its trophosome. The Riftia symbionts have been described as sulfide-oxidizing gamma proteobacteria that fix carbon via the Calvin– Benson Cycle.

In order to gain a better understanding of this uncultured symbiont, a metagenomic project was undertaken with symbionts purified from worms and named Canditus E. persephone. The genomic repertoire was compared with well-characterized cultured systems. The authors gave evidence for why their study was reliable and complete which all seemed fair and reassuring to trust their results.

An interesting find was that, despite the origin of DNA from two worms for this metagenomic study, the symbiont populations are nearly monoclonal.

The metagenome contained a partial Calvin–Benson Cycle and all necessary components of the reverse TCA (rTCA) cycle for carbon fixation. A couple of the ezymes involved in the prosess were missing which is similar for other simbionts. Canditus E. persephone had a different version of ATP citrate lyase (ACL) that shares a similarity with other symbiotic bacteria. It therefore appears that the ACL in Cand. E. persephone arose from lateral transfer rather than a recent gene duplication event, but additional sequencing of such genes is necessary to verify this theory. As in the known carbon fixation pathways, it appears that this gene exists among divergent lineages within the prokaryotes. Several transporters for the uptake of four carbon molecules were identified. It is therefore possible that at times carbon fixation is a combined effort between host and symbiont.

The large number of genes involved in chemotaxis and the ability to respond to external
carbon sources suggest that Cand. E. Persephone can survive as a heterotroph while free-living in the hydrothermal environment. While living in biofilms on the cuticle of the host or during the infection process, the symbionts would benefit by employing this metabolism.

Required enzymes were identified in the metagenome for the Riftia symbiont to perform sulfide oxidation via a reverse sulfate reduction pathway, involving the enzymes APS reductase and ATP sulfurylase Several genes encoding sulfurtransferases are also present, therefore the use of thiosulfate by the symbiont warrants further investigation. The genomic capacity required to sense and respond to nitrite and nitrate, and to use ammonia to synthesize glutamate and glutamine was also found The host is known to contain ureases and the resulting ammonium can be taken up by the symbiont for biosynthesis.

Clusters of orthologous groups (COG) are used to classify genomic components by functional
category. Campared to many phylogenetically similar species, Cand. E. persephone COG profiles show a commitment to energy production and conversion, signal transduction and defense. The symbionts must provide energy for their own productivity as well as their host’s. The functions of the majority of the signal transduction pathways are unknown and experimentation is necessary to determine their possible roles in host response. The dedication to defence processes in a symbiont may be because response to the initial symbiont infection through the cuticle and mesodermal tissues. Several of the ABC transporters in the genome are annotated as toxin or multidrug exporters.

Cand. E. Persephone also has the genes necessary for a functional flagellum, and 30% of genes in the motility category are involved in chemotaxis, to aid the symbiont in the search for suitable substrates in the highly variable environment of a hydrothermal vent.

The Cand. E. persephone metagenome sheds new light on the Riftia pachyptila symbiosis. The prospect of heterotrophic metabolism while free living opens new doors with respect to the source of bacteria for new generations of tubeworm larvae. Perhaps use of an organic carbon source will lead to successful cultivation of this adaptable bacterium and therefore further study.