Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment

Abstract

Horizontally transmitted symbioses usually house multiple and variable symbiont genotypes that are acquired from a much more diverse environmental pool via partner choice mechanisms. However, in the deep-sea hydrothermal vent tubeworm Riftia pachyptila (Vestimentifera, Siboglinidae), it has been suggested that the Candidatus Endoriftia persephone symbiont is monoclonal. Here, we show with high-coverage metagenomics that adult R. pachyptila house a polyclonal symbiont population consisting of one dominant and several low-frequency variants. This dominance of one genotype is confirmed by multilocus gene sequencing of amplified housekeeping genes in a broad range of host individuals where three out of four loci ( atpA , uvrD and recA ) revealed no genomic differences, while one locus ( gyrB ) was more diverse in adults than in juveniles. We also analysed a metagenome of free-living Endoriftia and found that the free-living population showed greater sequence variability than the host-associated population. Most juveniles and adults shared a specific dominant genotype, while other genotypes can dominate in few individuals. We suggest that although generally permissive, partner choice is selective enough to restrict uptake of some genotypes present in the environment.

Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis

“…Besides their putative function in effector protein export, symbiont membrane proteins may also lead to bacterial strain adaptation. The Riftia symbiont population is polyclonal, i.e., although there is only one 16S rRNA phylotype, this phylotype consists of several distinct strains (20). T4P system-mediated exchange of genetic material between different symbiont strains would add to this diversity in the symbiosis and might additionally enable exchange of symbiosis-related genes within the free-living “ Ca.…”

“…The uncultured gammaproteobacterial Riftia symbiont, a single 16S rRNA phylotype tentatively named “ Candidatus Endoriftia persephone” (19–21), densely populates bacteriocytes in the host trophosome, a specialized organ that fills most of the worm’s body cavity (14). The bacteria oxidize inorganic reduced compounds, such as hydrogen sulfide, to generate energy for carbon fixation (13, 22–26).…”

Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish

“…The bacterial housekeeping genes (atpA, recA, and gyrB) were selected (Polzin et al, 2019) for PCR amplifications with a set of custom primers ( Supplementary Table S2). DNA extracted from the guts was used as template.…”

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

“…Although the symbiont population consists of a single 16S rRNA phylotype (comprising one dominating and several minor genotypes; Polzin et al, 2019 ), it was previously shown to exhibit remarkable metabolic versatility and redundancy: As demonstrated by proteomic analyses, symbionts from the same host animal expressed enzymes of two CO 2 fixation pathways, the Calvin cycle and the reverse tricarboxylic acid (rTCA) cycle, as well as enzymes for both glycogen generation and glycogen degradation ( Markert et al, 2007 ; Markert et al, 2011 ; Gardebrecht et al, 2012 ; Hinzke et al, 2019 ). Moreover, proteins involved in utilization of hydrogen sulfide and thiosulfate as energy sources were expressed simultaneously by the same symbiont population; as were proteins for the use of nitrate and oxygen as electron acceptors ( Markert et al, 2011 ).…”