Metagenomic analyses of a deep-sea mussel symbiosis

Abstract

Symbiosis is ubiquitous across all domains of life. Deep-sea hydrothermal vents are home to extraordinary examples of symbiosis. Fascinating symbiotic communities are fuelled by reduced chemical compounds released from fissures in the oceanic crust. Chemosynthetic symbionts use the energy of reduced chemicals energy to produce biomass and to support their animal hosts to thrive in environments where nutrients are scarce. Bathymodiolus mussels are among the most successful fauna in such habitats. Within their gills, they host sulphur- and methane-oxidising symbionts, among others. These symbiotic bacteria are acquired from the environment, suggesting the existence of a free-living stage. The mussels are well studied for their symbionts’ physiology, host-symbiont interaction and the host's immune system. Some interesting questions, however, have remained unresolved. I used metagenomics, a versatile and cultivation-independent approach, to address some of these questions:

What can a mussel hybrid zone reveal about factors driving symbiont composition? Hybrid zones provide an opportune system to study evolutionary processes in their natural context. Analysis of symbionts from co-occurring hybrid and parental mussels at the Broken Spur vent field allowed me to identify whether host genetics, geography, or the environment, is driving the symbiont community composition. Phylogenomics revealed the presence of a new location-specific symbiont subspecies. Symbionts of hybrids and parental mussels could not be distinguished genetically. Thus, host genetics seem to have little influence on the symbiont community. Instead, geography explained much of the observed symbiont variation. Whether the symbiont population structure results from a geographical structuring of the free-living pool of symbionts remains to be elucidated.

Are free-living symbionts present in the water column? Knowledge about the free-living stage of horizontally transmitted symbionts can give insights into the symbiont uptake and the specificity of the association. To investigate the presence of symbionts in the free-living stage, I screened for symbiont marker genes in water metagenomes. While symbiont-related genes were detected, they always co-occurred with host DNA. This raises the question whether the symbionts in my data are free-living or still associated with their hosts. The results suggest that transmission via host particles may be more important than anticipated. To further future research based on the experiences of this work, I suggest sampling schemes to learn more about the free-living stage.

Are mitochondrial and nuclear genomes congruent in Bathymodiolus? Species assignment is often performed using mitochondrial marker genes. Mitochondrial inheritance in bivalves is often complex, and incongruent nuclear and mitochondrial genomes have been described for the Bathymodiolus hybrid zone. I compared mitochondrial clades to clustering based on the nuclear genome and found incongruences for 10 % of the 175 analysed mussels. The high-resolution analysis further revealed a lack of subpopulation structure in conspecific mussels from different sites. Both findings suggest a strong genetic connectivity of populations at the Mid-Atlantic Ridge, probably enabled by long-distance migration of planktotrophic larvae. The biological processes underlying the mitonuclear discordance are exciting topics for future analyses.

Altogether, the research presented in this thesis enhances our understanding of the symbiotic association in Bathymodiolus mussels and provides the basis for further population genomic studies of host, symbionts and the free-living bacterial community.