Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts

The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not been well studied in marine environments. Here, we analysed the composition of the symbiont community in two deep-sea, Bathymodiolus mussel species along their known distribution range at hydrothermal vents on the Mid-Atlantic Ridge, with a focus on the hybrid zone where they interbreed. In-depth metagenomic analyses of the sulphur-oxidising symbionts of 30 mussels from the hybrid zone, at a resolution of single nucleotide polymorphism analyses of ~2500 orthologous genes, revealed that parental and hybrid mussels (F2–F4 generation) have genetically indistinguishable symbionts. While host genetics does not appear to affect symbiont composition in these mussels, redundancy analyses showed that geographic location of the mussels on the Mid-Atlantic Ridge explained most of the symbiont genetic variability compared to the other factors. We hypothesise that geographic structuring of the free-living symbiont population plays a major role in driving the composition of the microbiome in these deep-sea mussels

Metagenomic analyses of a deep-sea mussel symbiosis

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

THE PLASTISPHERE – UNVEILING POLYMER SPECIFIC MICROORGANISMS

There is still no consistency concerning the microbial community compositions on synthetic polymers and other surfaces (e.g. glass) in the marine environment. Moreover, there is a need to identify those microorganisms that are preferentially able to colonize and interact with synthetic polymer surfaces, as opposed to generalists that colonize other surfaces. We hypothesized that i.) polymer specific microorganisms are tightly attached to the polymeric surface and ii.) a general core community is building the upper biofilm layers of all surfaces including plastics. Accordingly we developed a new high-pressure treatment technique to remove the upper biofilm layers and to further isolate polymer specific microorganisms. Five different synthetic polymer films and glass were incubated in situ for 21 months in a seawater flow through system. Those were high-pressure treated and thereafter used as a source for re-colonisation of the same sterile polymer. Re-colonization was proven by fluorescent microscopy. Re-colonized polymers were further incubated in vitro before subjected to enrichments and isolated on HaHa_100 agar. Isolates were dereplicated by MALDI-TOF (matrix assisted laser desorption/ionization time-of-flight). To characterize the re-colonization process isolates were identified by RNA gene sequencing and re-colonized polymers, the untreated biofilm and the polymer surface were visualized via Scanning Electron microscopy. Our findings indicate the presence of polymer specific microorganisms which could be involved in polymer degradation processes