Application of high-resolution metagenomics to study symbiont population structure across individual mussels

Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota and its consequences in shaping population pangenomes is poorly characterized. Here we show that chemosynthetic symbionts (Sulfur-oxidizing or SOX and Methane-oxidizing or MOX) of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strain sequences from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel lifespan, and individual hosts show a high degree of genetic isolation. By additionally reconstructing population pan genomes, we reveal that gene content differences between mussel symbiont communities reflect the differences in strain composition; thus, strains belonging to the same monophyletic group share most of their genes. Furthermore, for both symbionts, the accessory gene content is over-represented in functions related to genome integrity. Compared to SOX, the MOX pan-genome is larger and has a smaller fraction of accessory genes. We find that MOX contains more genes related to cell motility and mobile genetic elements. Altogether, our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We suggest that this geographic isolation among symbiont populations from individual mussels limits the exposure of symbionts to mobile genetic elements. In addition, the differences between both species suggest that the two symbionts have different ecological traits, where the association of MOX with the host occurred more recently and has a more facultative character that may involve an active free-living phase. We conclude that bacterial colonization dynamics over the host life cycle are an important determinant of population structure and genome evolution of horizontally transmitted symbionts

Currency, Exchange, and Inheritance in the Evolution of Symbiosis

Highlights: Inspired by the evolution of eukaryotic organelles, we propose a conceptual framework to study the evolutionary and ecological drivers of symbiosis, including three main elements: a currency, mechanisms of currency exchange, and inheritance. Currency in symbiosis is the type resources that species in a beneficial symbiosis gain from their partner. Currency exchange is a complex process that requires molecular adaptations in one or both partners. We identify two distinct but not mutually exclusive initial evolutionary imperatives for the establishment of symbiosis, termed currency first, in which the initial interaction stems from a common currency exchange between the interacting partners to complement their environmental requirements, and transmission first, in which stable transgenerational transmission precedes the evolution of currency exchange. Symbiotic interactions between eukaryotes and prokaryotes are widespread in nature. Here we offer a conceptual framework to study the evolutionary origins and ecological circumstances of species in beneficial symbiosis. We posit that mutual symbiotic interactions are well described by three elements: a currency, the mechanism of currency exchange, and mechanisms of symbiont inheritance. Each of these elements may be at the origin of symbiosis, with the other elements developing with time. The identity of currency in symbiosis depends on the ecological context of the symbiosis, while the specificity of the exchange mechanism underlies molecular adaptations for the symbiosis. The inheritance regime determines the degree of partner dependency and the symbiosis evolutionary trajectory. Focusing on these three elements, we review examples and open questions in the research on symbiosis

Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance

Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared with core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent HGT between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained