Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission

Abstract

Background: The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis.

Results: We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment.

Conclusion: Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome.

Keywords: Animal microbiomes; Holobiont; Horizontal transmission; Microbiome transmission; Oyster larvae microbiomes; Sydney Rock Oyster; Symbiosis; Vertical transmission.

Fig. 1

Stacked bar plot of the relative abundance of bacterial orders comprising microbial communities associated with oyster tissues (gill, mantle, stomach, gonad, gametes and larvae) and their environment (water and algae). Relative abundance was calculated within each sample and ASVs that made up less than 1% of the sample were excluded

Fig. 2

Non-metric multidimensional scaling (NMDS) plots of Sorensen-Dice dissimilarities of microbial communities associated with oyster larvae, gametes, and their environment. Colored by A larval stage day, adult tissues and gametes, B larvae stage day and environment, and C family. Group centroids are defined by the mean dissimilarities for each group

Fig. 3

Force directed network of the ASVs in our data set with a relative abundance > 0.001 (n = 4420). Every dot identifies an ASV and the edges connect the ASVs to the sample type they were found in. Colors represent different modules identified in modularity analysis of the network

Fig. 4

Heat map of the 30 ASVs that are the most important contributors to a Random Forest classification model that was trained to predict larval stage from microbial community composition. The heat map shows the relative abundance of the ASVs in samples of the different larval stages (Day), samples are clustered using Sorensen-Dice dissimilarity distances. More detailed taxonomic information can be found in Additional file 1: Table S4. Stars denote ASVs that were not detected in tank water and algae samples with a relative abundance greater than 1%

Fig. 5

Box and whisker plots of the relative abundances of ASVs identified as core members (present at greater than 1% abundance in more than 50% of samples) in the eggs, sperm, and all larval stages. This analysis excluded all ASVs detected in tank water and algae samples with a relative abundance greater than 1%. More detailed taxonomic information can be found in Additional file 1: Table S5

Fig. 6

Box and whiskers plots of the percentage of ASVs shared A between each larval stage and their parent eggs and sperm, and B between adjacent larval stages. This analysis excluded all ASVs detected in tank water and algae samples with a relative abundance greater than 1%