Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome

Abstract

The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we sampled the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.

Keywords: bacteriophage; carcharhinid; denticle; epidermis; metagenomics; shark; virome.

Figure 1

(A) Sampling locations on Norfolk Island, as indicated by red dots. The approximate location of the water sample is represented by a blue dot. (B) Photograph of a “super-sucker” microbiome sampling device. (C) Microbiome sampling on the dorsal flank of a C. obscurus individual.

Figure 2

Box-and-whisker plot of richness (red) and Simpson’s diversity (blue) at the strain level for each shark species and the lone water column sample.

Figure 3

Bubble plot showing the relative abundances of all viral genera that contributed at least 0.5% of the total annotated reads for at least one virome sample. Larger bubbles denote greater abundance. The bacterial host taxa commonly associated with each genus (according to the NCBI taxonomy browser) are listed in the column to the left. Pie charts indicate the proportions of annotated viruses that infect eukaryotic (black), prokaryotic (blue), and unknown (grey) hosts for each shark species.

Figure 4

Three-dimensional nMDS plots showing the similarity of virome community composition at the family, host-genus, and strain levels. Plots are angled to reflect the separation of shark viromes from the lone water column sample, as well as the dispersion of shark viromes relative to each other.

Figure 5

Electron microscopy images of the dermal denticles of C. obscurus (left) and G. cuvier (right) (photo by Erin Dillon and Jorge Ceballos). The scale bar represents a length of 100 μm.