Ephemeral signatures of phylosymbiosis in dermal microbiomes within the requiem shark family (Carcharhinidae)

The elasmobranch dermal microbiome may be important for buffering effects of environmental stress on host health and population viability via functional metabolic interactions. Dermal microbiomes among elasmobranch orders co-vary with host phylogeny (phylosymbiosis), indicating functional co-evolution with their hosts at deep phylogenetic splits. However, the extent of phylosymbiosis and potential for functional co-evolution within particularly species-rich elasmobranch families is unknown. Here we re-analyse Illumina amplicon sequence data from the 16S rRNA gene from eight Carcharhinid shark species (plus one Ginglymostomatid outgroup) across six independent studies and explicitly examine the extent of phylosymbiosis in dermal microbiomes within this family. We found extensive divergence in OTU abundance and functional metabolic capacity between studies, driven by disparity in OTU sharing and probably reflecting geographical and seasonal factors. Total microbiome structure was incongruent with shark phylogeny, providing no evidence for phylosymbiosis when considering all species and OTUs. However, using bootstrapping and subsampling methods, we identified several subsets of OTUs where Bray-Curtis dissimilarity supported perfect topological congruence with shark phylogeny or strong associations with phylogenetic distances, but not both. Partial Mantel tests identified ten candidate OTUs that supported a moderately strong signal of phylosymbiosis across all shark species and included the immunostimulant skin symbiont genera Lactiplantibacillus and Alcaligenes. Overall, this provides provisional evidence for phylosymbiosis in a minority fraction of the elasmobranch dermal microbiome within the Carcharhinidae family and will necessitate coordinated large-scale studies to establish generality of these findings.