Abstract
Profiles of symbiotic microbial communities (“microbiomes”) can provide insight into the natural history and ecology of their hosts. Using high throughput DNA sequencing of the 16S rRNA V4 region, microbiomes of five shark species in South Florida (nurse, lemon, sandbar, Caribbean reef, and tiger) have been characterized for the first time. The microbiomes show species specific microbiome composition, distinct from surrounding seawater. Shark anatomical location (gills, teeth, skin, cloaca) affected the diversity of microbiomes. An in-depth analysis of teeth communities revealed species specific microbial communities. For example, the genus Haemophilus, explained 7.0% of the differences of the teeth microbiomes of lemon and Caribbean reef sharks. Lemon shark teeth communities (n = 11) contained a high abundance of both Vibrio (10.8 ± 26.0%) and Corynebacterium (1.6 ± 5.1%), genera that can include human pathogenic taxa. The Vibrio (2.8 ± 6.34%) and Kordia (3.1 ± 6.0%) genera and Salmonella enterica (2.6 ± 6.4%) were the most abundant members of nurse shark teeth microbial communities. The Vibrio genus was highly represented in the sandbar shark (54.0 ± 46.0%) and tiger shark (5.8 ± 12.3%) teeth microbiomes. The prevalence of genera containing potential human pathogens could be informative in shark bite treatment protocols and future research to confirm or deny human pathogenicity. We conclude that South Florida sharks host species specific microbiomes that are distinct from their surrounding environment and vary due to differences in microbial community composition among shark species and diversity and composition among anatomical locations. Additionally, when considering the confounding effects of both species and location, microbial community diversity and composition varies.
Highlights
Microbiomes help compose the “holobiont” or the total individual, which includes microbiota co-adapted with the macro-organismal host
High-throughput sequencing of 120 samples from 30 sharks and 22 water samples which were taken once per trip produced a total of 12,374,571 high quality 16S rRNA reads, which resulted in 26,309 operational taxonomic unit (OTU) after QIIME processing
Non-metric dimensional scaling (R2 = 0.77, stress = 0.1833) demonstrates the similarities between surrounding water in shark microbial communities, which is consistent with shark-associated microbial communities that could be enriched from the water column
Summary
Microbiomes help compose the “holobiont” or the total individual, which includes microbiota co-adapted with the macro-organismal host. While there is no direct support for holobiont coevolution in sharks, the general concept as shown in other organisms is worth considering (Zilber-Rosenberg and Rosenberg, 2008; Pita et al, 2018; Pratte et al, 2018; Freed et al, 2019; van der Loos et al, 2019; Carthey et al, 2020). Various anatomical parts within an individual organism can harbor significantly different microbiome communities. For example, individuals have significantly different microbiome compositions by anatomical location, likely stemming from a complex combination of host behavior, habitat, pH, diet, and varying life stage exposure to microbes (Human Microbiome Project Consortium, 2012a,b; Lloyd-Price et al, 2017; Carlson et al, 2018)
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