The Epidermal Microbiome Within An Aggregation of Leopard Sharks (Triakis Semifasciata) Has Taxonomic Flexibility With Gene Functional Stability Across Three Time-Points

Background: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein rich mucus that influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) across three time-points to identify links between microbial groups and host metabolism. Our aims include 1) describing the variation of microbiome taxa over time and identify those members which are recurrent (present across all time-points, 2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points, 3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and 4) identifying whether the metabolisms are share across microbial genera or found in specific taxa. Results: Microbial members of the microbiome showed high similarity between all individuals (average similarity: 82.74) with relative abundance of those members varying across years, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter and Sphingopxis being consistently abundance across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relative abundant genera forming three recurrent groups. The microbiome also displayed high functional similarity between individuals (average similarity: 97.65) with gene function composition being consistent across time-points. Conclusion: These results show that while presence of microbial genera exhibit consistency across time-points, their abundances do fluctuate. Functions however remain stable across time points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We hypothesize this may be the result of the host’s epidermal attributes structuring the microbiome. In addition, we show the co-existence of many microbial genera that carry genes which may enable the microbes to use the nutrients provided by the elasmobranch’s metabolism.

Epidermal Microbiomes of Triakis Semifasciata Are Consistent Across Captive and Wild Environments

Background: Characterizations of sharks-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California), semi-captive (<1 year in captivity; Scripps Institute of Oceanography, California) and wild environments (Moss Landing and La Jolla, California). Results: Here we report captive environments do not drive microbiome composition of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as MAGs revealed a consistent relationship across captive, semi-captive, and wild populations. Conclusions: Our report illustrates the importance of conservation programs for coastal fishes as epidermally-associated microbes of near-shore shark species do not suffer detrimental impacts from long or short-term captivity. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel microbial associations that are consistent across captive gradients.

The Epidermal Microbiome Within An Aggregation of Leopard Sharks (Triakis Semifasciata) Has Taxonomic Flexibility With Gene Functional Stability Across Three Time-Points

Background: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein rich mucus that influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) across three time-points to identify links between microbial groups and host metabolism. Our aims include 1) describing the variation of microbiome taxa over time and identify those members which are recurrent (present across all time-points, 2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points, 3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and 4) identifying whether the metabolisms are share across microbial genera or found in specific taxa. Results: Microbial members of the microbiome showed high similarity between all individuals (average similarity: 82.74) with relative abundance of those members varying across years, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter and Sphingopxis being consistently abundance across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relative abundant genera forming three recurrent groups. The microbiome also displayed high functional similarity between individuals (average similarity: 97.65) with gene function composition being consistent across time-points. Conclusion: These results show that while presence of microbial genera exhibit consistency across time-points, their abundances do fluctuate. Functions however remain stable across time points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We hypothesize this may be the result of the host’s epidermal attributes structuring the microbiome. In addition, we show the co-existence of many microbial genera that carry genes which may enable the microbes to use the nutrients provided by the elasmobranch’s metabolism.

Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California

ABSTRACTDuring March to August of 2017, hundreds of leopard sharks (Triakis semifasciata) stranded and died on the shores of San Francisco Bay, California, USA. Similar mass stranding events occurred in 1967 and 2011, yet analysis of these epizootics was incomplete and no etiology was confirmed. Our investigation of the most recent epizootic revealed severe meningoencephalitis in stranded sharks, raising suspicion for infection. On this basis, we pursued a strategy for unbiased pathogen detection using metagenomic next-generation sequencing followed by orthogonal validation and further screening. We show that the ciliated protozoan pathogen, Miamiensis avidus, was present in the central nervous system of leopard (n=12) and other shark species (n=2) that stranded in San Francisco Bay, but absent in leopard sharks caught elsewhere. Whereas this protozoan has previously been implicated in devastating outbreaks in teleost marine fish, our findings represent the first report of a ciliated protozoan infection in wild elasmobranchs. This discovery highlights the benefits of adopting unbiased metagenomic sequencing in the study of wildlife health and disease.