Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari).

BACKGROUND: Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a 'natural' host microbiome. Focusing on an endangered elasmobranch species-the whitespotted eagle ray Aetobatus narinari-we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome. RESULTS: Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and ß-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. ß-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays. CONCLUSION: For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health.

The distribution of manta rays in the western North Atlantic Ocean off the eastern United States.

In 2018, the giant manta ray was listed as threatened under the U.S. Endangered Species Act. We integrated decades of sightings and survey effort data from multiple sources in a comprehensive species distribution modeling (SDM) framework to evaluate the distribution of giant manta rays off the eastern United States, including the Gulf of Mexico. Manta rays were most commonly detected at productive nearshore and shelf-edge upwelling zones at surface thermal frontal boundaries within a temperature range of approximately 20-30 °C. SDMs predicted highest nearshore occurrence off northeastern Florida during April, with the distribution extending northward along the shelf-edge as temperatures warm, leading to higher occurrences north of Cape Hatteras, North Carolina from June to October, and then south of Savannah, Georgia from November to March as temperatures cool. In the Gulf of Mexico, the highest nearshore occurrence was predicted around the Mississippi River delta from April to June and again from October to November. SDM predictions will allow resource managers to more effectively protect manta rays from fisheries bycatch, boat strikes, oil and gas activities, contaminants and pollutants, and other threats.

Elasmobranch microbiomes: emerging patterns and implications for host health and ecology.

Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has now begun to explore the role of body-associated microbiomes in shaping elasmobranch health. Here, we review the burgeoning efforts to understand elasmobranch microbiomes, highlighting microbiome variation among gastrointestinal, oral, skin, and blood-associated niches. We identify major bacterial lineages in the microbiome, challenges to the field, key unanswered questions, and avenues for future work. We argue for prioritizing research to determine how microbiomes interact mechanistically with the unique physiology of elasmobranchs, potentially identifying roles in host immunity, disease, nutrition, and waste processing. Understanding elasmobranch-microbiome interactions is critical for predicting how sharks and rays respond to a changing ocean and for managing healthy populations in managed care.

First insights into the vertical habitat use of the whitespotted eagle ray Aetobatus narinari revealed by pop-up satellite archival tags.

The whitespotted eagle ray Aetobatus narinari is a tropical to warm-temperate benthopelagic batoid that ranges widely throughout the western Atlantic Ocean. Despite conservation concerns for the species, its vertical habitat use and diving behaviour remain unknown. Patterns and drivers in the depth distribution of A. narinari were investigated at two separate locations, the western North Atlantic (Islands of Bermuda) and the eastern Gulf of Mexico (Sarasota, Florida, U.S.A.). Between 2010 and 2014, seven pop-up satellite archival tags were attached to A. narinari using three methods: a through-tail suture, an external tail-band and through-wing attachment. Retention time ranged from 0 to 180 days, with tags attached via the through-tail method retained longest. Tagged rays spent the majority of time (82.85 ± 12.17% S.D.) within the upper 10 m of the water column and, with one exception, no rays travelled deeper than ~26 m. One Bermuda ray recorded a maximum depth of 50.5 m, suggesting that these animals make excursions off the fore-reef slope of the Bermuda Platform. Individuals occupied deeper depths (7.42 ± 3.99 m S.D.) during the day versus night (4.90 ± 2.89 m S.D.), which may be explained by foraging and/or predator avoidance. Each individual experienced a significant difference in depth and temperature distributions over the diel cycle. There was evidence that mean hourly depth was best described by location and individual variation using a generalized additive mixed model approach. This is the first study to compare depth distributions of A. narinari from different locations and describe the thermal habitat for this species. Our study highlights the importance of region in describing A. narinari depth use, which may be relevant when developing management plans, whilst demonstrating that diel patterns appear to hold across individuals.

Phylogenomics and species delimitation for effective conservation of manta and devil rays.

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

Fishery gear interactions from stranded bottlenose dolphins, Florida manatees and sea turtles in Florida, U.S.A.

Documenting the extent of fishery gear interactions is critical to wildlife conservation efforts, especially for reducing entanglements and ingestion. This study summarizes fishery gear interactions involving common bottlenose dolphins (Tursiops truncatus truncatus), Florida manatees (Trichechus manatus latirostris) and sea turtles: loggerhead (Caretta caretta), green turtle (Chelonia mydas), leatherback (Dermochelys coriacea), hawksbill (Eretmochelys imbricata), Kemp's ridley (Lepidochelys kempii), and olive ridley (Lepidochelys olivacea) stranding in Florida waters during 1997-2009. Fishery gear interactions for all species combined were 75.3% hook and line, 18.2% trap pot gear, 4.8% fishing nets, and 1.7% in multiple gears. Total reported fishery gear cases increased over time for dolphins (p<0.05), manatees (p<0.01), loggerheads (p<0.05) and green sea turtles (p<0.05). The proportion of net interaction strandings relative to total strandings for loggerhead sea turtles increased (p<0.05). Additionally, life stage and sex patterns were examined, fishery gear interaction hotspots were identified and generalized linear regression modeling was conducted.

Lacaziosis and lacaziosis-like prevalence among wild, common bottlenose dolphins Tursiops truncatus from the west coast of Florida, USA.

Lacaziosis (lobomycosis; Lacazia loboi) is a fungal skin disease that naturally occurs only in humans and dolphins. The first reported case of lacaziosis in a bottlenose dolphin Tursiops truncatus occurred in 1970 in Sarasota Bay, Florida, USA, and subsequent photo-ID monitoring of the Sarasota Bay dolphin population has revealed persistence of the disease. The objectives of this study were to estimate lacaziosis prevalence (P) in 2 bottlenose dolphin populations on the west coast of Florida (Sarasota Bay and Charlotte Harbor) and compare disease occurrence to other published estimates of lacaziosis in dolphin populations across the globe. Historic photographic records of dolphins captured and released for health assessment purposes (Sarasota Bay) and photo-ID studies (Charlotte Harbor) were screened for evidence of lesions consistent with lacaziosis. Health assessment data revealed a prevalence of lacaziosis in the Sarasota Bay bottlenose dolphin population between 2 and 3%, and analyses of photo-ID data provided a lacaziosis-like prevalence estimate of 2% for Charlotte Harbor dolphins. With the exception of lacaziosis prevalence estimates for dolphins inhabiting the Indian River Lagoon (P = 0.068; P = 0.12), no statistically significant differences were seen among Sarasota Bay, Charlotte Harbor, and other published estimates. Although lacaziosis is a rare disease among these dolphin populations, studies that assess disease burden among different populations can assist with the surveillance of this zoonotic pathogen.