Through the looking glass: Using epidermal microbiomes to peer into the health of Bristol Bay and Cook Inlet beluga whales

Amy Van Cise, Cascadia Research Collective, Olympia, WA, United States; Woods Hole Oceanographic Institution, Woods Hole, WA, United States, Paul R Wade, NOAA Fisheries, Alaska Fisheries Science Center, Seattle, WA, United States, Caroline EC Goertz, Alaska SeaLife Center, Seward, AK, United States, Kathy Burek-Huntington, Alaska Veterinary Pathology Service, Eagle River, AK, United States, Kim Parsons, NOAA Northwest Fisheries Science Center, Seattle, WA, United States, Rod Hobbs, NOAA Fisheries, Alaska Fisheries Science Center, retired, Seattle, WA, United States and Amy Apprill, Woods Hole Oceanographic Institution, Department of Marine Chemistry & Geochemistry, Woods Hole, MA, United States
Abstract:
The Cook Inlet, Alaska population of beluga whales suffered a 47% reduction in abundance between 1994 and 1998, and shows no sign of recovery in the 12 years since the 2006 moratorium on hunting in the region. We examine the epidermal microbiome from individuals in the Cook Inlet population, and compare with healthy and diseased individuals in nearby Bristol Bay, to determine whether individual health status is related to depressed population growth in the region. Skin diseases have been linked to poor health condition in several cetacean species, and changes in epidermal microbiomes have been linked to skin disease in some mammalian species. Ninety samples were collected either from stranded individuals or via biopsy dart from free-ranging whales between 2008 and 2018 in Bristol Bay and Cook Inlet. Whole DNA was extracted from epidermal tissue, and the hypervariable IV region of the small subunit ribosomal RNA gene was targeted and amplified by PCR using primers that target bacteria and archaea. The resulting 8.8 million sequences were aligned to the SSU rRNA gene and filtered for quality, resulting in 6.32 million high-quality sequences that were classified into amplicon sequence variants (ASVs) operational taxonomic units (OTUs) for analyses of phylogeny and biodiversity. Using nonmetric multidimensional scaling (NMDS) to cluster samples, we find strong correlations in microbiome composition between the two regional populations, as well as among years within the Cook Inlet population. Among animals of known health status, we find that microbiome composition varies with health. By identifying the characteristics of epidermal microbiomes associated with unhealthy individuals, we can identify potential health concerns in the Cook Inlet beluga population. Results of these analyses provide insight into the health status of the Cook Inlet beluga population, and may help determine a strategy for their conservation.