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Marine Ecology Progress Series

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MEPS 704:131-147 (2023)  -  DOI:

Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations

Megan Franz1, Lyle Whyte1, Todd C. Atwood2, Damian Menning2, Sarah A. Sonsthagen2,3, Sandra L. Talbot2,4, Kristin L. Laidre5,6, Emmanuel Gonzalez7,8,9, Melissa A. McKinney1,*

1Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
2U.S. Geological Survey (USGS), Alaska Science Center, University Drive, Anchorage, AK 99508, USA
3U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Research Unit, University of Nebraska-Lincoln, School of Natural Resources, Lincoln, NE 68583, USA
4Far Northwestern Institute for Art and Science, Anchorage, AK 99501, USA
5Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA
6Greenland Institute of Natural Resources, PO Box 570, Nuuk 3900, Greenland
7Canadian Centre for Computational Genomics, McGill Genome Centre, Montréal, QC H3A 0G1, Canada
8Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
9Gerald Bronfman Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada
*Corresponding author:

ABSTRACT: This study developed and evaluated DNA metabarcoding to identify the presence of pinniped and cetacean prey DNA in fecal samples of East Greenland (EG) and Southern Beaufort Sea (SB) polar bears Ursus maritimus sampled in the spring of 2015-2019. Prey DNA was detected in half (49/92) of all samples, and when detected, ringed seal Pusa hispida was the predominant prey species, identified in 100% (22/22) of EG and 81% (22/27) of SB polar bear samples with prey DNA detected. Bearded seal Erignathus barbatus DNA was found in 19% (5/27) of SB polar bear samples for which prey DNA was detected. Prey DNA detection frequencies and relative abundances were compared to estimates from quantitative fatty acid signature analysis (QFASA) for a subset of SB polar bears. Ringed seal and bearded seal were the main prey identified by both methods, but QFASA also identified 2 cetacean prey species not found by prey DNA. Differences in DNA metabarcoding vs. QFASA results were likely related to the different dietary timescales captured by each approach, i.e. short-term vs. long-term diet, respectively. Prey DNA detection, sex/age class, and subpopulation significantly explained variation in polar bear gut bacterial composition. Polar bear samples with prey DNA detected were associated with higher abundances of the bacterial classes Clostridia and Bacilli and lower abundances of Negativicutes. Fecal DNA metabarcoding is thus useful for identifying recent prey of polar bears, complementing quantitative and likely longer-term QFASA estimates, and may help understand variation in the polar bear gut microbiome.

KEY WORDS: Diet composition · DNA metabarcoding · QFASA · Fatty acid signatures · Marine mammal · Genomics · Arctic marine ecology

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Cite this article as: Franz M, Whyte L, Atwood TC, Menning D and others (2023) Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations. Mar Ecol Prog Ser 704:131-147.

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