Southern Beaufort Sea Polar Bear Diet and Gut Microbiota Data, 2015-2019

Polar bears were captured or biopsy-darted on the sea ice of Alaska's southern Beaufort Sea region in spring, 2015-2016 and 2018-2019. Upon observation, polar bear age class and sex class were determined and recorded. Age and sex class for captured bears was confirmed via physical examination. Captured bears were measured and weighed. Adipose tissue iopsy samples were collected from the rump and stored in a glass vial. Fecal samples were collected from the rectum and stored in a Whirlpack plastic bag. Samples were collected from yearling, subadult, and adult individuals. Unmarked bears were microchipped, tattooed, and ear-tagged with a unique number. Buccal swabs were collected from all captured bears and used to determine each individual's genetic ID. Samples collected from biopsy darted bears consist of hair, skin, and adipose tissue. The skin was separated from the adipose tissue sample and used to derive a genetic ID for each bear darted. Adipose tissue and fecal samples were then used in diet and gut microbiome analyses, respectively, as described below.

Adipose tissue samples were collected from yearling, subadult and adult polar bears from Alaska's southern Beaufort Sea region in spring, 2015-2016 and 2018-2019. Adipose tissue samples were placed in a glass vial and into a cooler immediately after collection and later transferred to a -80 degree Fahrenheit freezer for long-term storage (McKinney et al. 2017).

Fecal samples were collected from yearling, subadult and adult polar bears from Alaska's southern Beaufort Sea region in spring, 2015-2016 and 2018-2019. Fecal samples were placed in plastic whirlpack bags, stored at 0 degrees Fahrenheit initially, and later transferred to a -80 degree Fahrenheit freezer for long-term storage.

Fatty acid analysis was performed on polar bear adipose tissues. Diet estimates based on fatty acid signatures were determined via quantitative fatty acid signature analysis (QFASA; Iverson et al. 2004, McKinney et al. 2017) using the QFASA package in R (Bromaghin 2016). QFASA determines the proportion of individual prey species consumed based on the weighted mixture of prey fatty acid signatures. Estimates from QFASA were adjusted using calibration coefficients (CC) from mink (Mustela vison) fed a marine diet. CC-corrected polar bear signatures were analyzed using the Kullback-Liebler distance measure (McKinney et al. 2017).

Fecal samples were analyzed using 16S rRNA bacterial DNA amplification and sequencing protocols as described in Watson et al. (2019, 2021) to characterize gut microbiome communities. Shannon, Faith's, and inverse Simpson indices of bacterial alpha diversity were calculated as described in Watson et al. (2019, 2021) and below.

Prey-specific primer sets to amplify pinniped DNA were developed as described in Menning (2017). Briefly, complementary DNA sequences of mitochondrial loci, cytochrome b (Cytb), and cytochrome oxidase 1 (CO1) were compiled from the NCBI GenBank nucleotide repository (http://www.ncbi.nlm.nih.gov) for marine vertebrate species known to co-occur with or be a component of southern Beaufort Sea polar bear diets and used for primer design. The selected primer pairs were tested for successful amplification in prey samples that were available in the lab from earlier projects.

The fecal microbiota of sampled bears was composed of 1221 operational taxonomic units (OTUs) encompassing 25 bacterial phyla. The diversity of phyla was measured using Shannon, Inverse Simpson, and Faith's Phylogenetic diversity indices (Watson et al. 2019). The Shannon Index takes into account both abundance and evenness of phyla present; the Inverse Simpson Index is less sensitive to taxa richness; and Faith's Phylogenetic Index differs from the other two indices in that it uses phylogenetic distance to calculate diversity. Taken together, the three diversity indices can be used to infer the robustness of bacterial phyla diversity estimates.