Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions

Megan Franz,Todd C Atwood,Kristin L Laidre,Lyle Whyte,Melissa A Mckinney,Esteban Góngora,Denis Roy,Sophie E Watson

doi:10.1038/s41598-021-04340-2

Abstract

Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.

Highlights

Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of iceassociated prey nearly year-round
Mean alpha diversity was qualitatively higher in SB than in EG polar bears for Shannon (SB: 2.74 +/− 0.06; EG: 2.65 +/− 0.07), Inverse Simpson (SB: 9.2 +/− 0.6; EG: 8.3 +/− 0.6), and Faith’s Phylogenetic Diversity (SB: 13.3 +/− 0.4; EG: 12.9 +/− 0.5) (Supplementary Fig. S1), linear models showed no effect of subpopulation for any of these alpha diversity indices (Supplementary Table S1)
Polar bears from the SB subpopulation showed significant differences in gut bacterial composition at multiple bacterial taxonomic levels compared to EG polar bears and an overall greater number of unique and total bacterial genera and amplicon sequence variants (ASVs)

Summary

Introduction

Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of iceassociated prey nearly year-round. Far less studied than those of human, laboratory, or domestic animals[5], the gut microbiomes of many wild animal species have recently been characterized[6] Many of these species host Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Verrucomicrobia as the major bacterial phyla[1]. With climate change-mediated loss of sea ice over the last four decades, SB polar bears spend longer periods of time onshore during the reduced ice season[25,26] This has led to increased access to onshore foods, including blubber, meat, and bones of bowhead whales leftover from local subsistence harvests (‘bone piles’), as well as carcasses of fish, caribou, and birds left nearby[27]

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Results

Conclusion