Dataset Information

High contributions of sea ice derived carbon in polar bear (Ursus maritimus) tissue.

ABSTRACT: Polar bears (Ursus maritimus) rely upon Arctic sea ice as a physical habitat. Consequently, conservation assessments of polar bears identify the ongoing reduction in sea ice to represent a significant threat to their survival. However, the additional role of sea ice as a potential, indirect, source of energy to bears has been overlooked. Here we used the highly branched isoprenoid lipid biomarker-based index (H-Print) approach in combination with quantitative fatty acid signature analysis to show that sympagic (sea ice-associated), rather than pelagic, carbon contributions dominated the marine component of polar bear diet (72-100%; 99% CI, n = 55), irrespective of differences in diet composition. The lowest mean estimates of sympagic carbon were found in Baffin Bay bears, which were also exposed to the most rapidly increasing open water season. Therefore, our data illustrate that for future Arctic ecosystems that are likely to be characterised by reduced sea ice cover, polar bears will not only be impacted by a change in their physical habitat, but also potentially in the supply of energy to the ecosystems upon which they depend. This data represents the first quantifiable baseline that is critical for the assessment of likely ongoing changes in energy supply to Arctic predators as we move into an increasingly uncertain future for polar ecosystems.

SUBMITTER: Brown TA

PROVIDER: S-EPMC5780053 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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High contributions of sea ice derived carbon in polar bear (Ursus maritimus) tissue.

Brown Thomas A TA Galicia Melissa P MP Thiemann Gregory W GW Belt Simon T ST Yurkowski David J DJ Dyck Markus G MG

PloS one 20180123 1

Polar bears (Ursus maritimus) rely upon Arctic sea ice as a physical habitat. Consequently, conservation assessments of polar bears identify the ongoing reduction in sea ice to represent a significant threat to their survival. However, the additional role of sea ice as a potential, indirect, source of energy to bears has been overlooked. Here we used the highly branched isoprenoid lipid biomarker-based index (H-Print) approach in combination with quantitative fatty acid signature analysis to sho ...[more]

PMID: 29360849

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Project description:Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result, long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9-based depletion method (depletion of abundant sequences by hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion, we discovered ?6,000 high-confidence isoforms and a number of novel genes. This indicates that there is a high diversity of gene isoforms within U. maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.

Dataset Information

High contributions of sea ice derived carbon in polar bear (Ursus maritimus) tissue.

Publications

High contributions of sea ice derived carbon in polar bear (Ursus maritimus) tissue.

Similar Datasets

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