The skin microbiome (based on 16S) of Antarctic Humpback whales (Megaptera novaeangliae)

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (Illumina MiSeq) of the microbiome (16S) on skin samples of Humpback whales (Megaptera novaeangliae)

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Researchers should cite this work as follows:

Bierlich K, Miller C, DeForce E, Friedlaender A, Johnston D, Apprill A (2019): The skin microbiome (based on 16S) of Antarctic Humpback whales (Megaptera novaeangliae). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antactice_humpback_whale_skin_microbiome&v=1.1

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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This resource has been registered with GBIF, and assigned the following GBIF UUID: 0144ad97-f933-4557-a599-0dd4c736066e.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

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Contacts

Who created the resource:

Kevin Bierlich
Woods Hole Oceanographic Institution Woods Hole US
Carolyn Miller
Woods Hole Oceanographic Institution Woods Hole US
Emelia DeForce
Woods Hole Oceanographic Institution Woods Hole US
Ari Friedlaender
Oregon State University Newport US
David Johnston
Duke University Marine Laboratory Beaufort US
Amy Apprill
Woods Hole Oceanographic Institution Woods Hole US

Who can answer questions about the resource:

Kevin Bierlich
Woods Hole Oceanographic Institution Woods Hole US

Who filled in the metadata:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels BE

Who else was associated with the resource:

User

Geographic Coverage

Healthy humpback whales in te Gerlache Strait, Palmer Deep Canyon and Bransfield Strait (Antarctica)

Bounding Coordinates South West [-68.077, -69.898], North East [-64.046, -61.605]

Taxonomic Coverage

Bacteria and Archaea were targeted using universal primers for the 16S ssu rRNA gene (V4 region)

Domain  Bacteria (Bacteria),  Archaea (Archaea)

Temporal Coverage

Formation Period 2010-2013

Project Data

No Description available

Title The skin microbiome (based on 16S) of Antarctic Humpback whales (Megaptera novaeangliae)
Funding Humpback whale skin biopsy samples were collected under NOAA permit 808-735 and ACA permit 2009-14 as part of NSF OPP awards ANT-07-39483 and 1250208. This project was supported by 67 donors to the “Whale Bacterial Buddies” crowd- funded project supported by WHOI, the Edna Bailey Sussman Fund, and the Michael K. Orbach Enrichment Fund awarded.

The personnel involved in the project:

Kevin Bierlich

Sampling Methods

Skin samples were collected from the upper flank near the dorsal fin of humpback whales via standard biopsy techniques. Specifically, a 68-kg pull crossbow and floating Ceta-Dart darts with 40-mm surgical stainless steel tips collected a small skin and blubber sample roughly 5 mm wide and 20 to 30 mm deep, depending on the angle of the sampling dart on impact. Tips were sterilized using 8.25% concentrated bleach, allowed to dry, cleaned, and then doused in 100% ethyl alcohol before each use. The darts were retrieved by hand and the tips immediately placed into a sterile bag (such that the sample was not contaminated) and on ice for no more than 10 h before transfer to a cryovial via sterile tools for freezing at 80°C. The global positioning system (GPS) location and the regional names of the bay, strait, etc. were recorded for each skin sample collected. One skin sample, w132a, was collected from an acoustic tag placed on the animal.

Study Extent Ninety-four skin samples were collected from 89 humpback whales in 12 different locations along the Western Antarctic Peninsula (WAP) during May and June 2010 (fall/late foraging season) and January and February 2013 (early summer/early foraging season). Five individuals were sampled twice during the study; three individuals were resampled on the same day, one a week later, and one was sampled in 2010 and 2013.

Method step description:

  1. DNA was extracted from 1 to 30 mg of the top layer of the epidermis, with an average of 13 mg, from each sample using a DNeasy tissue kit (Qiagen, Valencia, CA, USA) and quantified using the Invitrogen Qubit 2.0 assay fluorometer (Life Technologies, Beverly, MA, USA). The V4 region of the SSU rRNA gene was amplified using barcoded primers (515F-Y, 5=-GTGYCAGCMGCCGCGGTAA-3=; and 806RB, 5=-GGACTACNVGGGTWTCTAAT-3=), broadly targeting bacteria and archaea. Samples and sterile water (negative control) were amplified in triplicate using PCR on a S1000 thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA), as follows: 2 min at 95°C, followed by 30 to 35 cycles of 20 s at 95°C, 15 s at 55°C, and 5 min at 72°C, followed by 10 min at 72°C. Triplicate PCR mixtures contained 1 ul of DNA, 5 ul of GoTaq 5 Flexi buffer, 14.75 l of H2O, 2.5 l of a 25 nM MgCl2 solution, 200 nM each dinucleoside triphosphate (dNTP), and 0.25 l of a 5 units/ l GoTaq DNA polymerase solution per sample, along with 200 nM each primer. After PCR, amplification was assessed by mixing 5u l of each sample with 1 ul of 10,000 Sybr Safe dye run on a 1% agarose–Tris- borate-EDTA (agarose-TBE) gel. The replicate reaction mixtures were purified using Agencourt AMPure XP beads (Beckman Coulter, Inc., Pasadena, CA, USA) and quantified using the Qubit assay. Barcoded amplicons were sequenced using a 2x250-bp MiSeq Illumina format at the University of Illinois W. M. Keck Center for Comparative and Functional Genomics.

Bibliographic Citations

  1. Bierlich, K. C., Miller, C., DeForce, E., Friedlaender, A. S., Johnston, D. W., & Apprill, A. (2018). Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula. Appl. Environ. Microbiol., 84(5), e02574-17. https://doi.org/10 .1128/AEM.02574-17

Additional Metadata

Alternative Identifiers 0144ad97-f933-4557-a599-0dd4c736066e
https://ipt.biodiversity.aq/resource?r=antactice_humpback_whale_skin_microbiome