Document of dataset 6266

Dataset record

Type
Metadata dataset
title in English
The skin microbiome (based on 16S) of Antarctic Humpback whales (Megaptera novaeangliae)
Description in English
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.
Abstract in English
Amplicon sequencing dataset (Illumina MiSeq) of the microbiome (16S) on skin samples of Humpback whales (Megaptera novaeangliae).
License
https://spdx.org/licenses/CC-BY-4.0.html
bibliographicCitation
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
Version
1.1

Temporal coverage

Temporal
Start date
2010-01-01
End date
2013-01-01

Geographical coverage

Spatial
PSW, Antarctica, Bransfield Strait

Thesaurus terms

Keyword
Dna sequencing
Metadata

Taxonomic terms

Taxon keywords
archaea
Bacteria
Megaptera novaeangliae

Ownerships

creator
Kevin Charles Bierlich
creator
Woods Hole Oceanographic Institution
creator
Carolyn Miller
creator
Woods Hole Oceanographic Institution
creator
Emelia DeForce
creator
Woods Hole Oceanographic Institution
creator
Ari Friedlaender
creator
Oregon State University
creator
David Johnston
creator
Marine Laboratory
creator
Amy Apprill
creator
Woods Hole Oceanographic Institution
contactPoint
Kevin Charles Bierlich
contactPoint
Woods Hole Oceanographic Institution

Dataset references

record
Antarctic Ocean Biodiversity Information System
related
Register of Antarctic Species(had role: partially included in)

Document metadata

date created
2019-04-08
date modified
2019-04-10