Presence and absence of iron and light-related functional genes collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project) (NCEI Accession 0277906)
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title: Presence and absence of iron and light-related functional genes collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project) (NCEI Accession 0277906)
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abstract: This dataset contains biological and survey - biological data collected on ARSV Laurence M. Gould during cruise LMG1401 at Antarctica from 2014-01-01 to 2014-12-31. These data include species. The instruments used to collect these data include Bioanalyzer and Inverted Microscope. These data were collected by Dr Adrian Marchetti of University of North Carolina at Chapel Hill as part of the "Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators (Polar_Transcriptomes)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2019-04-18. The following is the text of the dataset description provided by BCO-DMO: Protein information obtained from samples collected on LMG1411. Dataset Description: Presence absence of iron and light-related functional genes. Protein information obtained from samples collected on LMG1411. Diatom isolates were obtained from the Western Antarctic Peninsula surface waters.
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title: Marchetti, A. (2016) Presence and absence of iron and light-related functional genes collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Dataset version 2016-11-21. https://doi.org/10.1575/1912/bco-dmo.665407.1
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supplementalInformation: Acquisition Description: Nine species of diatoms were isolated from the Western Antarctic Peninsula along the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed using an Olympus CKX41 inverted microscope by single cell isolation with a micropipette (Anderson 2005). Diatom species were identified by morphological characterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with the DNeasy Plant Mini Kit according to the manufacturer’s protocols (Qiagen). Amplification of the nuclear 18S rDNA region was achieved with standard PCR protocols using eukaryotic-specific, universal 18S forward and reverse primers. Primer sequences were obtained from Medlin et al. (1982). The length of the region amplified is approximately 1800 base pairs (bp). Pseudo-nitzschia species are often difficult to identify by their 18S rDNA sequence, therefore, additional support of the taxonomic identification of P. subcurvata was provided through sequencing of the 18S-ITS1-5.8S regions. Amplification of this region was performed with the 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were purified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT (Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were edited using Geneious Pro software ( http://www.geneious.com , Kearse et al., 2012) and BLASTn sequence homology searches were performed against the NCBI nucleotide non-redundant (nr) database to determine species with a cutoff identity of 98%. Diatom phylogenetic analysis was performed with Geneious Pro and included 71 additional diatom 18S rDNA sequences from publically available genomes and transcriptomes, including those in the MMETSP database. Diatom sequences were trimmed to the same length and aligned with MUSCLE (Edgar 2004). A phylogenetic tree was created in Mega with the Maximum-likelihood method of tree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor 1969), and 100 bootstrap replicates. Isolates were maintained at 4 deg C in constant irradiance at intensities of either 10 umol photons m-2 s-1 (low light) or 90 umol photons m-2 s-1 (growth saturating light) and with media containing high and low iron concentrations. Cultures were grown in the synthetic seawater medium, AQUIL, enriched with filter sterilized vitamin and trace metal ion buffer containing 100 umol L-1 EDTA. The growth media also contained 300 μmol L-1 nitrate, 200 umol L-1 silicic acid and 20 umol L-1 phosphate. Premixed Fe-EDTA (1:1) was added separately for total iron concentrations of either 1370 nmol L-1 or 3.1 nmol L-1. Cultures were grown in acid-washed 28 mL polycarbonate centrifuge tubes (Nalgene) and maintained in exponential phase by dilution. Specific growth rates of successive transfers were calculated from the linear regression of the natural log of in vivo chlorophyll a fluorescence using a Turner 10-AU fluorometer (Brand et al. 1981). Photophysiological parameters were measured with a Fluorescence Induction Relaxation System (FIRe) (Satatlantic). Samples were dark acclimated for at least 10 minutes and measurements were taken of each culture for photosynthetic efficiency (Fv:Fm), and functional absorption cross-section of PSII (oPSII [A2 quanta-1]). FIRe parameters were set to measure single turnover flash of PSII reaction centers (single closure event) with a sample delay of 100, and a total of 50 samples (Gorbunov and Falkowski 2004).
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electronicMailAddress: NCEI.Info@noaa.gov
role: (CI_RoleCode) pointOfContact
distributionOrderProcess: (MD_StandardOrderProcess)
fees: In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
orderingInstructions: Contact NCEI for other distribution options and instructions.
distributorFormat: (MD_Format)
name: TSV
version: (unknown)
distributorTransferOptions: (MD_DigitalTransferOptions)
transferSize:
Real: 0.164
onLine: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/0277906
protocol: HTTPS
applicationProfile: Web browser
name: NCEI Dataset Landing Page
description: Navigate directly to the URL for a descriptive web page with download links.
function: (CI_OnLineFunctionCode) information
onLine: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/oas/277906
protocol: HTTPS
applicationProfile: Web browser
name: Descriptive Information
description: Navigate directly to the URL for a descriptive web page with download links.
function: (CI_OnLineFunctionCode) information
onLine: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/download/277906
protocol: HTTPS
applicationProfile: Web browser
name: HTTPS
description: Navigate directly to the URL for data access and direct download.
function: (CI_OnLineFunctionCode) download
onLine: (CI_OnlineResource)
linkage: ftp://ftp-oceans.ncei.noaa.gov/nodc/archive/arc0212/0277906/
protocol: FTP
applicationProfile: Any FTP client
name: FTP
description: These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
function: (CI_OnLineFunctionCode) download
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dataQualityInfo: (DQ_DataQuality)
scope: (DQ_Scope)
level: (MD_ScopeCode) dataset
lineage: (LI_Lineage)
processStep: (LE_ProcessStep)
description: NCEI Accession 0277906 v1.1 was published.
dateTime:
DateTime: 2023-05-05T04:38:32Z
output: (LE_Source)
sourceCitation: (CI_Citation)
title: NCEI Accession 0277906 v1.1
date: (CI_Date)
date: (inapplicable)
dateType: (CI_DateTypeCode) publication
citedResponsibleParty: (CI_ResponsibleParty)
individualName: (inapplicable)
contactInfo: (CI_Contact)
onlineResource: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/0277906/1.1
protocol: HTTPS
name: NCEI Accession 0277906 v1.1
description: published 2023-05-05T04:38:32Z
function: (CI_OnLineFunctionCode) download
role: (inapplicable)
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metadataMaintenance: (MD_MaintenanceInformation)
maintenanceAndUpdateFrequency: (MD_MaintenanceFrequencyCode) asNeeded
maintenanceNote: Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
contact: (CI_ResponsibleParty)
organisationName: NOAA National Centers for Environmental Information
role: (CI_RoleCode) custodian
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acquisitionInformation: (MI_AcquisitionInformation)
platform: (MI_Platform)
identifier: (MD_Identifier)
code: R/V Laurence M. Gould
description: Flag: United States of America Vessel Type: Research Vessel; Ice Breaker DOB: Dec 1997 IMO: 9137337 The RV Laurence M. Gould is an icebreaker used by researchers from the United States' National Science Foundation for research in the Southern Ocean. The vessel is named after Laurence McKinley Gould a widely recognized American scientist, who had explored both the Arctic and Antarctic. She was built in Louisiana to replace the RV Polar Duke.
instrument: (missing)