http://lod.bco-dmo.org/id/dataset/666201
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-11-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Diatom growth rates from samples collected on the Gould cruise LMG1411 in the Western Antarctica Peninsula from 2014 (Polar Transcriptomes project)
2016-11-28
publication
2016-11-28
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-04-17
publication
https://doi.org/10.1575/1912/bco-dmo.666201.1
Adrian Marchetti
University of North Carolina at Chapel Hill
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Marchetti, A. (2016) Diatom growth rates from samples collected on the Gould cruise LMG1411 in the Western Antarctica Peninsula from 2014 (Polar Transcriptomes project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-11-28 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.666201.1 [access date]
Cell growth rates from samples obtained on LMG1411. Dataset Description: <pre>
<span style="font-family:arial,helvetica,sans-serif">Diatom growth rates from samples obtained on LMG1411.</span>
</pre>
<p>Diatom isolates were obtained from the Western Antarctic Peninsula surface waters.</p> Methods and Sampling: <p>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).&nbsp;Pseudo-nitzschia&nbsp;species are often difficult to identify by their 18S rDNA sequence, therefore, additional support of the taxonomic identification of&nbsp;P.&nbsp;subcurvata&nbsp;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 (<a href="http://www.geneious.com" target="_blank">http://www.geneious.com</a>, 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%.</p>
<p>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.</p>
<p>Isolates were maintained at 4 deg C in constant irradiance at intensities of either 10&nbsp;umol&nbsp;photons m-2&nbsp;s-1&nbsp;(low light) or 90&nbsp;umol&nbsp;photons m-2&nbsp;s-1&nbsp;(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&nbsp;umol&nbsp;L-1&nbsp;EDTA. The growth media also contained 300 μmol L-1&nbsp;nitrate, 200&nbsp;umol&nbsp;L-1&nbsp;silicic acid and 20&nbsp;umol&nbsp;L-1&nbsp;phosphate. Premixed Fe-EDTA (1:1) was added separately for total iron concentrations of either 1370 nmol L-1&nbsp;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&nbsp;log of&nbsp;in vivo&nbsp;chlorophyll&nbsp;a&nbsp;fluorescence using a Turner 10-AU fluorometer (Brand et al. 1981).&nbsp;</p>
<p>Statistical analyses of growth rates and photophysiological data were performed with SigmaPlot 12.5 (SysStat Software Inc.). To test for significant differences between treatments, Two-Way Analysis of Variance (ANOVA) was performed with a significance level set&nbsp;to&nbsp;p&lt;0.05. ANOVA also tests for normality using Shapiro-Wilks and Equal Variance tests. Because ANOVA does not test all interactions, an unpaired t-test was performed between –FeLL and +FeSL for u, Fv:Fm, and &nbsp;oPSII. All tests passed the Shapiro-Wilks Normality tests unless otherwise stated, in which case&nbsp;p-values are representative of the Mann-Whitney Rank Sum test. Post-hoc Tukey tests were also performed in order to determine which treatments differed significantly (p&nbsp;&lt; 0.05).</p>
<p>Cultures for high throughput sequencing of mRNA were grown in acid-washed 2L polycarbonate bottles in iron-replete conditions under growth-saturating light (90&nbsp;umol&nbsp;photons m-2&nbsp;s-1). After reaching late exponential/early stationary phase, cultures were harvested onto polycarbonate filters (3.0 um pore size, 25 mm) and stored at -80 deg C. Total RNA was extracted using the RNAqueous 4PCR Kit (Ambion) according to the manufacturer’s protocols. Residual genomic DNA was eliminated by DNAseI digestion at 37 deg C for 45 min. An Agilent Bioanalyzer 2100 was used to determine RNA integrity. mRNA libraries were generated with ~2&nbsp;ug&nbsp;of total RNA and prepared with the Illumina TruSeq Stranded mRNA Library Preparation Kit. Samples were individually barcoded and pooled prior to sequencing on the Illumina MiSeq platform at the High Throughput Sequencing Facility (HTSF) at UNC-Chapel Hill. Sequencing resulted in approximately 0.7-2 million paired-end reads of 2x300bp per sample.</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1341479 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1341479
completed
Adrian Marchetti
University of North Carolina at Chapel Hill
919-843-3473
123 South Rd.
Chapel Hill
NC
27514
USA
amarchet@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
treatment
mean_specific_u
relative_u
std_error_u
propogation_error_u
sample_size_u
mean_FvFm
relative_FvFm
std_error_FvFm
propogation_error_FvFm
sample_size_FvFm
mean_sigma
relative_sigma
std_error_sigma
propogation_error_sigma
sample_size_sigma
Agilent Bioanalyzer 2100
Turner 10-AU
Olympus CKX41
theme
None, User defined
species scientific name (binomial)
treatment
mean
growth
standard error
number
Fv to Fm ratio
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Bioanalyzer
Fluorometer
Inverted Microscope
instrument
BCO-DMO Standard Instruments
LMG1401
service
Deployment Activity
Antarctica
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
http://www.nsf.gov/awardsearch/showAward?AWD_ID=1341479
Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
<p>The Southern Ocean surrounding Antarctica is changing rapidly in response to Earth's warming climate. These changes will undoubtedly influence communities of primary producers (the organisms at the base of the food chain, particularly plant-like organisms using sunlight for energy) by altering conditions that influence their growth and composition. Because primary producers such as phytoplankton play an important role in global biogeochemical cycling, it is essential to understand how they will respond to changes in their environment. The growth of phytoplankton in certain regions of the Southern Ocean is constrained by steep gradients in chemical and physical properties that vary in both space and time. Light and iron have been identified as key variables influencing phytoplankton abundance and distribution within Antarctic waters. Microscopic algae known as diatoms are dominant members of the phytoplankton and sea ice communities, accounting for significant proportions of primary production. The overall objective of this project is to identify the molecular bases for the physiological responses of polar diatoms to varying light and iron conditions. The project should provide a means of evaluating the extent these factors regulate diatom growth and influence net community productivity in Antarctic waters. The project will also further the NSF goals of making scientific discoveries available to the general public and of training new generations of scientists. It will facilitate the teaching and learning of polar-related topics by translating the research objectives into readily accessible educational materials for middle-school students. This project will also provide funding to enable a graduate student and several undergraduate students to be trained in the techniques and perspectives of modern biology.</p>
<p>Although numerous studies have investigated how polar diatoms are affected by varying light and iron, the cellular mechanisms leading to their distinct physiological responses remain unknown. Using comparative transcriptomics, the expression patterns of key genes and metabolic pathways in several ecologically important polar diatoms recently isolated from Antarctic waters and grown under varying iron and irradiance conditions will be examined. In addition, molecular indicators for iron and light limitation will be developed within these polar diatoms through the identification of iron- and light-responsive genes -- the expression patterns of which can be used to determine their physiological status. Upon verification in laboratory cultures, these indicators will be utilized by way of metatranscriptomic sequencing to examine iron and light limitation in natural diatom assemblages collected along environmental gradients in Western Antarctic Peninsula waters. In order to fully understand the role phytoplankton play in Southern Ocean biogeochemical cycles, dependable methods that provide a means of elucidating the physiological status of phytoplankton at any given time and location are essential.</p>
Polar_Transcriptomes
largerWorkCitation
project
eng; USA
oceans
Antarctica
2014-01-01
2014-12-31
Antarctica
0
BCO-DMO catalogue of parameters from Diatom growth rates from samples collected on the Gould cruise LMG1411 in the Western Antarctica Peninsula from 2014 (Polar Transcriptomes project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/666215.rdf
Name: species
Units: unitless
Description: <p>Species analyzed</p>
http://lod.bco-dmo.org/id/dataset-parameter/666216.rdf
Name: treatment
Units: unitless
Description: <p>Treatment condition</p>
http://lod.bco-dmo.org/id/dataset-parameter/666217.rdf
Name: mean_specific_u
Units: d -1
Description: <p>Average growth rate in a specific treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/666218.rdf
Name: relative_u
Units: unitless
Description: <p>Relative growth rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/666219.rdf
Name: std_error_u
Units: unitless
Description: <p>Standard error of relative growth rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/666220.rdf
Name: propogation_error_u
Units: unitless
Description: <p>Relative growth rate error</p>
http://lod.bco-dmo.org/id/dataset-parameter/666221.rdf
Name: sample_size_u
Units: unitless
Description: <p>Number of samples recorded</p>
http://lod.bco-dmo.org/id/dataset-parameter/666222.rdf
Name: mean_FvFm
Units: unitless
Description: <p>Average photosynthetic efficiency</p>
http://lod.bco-dmo.org/id/dataset-parameter/666223.rdf
Name: relative_FvFm
Units: unitless
Description: <p>Relative photosynthetic efficiency</p>
http://lod.bco-dmo.org/id/dataset-parameter/666224.rdf
Name: std_error_FvFm
Units: unitless
Description: <p>Relative photosynthetic efficiency standard error</p>
http://lod.bco-dmo.org/id/dataset-parameter/666225.rdf
Name: propogation_error_FvFm
Units: unitless
Description: <p>Relative photosynthetic efficiency error</p>
http://lod.bco-dmo.org/id/dataset-parameter/666226.rdf
Name: sample_size_FvFm
Units: unitless
Description: <p>Relative photosynthetic efficiency number of samples recorded</p>
http://lod.bco-dmo.org/id/dataset-parameter/666227.rdf
Name: mean_sigma
Units: A2 quanta -1
Description: <p>Average functional absorption cross-section of PSII</p>
http://lod.bco-dmo.org/id/dataset-parameter/666228.rdf
Name: relative_sigma
Units: unitless
Description: <p>Relative function absorption cross-section of PSII</p>
http://lod.bco-dmo.org/id/dataset-parameter/666229.rdf
Name: std_error_sigma
Units: unitless
Description: <p>Functional absorption cross-section of PSII standard error</p>
http://lod.bco-dmo.org/id/dataset-parameter/666230.rdf
Name: propogation_error_sigma
Units: unitless
Description: <p>Functional absorption cross-section of PSII error</p>
http://lod.bco-dmo.org/id/dataset-parameter/666231.rdf
Name: sample_size_sigma
Units: unitless
Description: <p>Functional absorption cross-section of PSII number of samples recorded</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
3809
https://darchive.mblwhoilibrary.org/bitstream/1912/24035/1/dataset-666201_diatom-growth-rates__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.666201.1
download
onLine
dataset
<p>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).&nbsp;Pseudo-nitzschia&nbsp;species are often difficult to identify by their 18S rDNA sequence, therefore, additional support of the taxonomic identification of&nbsp;P.&nbsp;subcurvata&nbsp;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 (<a href="http://www.geneious.com" target="_blank">http://www.geneious.com</a>, 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%.</p>
<p>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.</p>
<p>Isolates were maintained at 4 deg C in constant irradiance at intensities of either 10&nbsp;umol&nbsp;photons m-2&nbsp;s-1&nbsp;(low light) or 90&nbsp;umol&nbsp;photons m-2&nbsp;s-1&nbsp;(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&nbsp;umol&nbsp;L-1&nbsp;EDTA. The growth media also contained 300 μmol L-1&nbsp;nitrate, 200&nbsp;umol&nbsp;L-1&nbsp;silicic acid and 20&nbsp;umol&nbsp;L-1&nbsp;phosphate. Premixed Fe-EDTA (1:1) was added separately for total iron concentrations of either 1370 nmol L-1&nbsp;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&nbsp;log of&nbsp;in vivo&nbsp;chlorophyll&nbsp;a&nbsp;fluorescence using a Turner 10-AU fluorometer (Brand et al. 1981).&nbsp;</p>
<p>Statistical analyses of growth rates and photophysiological data were performed with SigmaPlot 12.5 (SysStat Software Inc.). To test for significant differences between treatments, Two-Way Analysis of Variance (ANOVA) was performed with a significance level set&nbsp;to&nbsp;p&lt;0.05. ANOVA also tests for normality using Shapiro-Wilks and Equal Variance tests. Because ANOVA does not test all interactions, an unpaired t-test was performed between –FeLL and +FeSL for u, Fv:Fm, and &nbsp;oPSII. All tests passed the Shapiro-Wilks Normality tests unless otherwise stated, in which case&nbsp;p-values are representative of the Mann-Whitney Rank Sum test. Post-hoc Tukey tests were also performed in order to determine which treatments differed significantly (p&nbsp;&lt; 0.05).</p>
<p>Cultures for high throughput sequencing of mRNA were grown in acid-washed 2L polycarbonate bottles in iron-replete conditions under growth-saturating light (90&nbsp;umol&nbsp;photons m-2&nbsp;s-1). After reaching late exponential/early stationary phase, cultures were harvested onto polycarbonate filters (3.0 um pore size, 25 mm) and stored at -80 deg C. Total RNA was extracted using the RNAqueous 4PCR Kit (Ambion) according to the manufacturer’s protocols. Residual genomic DNA was eliminated by DNAseI digestion at 37 deg C for 45 min. An Agilent Bioanalyzer 2100 was used to determine RNA integrity. mRNA libraries were generated with ~2&nbsp;ug&nbsp;of total RNA and prepared with the Illumina TruSeq Stranded mRNA Library Preparation Kit. Samples were individually barcoded and pooled prior to sequencing on the Illumina MiSeq platform at the High Throughput Sequencing Facility (HTSF) at UNC-Chapel Hill. Sequencing resulted in approximately 0.7-2 million paired-end reads of 2x300bp per sample.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>-reformatted column names to comply with BCO-DMO standards<br />
-replaced spaces with underscores<br />
-replaced blank cells with "nd"<br />
-added a species column<br />
-filled in blank column name</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Agilent Bioanalyzer 2100
Agilent Bioanalyzer 2100
PI Supplied Instrument Name: Agilent Bioanalyzer 2100 PI Supplied Instrument Description:Used to determine RNA integrity Instrument Name: Bioanalyzer Instrument Short Name:Bioanalyzer Instrument Description: A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.
Turner 10-AU
Turner 10-AU
PI Supplied Instrument Name: Turner 10-AU PI Supplied Instrument Description:Used to determine cell growth rates Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Olympus CKX41
Olympus CKX41
PI Supplied Instrument Name: Olympus CKX41 PI Supplied Instrument Description:Used to perform isolations Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: LMG1401
LMG1401
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel