http://lod.bco-dmo.org/id/dataset/628290
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
2015-12-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Iron and vitamin B12 metatranscriptomincs co-limitation in sea water collected from the Ross Sea in 2014 (Ross Sea Microb Ecophys project)
2015-12-07
publication
2015-12-07
revision
BCO-DMO Linked Data URI
2015-12-07
creation
http://lod.bco-dmo.org/id/dataset/628290
Andrew E. Allen
J. Craig Venter Institute
principalInvestigator
Deborah A. Bronk
Virginia Institute of Marine Science
principalInvestigator
David A. Hutchins
University of Southern California
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: Allen, A. E., Bronk, D. A., Hutchins, D. A. (2015) Iron and vitamin B12 metatranscriptomincs co-limitation in sea water collected from the Ross Sea in 2014 (Ross Sea Microb Ecophys project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-12-07) Version Date 2015-12-07 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/628290 [access date]
Iron and vitamin B12 metatranscriptomincs co-limitation in Ross Sea waters, 2014 Dataset Description: <p>We examined the short-term transcriptional response of the 16 Jan 2013 community to cobalamin and iron addition in order to further characterize the nature and implications of this colimitation. RNA sequencing was performed on triplicate samples, 24 h after micronutrient addition. Sequencing and assembly statistics are given in Bertrand et al. 2015.</p>
<p>Data deposition: The data reported in this paper have been deposited in the NCBI sequence read archive (BioProject accession no. <a href="http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA281813" target="_blank">PRJNA281813</a>; BioSample accession nos.SAMN03565520–SAMN03565531). Assembled contigs, predicted peptides, annotation, and transcript abundance data for this study can be found at https://scripps.ucsd.edu/labs/aallen/data/. These files are also accessible via the '<strong>Get Data</strong>' link above.</p> Methods and Sampling: <p>Near-surface water samples were collected by helicopter in the Ross Sea near McMurdo Station, Antarctica.</p>
<p><strong>Methodology</strong>: From Bertrand, E.M., McCrow, J.P., Moustafa, A., Zheng, H., McQuaid, J., Delmont, T., Post, A.F., Sipler, R., Spackeen, J.L., Xu, K., Bronk, D.A., Hutchins, D.A., Allen, A.E. (2015) <a href="http://scrippsscholars.ucsd.edu/node/36287">Phytoplanktont-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge</a>. Proceedings of the National Academy of Sciences. <a href="http://dx.doi.org/10.1073%2Fpnas.1501615112">10.1073/pnas.1501615112</a></p>
<p>On January 16, 2013, seawater was collected from3mdepth at the sea ice edge in McMurdo Sound of the Ross Sea (77° 36.999' S 165° 28.464' E), using trace metal clean technique. Triplicate bottles (2.7 L) of each treatment (unamended control, + 1 nM added FeCl3, + 200 pM added cyanocobalamin, and + 200 pM cyanocobalamin and 1 nM Fe) were placed in an indoor incubator at 0 °C, ~45 µmol photonsm-2·s-1 of constant light. After 24 h, RNA sampleswere collected (450 mL) and nitrate uptake and primary productivity rates were measured. Samples were taken for Chl a at 0, 24, and 96 h. RNA was extracted using the TRIzol reagent (Life Technologies). Ribosomal RNA was removed with Ribo-Zero Magnetic kits, and the resulting mRNA enrichment was purified and subjected to amplification and cDNA synthesis, using the Ovation RNA-Seq System V2 (NuGEN). One microgram of the resulting high-quality cDNA pool was fragmented to a mean length of 200 bp, and Truseq (Illumina) libraries were prepared and subjected to paired-end sequencing via Illumina HiSeq. Reads were trimmed and filtered, contigs were assembled in CLC Assembly Cell (CLCbio), and ORFs were predicted (41). ORFs were annotated de novo for function via KEGG, KO, KOG, Pfam, and TigrFam assignments. Taxonomic classification was assigned to each ORF using a reference dataset, as described in the SI Appendix (Bertrand, 2015), and the Lineage Probability Index (LPI, as calculated in ref. 18). edgeR was used to assign normalized fold change and determine which ORFs were significantly differentially expressed in pairwise comparisons between treatments, considering triplicates, within a given phylogenetic grouping (42). For Fig. 2, diatom ORFs [identified as diatom via LPI analyses; LPI &gt; 0.8 (18)] were clustered using MCL (Markov cluster algorithm) (21), and these clusters were used to produce MANTA plots (20). For Oceanospirillaceae ASP10-02a genome assembly, water was collected from 10 m in the Amundsen Sea on December 19, 2010. Metagenomic libraries were created with the OVATION ultralow kit (NuGen). Overlapping and gapped metagenomic DNA libraries were prepared for sequencing on a HiSeq platform (Illumina). CLC was used to assemble scaffolds, tetranucleotide frequencies of scaffolds were analyzed (43), and draft genomes were generated via binning scaffolds clustered (hierarchical) together in well-supported clades, refined using GC content and taxonomical affiliation (44). ORFs identified in metatranscriptomic analyses were mapped to the Oceanospirillaceae ASP10-02a genome bin from the best-scoring nucleotide alignment, using BWA-MEM with default parameters (45). ORFs with &gt;99%similarity to the genome scaffold sequences were used for subsequent analyses of gene expression patterns within this population. Complete materials and methods are given in the SI Appendix (Bertrand, 2015).</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1043671 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1043671
completed
Andrew E. Allen
J. Craig Venter Institute
858-200-1826
4120 Capricorn Lane
La Jolla
CA
92037
USA
aallen@jcvi.org
pointOfContact
Deborah A. Bronk
Virginia Institute of Marine Science
207-315-2567
60 Bigelow Drive
East Boothbay
ME
04544
USA
dbronk@bigelow.org
pointOfContact
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
asNeeded
Dataset Version: 2015-12-07
Unknown
description
NCBI_BioProject
file_size_MB
download_link
theme
None, User defined
No BCO-DMO term
file_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
helicopter_Allen
service
Deployment Activity
Ross Sea
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.
Synergistic Effects of Iron, Carbon Dioxide and Temperature on the Fate of Nitrate: Implications for Future Changes in Export Production in the Southern Ocean
https://osprey.bco-dmo.org/project/626702
Synergistic Effects of Iron, Carbon Dioxide and Temperature on the Fate of Nitrate: Implications for Future Changes in Export Production in the Southern Ocean
<p><em>Description from NSF award abstract:</em><br />
This award provides support for "Collaborative Research: Synergistic Effects of Iron, Carbon Dioxide, and Temperature on the Fate of Nitrate: Implications for Future Changes in Export Production in the Southern Ocean" from the Antarctic Organisms and Ecosystems program in the Office of Polar Programs at NSF. The project will use a novel combination of research approaches to evaluate the effects of temperature, carbon dioxide, and iron on three ecologically- and biogeochemically-critical Southern Ocean phytoplankton functional groups: Large centric diatoms, small pennate diatoms, and Phaeocystis antarctica.</p>
<p>The Southern Ocean around Antarctic is undergoing several changes including increased temperature and carbon dioxide content, as well as changing levels of biologically available iron. The project goals are to understand how the individual and combined influences of these three variables affect Southern Ocean phytoplankton community structure, and to determine how these assemblage-level responses are linked to fundamental cellular responses at the levels of nutrient physiology and gene expression. The research team will focus on three different types of marine algae: large and small diatoms, and the prymnesiophyte, Phaeocystis antarctica. Shifts between these three major algal groups have very different consequences for nutrient and carbon biogeochemistry in the rapidly changing Antarctic marine environments. However, the mechanistic underpinnings of these environmentally-driven community shifts are not known. The project includes a US-based laboratory component with Antarctic isolates, field study at McMurdo Station, and then a cruise of opportunity in the upwelling areas directly south of the Antarctic Circumpolar Current. The study also includes collection and analysis of environmental gene expression data, or meta-transcriptomics, both from the field and experimental settings. The transcriptomes will be generated under environmentally relevant conditions and will thus contain information critical for decoding the genomes of several newly sequenced polar phytoplankton species in addition to the three groups highlighted above.</p>
<p><em>Related publications:</em><br />
Bertrand, E.M., McCrow, J.P., Moustafa, A., Zheng, H., McQuaid, J., Delmont, T., Post, A.F., Sipler, R., Spackeen, J.L., Xu, K., Bronk, D.A., Hutchins, D.A., Allen, A.E. 2015. Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. Proceedings of the National Academy of Sciences. <a href="http://dx.doi.org/10.1073%2Fpnas.1501615112" target="_blank">10.1073/pnas.1501615112</a></p>
Ross_Sea_Microb_Ecophys
largerWorkCitation
project
eng; USA
biota
oceans
Ross Sea
2015-12-07
McMurdo Sound of the Ross Sea
0
BCO-DMO catalogue of parameters from Iron and vitamin B12 metatranscriptomincs co-limitation in sea water collected from the Ross Sea in 2014 (Ross Sea Microb Ecophys 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/628729.rdf
Name: description
Units: unitless
Description: <p>description of file type</p>
http://lod.bco-dmo.org/id/dataset-parameter/628730.rdf
Name: NCBI_BioProject
Units: unitless
Description: <p>NCBI BioProject identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/628731.rdf
Name: file_size_MB
Units: MegaBytes
Description: <p>size of file available for download</p>
http://lod.bco-dmo.org/id/dataset-parameter/628732.rdf
Name: download_link
Units: unitless
Description: <p>link to download file or to NCBI accession page</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
2228
https://datadocs.bco-dmo.org/file/rggpGKnFrNMQLQ/cDNA.csv
cDNA.csv
Primary data file for dataset ID 628290
download
https://osprey.bco-dmo.org/dataset/628290/data/download
download
onLine
dataset
<p>Near-surface water samples were collected by helicopter in the Ross Sea near McMurdo Station, Antarctica.</p>
<p><strong>Methodology</strong>: From Bertrand, E.M., McCrow, J.P., Moustafa, A., Zheng, H., McQuaid, J., Delmont, T., Post, A.F., Sipler, R., Spackeen, J.L., Xu, K., Bronk, D.A., Hutchins, D.A., Allen, A.E. (2015) <a href="http://scrippsscholars.ucsd.edu/node/36287">Phytoplanktont-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge</a>. Proceedings of the National Academy of Sciences. <a href="http://dx.doi.org/10.1073%2Fpnas.1501615112">10.1073/pnas.1501615112</a></p>
<p>On January 16, 2013, seawater was collected from3mdepth at the sea ice edge in McMurdo Sound of the Ross Sea (77° 36.999' S 165° 28.464' E), using trace metal clean technique. Triplicate bottles (2.7 L) of each treatment (unamended control, + 1 nM added FeCl3, + 200 pM added cyanocobalamin, and + 200 pM cyanocobalamin and 1 nM Fe) were placed in an indoor incubator at 0 °C, ~45 µmol photonsm-2·s-1 of constant light. After 24 h, RNA sampleswere collected (450 mL) and nitrate uptake and primary productivity rates were measured. Samples were taken for Chl a at 0, 24, and 96 h. RNA was extracted using the TRIzol reagent (Life Technologies). Ribosomal RNA was removed with Ribo-Zero Magnetic kits, and the resulting mRNA enrichment was purified and subjected to amplification and cDNA synthesis, using the Ovation RNA-Seq System V2 (NuGEN). One microgram of the resulting high-quality cDNA pool was fragmented to a mean length of 200 bp, and Truseq (Illumina) libraries were prepared and subjected to paired-end sequencing via Illumina HiSeq. Reads were trimmed and filtered, contigs were assembled in CLC Assembly Cell (CLCbio), and ORFs were predicted (41). ORFs were annotated de novo for function via KEGG, KO, KOG, Pfam, and TigrFam assignments. Taxonomic classification was assigned to each ORF using a reference dataset, as described in the SI Appendix (Bertrand, 2015), and the Lineage Probability Index (LPI, as calculated in ref. 18). edgeR was used to assign normalized fold change and determine which ORFs were significantly differentially expressed in pairwise comparisons between treatments, considering triplicates, within a given phylogenetic grouping (42). For Fig. 2, diatom ORFs [identified as diatom via LPI analyses; LPI &gt; 0.8 (18)] were clustered using MCL (Markov cluster algorithm) (21), and these clusters were used to produce MANTA plots (20). For Oceanospirillaceae ASP10-02a genome assembly, water was collected from 10 m in the Amundsen Sea on December 19, 2010. Metagenomic libraries were created with the OVATION ultralow kit (NuGen). Overlapping and gapped metagenomic DNA libraries were prepared for sequencing on a HiSeq platform (Illumina). CLC was used to assemble scaffolds, tetranucleotide frequencies of scaffolds were analyzed (43), and draft genomes were generated via binning scaffolds clustered (hierarchical) together in well-supported clades, refined using GC content and taxonomical affiliation (44). ORFs identified in metatranscriptomic analyses were mapped to the Oceanospirillaceae ASP10-02a genome bin from the best-scoring nucleotide alignment, using BWA-MEM with default parameters (45). ORFs with &gt;99%similarity to the genome scaffold sequences were used for subsequent analyses of gene expression patterns within this population. Complete materials and methods are given in the SI Appendix (Bertrand, 2015).</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Illumina HiSeq platform Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: PI Supplied Instrument Description:Life Technologies AccuPrime PCR system
Life Technologies ProFlex PCR system Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: helicopter_Allen
helicopter_Allen
McMurdo Station
laboratory
helicopter_Allen
Andrew E. Allen
J. Craig Venter Institute
McMurdo Station
laboratory