http://lod.bco-dmo.org/id/dataset/722731
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
2018-01-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
18S rRNA gene sequence from the euphotic zone at Station ALOHA from near-monthly samples collected during Hawaii Ocean Time-series (HOT) program cruises 230-252 between 2011 and 2013 (PhytoNsubResponse project)
2017-08-25
publication
2017-08-25
revision
BCO-DMO Linked Data URI
2017-08-25
creation
http://lod.bco-dmo.org/id/dataset/722731
Matthew J. Church
University of Montana
principalInvestigator
Kevin R. Arrigo
Stanford University
principalInvestigator
Dr Zbigniew Kolber
University of California-Santa Cruz
principalInvestigator
Jonathan P. Zehr
University of California-Santa Cruz
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: Church, M. J., Zehr, J. P., Arrigo, K. R., Kolber, Z. (2017) 18S rRNA gene sequence from the euphotic zone at Station ALOHA from near-monthly samples collected during Hawaii Ocean Time-series (HOT) program cruises 230-252 between 2011 and 2013 (PhytoNsubResponse project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-08-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/722731 [access date]
18S rRNA gene sequence Dataset Description: <p>18S rRNA gene sequences from the euphotic zone (0-175 m) at Station ALOHA.&nbsp; Samples were collected at near-monthly intervals over ~2 year period (2011-2013); the V9 region of the 18S rRNA gene was PCR amplified and sequenced on an Illumina MiSeq.</p>
<p>&nbsp;</p> Methods and Sampling: <p><strong>Sampling and Analytical Methodology:&nbsp; </strong></p>
<p>Seawater was collected in 12-L polyvinylchloride bottles affixed to a 24-bottle rosette</p>
<p>sampler, equipped with a Sea-Bird 911+ conductivity, temperature, and pressure profiler. Seawater samples were sequentially filtered using a peristaltic pump onto 25-mm diameter, 3-μm pore size polycarbonate membranes (Millipore IsoporeTM), followed by filtration through 25-mm diameter, 0.2-μm pore size polyethersulfone filters (Pall Supor®). After filtration, filters were placed in sterile 1.5-mL microcentrifuge tubes, immediately flash-frozen in liquid nitrogen, and stored at -80°C until analysis. Back in the shore-based laboratory, DNA from the 0.2-μm filter membranes was extracted and purified using the QIAGEN DNeasy Plant Mini Kit including a bead-beating step (with 0.1- and 0.5-mm beads) and Proteinase K (QIAGEN) for additional cell disruption and lysing. Extracts were eluted in 200 μL of nuclease-free PCR grade water and quantified using the Qubit® fluorometer. Triplicate PCR products were pooled, fragment size was determined using 1.5% agarose gel electrophoresis, and quantity was measured with the Qubit® 2.0 fluorometer with Qubit® dsDNA High Sensitivity Assay kit (Molecular Probes). From each sample, ~50 ng of PCR product was combined and purified using the UltraClean PCR Clean-Up Kit (MoBio).</p>
<p>&nbsp;</p>
<p><strong>Data Processing: </strong></p>
<p>Sequences were merged using PEAR (Zhang et al., 2014) and quality-filtered with reads trimmed to 100-150 bp, a maximum expected error of 1%, no ambiguous bases allowed, and an</p>
<p>average Phred quality threshold &gt;34. Reference-based and de novo 70 chimeras were detected using</p>
<p>USEARCH v7.0.1090 (Edgar et al., 2011) with the SILVA 119 database pre-clustered at 97% sequence identity (Quast et al., 2013) and removed. Sequences were deposited into</p>
<p>NCBI’s Sequence Read Archive as BioProject ID PRJNA351881 (accession SRP092782).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1241263 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1241263
completed
Matthew J. Church
University of Montana
(406) 982-3301
Flathead Lake Biological Station, University of Montana 321225 Bio Station Lane
Polson
MT
59860-6815
USA
matt.church@flbs.umt.edu
pointOfContact
Kevin R. Arrigo
Stanford University
650-723-3599
Department of Earth System Science/ Y2E2 Building Room 141
Stanford
CA
94305
USA
arrigo@stanford.edu
pointOfContact
Dr Zbigniew Kolber
University of California-Santa Cruz
zkolber@gmail.com
pointOfContact
Jonathan P. Zehr
University of California-Santa Cruz
831-459 4009
E&MS A438, Ocean Sciences Department 1156 High Street
Santa Cruz
CA
95064
USA
zehrj@ucsc.edu
pointOfContact
asNeeded
Unknown
HOT_cruises
service
Deployment Activity
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Oligotrophic phytoplankton community response to changes in N substrates and the resulting impact on genetic, taxonomic and functional diversity
https://osprey.bco-dmo.org/project/471899
Oligotrophic phytoplankton community response to changes in N substrates and the resulting impact on genetic, taxonomic and functional diversity
<p>(Extracted from NSF award abstract)</p>
<p>Marine phytoplankton are a diverse group of Prokaryotic and Eukaryotic unicellular organisms that account for approximately 50% of global carbon fixation. Nitrogen (N) is an essential element for microbial growth, but concentrations of bioavailable nitrogen in vast regions of subtropical ocean gyres are extremely low (submicromolar to nanomolar concentrations), and generally limit phytoplankton growth. Phytoplankton taxa differ in their genetic capabilities to take up and assimilate nutrients, and thus competition for different chemical forms of N (NH4+, NO3- and urea) and supply of these N-containing compounds are important controls on phytoplankton growth, productivity, and ultimately ecosystem function. The form and supply of N to phytoplankton have already been altered by anthropogenic activities, and with increasing environmental perturbations the effects will accelerate. To date however, there is limited information on how the N forms and fluxes impact the marine phytoplankton community composition and primary production. Similarly, determining the mechanisms of the response are crucial to assessing how ocean ecosystem function will respond to global climate change.</p>
<p>This project seeks to determine how taxonomic, genetic and functional dimensions of phytoplankton diversity are linked with community-level responses to the availability of different N substrates (NH4+, NO3-, and urea) in one of Earth's largest aquatic habitats, the North Pacific Subtropical Gyre. The project will characterize phytoplankton community composition change and gene expression, photosynthetic performance, carbon fixation, and single-cell level N and C uptake in different taxa within the phytoplankton assemblage in response to different N compounds. The research project is unique in investigating community-to-single-cell level function and species (strain)-specific gene expression patterns using state-of-the-art methods including fast repetition rate fluorometry, nanoscale secondary ion mass spectrometry and a comprehensive marine microbial community microarray. The results will provide predictive understanding of how changes in the availability of key nitrogen pools (N) may impact phytoplankton dynamics and function in the ocean.</p>
<p>References:</p>
<p>Karl, D. M., Bjorkman, K. M., Dore, J. E., Fujieki, L., Hebel, D. V., Houlihan, T., Letelier, R. M., Tupas, L. M. 2001. Ecological nitrogen-to-phosphorus stoichiometry at station ALOHA. Deep-Sea Research II. 48:1529 - 1566.</p>
<p>Karl, D. M., Letelier, R., Tupas, L., Dore, J., Christian, J. & Hebel, D. 1997. The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean. Nature. 388:533-538.</p>
<p>McCarthy, J., Taylor, W. R., Taft, J. 1997. Nitrogenous nutrition of the plankton in the Chesapeake Bay. Limnology and Oceanography. 35:822 - 829.</p>
<p>Letelier, R., Karl, D. M. 1996. Role of Trichodesmium spp. in the productivity of the subtropical North Pacific Ocean. Marine Ecology Progress Series. 133:263 - 273.</p>
<p>Lipschultz, F. 1995. Nitrogen-specific uptake rates of marine phytoplankton isolated from natura populations of particles by flow cytometry. Marine Ecology Progress Series. 123:245-258.</p>
PhytoNsubResponse
largerWorkCitation
project
eng; USA
oceans
-158
-158
22.75
22.75
2017-08-25
North Pacific Subtropical Gyre at Station ALOHA, and a transect from San Diego, CA to Hawaii
0
BCO-DMO catalogue of parameters from 18S rRNA gene sequence from the euphotic zone at Station ALOHA from near-monthly samples collected during Hawaii Ocean Time-series (HOT) program cruises 230-252 between 2011 and 2013 (PhytoNsubResponse 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
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
38294
https://datadocs.bco-dmo.org/file/4WW2j6LiYwlEE4/sequences.csv
sequences.csv
Primary data file for dataset ID 722731
download
https://osprey.bco-dmo.org/dataset/722731/data/download
download
onLine
dataset
<p><strong>Sampling and Analytical Methodology:&nbsp; </strong></p>
<p>Seawater was collected in 12-L polyvinylchloride bottles affixed to a 24-bottle rosette</p>
<p>sampler, equipped with a Sea-Bird 911+ conductivity, temperature, and pressure profiler. Seawater samples were sequentially filtered using a peristaltic pump onto 25-mm diameter, 3-μm pore size polycarbonate membranes (Millipore IsoporeTM), followed by filtration through 25-mm diameter, 0.2-μm pore size polyethersulfone filters (Pall Supor®). After filtration, filters were placed in sterile 1.5-mL microcentrifuge tubes, immediately flash-frozen in liquid nitrogen, and stored at -80°C until analysis. Back in the shore-based laboratory, DNA from the 0.2-μm filter membranes was extracted and purified using the QIAGEN DNeasy Plant Mini Kit including a bead-beating step (with 0.1- and 0.5-mm beads) and Proteinase K (QIAGEN) for additional cell disruption and lysing. Extracts were eluted in 200 μL of nuclease-free PCR grade water and quantified using the Qubit® fluorometer. Triplicate PCR products were pooled, fragment size was determined using 1.5% agarose gel electrophoresis, and quantity was measured with the Qubit® 2.0 fluorometer with Qubit® dsDNA High Sensitivity Assay kit (Molecular Probes). From each sample, ~50 ng of PCR product was combined and purified using the UltraClean PCR Clean-Up Kit (MoBio).</p>
<p>&nbsp;</p>
<p><strong>Data Processing: </strong></p>
<p>Sequences were merged using PEAR (Zhang et al., 2014) and quality-filtered with reads trimmed to 100-150 bp, a maximum expected error of 1%, no ambiguous bases allowed, and an</p>
<p>average Phred quality threshold &gt;34. Reference-based and de novo 70 chimeras were detected using</p>
<p>USEARCH v7.0.1090 (Edgar et al., 2011) with the SILVA 119 database pre-clustered at 97% sequence identity (Quast et al., 2013) and removed. Sequences were deposited into</p>
<p>NCBI’s Sequence Read Archive as BioProject ID PRJNA351881 (accession SRP092782).</p>
from Cruise: HOT_cruises <p>Hawaii Ocean Time-series (HOT) program cruises 230-252</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
*&nbsp;added column biosample link which is the direct link to the accession at NCBI<br />
* added lat/lon of Station ALOHA 22.75,-158</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
Cruise: HOT_cruises
HOT_cruises
Multiple Vessels
vessel
HOT_cruises
Angelicque E. White
University of Hawaiʻi at Mānoa
http://hahana.soest.hawaii.edu/hot/
Report describing HOT_cruises
Multiple Vessels
vessel