http://lod.bco-dmo.org/id/dataset/3443
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
2011-03-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI Accessions for 16S rRNA clone libraries made with bacterial 8F and 519R primers collected on R/V Knorr KN192-05 in the South Atlantic subtropical gyre and Benguela upwelling region from November to December 2007 (CoFeMUG project)
2011-03-10
publication
2011-03-10
revision
BCO-DMO Linked Data URI
2011-03-10
creation
http://lod.bco-dmo.org/id/dataset/3443
Gabrielle Rocap
University of Washington
principalInvestigator
Robert Morris
University of Washington
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: Rocap, G., Morris, R. (2011) NCBI Accessions for 16S rRNA clone libraries made with bacterial 8F and 519R primers collected on R/V Knorr KN192-05 in the South Atlantic subtropical gyre and Benguela upwelling region from November to December 2007 (CoFeMUG project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 10 March 2011) Version Date 2011-03-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3443 [access date]
NCBI Accessions for 16S rRNA clone libraries made with bacterial 8F and 519R primers. Dataset Description: <p>NCBI Accessions for 16S rRNA clone libraries made with bacterial 8F and 519R primers. GenBank Accession: GU460426-GU461274.</p>
<p>Reference:<br />
Morris, R. M., B. Nunn, C. Frazar, D. Goodlett, Y.S. Ting and G. Rocap. 2010. Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction ISME Journal 4:673-685</p> Methods and Sampling: <p>Microorganisms were concentrated from large volume (100-200 l) surface seawater samples (5-8 m) collected from either a Niskin rosette or a surface pump. We targeted the &lt; 0.8 um size fraction to obtain the same bacterioplankton community used for GOS shotgun sequencing (Rusch et al., 2007). All concentrations were performed in a 50 l polystyrene reservoir using a Pellicon 2 cassette tangential flow filtration system equipped with one 30kD Biomax Polyethersulfone cassette (Millipore Corporation, Billerica, MA, USA). Seawater was continuously added to the concentration reservoir until cell densities reached ~10^8 cells/ml. In all, 100-200 ml of cell concentrate was obtained in 1.5-3h. Concentrated cells were flash frozen in liquid nitrogen and stored at -80 C until further processing on shore.</p>
<p>A cell pellet was prepared from each tangential flow filtration concentrated sample by centrifugation at 4 C for 60 min (17 000 g). The supernatant was discarded and cell pellets were resuspended in 3 ml of 20 mM Tris buffer pH 7.4. Crude extracts were prepared by passing the cells through a French pressure mini cell at 8000 lb/inch - 2 two times and subsequent centrifugation at 4 1C for 30 min (18 000 g). Crude pellet and soluble fractions were separated and pellets were rinsed with 100ml 20mM Tris buffer pH 7.4. Bacterial 16S rRNA gene clone libraries were constructed from the soluble cell fractions.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0723866 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0723866
onGoing
Gabrielle Rocap
University of Washington
206-685-9994
School of Oceanography Box 357940
Seattle
WA
98195
USA
rocap@ocean.washington.edu
pointOfContact
Robert Morris
University of Washington
206-221-7228
School of Oceanography Box 357940
Seattle
WA
98195-7940
USA
morrisrm@uw.edu
pointOfContact
asNeeded
Dataset Version: 10 March 2011
Unknown
NCBI_Accession
New_ARB_Grouping
Subgroup
Publication_Grouping
Publication_Subgrouping
Clone_STNno
Station
Cast
Depth
Niskin bottle
Pump surface
theme
None, User defined
accession number
No BCO-DMO term
station
cast
depth
featureType
BCO-DMO Standard Parameters
Niskin bottle
Pump - Surface Underway Ship Intake
instrument
BCO-DMO Standard Instruments
KN192-05
service
Deployment Activity
South Atlantic subtropical gyre and Benguela upwelling region
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.
Ocean Carbon and Biogeochemistry
http://us-ocb.org/
Ocean Carbon and Biogeochemistry
The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.
The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.
The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.
The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.
OCB
largerWorkCitation
program
U.S. GEOTRACES
http://www.geotraces.org/
U.S. GEOTRACES
GEOTRACES is a SCOR sponsored program; and funding for program infrastructure development is provided by the U.S. National Science Foundation.
GEOTRACES gained momentum following a special symposium, S02: Biogeochemical cycling of trace elements and isotopes in the ocean and applications to constrain contemporary marine processes (GEOSECS II), at a 2003 Goldschmidt meeting convened in Japan. The GEOSECS II acronym referred to the Geochemical Ocean Section Studies To determine full water column distributions of selected trace elements and isotopes, including their concentration, chemical speciation, and physical form, along a sufficient number of sections in each ocean basin to establish the principal relationships between these distributions and with more traditional hydrographic parameters;
* To evaluate the sources, sinks, and internal cycling of these species and thereby characterize more completely the physical, chemical and biological processes regulating their distributions, and the sensitivity of these processes to global change; and
* To understand the processes that control the concentrations of geochemical species used for proxies of the past environment, both in the water column and in the substrates that reflect the water column.
GEOTRACES will be global in scope, consisting of ocean sections complemented by regional process studies. Sections and process studies will combine fieldwork, laboratory experiments and modelling. Beyond realizing the scientific objectives identified above, a natural outcome of this work will be to build a community of marine scientists who understand the processes regulating trace element cycles sufficiently well to exploit this knowledge reliably in future interdisciplinary studies.
Expand "Projects" below for information about and data resulting from individual US GEOTRACES research projects.
U.S. GEOTRACES
largerWorkCitation
program
Cobalt, Iron and Micro-organisms from the Upwelling zone to the Gyre (GAc01)
https://osprey.bco-dmo.org/project/2067
Cobalt, Iron and Micro-organisms from the Upwelling zone to the Gyre (GAc01)
<p>The geochemistries of dissolved cobalt (Co) and iron (Fe) in the oceanic water column share several characteristics such as extremely low concentrations, redox chemistry, low solubility,and utilization as micronutrients by marine microbes. Iron has been the subject of considerable research focus in recent years due to its role in limiting phytoplankton productivity in oceanic and coastal upwelling environments. Cobalt has been much less studied, but recent data show it may be important in influencing primary productivity or phytoplankton community composition in certain geographical areas.</p>
<p>The CoFeMUG project predated GEOTRACES, so while it is not formally recognized as a GEOTRACES section, it is considered a GEOTRACES-related project and the CoFeMUG data are GEOTRACES compliant.</p>
<p>State-of-the-art geochemical and molecular biological techniques were used to address biogeochemical questions in the South Atlantic, and focus especially on the two trace metals, cobalt and iron. The 27-day cruise in November and December 2007 to the South Atlantic was designed to study cobalt and iron biogeochemistry and focus on four major hypotheses.</p>
<p>(1) Large fluxes of labile cobalt are associated with upwelling systems even in Aeolian dominated environments.<br />
(2) Cobalt and phosphate show correlations in (and only in) surface waters due to micronutrient utilization and rapid remineralization. The slope of the correlation is dependent on the chemical speciation of cobalt.<br />
(3) The absence of Trichodesmium populations in the subtropical and tropical South Atlantic is caused by iron limitation.<br />
(4) Based on work from the California and Peru Upwelling regimes, primary productivity in the Benguela upwelling regime off of South West Africa may be iron limited or iron-cobalt colimited.</p>
<p>A combination of geochemical and biological/molecular analyses were made across an oligotrophic-upwelling transition to examine how changing metal regimes affect the physiology and growth of the important primary producers Trichodesmium and Synechococcus.</p>
<p>CoFeMUG project results are published in:<br />
Noble, Abigail E., Carl H. Lamborg, Dan C. Ohnemus, Phoebe J. Lam, Tyler J. Goepfert, Chris I. Measures, Caitlin H. Frame, Karen L. Casciotti, Giacomo R. DiTullio, Joe Jennings, and Mak A. Saito (2012) Basin-scale inputs of cobalt, iron, and manganese from the Benguela-Angola front to the South Atlantic Ocean. Limnology & Oceanography. Vol. 57(4), July 2012. pgs 989-1010. doi:10.4319/lo.2012.57.4.0989 (<a href="http://www.aslo.org/lo/toc/vol_57/issue_4/0989.pdf">www.aslo.org/lo/toc/vol_57/issue_4/0989.pdf</a>)</p>
CoFeMUG
largerWorkCitation
project
eng; USA
oceans
South Atlantic subtropical gyre and Benguela upwelling region
2011-03-10
South Atlantic subtropical gyre and Benguela upwelling region
0
BCO-DMO catalogue of parameters from NCBI Accessions for 16S rRNA clone libraries made with bacterial 8F and 519R primers collected on R/V Knorr KN192-05 in the South Atlantic subtropical gyre and Benguela upwelling region from November to December 2007 (CoFeMUG 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/23709.rdf
Name: NCBI_Accession
Units: text
Description: <p>NCBI Accession linked to GenBank.</p>
http://lod.bco-dmo.org/id/dataset-parameter/23710.rdf
Name: New_ARB_Grouping
Units: text
Description: <p>New ARB Grouping</p>
http://lod.bco-dmo.org/id/dataset-parameter/23711.rdf
Name: Subgroup
Units: text
Description: <p>Subgroup</p>
http://lod.bco-dmo.org/id/dataset-parameter/23712.rdf
Name: Publication_Grouping
Units: text
Description: <p>Publication Grouping</p>
http://lod.bco-dmo.org/id/dataset-parameter/23713.rdf
Name: Publication_Subgrouping
Units: text
Description: <p>Publication Subgrouping</p>
http://lod.bco-dmo.org/id/dataset-parameter/23714.rdf
Name: Clone_STNno
Units: text
Description: <p>Clone (STN #)</p>
http://lod.bco-dmo.org/id/dataset-parameter/23715.rdf
Name: Station
Units: integer
Description: <p>Station</p>
http://lod.bco-dmo.org/id/dataset-parameter/23716.rdf
Name: Cast
Units: text
Description: <p>Cast</p>
http://lod.bco-dmo.org/id/dataset-parameter/23717.rdf
Name: Depth
Units: integer
Description: <p>Depth</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
173037
https://datadocs.bco-dmo.org/file/1VVMoyLUqx67ng/GenBankClones.csv
GenBankClones.csv
Primary data file for dataset ID 3443
download
https://osprey.bco-dmo.org/dataset/3443/data/download
download
onLine
dataset
<p>Microorganisms were concentrated from large volume (100-200 l) surface seawater samples (5-8 m) collected from either a Niskin rosette or a surface pump. We targeted the &lt; 0.8 um size fraction to obtain the same bacterioplankton community used for GOS shotgun sequencing (Rusch et al., 2007). All concentrations were performed in a 50 l polystyrene reservoir using a Pellicon 2 cassette tangential flow filtration system equipped with one 30kD Biomax Polyethersulfone cassette (Millipore Corporation, Billerica, MA, USA). Seawater was continuously added to the concentration reservoir until cell densities reached ~10^8 cells/ml. In all, 100-200 ml of cell concentrate was obtained in 1.5-3h. Concentrated cells were flash frozen in liquid nitrogen and stored at -80 C until further processing on shore.</p>
<p>A cell pellet was prepared from each tangential flow filtration concentrated sample by centrifugation at 4 C for 60 min (17 000 g). The supernatant was discarded and cell pellets were resuspended in 3 ml of 20 mM Tris buffer pH 7.4. Crude extracts were prepared by passing the cells through a French pressure mini cell at 8000 lb/inch - 2 two times and subsequent centrifugation at 4 1C for 30 min (18 000 g). Crude pellet and soluble fractions were separated and pellets were rinsed with 100ml 20mM Tris buffer pH 7.4. Bacterial 16S rRNA gene clone libraries were constructed from the soluble cell fractions.</p>
Specified by the Principal Investigator(s)
<p>Community genomic DNA was extracted from 200 ml of cell lysate using a DNeasy Blood and Tissue kit (QIAGEN, Germantown, MD, USA). DNA was extracted according to the manufacturer’s instructions. Ribosomal RNA genes were amplified from community genomic DNA for cloning by PCR with Taq polymerase (Fermentas, Hanover, MD, USA) and variations of commonly used bacterial primers, 8F and 519R. Briefly, amplifications were performed in a C1000 thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA) using the following conditions: 35 cycles, annealing at 55 1C for 1 min, elongation at 72 1C for 2 min and denaturation at 94 1C for 30 s. A single band of the predicted length was observed by agarose gel electrophoresis, excised and purified using a DNeasy minelute kit (QIAGEN) according to the manufacturer’s instructions. Clone libraries were constructed using the resulting mixed-template amplicons and the pGEM-T-Easy vector (Promega) following the manufacturer’s instructions. Clone sequences were obtained from transformations by plating, rolling-circle amplification and cycle sequencing at the High-Throughput Genomics Unit (University of Washington, Seattle, WA, USA). Clones from each station were assigned library and station prefixes and numbered sequentially from 1 to 96 (GenBank Accession: GU460426-GU461274). Cloned 16S rRNA gene sequences were aligned in the ARB software package (Ludwig et al., 2004) using a custom database that contained 151 952 sequences from cultured organisms and environmental gene clone libraries. Unambiguously aligned nucleotide sequences were added to a custom tree using the parsimony insertion tool for phylogenetic identification available in ARB. Taxonomic assignments were determined by phylogenetic inference.</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
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Pump surface
Pump surface
PI Supplied Instrument Name: Pump surface Instrument Name: Pump - Surface Underway Ship Intake Instrument Short Name:Pump-Ship Intake Instrument Description: The 'Pump-underway ship intake' system indicates that samples are from the ship's clean water intake pump. This is essentially a surface water sample from a source of uncontaminated near-surface (commonly 3 to 7 m) seawater that can be pumped continuously to shipboard laboratories on research vessels. There is typically a temperature sensor near the intake (known as the hull temperature) to provide measurements that are as close as possible to the ambient water temperature. The flow from the supply is typically directed through continuously logged sensors such as a thermosalinograph and a fluorometer. Water samples are often collected from the underway supply that may also be referred to as the non-toxic supply. Ideally the data contributor has specified the depth in the ship's hull at which the pump is mounted. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/31/
Cruise: KN192-05
KN192-05
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN192-05
Mak A. Saito
Woods Hole Oceanographic Institution
http://bcodata.whoi.edu/CoFeMUG/CruiseReport_KN192-5.pdf
Report describing KN192-05
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel