http://lod.bco-dmo.org/id/dataset/841640
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
2021-02-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cellular trace elements collected on cruise TN280 (GeoMICS project) along Line P in the NE Pacific in May 2012
2021-02-24
publication
2021-02-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-18
publication
https://doi.org/10.26008/1912/bco-dmo.841640.1
Benjamin Twining
Bigelow Laboratory for Ocean Sciences
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: Twining, B. (2021) Cellular trace elements collected on cruise TN280 (GeoMICS project) along Line P in the NE Pacific in May 2012. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-02-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.841640.1 [access date]
Cellular trace elements from TN280 Dataset Description: Methods and Sampling: <p>Samples were collected with trace-metal clean rosette and GO-FLO bottles. A small aliquot of unfiltered seawater was collected following protocols described in Twining et al. (2015). Cellular metals were analyzed with the 2-ID-E microprobe beamline at the Advanced Photon Source, Argonne National Laboratory. Incident beam energy was 10 keV to enable the excitation of K<sub>α</sub> fluorescence for elements ranging in atomic number from Si (14) to Zn (30). Element quantification was performed by averaging the spectra from pixels representing the cells of interest. Spectra were also extracted from a background area close to each cell. The spectra were then fit with MAPS, a custom fitting software package (Vogt, 2003).&nbsp; Concentrations were calculated based on conversion factors obtained by running the thin-film standards NBS 1832, NBS 1833, and custom Si, P, and Fe standards made by Micromatter XRF. Cell volume was calculated based on measurements taken from bright field images of the cells and using the equations of Hillebrand et al. (1999). Cellular C was then calculated from the volumes using the equations described in Menden-Deuer and Lessard (2000).</p>
<p>Complete methodology is published in Twining et al. (2020).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1205232 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1205232
completed
Benjamin Twining
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive PO Box 380
East Boothbay
ME
04544-0380
USA
btwining@bigelow.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
Lat_N
Lon_E
Depth
CellType
Run
MDA
Volume
cellC
cellSi
cellMn
cellFe
cellCo
cellNi
cellZn
GO-FLO bottles
trace-metal clean rosette bottles
2-ID-E X-ray microprobe beamline
theme
None, User defined
station
latitude
longitude
depth
sample description
sample identification
biovolume
Elemental carbon (C)
Silicon
Manganese
Iron
Cobalt
Nickel
Zinc
featureType
BCO-DMO Standard Parameters
GO-FLO Bottle
Trace Metal Bottle
X-ray fluorescence analyzer
instrument
BCO-DMO Standard Instruments
TN280
service
Deployment Activity
Line P in the northeast Pacific Ocean
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.
GeoMICS
https://osprey.bco-dmo.org/program/517517
GeoMICS
The GeoMICS (Global scale Microbial Interactions across Chemical Surveys) research effort grew out of an Ocean Carbon and Biogeochemistry (OCB) workshop that discussed how molecular ecologists might collaborate with geochemists to better understand biogeochemical processes in the world oceans. The workshop highlighted the potential of bringing these two communities together. The first GeoMICS cruise was carried out in May 2012 on the R/V Thompson along a subset of Line P. Goals included:
Identify interactions between changes in microbial diversity, community functions, and chemical features across a gradient.
Coordinate sampling protocols: inorganic geochemistry, organic geochemistry, and molecular biology.
In February 2013, an OCB-sponsored workshop was held to coordinate data analysis among the groups of participants (inorganic geochemists, organic geochemists, molecular ecologists, modelers, and computer scientists).
GeoMICS
largerWorkCitation
program
GeoMICS
https://osprey.bco-dmo.org/program/517517
GeoMICS
The GeoMICS (Global scale Microbial Interactions across Chemical Surveys) research effort grew out of an Ocean Carbon and Biogeochemistry (OCB) workshop that discussed how molecular ecologists might collaborate with geochemists to better understand biogeochemical processes in the world oceans. The workshop highlighted the potential of bringing these two communities together. The first GeoMICS cruise was carried out in May 2012 on the R/V Thompson along a subset of Line P. Goals included:
Identify interactions between changes in microbial diversity, community functions, and chemical features across a gradient.
Coordinate sampling protocols: inorganic geochemistry, organic geochemistry, and molecular biology.
In February 2013, an OCB-sponsored workshop was held to coordinate data analysis among the groups of participants (inorganic geochemists, organic geochemists, molecular ecologists, modelers, and computer scientists).
GeoMICS
largerWorkCitation
program
The relationship between microbial biogeography and ocean chemistry across a persistent oceanographic "hot spot" in the NE Pacific Ocean
https://osprey.bco-dmo.org/project/517510
The relationship between microbial biogeography and ocean chemistry across a persistent oceanographic "hot spot" in the NE Pacific Ocean
<p><em>NSF Award Abstract:</em><br />
The oceans are undergoing dramatic changes. Currently, two largely independently operating research communities -- geochemists and molecular ecologists -- examine potential biological repercussions of changes in ocean chemistry and physics. Geochemists focus primarily on large-scale resultant chemical features, with limited knowledge of underlying biological drivers. Molecular ecologists focus primarily on biodiversity of microbial ecosystems, with few direct linkages to process rates.</p>
<p>With funding from this Early-Concept Grant for Exploratory Research (EAGER), a marine molecular biologist from the University of Washington, a marine inorganic biochemist from the University of Southern California, and a marine trace metal geochemist from Old Dominion University will conduct a multi-parameter exploratory survey cruise to collect and analyze shared geochemical and molecular data to identify chemical and physical drivers of distinct biogeochemical provinces in the sea. They have targeted a well-defined gradient in biogeochemical properties in the northeast Pacific where high nutrient, low chlorophyll waters limited by iron meet low nutrient, iron-replete waters with the long-term goal of understanding the sensitivity of province boundaries to climate change. The transition zone is a surrogate for a geochemical province boundary and is characterized by high biological activity and strong gradients in chemical parameters.</p>
<p>The team hypothesizes that the physical/chemical front creates a distinctive biome with a disproportionate impact on the biogeochemistry of the region, an attribute that may be a fundamental feature of province boundaries. Accordingly, they will characterize multiple biological and chemical parameters on a detailed surface to seafloor zonal survey across this zone. Biological parameters include metagenomes and metatranscriptomes of the microbial community from surface to seafloor at carefully selected stations and gene-focused surveys at more broadly distributed stations. Chemical parameters at all stations include nutrients and dissolved concentrations of Fe, Cu, Zn, Cd, Mn, Co and Ni, key parameters in the GEOTRACES program. Shipboard work will include short-term (12-24 hr) on-deck incubations to examine relationships between rate processes and changes in community composition.</p>
<p>This project is well suited to EAGER funding. The high risk associated with bringing these two research communities together to synthesize resulting data in meaningful ways is mitigated by the high reward associated with learning how to conduct oceanographic work in entirely new ways, moving beyond correlations to causations between biology and chemistry.</p>
<p>This study is motivated by the results from an NSF-sponsored community workshop that highlighted the transformative potential of bringing these two communities together to address underlying drivers of geochemical provinces. The team will invite cruise participation by a broad representation of the two communities, with a central requisite that all participants are broad thinkers that will readily share data in a timely fashion. Member of the U.S. Ocean Carbon and Biogeochemistry (OCB) Scientific Steering Committee have encouraged submission of a proposal for a post-cruise meeting to share successes and "lessons learned". The results of this EAGER project will allow evaluation of the feasibility of joint molecular/geochemical sectional surveys on the scale of programs such as CLIVAR and GEOTRACES</p>
GeoMICS Chem
largerWorkCitation
project
Characterizing biological function across a persistent oceanographic "hotspot" in the NE Pacific Ocean
https://osprey.bco-dmo.org/project/517513
Characterizing biological function across a persistent oceanographic "hotspot" in the NE Pacific Ocean
<p><em>NSF Award Abstract:</em><br />
Every cubic centimeter of oceanic water is home to millions of single celled organisms that are the engines of the majority of biological activity in the ocean. These organisms form functional communities that are key to our understanding of how the ocean benefits us through providing ecosystem services and hinders us through disease and harmful algal blooms. The underlying causes that shape the distribution and activity of organisms remain elusive, resulting in impaired predictive ability. This project will bring oceanographic research into the post-genomic era by joining genomics and transciptomics with state of the art tools in proteomics, metabolomics and trace metal analyses to understand the causes for observed biogeography and biological activity. The project is a multi-faceted study of the structure and function of microbial communities along a transect in the Northeast Pacific that crosses an oceanographic "hotspot" that results from the mixing of high nutrient low chlorophyll waters with coastal iron rich waters.</p>
<p>This project is appropriate as an EAGER award due to the high risk associated with combining numerous cutting edge techniques carried out by a highly multidisciplinary team for the first time. The team includes individuals in the geochemistry community that are accustomed to viewing the end result of biological activity on a large spatial and time integrated scale, and molecular ecologists who interrogate organisms and communities for their evolutionary roots, metabolic capabilities and physiological status. The project is a test bed for an integrated study that includes a complete set of "omics" data along with cell quotas for trace metals. The project will generate a large data set that will be shared with the broader community as well as analyzed by the PIs. Cells in the environment carry out their metabolic processes in the context of a chemical environment. By interrogating cellular functions in the form of the proteome, metabolome and metallome, the investigators are asking the cells to tell us what they sense in the environment and how they respond to what they are sensing. These findings will represent a major step toward redefining how we do oceanography such that a complete understanding of microbial communities can lead us to predictions of how the ocean will respond to ongoing change.</p>
<p>This project follows on an ocean carbon and biogeochemistry workshop that discussed how molecular ecologists might collaborate with geochemists to better understand biogeochemical processes in the world oceans. It is expected that successful completion of this proof of concept cruise will lead to larger interdisciplinary program with the ongoing U.S. Geotraces program. This particular project will demonstrate how using -omics approaches, in conjunction with metagenomic and geochemical sampling, can provide the key to linking structure with function across ocean biomes. As part of this project there will be training for the next generation of oceanographers to work in a multidisciplinary community. Undergraduate students will participate on the cruise and will be entrained in research projects using the data generated. A large data set will be made available to the entire oceanographic community, so that participation will be considerably larger than the small group of investigators participating in the cruise.</p>
GeoMICS Bio
largerWorkCitation
project
eng; USA
oceans
Line P in the northeast Pacific Ocean
-128.67
-125.5
48.58
48.82
2021-02-24
Northeast Pacific Ocean: 48.5N 126W
0
BCO-DMO catalogue of parameters from Cellular trace elements collected on cruise TN280 (GeoMICS project) along Line P in the NE Pacific in May 2012
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/841656.rdf
Name: Station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/841657.rdf
Name: Lat_N
Units: degrees N
Description: <p>station latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/841658.rdf
Name: Lon_E
Units: degrees E
Description: <p>station longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/841659.rdf
Name: Depth
Units: meters (m)
Description: <p>depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/841660.rdf
Name: CellType
Units: unitless
Description: <p>classification of diatom type</p>
http://lod.bco-dmo.org/id/dataset-parameter/841661.rdf
Name: Run
Units: unitless
Description: <p>analysis year and run</p>
http://lod.bco-dmo.org/id/dataset-parameter/841662.rdf
Name: MDA
Units: unitless
Description: <p>unique identifier for each cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/841663.rdf
Name: Volume
Units: cubic micrometers (um^3)
Description: <p>biovolume of cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/841664.rdf
Name: cellC
Units: moles per cell (mol/cell)
Description: <p>cellular carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/841665.rdf
Name: cellSi
Units: moles per cell (mol/cell)
Description: <p>cellular silicon</p>
http://lod.bco-dmo.org/id/dataset-parameter/841666.rdf
Name: cellMn
Units: moles per cell (mol/cell)
Description: <p>cellular manganese</p>
http://lod.bco-dmo.org/id/dataset-parameter/841667.rdf
Name: cellFe
Units: moles per cell (mol/cell)
Description: <p>cellular iron</p>
http://lod.bco-dmo.org/id/dataset-parameter/841668.rdf
Name: cellCo
Units: moles per cell (mol/cell)
Description: <p>cellular cobalt</p>
http://lod.bco-dmo.org/id/dataset-parameter/841669.rdf
Name: cellNi
Units: moles per cell (mol/cell)
Description: <p>cellular nickel</p>
http://lod.bco-dmo.org/id/dataset-parameter/841670.rdf
Name: cellZn
Units: moles per cell (mol/cell)
Description: <p>cellular zinc</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
7896
https://darchive.mblwhoilibrary.org/bitstream/1912/27125/1/dataset-841640_cellular-trace-elements-tn280__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.841640.1
download
onLine
dataset
<p>Samples were collected with trace-metal clean rosette and GO-FLO bottles. A small aliquot of unfiltered seawater was collected following protocols described in Twining et al. (2015). Cellular metals were analyzed with the 2-ID-E microprobe beamline at the Advanced Photon Source, Argonne National Laboratory. Incident beam energy was 10 keV to enable the excitation of K<sub>α</sub> fluorescence for elements ranging in atomic number from Si (14) to Zn (30). Element quantification was performed by averaging the spectra from pixels representing the cells of interest. Spectra were also extracted from a background area close to each cell. The spectra were then fit with MAPS, a custom fitting software package (Vogt, 2003).&nbsp; Concentrations were calculated based on conversion factors obtained by running the thin-film standards NBS 1832, NBS 1833, and custom Si, P, and Fe standards made by Micromatter XRF. Cell volume was calculated based on measurements taken from bright field images of the cells and using the equations of Hillebrand et al. (1999). Cellular C was then calculated from the volumes using the equations described in Menden-Deuer and Lessard (2000).</p>
<p>Complete methodology is published in Twining et al. (2020).</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
SXRF data were excluded if the relative standard deviation of the element peak fit by the model was greater than 20%, indicating poor precision of the model fit.</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
GO-FLO bottles
GO-FLO bottles
PI Supplied Instrument Name: GO-FLO bottles Instrument Name: GO-FLO Bottle Instrument Short Name:GO-FLO Instrument Description: GO-FLO bottle cast used to collect water samples for pigment, nutrient, plankton, etc. The GO-FLO sampling bottle is specially designed to avoid sample contamination at the surface, internal spring contamination, loss of sample on deck (internal seals), and exchange of water from different depths. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/30/
trace-metal clean rosette bottles
trace-metal clean rosette bottles
PI Supplied Instrument Name: trace-metal clean rosette bottles Instrument Name: Trace Metal Bottle Instrument Short Name:TM Bottle Instrument Description: Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/30/
2-ID-E X-ray microprobe beamline
2-ID-E X-ray microprobe beamline
PI Supplied Instrument Name: 2-ID-E X-ray microprobe beamline PI Supplied Instrument Description:The 2-ID-E X-ray microprobe beamline at the Advanced Photon Source, Argonne National Laboratory, was used for cellular element analysis. Instrument Name: X-ray fluorescence analyzer Instrument Short Name:XRF analyzer Instrument Description: Instruments that identify and quantify the elemental constituents of a sample from the spectrum of electromagnetic radiation emitted by the atoms in the sample when excited by X-ray radiation.
Cruise: TN280
TN280
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN280
E. Virginia Armbrust
University of Washington
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel