http://lod.bco-dmo.org/id/dataset/517634
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
2014-06-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
HPLC pigment analyses of CTD-collected samples from R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE project)
2014-09-17
publication
2014-09-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-12-30
publication
https://doi.org/10.1575/1912/bco-dmo.517634.1
Giacomo DiTullio
Grice Marine Laboratory - College of Charleston
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: DiTullio, G. (2014) HPLC pigment analyses of CTD-collected samples from R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2014-09-17 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.517634.1 [access date]
HPLC pigment analyses of CTD collected samples on KN207-03 cruise (NA-VICE). Dataset Description: <p>Dataset includes HPLC pigment analyses of CTD collected samples from the KN207-03 cruise (Northeast Atlantic Ocean transect from Azores to Iceland).</p> Methods and Sampling: <p>Water samples were collected from CTD Niskin bottles. Water samples for HPLC analyses were taken from one Niskin bottle per cast-depth combination included in the dataset. Note that the niskin_sampled column indicates which Niskin bottle the HPLC sample was taken from. The niskins_fired column indicates all Niskin bottle numbers fired at the specified depth, though the HPLC sample was taken from only one of those bottles.</p>
<p>Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100). Culture aliquots were filtered on Whatmann GF/F filters, flash frozen in liquid nitrogen, and stored at -80°C until analysis. Just prior to analysis, pigments were extracted overnight in acetone at -20°C. The following day extracted pigments were centrifuged and measured using a gradient elution method (DiTullio and Geesey, 2003), a modification of the Zapata et al 2000 method. Chromatographic separation was performed using a Waters C8 symmetry column, photodiode array and fluorescence detectors. The internal standard, β-Apo-8-carotenal-trans standard (Fluka Chemical Corp., USA) was added to extracted pigments as a peak reference. Individual pigment peaks were quantified with Chemstation software (revision B.03.01, Agilent) and our pigment action spectra library calibrated using pigment standards from DHI LABS (Hoersholm, Denmark) and in-house purifications of non-commercially available pigments. Coefficient of variation among replicate HPLC injections is &lt; 3% and our limit of detection is approximately 1 ng L<sup>-1</sup>.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1061876 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1061876
completed
Giacomo DiTullio
Grice Marine Laboratory - College of Charleston
843-953-9196
Hollings Marine Lab 205 Fort Johnson Rd.
Charleston
SC
29412
USA
ditullioj@cofc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
cast
station
date_gmt
time_gmt
date_local
time_local
lat
lon
lat_deg
lat_min
lon_deg
lon_min
ISO_DateTime_UTC
depth
amb_bot
niskin_sampled
niskins_fired
filt_vol
pigment
concentration
HPLC
Niskin bottle
theme
None, User defined
cast
station
date_gmt
time_gmt
date_local
time_local
latitude
longitude
lat_degs
lat_mins
lon_degs
lon_mins
ISO_DateTime_UTC
depth
bottle
bottles
volume of water filtered
pigment concentration
featureType
BCO-DMO Standard Parameters
High-Performance Liquid Chromatograph
Niskin bottle
instrument
BCO-DMO Standard Instruments
KN207-03
service
Deployment Activity
North Atlantic; transect from Ponta Delgada, Azores to Reykjavik, Iceland
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
Lipid lubrication of oceanic carbon and sulfur biogeochemistry via a host-virus chemical arms race
https://osprey.bco-dmo.org/project/2136
Lipid lubrication of oceanic carbon and sulfur biogeochemistry via a host-virus chemical arms race
<p>This project is also called "<strong>NA-VICE</strong>" (North Atlantic Virus Infection of Coccolithophores Expedition).</p>
<p><em>Project description from NSF award abstract:</em><br />
Despite the critical importance of viruses in shaping marine microbial ecosystems, very little is known about the molecular mechanisms mediating phytoplankton-virus interactions. As a consequence, we currently lack biomarkers to quantify active viral infection in the oceans, significantly hindering our understanding of its ecological and biogeochemical impacts.</p>
<p>The coccolithophore <em>Emiliania huxleyi</em> (Prymnesiophyceae, Haptophyte) is a cosmopolitan unicellular photoautotroph whose calcite skeletons account for about a third of the total marine CaCO3 production. <em>E. huxleyi</em> forms massive annual spring blooms in the North Atlantic that are infected and terminated by lytic, giant double-stranded DNA containing coccolithoviruses. Findings that lytic viral infection of <em>E. huxleyi</em> recruits the hosts programmed cell death (PCD) machinery demonstrate that viruses employ a sophisticated, co-evolutionary “arms race” in mediating host-virus interactions. The investigators recently demonstrated that viral glycosphingolipids (vGSLs), derived from unexpected cluster of sphingolipid biosynthetic genes, a pathway never before described in a viral genome, play a crucial functional role in facilitating infection of <em>E. huxleyi</em>. The observations of vGSLs in the North Atlantic and Norwegian fjords further suggest that they may be novel, diagnostic biomarkers for viral infection of coccolithophore populations. At the same time, the discovery of vGSLs and a distinct, protective 802 lipid argues that a host-virus, co-evolutionary chemical arms race plays a pivotal role in regulating viral infection and in lubricating upper ocean biogeochemical fluxes of carbon and sulfur.</p>
<p><strong>The focus of this collaborative research project is to elucidate the molecular, ecological, and biogeochemical links between vGSLs (and other polar lipids) and the global cycles of carbon and sulfur.</strong></p>
<p>The team of investigators proposes a multi-pronged approach combing a suite of lab-based, mechanistic studies using several haptophyte-virus model systems along with observational studies and manipulative field-based experiments the Northeast Atlantic. Using these diagnostic markers, they will document active viral infection of natural coccolithophore populations and couple it with a suite of oceanographic measurements in order to quantify how viral infection (via vGSLs) influences cell fate, the dissolved organic carbon (DOC) pool, vertical export of particular organic (POC) and inorganic carbon (PIC; as calcium carbonate, CaCO3) (along with associated alkenone lipid biomarkers and genetic signatures of viruses and their hosts) and the upper ocean sulfur cycle (via the cycling of dimethylsulfide [DMS] and other biogenic sulfur compounds). Furthermore, given they are unique to viruses, the investigators propose that vGSLs can be used to trace the flow of virally-derived carbon and provide quantitative insights into a “viral shunt” that diverts fixed carbon from higher trophic levels and the deep sea.</p>
<p><strong>The overarching hypothesis for this study is that vGSLs are cornerstone molecules in the upper ocean, which facilitate viral infection on massive scales and thereby mechanistically "lubricate" the biogeochemical fluxes of C and S in the ocean.</strong></p>
NA-VICE
largerWorkCitation
project
eng; USA
oceans
North Atlantic; transect from Ponta Delgada, Azores to Reykjavik, Iceland
-35.0733
-26.102033
42.963
65.447967
2012-06-17
2012-07-13
North Atlantic; Azores to Iceland
0
BCO-DMO catalogue of parameters from HPLC pigment analyses of CTD-collected samples from R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE 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/517644.rdf
Name: cast
Units: alphanumeric
Description: <p>Cast number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517645.rdf
Name: station
Units: text
Description: <p>Station name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517646.rdf
Name: date_gmt
Units: unitless
Description: <p>Date of cast (GMT). in the format mmddyyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/517647.rdf
Name: time_gmt
Units: unitless
Description: <p>Time of cast (GMT). in the format hhmmss</p>
http://lod.bco-dmo.org/id/dataset-parameter/517648.rdf
Name: date_local
Units: unitless
Description: <p>Date of cast (local time zone). in the format mmddyyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/517649.rdf
Name: time_local
Units: unitless
Description: <p>Time of cast (local time zone). in the format hhmmss</p>
http://lod.bco-dmo.org/id/dataset-parameter/517650.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude. Positive values = North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517651.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude. Positive values = East.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517652.rdf
Name: lat_deg
Units: degrees North
Description: <p>Degrees latitude.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517653.rdf
Name: lat_min
Units: minutes North
Description: <p>Minutes latitude.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517654.rdf
Name: lon_deg
Units: degrees West
Description: <p>Degrees longitude. Positive = West.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517655.rdf
Name: lon_min
Units: minutes West
Description: <p>Minutes longitude. Positive = West.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528415.rdf
Name: ISO_DateTime_UTC
Units: yyyy-MM-dd'T'HH:mm:ss.SS
Description: <p>Date and time of cast formatted to ISO8601 standard.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528416.rdf
Name: depth
Units: meters
Description: <p>Depth of Niskin bottle firing.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528417.rdf
Name: amb_bot
Units: integer
Description: <p>Amber bottle identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528418.rdf
Name: niskin_sampled
Units: integer
Description: <p>Niskin bottle number from which HPLC sample was taken.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528419.rdf
Name: niskins_fired
Units: range of integers
Description: <p>Niskin bottle numbers fired at depth; HPLC sample was taken from one Niskin bottle.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528420.rdf
Name: filt_vol
Units: liters (L)
Description: <p>Volume of water filtered.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528421.rdf
Name: pigment
Units: text
Description: <p>Name of the pigment measured:<br />
chl_c3 = Chlorophyll c3;<br />
chl_ide = Chlorophyllide a;<br />
mg_dvp = Magnesium-2;4-divinyl phaeoporphyrin a5 monomethyl ester;<br />
chl_c2 = Chlorophyll c2;<br />
chl_c1 = Chlorophyll c1;<br />
peridinin = Peridinin;<br />
but19 = 19-butanoyloxyfucoxanthin;<br />
fucox = Fucoxanthin;<br />
ph_ide = Pheophorbide a;<br />
neox = Neoxanthin;<br />
prasinox = Prasinoxanthin;<br />
violax = Violaxanthin;<br />
hex19 = 19'-hexanoyloxyfucoxanthin;<br />
diadinox = Diadinoxanthin;<br />
cis_fucox = cis-Fucoxanthin;<br />
allox = Alloxanthin;<br />
diatox = Diatoxanthin;<br />
monad = Monadoxanthin;<br />
zeax = Zeaxanthin;<br />
lutein = lutein;<br />
crocox = Crocoxanthin;<br />
chl_b = Chlorophyll b;<br />
dv_chl_a = Divinyl Chlorophyll a;<br />
chl_a = Chlorophyll a;<br />
p_phytin = Phaeophytin a;<br />
carotene_a = alpha Carotene;<br />
carotene_b = beta Carotene.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528422.rdf
Name: concentration
Units: nanograms per liter (ng/L)
Description: <p>Concentration of the pigment as determined by HPLC.</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
833875
https://darchive.mblwhoilibrary.org/bitstream/1912/25082/1/dataset-517634_hplc-pigments__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.517634.1
download
onLine
dataset
<p>Water samples were collected from CTD Niskin bottles. Water samples for HPLC analyses were taken from one Niskin bottle per cast-depth combination included in the dataset. Note that the niskin_sampled column indicates which Niskin bottle the HPLC sample was taken from. The niskins_fired column indicates all Niskin bottle numbers fired at the specified depth, though the HPLC sample was taken from only one of those bottles.</p>
<p>Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100). Culture aliquots were filtered on Whatmann GF/F filters, flash frozen in liquid nitrogen, and stored at -80°C until analysis. Just prior to analysis, pigments were extracted overnight in acetone at -20°C. The following day extracted pigments were centrifuged and measured using a gradient elution method (DiTullio and Geesey, 2003), a modification of the Zapata et al 2000 method. Chromatographic separation was performed using a Waters C8 symmetry column, photodiode array and fluorescence detectors. The internal standard, β-Apo-8-carotenal-trans standard (Fluka Chemical Corp., USA) was added to extracted pigments as a peak reference. Individual pigment peaks were quantified with Chemstation software (revision B.03.01, Agilent) and our pigment action spectra library calibrated using pigment standards from DHI LABS (Hoersholm, Denmark) and in-house purifications of non-commercially available pigments. Coefficient of variation among replicate HPLC injections is &lt; 3% and our limit of detection is approximately 1 ng L<sup>-1</sup>.</p>
Specified by the Principal Investigator(s)
<p>Response factors for pigments were performed using dilutions of calibration standards. Full details of data processing and methods used can be found in:<br />
DiTullio, G. R. &amp; Geesey, M. E. (2002) Photosynthetic pigments in marine algae and bacteria. <em>In:</em> BITTON, G. (ed.) <em>The Encyclopedia of Environmental Microbiology.</em> New York: John Wiley &amp; Sons Inc.</p>
<p>BCO-DMO Processing Notes:<br />
- Modified parameter names to conform to BCO-DMO conventions;<br />
- Blanks (missing data) replaced with "nd" meaning "no data";<br />
- Separated the original "niskin" column into two columns: "niskin_sampled" and "niskins_fired";<br />
- Converted original longitude values provided as positive degrees West to negative degrees East;<br />
- Added ISO_DateTime_UTC column from original date_gmt and time_gmt fields;<br />
- Transposed data to convert columns containing pigment concentrations into rows.</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
HPLC
HPLC
PI Supplied Instrument Name: HPLC PI Supplied Instrument Description:Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100). Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
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/
Cruise: KN207-03
KN207-03
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN207-03
Kay D. Bidle
Rutgers University
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel