http://lod.bco-dmo.org/id/dataset/556400
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
2015-04-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Water column (community) respiration rates from changes in DO in incubations from samples collected on R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE project)
2015-04-20
publication
2015-04-20
revision
BCO-DMO Linked Data URI
2015-04-20
creation
http://lod.bco-dmo.org/id/dataset/556400
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
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: Van Mooy, B. A. (2015) Water column (community) respiration rates from changes in DO in incubations from samples collected on 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 20 April 2015) Version Date 2015-04-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/556400 [access date]
Water column (community) respiration rates from changes in DO in incubations. Dataset Description: <p>Water column (community) respiration rates from changes in DO in incubations.</p> Methods and Sampling: <p>Refer to Collins et al., <em>Global Biogeochem. Cycles </em>(2015), in review. Excerpted from methods section:</p>
<p>Estimates of aerobic respiration by the water column microbial community (WCR) were calculated by linear regression of measurements of dissolved oxygen concentration in a series of 300 mL shipboard bottle incubations. Determination of dissolved oxygen was made at 3- to 9-hour intervals in at least five replicates using optode spot minisensors (PreSens PSt3; Precision Sensing GmbH, Regensburg, Germany) that were glued to the inside surfaces of the bottles using food-quality silicone cement (M Warkentin et al., 2007). The use of these optode spots eliminated the need for drawing of aliquots from the sample bottles. Incubations were conducted in the dark at in situ temperature as described in Edwards et al. (2011). We validated the rates from these incubations using a series of Winkler titrations; methods are described in the Auxiliary Material to Collins et al. (2015). We used the standard error of the slope parameter from these regressions as the uncertainty in our estimates of WCR.</p>
<p><strong>References:</strong><br />
Collins, J. R., B. R. Edwards, K. Thamatrakoln, J. E. Ossolinksi, G. R. DiTullio, K. D. Bidle, S. C. Doney, and B. A. S. Van Mooy (2015), The multiple fates of sinking particles in the North Atlantic Ocean, <em>Global Biogeochem. Cycles, </em>in review.</p>
<p>Edwards, B. R., C. M. Reddy, R. Camilli, C. A. Carmichael, K. Longnecker, and B. A. S. Van Mooy (2011), Rapid microbial respiration of oil from the Deepwater Horizon spill in offshore surface waters of the Gulf of Mexico, <em>Environmental Research Letters</em>, <em>6</em>(3), doi:<a href="http://dx.doi.org/10.1088/1748-9326/6/3/035301" target="_blank">10.1088/1748-9326/6/3/035301</a>.</p>
<p>Warkentin, M., H. M. Freese, U. Karsten, and R. Schumann (2007), New and fast method to quantify respiration rates of bacterial and plankton communities in freshwater ecosystems by using optical oxygen sensor spots, <em>Appl. Environ. Microbiol.</em>, <em>73</em>(21), 6722-6729, doi:<a href="http://dx.doi.org/10.1128/Aem.00405-07" target="_blank">10.1128/Aem.00405-07</a>.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1059884 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1059884
completed
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
(508) 289 2322
Department of Marine Chemistry and Geochemistry, MS #4, Fye 117 Woods Hole Oceanographic Institution
Woods Hole
MA
02543
USA
bvanmooy@whoi.edu
pointOfContact
asNeeded
Dataset Version: 20 April 2015
Unknown
station_ctd
depth
incub_temp
lat_CTD
lon_CTD
delta_O2
delta_O2_stdev
mean_R2
ISO_DateTime_UTC
theme
None, User defined
station number
depth
incubation temperature
latitude
longitude
No BCO-DMO term
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
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
2015-04-20
North Atlantic; Azores to Iceland
0
BCO-DMO catalogue of parameters from Water column (community) respiration rates from changes in DO in incubations from samples collected on 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/556410.rdf
Name: station_ctd
Units: dimensionless
Description: <p>CTD station number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556411.rdf
Name: depth
Units: meters
Description: <p>Sample depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556412.rdf
Name: incub_temp
Units: degrees Celsius ( C)
Description: <p>Incubation temperature.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556413.rdf
Name: lat_CTD
Units: decimal degrees
Description: <p>Latitude of CTD station.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556414.rdf
Name: lon_CTD
Units: decimal degrees
Description: <p>Longitude of CTD station.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556415.rdf
Name: delta_O2
Units: millimoles O2 per cubic meter per day (mmol O2 m-3 d-1)
Description: <p>Delta O2.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556416.rdf
Name: delta_O2_stdev
Units: millimoles O2 per cubic meter per day (mmol O2 m-3 d-1)
Description: <p>Standard deviation of delta O2.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556417.rdf
Name: mean_R2
Units: dimensionless
Description: <p>Mean r-squared value of regressions DO on time.</p>
http://lod.bco-dmo.org/id/dataset-parameter/556418.rdf
Name: ISO_DateTime_UTC
Units: YYYY-mm-ddTHH:MM:SS.xxZ
Description: <p>Date and time, UTC, (from CTD timestamp) formatted to ISO 8601 standard. T represents the start of the time string and Z indicates UTC.</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
1963
https://datadocs.bco-dmo.org/file/YVVZJ25SkKyWPg/KN207-03_resp.csv
KN207-03_resp.csv
Primary data file for dataset ID 556400
download
https://osprey.bco-dmo.org/dataset/556400/data/download
download
onLine
dataset
<p>Refer to Collins et al., <em>Global Biogeochem. Cycles </em>(2015), in review. Excerpted from methods section:</p>
<p>Estimates of aerobic respiration by the water column microbial community (WCR) were calculated by linear regression of measurements of dissolved oxygen concentration in a series of 300 mL shipboard bottle incubations. Determination of dissolved oxygen was made at 3- to 9-hour intervals in at least five replicates using optode spot minisensors (PreSens PSt3; Precision Sensing GmbH, Regensburg, Germany) that were glued to the inside surfaces of the bottles using food-quality silicone cement (M Warkentin et al., 2007). The use of these optode spots eliminated the need for drawing of aliquots from the sample bottles. Incubations were conducted in the dark at in situ temperature as described in Edwards et al. (2011). We validated the rates from these incubations using a series of Winkler titrations; methods are described in the Auxiliary Material to Collins et al. (2015). We used the standard error of the slope parameter from these regressions as the uncertainty in our estimates of WCR.</p>
<p><strong>References:</strong><br />
Collins, J. R., B. R. Edwards, K. Thamatrakoln, J. E. Ossolinksi, G. R. DiTullio, K. D. Bidle, S. C. Doney, and B. A. S. Van Mooy (2015), The multiple fates of sinking particles in the North Atlantic Ocean, <em>Global Biogeochem. Cycles, </em>in review.</p>
<p>Edwards, B. R., C. M. Reddy, R. Camilli, C. A. Carmichael, K. Longnecker, and B. A. S. Van Mooy (2011), Rapid microbial respiration of oil from the Deepwater Horizon spill in offshore surface waters of the Gulf of Mexico, <em>Environmental Research Letters</em>, <em>6</em>(3), doi:<a href="http://dx.doi.org/10.1088/1748-9326/6/3/035301" target="_blank">10.1088/1748-9326/6/3/035301</a>.</p>
<p>Warkentin, M., H. M. Freese, U. Karsten, and R. Schumann (2007), New and fast method to quantify respiration rates of bacterial and plankton communities in freshwater ecosystems by using optical oxygen sensor spots, <em>Appl. Environ. Microbiol.</em>, <em>73</em>(21), 6722-6729, doi:<a href="http://dx.doi.org/10.1128/Aem.00405-07" target="_blank">10.1128/Aem.00405-07</a>.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO processing notes:<br />
- Modified parameter names to conform with BCO-DMO naming conventions.<br />
- Modified format of date/time to fit ISO8601 format.<br />
- Replaced blanks (missing data) and 'NaN' with 'nd' to indicate 'no data'.</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: 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