http://lod.bco-dmo.org/id/dataset/555950
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
2015-04-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial production data from R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE project)
2015-04-16
publication
2015-04-16
revision
BCO-DMO Linked Data URI
2015-04-16
creation
http://lod.bco-dmo.org/id/dataset/555950
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) Bacterial production data 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 16 April 2015) Version Date 2015-04-16 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/555950 [access date]
Bacterial production data from the KN207-03 cruise. Dataset Description: <p>Water column bacterial production (BP) rates measured using the 3H-leucine incorporation microcentrifuge method.</p> Methods and Sampling: <p>Refer to Collins et al., <em>Global Biogeochem. Cycles </em>(2015), in review. Excerpted from methods section:</p>
<p>Water column bacterial production (BP) rates were measured using the 3H-leucine incorporation microcentrifuge method of Simon and Azam (1989), as modified by Kirchman (2001). Incubations were conducted following each CTD cast using water samples from six depths; the first and sixth samples were always from the immediate surface layer (3-5 m) and 150 m. Triplicate 1 mL samples from each chosen depth or net trap were incubated with 3H-leucine (PerkinElmer, Inc., Waltham, MA; 146.5 Ci mmol-1, diluted to achieve 20 nM final concentration) for 4-12 hours at the temperature of the mixed layer. At the conclusion of the cruise, samples were processed and analyzed in a laboratory ashore according to Kirchman (2001) using Ultima Gold Low-Level Tritium cocktail (PerkinElmer, Inc.). Decay per minute counts in killed control samples were subtracted from the mean of each set of triplicates and divided by the incubation time to obtain a blank-corrected leucine incorporation rate in units of pmol leucine L-1 h-1.</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>Simon, M., and F. Azam (1989), Protein-content and protein-synthesis rates of planktonic marine bacteria, <em>Mar. Ecol. Prog. Ser.</em>, <em>51</em>(3), 201-213, doi:<a href="http://dx.doi.org/10.3354/Meps051201" target="_blank">10.3354/Meps051201</a>.</p>
<p>Kirchman, D. (2001), Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments, in <em>Methods in Microbiology</em>, edited by J. H. Paul, pp. 227-237, Academic Press, doi:<a href="http://dx.doi.org/10.1016/S0580-9517(01)30047-8" target="_blank">10.1016/S0580-9517(01)30047-8</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: 16 April 2015
Unknown
station_ctd
incub_duration
ISO_DateTime_UTC
lat_CTD
lon_CTD
depth
DPM_live_samples_mean
DPM_live_samples_stdev
DPM_of_killed_control
trit_leu_uptake_live_mean_dpm
trit_leu_uptake_live_stdev_dpm
trit_leu_uptake_killed_dpm
trit_leu_uptake_dpm
trit_leu_uptake_stdev_dpm
trit_leu_uptake_live_mean_pmol
trit_leu_uptake_live_stdev_pmol
trit_leu_uptake_killed_pmol
trit_leu_uptake_pmol
trit_leu_uptake_stdev_pmol
signal_to_noise
incub_temp
theme
None, User defined
station number
incubation time or duration
ISO_DateTime_UTC
latitude
longitude
depth
No BCO-DMO term
incubation temperature
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
2015-04-16
North Atlantic; Azores to Iceland
0
BCO-DMO catalogue of parameters from Bacterial production data 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/555960.rdf
Name: station_ctd
Units: dimensionless
Description: <p>CTD station number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555961.rdf
Name: incub_duration
Units: minutes
Description: <p>Incubation duration.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555962.rdf
Name: ISO_DateTime_UTC
Units: YYYY-mm-ddTHH:MM:SS.xxZ
Description: <p>Date and time (from CTD timestamp) formatted to ISO 8601 standard. T represents the start of the time string and Z indicates UTC.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555963.rdf
Name: lat_CTD
Units: decimal degrees
Description: <p>Latitude of CTD station.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555964.rdf
Name: lon_CTD
Units: decimal degrees
Description: <p>Longitude of CTD station.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555965.rdf
Name: depth
Units: meters (m)
Description: <p>Sample depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555966.rdf
Name: DPM_live_samples_mean
Units: dpm (disintegrations per minute)
Description: <p>Mean DPM (disintegrations per minute), live samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555967.rdf
Name: DPM_live_samples_stdev
Units: dpm (disintegrations per minute)
Description: <p>Standard deviation DPM (disintegrations per minute), live samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555968.rdf
Name: DPM_of_killed_control
Units: dpm (disintegrations per minute)
Description: <p>DPM (disintegrations per minute) of killed control.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555969.rdf
Name: trit_leu_uptake_live_mean_dpm
Units: dpm per liter per hour (dpm/L/hr)
Description: <p>Mean tritium-labeled leucine (3H-Leu) uptake, live samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555970.rdf
Name: trit_leu_uptake_live_stdev_dpm
Units: dpm per liter per hour (dpm/L/hr)
Description: <p>Standard deviation of tritium-labeled leucine (3H-Leu) uptake, live samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555971.rdf
Name: trit_leu_uptake_killed_dpm
Units: dpm per liter per hour (dpm/L/hr)
Description: <p>Tritium-labeled leucine (3H-Leu) uptake, killed control.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555972.rdf
Name: trit_leu_uptake_dpm
Units: dpm per liter per hour (dpm/L/hr)
Description: <p>Tritium-labeled leucine (3H-Leu) uptake.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555973.rdf
Name: trit_leu_uptake_stdev_dpm
Units: dpm per liter per hour (dpm/L/hr)
Description: <p>Standard deviation of tritium-labeled leucine (3H-Leu) uptake.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555974.rdf
Name: trit_leu_uptake_live_mean_pmol
Units: picomoles per liter per hour (pmol/L/hr)
Description: <p>Mean tritium-labeled leucine (3H-Leu) uptake, live samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555975.rdf
Name: trit_leu_uptake_live_stdev_pmol
Units: picomoles per liter per hour (pmol/L/hr)
Description: <p>Standard deviation tritium-labeled leucine (3H-Leu) uptake, live samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555976.rdf
Name: trit_leu_uptake_killed_pmol
Units: picomoles per liter per hour (pmol/L/hr)
Description: <p>Tritium-labeled leucine (3H-Leu) uptake, killed control.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555977.rdf
Name: trit_leu_uptake_pmol
Units: picomoles 3H-leucine per liter per hour (pmol 3H-leu/L/hr)
Description: <p>The final, blank-corrected, replicate-averaged rates of leucine incorporation for each CTD station and depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555978.rdf
Name: trit_leu_uptake_stdev_pmol
Units: picomoles 3H-leucine per liter per hour (pmol 3H-leu/L/hr)
Description: <p>Standard deviation of the final, blank-corrected, replicate-averaged rates of leucine incorporation for each CTD station and depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555979.rdf
Name: signal_to_noise
Units: dimensionless (ratio)
Description: <p>The "signal to noise" ratio for each measurement, i.e., the ratio of the incorporation rate in the live samples to the killed control at that depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/555980.rdf
Name: incub_temp
Units: degrees Celsius (C)
Description: <p>Incubation temperature.</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
49082
https://datadocs.bco-dmo.org/file/QAAXxQ6SlJyA9g/KN207-03_bact_prod.csv
KN207-03_bact_prod.csv
Primary data file for dataset ID 555950
download
https://osprey.bco-dmo.org/dataset/555950/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>Water column bacterial production (BP) rates were measured using the 3H-leucine incorporation microcentrifuge method of Simon and Azam (1989), as modified by Kirchman (2001). Incubations were conducted following each CTD cast using water samples from six depths; the first and sixth samples were always from the immediate surface layer (3-5 m) and 150 m. Triplicate 1 mL samples from each chosen depth or net trap were incubated with 3H-leucine (PerkinElmer, Inc., Waltham, MA; 146.5 Ci mmol-1, diluted to achieve 20 nM final concentration) for 4-12 hours at the temperature of the mixed layer. At the conclusion of the cruise, samples were processed and analyzed in a laboratory ashore according to Kirchman (2001) using Ultima Gold Low-Level Tritium cocktail (PerkinElmer, Inc.). Decay per minute counts in killed control samples were subtracted from the mean of each set of triplicates and divided by the incubation time to obtain a blank-corrected leucine incorporation rate in units of pmol leucine L-1 h-1.</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>Simon, M., and F. Azam (1989), Protein-content and protein-synthesis rates of planktonic marine bacteria, <em>Mar. Ecol. Prog. Ser.</em>, <em>51</em>(3), 201-213, doi:<a href="http://dx.doi.org/10.3354/Meps051201" target="_blank">10.3354/Meps051201</a>.</p>
<p>Kirchman, D. (2001), Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments, in <em>Methods in Microbiology</em>, edited by J. H. Paul, pp. 227-237, Academic Press, doi:<a href="http://dx.doi.org/10.1016/S0580-9517(01)30047-8" target="_blank">10.1016/S0580-9517(01)30047-8</a>.</p>
Specified by the Principal Investigator(s)
<p>The "signal_to_noise" column gives the ratio for each measurement, i.e., the ratio of the incorporation rate in the live samples to the killed control at that depth.</p>
<p>BCO-DMO processing notes:<br />
- Replaced 'NaN' with 'nd' to indicate 'no data'.<br />
- Modified parameter names to conform with BCO-DMO naming conventions.<br />
- Modified format of date/time to fit ISO8601 format.</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