http://lod.bco-dmo.org/id/dataset/713842
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
2017-08-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Size fractionated and group-specific rates of 14C-primary production by Prochlorococcus, Synechococcus, and photosynthetic picoeukaryotes from samples collected during Hawaii Ocean Time-series (HOT) program cruises 230-252 between 2012 and 2013
2017-08-25
publication
2017-08-25
revision
BCO-DMO Linked Data URI
2017-08-25
creation
http://lod.bco-dmo.org/id/dataset/713842
Matthew J. Church
University of Montana
principalInvestigator
Kevin R. Arrigo
Stanford University
principalInvestigator
Dr Zbigniew Kolber
University of California-Santa Cruz
principalInvestigator
Jonathan P. Zehr
University of California-Santa Cruz
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: Church, M. J., Zehr, J. P., Arrigo, K. R., Kolber, Z. (2017) Size fractionated and group-specific rates of 14C-primary production by Prochlorococcus, Synechococcus, and photosynthetic picoeukaryotes from samples collected during Hawaii Ocean Time-series (HOT) program cruises 230-252 between 2012 and 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-08-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/713842 [access date]
Size fractionated and group-specific rates of 14C-primary production by Prochlorococcus, Synechococcus, and photosynthetic picoeukaryotes Dataset Description: <p>This dataset contains&nbsp;size fractionated rates of 14C-bicarbonate assimilation and the “group-specific” rates of 14C-bicarbonate assimilation. &nbsp;The group-specific rates were derived from flow cytometrically sorting radiolabeled cells (post-incubation) including Prochlorococcus, Synechococcus, and photosynthetic picoeukaryotes.</p>
<p>These results were published in the following publication:</p>
<p>Rii YM, Karl DM, Church MJ (2016) Temporal and vertical variability in picophytoplankton primary productivity in the North Pacific Subtropical Gyre. Mar Ecol Prog Ser 562:1-18. <a href="https://doi.org/10.3354/meps11954" target="_blank">https://doi.org/10.3354/meps11954&nbsp;</a></p> Methods and Sampling: <p>Seawater was collected in 12-L polyvinylchloride bottles affixed to a 24-bottle rosette sampler, equipped with a Sea-Bird 911+ conductivity, temperature, and pressure profiler. Rates of size-fractionated (&gt;3 μm and 0.2-3 um) and group-specific particulate 14C-based primary production were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m)&nbsp;throughout the euphotic zone.&nbsp; Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes (Nalgene (TM) Oak Ridge) from a pre-dawn cast, inoculated under subdued light with 70 uL of NaH14CO3- (final activity = ~0.14 MBq/mL; MP Biomedicals 17441H), then incubated over the full photoperiod (~12-14 hours) in white mesh bags affixed to a floating in situ array at the corresponding depths where the water was collected.&nbsp; At the end of the incubation period (after sundown), each polycarbonate tube was sampled for size-fractionated and group-specific rates of 14C primary productivity. Aliquots (25 µl) were subsampled from each tube and stored in 20-mL glass scintillation vials containing 500&nbsp;µL of B–phenylethylamine to determine the total activity of&nbsp;14C added to each sample. Next, 5 mL of each sample was preserved in cryotubes containing 30 uL of 16% (final concentration 0.24% w/v) microscopy-grade paraformaldehyde (PFA, Alfa Aesar 43368), flash-frozen in liquid nitrogen, and stored at -80C for subsequent flow cytometric sorting. The remaining sample volume (~25 mL) was vacuum-filtered first onto a 25-mm diameter 3-μm pore size polycarbonate membrane (Millipore IsoporeTM), then the filtrate was vacuum-filtered onto a 25-mm diameter 0.2-um pore size polycarbonate membrane filter (GE Osmonics).&nbsp;After filtration, each filter was placed into a 20-mL glass scintillation vial and stored at -20C until analyzed back&nbsp;at the shore-based laboratory. Upon return to shore, vials were uncapped, 1 mL of 2 M hydrochloric acid was added to each filter, and vials were vented for at least 24 hours to remove remaining inorganic 14C. After venting, 10 mL of Ultima Gold liquid scintillation cocktail was added to each vial, and vials were placed in a liquid scintillation counter (Packard TRI-Carb 4640) for the determination of&nbsp;14C activities.&nbsp; Group-specific rates of 14C-assimilation by&nbsp;<em>Prochlorococcus</em>,&nbsp;<em>Synechococcus</em>, and PPE were determined by measuring the amount of 14C assimilated into populations sorted using the BD InfluxTM (100-μm nozzle tip, 1X BioSure® sheath solution). Calibration of the # of cells sorted was conducted at the beginning of each sorting session; a known number of fluorescent microspherical beads (1 um, Fluoresbrite, Polysciences) were gated through the data acquisition software Spigot, sorted onto a slide, and checked for accuracy under the microscope. The ‘1.0 drop purity’ setting in the Spigot software was utilized as a conservative way of ensuring accuracy of the types of cells sorted into two 6.5-mL HDPE scintillation vials with the ‘two tube sort’ setting. Beads were included with the samples for size reference, and 0.2 x 103 to 4 x 103 beads were sorted for the determination of background levels of radioactivity (both organic 14C in the seawater and 14C absorbed to the beads). Picophytoplankton cells were triggered on forward scatter (FSC) and enumerated based on FSC and side scatter, chlorophyll-based red fluorescence (692 +- 20 nm), and phycoerythrin-based orange fluorescence (585 +- 20 nm) following excitation with two lasers, 488 nm (200 mW) and 457 nm (300 mW).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1241263 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1241263
completed
Matthew J. Church
University of Montana
(406) 982-3301
Flathead Lake Biological Station, University of Montana 321225 Bio Station Lane
Polson
MT
59860-6815
USA
matt.church@flbs.umt.edu
pointOfContact
Kevin R. Arrigo
Stanford University
650-723-3599
Department of Earth System Science/ Y2E2 Building Room 141
Stanford
CA
94305
USA
arrigo@stanford.edu
pointOfContact
Dr Zbigniew Kolber
University of California-Santa Cruz
zkolber@gmail.com
pointOfContact
Jonathan P. Zehr
University of California-Santa Cruz
831-459 4009
E&MS A438, Ocean Sciences Department 1156 High Street
Santa Cruz
CA
95064
USA
zehrj@ucsc.edu
pointOfContact
asNeeded
Unknown
Cruise
Date
Time
ISO_DateTime_UTC
Lat
Lon
Cast
Bottle
Depth
Pico_SzFxPP_mean
Pico_SzfxPP_sd
ndno_SzFxPP_mean
ndno_SzfxPP_sd
Pro_PP_mean
Syn_PP_mean
Peuk_PP_mean
Packard TRI-Carb 4640
theme
None, User defined
cruise_id
date
time of day
ISO_DateTime_UTC
latitude
longitude
cast
bottle
depth nominal
primary production
featureType
BCO-DMO Standard Parameters
Liquid Scintillation Counter
instrument
BCO-DMO Standard Instruments
HOT_cruises
service
Deployment Activity
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Oligotrophic phytoplankton community response to changes in N substrates and the resulting impact on genetic, taxonomic and functional diversity
https://osprey.bco-dmo.org/project/471899
Oligotrophic phytoplankton community response to changes in N substrates and the resulting impact on genetic, taxonomic and functional diversity
<p>(Extracted from NSF award abstract)</p>
<p>Marine phytoplankton are a diverse group of Prokaryotic and Eukaryotic unicellular organisms that account for approximately 50% of global carbon fixation. Nitrogen (N) is an essential element for microbial growth, but concentrations of bioavailable nitrogen in vast regions of subtropical ocean gyres are extremely low (submicromolar to nanomolar concentrations), and generally limit phytoplankton growth. Phytoplankton taxa differ in their genetic capabilities to take up and assimilate nutrients, and thus competition for different chemical forms of N (NH4+, NO3- and urea) and supply of these N-containing compounds are important controls on phytoplankton growth, productivity, and ultimately ecosystem function. The form and supply of N to phytoplankton have already been altered by anthropogenic activities, and with increasing environmental perturbations the effects will accelerate. To date however, there is limited information on how the N forms and fluxes impact the marine phytoplankton community composition and primary production. Similarly, determining the mechanisms of the response are crucial to assessing how ocean ecosystem function will respond to global climate change.</p>
<p>This project seeks to determine how taxonomic, genetic and functional dimensions of phytoplankton diversity are linked with community-level responses to the availability of different N substrates (NH4+, NO3-, and urea) in one of Earth's largest aquatic habitats, the North Pacific Subtropical Gyre. The project will characterize phytoplankton community composition change and gene expression, photosynthetic performance, carbon fixation, and single-cell level N and C uptake in different taxa within the phytoplankton assemblage in response to different N compounds. The research project is unique in investigating community-to-single-cell level function and species (strain)-specific gene expression patterns using state-of-the-art methods including fast repetition rate fluorometry, nanoscale secondary ion mass spectrometry and a comprehensive marine microbial community microarray. The results will provide predictive understanding of how changes in the availability of key nitrogen pools (N) may impact phytoplankton dynamics and function in the ocean.</p>
<p>References:</p>
<p>Karl, D. M., Bjorkman, K. M., Dore, J. E., Fujieki, L., Hebel, D. V., Houlihan, T., Letelier, R. M., Tupas, L. M. 2001. Ecological nitrogen-to-phosphorus stoichiometry at station ALOHA. Deep-Sea Research II. 48:1529 - 1566.</p>
<p>Karl, D. M., Letelier, R., Tupas, L., Dore, J., Christian, J. & Hebel, D. 1997. The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean. Nature. 388:533-538.</p>
<p>McCarthy, J., Taylor, W. R., Taft, J. 1997. Nitrogenous nutrition of the plankton in the Chesapeake Bay. Limnology and Oceanography. 35:822 - 829.</p>
<p>Letelier, R., Karl, D. M. 1996. Role of Trichodesmium spp. in the productivity of the subtropical North Pacific Ocean. Marine Ecology Progress Series. 133:263 - 273.</p>
<p>Lipschultz, F. 1995. Nitrogen-specific uptake rates of marine phytoplankton isolated from natura populations of particles by flow cytometry. Marine Ecology Progress Series. 123:245-258.</p>
PhytoNsubResponse
largerWorkCitation
project
eng; USA
oceans
-158
-158
22.75
22.75
2012-05-30
2013-05-18
North Pacific Subtropical Gyre at Station ALOHA, and a transect from San Diego, CA to Hawaii
0
BCO-DMO catalogue of parameters from Size fractionated and group-specific rates of 14C-primary production by Prochlorococcus, Synechococcus, and photosynthetic picoeukaryotes from samples collected during Hawaii Ocean Time-series (HOT) program cruises 230-252 between 2012 and 2013
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/722714.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/722715.rdf
Name: Date
Units: unitless
Description: <p>Date of cast in format mmddyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/722716.rdf
Name: Time
Units: unitless
Description: <p>Time of cast in format hhmm (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/722717.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>ISO timestamp based on the ISO 8601:2004(E) standard in format YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/722718.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/722719.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/722720.rdf
Name: Cast
Units: unitless
Description: <p>Cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/722721.rdf
Name: Bottle
Units: unitless
Description: <p>Bottle numbers samples came from (separated by semicolons)</p>
http://lod.bco-dmo.org/id/dataset-parameter/722722.rdf
Name: Depth
Units: meters
Description: <p>Nominal bottle depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/722723.rdf
Name: Pico_SzFxPP_mean
Units: mmol C/m3/d
Description: <p>Mean picophytoplankton (size fraction between 0.2-3 um) primary production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/722724.rdf
Name: Pico_SzfxPP_sd
Units: mmol C/m3/d
Description: <p>Standard deviation of picophytoplankton (size fraction between 0.2-3 um) primary production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/722725.rdf
Name: ndno_SzFxPP_mean
Units: mmol C/m3/d
Description: <p>Mean picophytoplankton (size fraction greater thatn 3 um) primary production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/722726.rdf
Name: ndno_SzfxPP_sd
Units: mmol C/m3/d
Description: <p>Standard deviation of picophytoplankton (size fraction greater than 3 um) primary production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/722727.rdf
Name: Pro_PP_mean
Units: mmolC/m3/d
Description: <p>Mean Prochlorococcus primary production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/722728.rdf
Name: Syn_PP_mean
Units: mmolC/m3/d
Description: <p>Mean Synechococcus primary production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/722729.rdf
Name: Peuk_PP_mean
Units: mmolC/m3/d
Description: <p>Mean picoeukaryotes primary production rate</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
6993
https://datadocs.bco-dmo.org/file/l880lxYt2WDpxB/14C_SizeFrac.csv
14C_SizeFrac.csv
Primary data file for dataset ID 713842
download
https://osprey.bco-dmo.org/dataset/713842/data/download
download
onLine
dataset
<p>Seawater was collected in 12-L polyvinylchloride bottles affixed to a 24-bottle rosette sampler, equipped with a Sea-Bird 911+ conductivity, temperature, and pressure profiler. Rates of size-fractionated (&gt;3 μm and 0.2-3 um) and group-specific particulate 14C-based primary production were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m)&nbsp;throughout the euphotic zone.&nbsp; Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes (Nalgene (TM) Oak Ridge) from a pre-dawn cast, inoculated under subdued light with 70 uL of NaH14CO3- (final activity = ~0.14 MBq/mL; MP Biomedicals 17441H), then incubated over the full photoperiod (~12-14 hours) in white mesh bags affixed to a floating in situ array at the corresponding depths where the water was collected.&nbsp; At the end of the incubation period (after sundown), each polycarbonate tube was sampled for size-fractionated and group-specific rates of 14C primary productivity. Aliquots (25 µl) were subsampled from each tube and stored in 20-mL glass scintillation vials containing 500&nbsp;µL of B–phenylethylamine to determine the total activity of&nbsp;14C added to each sample. Next, 5 mL of each sample was preserved in cryotubes containing 30 uL of 16% (final concentration 0.24% w/v) microscopy-grade paraformaldehyde (PFA, Alfa Aesar 43368), flash-frozen in liquid nitrogen, and stored at -80C for subsequent flow cytometric sorting. The remaining sample volume (~25 mL) was vacuum-filtered first onto a 25-mm diameter 3-μm pore size polycarbonate membrane (Millipore IsoporeTM), then the filtrate was vacuum-filtered onto a 25-mm diameter 0.2-um pore size polycarbonate membrane filter (GE Osmonics).&nbsp;After filtration, each filter was placed into a 20-mL glass scintillation vial and stored at -20C until analyzed back&nbsp;at the shore-based laboratory. Upon return to shore, vials were uncapped, 1 mL of 2 M hydrochloric acid was added to each filter, and vials were vented for at least 24 hours to remove remaining inorganic 14C. After venting, 10 mL of Ultima Gold liquid scintillation cocktail was added to each vial, and vials were placed in a liquid scintillation counter (Packard TRI-Carb 4640) for the determination of&nbsp;14C activities.&nbsp; Group-specific rates of 14C-assimilation by&nbsp;<em>Prochlorococcus</em>,&nbsp;<em>Synechococcus</em>, and PPE were determined by measuring the amount of 14C assimilated into populations sorted using the BD InfluxTM (100-μm nozzle tip, 1X BioSure® sheath solution). Calibration of the # of cells sorted was conducted at the beginning of each sorting session; a known number of fluorescent microspherical beads (1 um, Fluoresbrite, Polysciences) were gated through the data acquisition software Spigot, sorted onto a slide, and checked for accuracy under the microscope. The ‘1.0 drop purity’ setting in the Spigot software was utilized as a conservative way of ensuring accuracy of the types of cells sorted into two 6.5-mL HDPE scintillation vials with the ‘two tube sort’ setting. Beads were included with the samples for size reference, and 0.2 x 103 to 4 x 103 beads were sorted for the determination of background levels of radioactivity (both organic 14C in the seawater and 14C absorbed to the beads). Picophytoplankton cells were triggered on forward scatter (FSC) and enumerated based on FSC and side scatter, chlorophyll-based red fluorescence (692 +- 20 nm), and phycoerythrin-based orange fluorescence (585 +- 20 nm) following excitation with two lasers, 488 nm (200 mW) and 457 nm (300 mW).&nbsp;</p>
from Cruise: HOT_cruises <p>Hawaii Ocean Time-series (HOT) program cruises 230-252</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* "na" values changed to "nd" for no data.<br />
*&nbsp;split location column into two columns (lat,lon) in decimal degree format.<br />
* removed the directional (N|W) and made longitude negative for west.<br />
*&nbsp;changed comma delimited bottle list in one column to ; delimited<br />
* added ISO_DateTime_UTC timestamp from date and time columns</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
Packard TRI-Carb 4640
Packard TRI-Carb 4640
PI Supplied Instrument Name: Packard TRI-Carb 4640 Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
Cruise: HOT_cruises
HOT_cruises
Multiple Vessels
vessel
HOT_cruises
Angelicque E. White
University of Hawaiʻi at Mānoa
http://hahana.soest.hawaii.edu/hot/
Report describing HOT_cruises
Multiple Vessels
vessel