http://lod.bco-dmo.org/id/dataset/773802
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
2019-07-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Dissolved organic matter (DOM) and base-extracted particulate organic matter (BEPOM) collected from a plankton senescence experiment from water samples offshore of North Carolina
2019-08-01
publication
2019-08-01
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-08-01
publication
https://doi.org/10.1575/1912/bco-dmo.773802.1
Chris Osburn
North Carolina State University
principalInvestigator
Thomas Bianchi
University of Florida
principalInvestigator
Astrid Schnetzer
North Carolina State University
principalInvestigator
Kai Ziervogel
University of New Hampshire
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: Osburn, C., Bianchi, T., Schnetzer, A., Ziervogel, K. (2019) Dissolved organic matter (DOM) and base-extracted particulate organic matter (BEPOM) collected from a plankton senescence experiment from water samples offshore of North Carolina. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-08-01 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.773802.1 [access date]
Dissolved organic matter (DOM) and base-extracted particulate organic matter (BEPOM) collected from a plankton senescence experiment from water samples offshore of North Carolina Dataset Description: <p>A mixed assemblage of natural phytoplankton community collected from waters offshore of North Carolina were used to create planktonic dissolved organic matter (DOM) and particulate organic matter (POM). The latter was extracted with 0.1 M NaOH to create base-extracted POM (BEPOM). Methods are reported in Kinsey et al. (2018) and Osburn et al. (2019).&nbsp;<br />
The medium used was: Natural Assemblage 2x filtered North Atlantic Surface water with f/2 nutrients; Whole water experiment - unfiltered North Atlantic Surface water with f/20 nutrients Irradiance ~70-100 umol photon m-2 s-1 (cool white bulbs); on roller table; diel cycle, 19 °C&nbsp;</p>
<p>Controls:&nbsp; 0.2 um Filtered Sargasso seawater amended with f/2 nutrients; NASW (or WW) unfiltered Sargasso Seawater amended with f/20 nutrients; NASW: Sargasso seawater amended with plankton tow sample and f/2 nutrients.&nbsp; All samples were in 1.9 L bottles with minimal headspace.</p> Methods and Sampling: <p>Inoculated bottles and seawater controls (medium without cells) were grown on a Wheaton roller apparatus rotating at ~1 rpm (Kinsey et al. 2018; Osburn et al. 2019) and maintained at 19 °C with a 12:12 light:dark cycle at ~90 μEs m−2 s−1 under cool-white fluorescent light in a growth incubator (Percival Scientific, Iowa). The algal assemblages reached stationary phase within ~20 days with cell densities at approximately 30,000 cells mL−1 with an average specific growth rate of 0.5. Changes in cell densities (mL−1) were based on microscopical cell counts (Olympus BX53) to monitor algal growth after preservation with acid Lugol's solution (5%) and settling varied volumes depending on growth phase. The remaining bottles were placed in the dark for 60 days of degradation to simulate transport of POM from surface waters to the mesopelagic ocean.&nbsp;</p>
<p>Sample aliquots were gently vacuum filtered through pre-combusted (450 °C, minimum 6 h) GF/F filters to collect particles for base extraction. The filtrate was collected in polycarbonate bottles for optical measurements and in pre-combusted borosilicate vials for DOC analysis. POM collected on GF/F filters was base-extracted with 0.1 M sodium hydroxide (NaOH) as described in Kinsey et al. (2018). DOC and base-extracted particulate organic carbon (from BEPOM solutions) were prepared and analyzed using an OI Analytical 1030D TOC analyzer as described in Kinsey et al. (2018). Limit of detection of this measurement was 0.11 mg C L-1; precision on standards (including the Hansell Deep Sea Reference material) was ± 0.04 mg C L−1.</p>
<p>Sodium borohydride (NaBH4) was used to reduce carbonyl groups (aldehydes, ketones) to their corresponding alcohols (Schendorf et al., 2016). CDOM and BEPOM samples from stationary and degradation stages were treated with 25-mass excess of NaBH4 (i.e., 15 mol borohydride per mole C per sample), using a basified 1M NaBH4 stock solution, and sparged with ultra-high purity argon gas for 24 h. Following reduction, samples were neutralized to their original pH and analyzed for absorbance and fluorescence as described below. For comparison, 2 mg C L−1 and 4 mg C L−1 samples of both SRFA (Lot 1R101F) and PLFA (Lot 1R109F) were prepared in MilliQ water. Optical measurements were taken before and after NaBH4 reduction for all samples.</p>
<p>Absorbance and fluorescence was measured from 200 to 800 nm on a Horiba Aqualog fluorescence spectrophotometer in 1 cm quartz cells (Starna Cells, Inc.). MilliQ water or a neutralized NaOH solution was used as a blank for initial DOM and BEPOM optical measurements, respectively. MilliQ water treated with NaBH4 was used as a blank following NaBH4 reduction. After blank subtraction, absorbance values (Aλ) were then converted to Napierian absorption coefficients (aλ) (Green and Blough, 1994).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1547976 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1547976
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459406 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1459406
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459294 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1459294
completed
Chris Osburn
North Carolina State University
919.515.0382
Marine, Earth, and Atmospheric Sciences Dept. 2800 Faucette Drive
Raleigh
NC
27695
USA
closburn@ncsu.edu
pointOfContact
Thomas Bianchi
University of Florida
pointOfContact
Astrid Schnetzer
North Carolina State University
919-515-7837
2800 Faucette Drive 4148 Jordan Hall
Raleigh
NC
27695
USA
aschnet@ncsu.edu
pointOfContact
Kai Ziervogel
University of New Hampshire
6038625478
kai.ziervogel@unh.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_id
sample_date
days
growth
label_time_rep
bottle_nr
raw_invivo_flu
bact_abund
doc
dom_b
dom_t
dom_a
dom_c
dom_m
dom_n
dom_bix
dom_hix
dom_a254
dom_a300
dom_a320
dom_slope
dom_S275_295
dom_S350_400
dom_SR
BEPOC
bepom_b
bepom_t
bepom_a
bepom_c
bepom_m
bepom_n
bepom_bix
bepom_hix
bepom_a254
bepom_a300
bepom_a320
bepom_slope
bepom_S275_295
bepom_S350_400
bepom_SR
OI Analytical Aurora 1030 W Total Organic Carbon (TOC) Analyzer
Horiba Aqualog Fluorescence Spectrometer
theme
None, User defined
sample identification
date
days
No BCO-DMO term
bottle number
fluorescence
abundance
dissolved organic Carbon
absorption coefficient
particulate organic Carbon (POC)
featureType
BCO-DMO Standard Parameters
Total Organic Carbon Analyzer
Spectrometer
instrument
BCO-DMO Standard Instruments
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.
Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater
https://www.bco-dmo.org/project/734581
Collaborative Research: Planktonic Sources of Chromophoric Dissolved Organic Matter in Seawater
<p>NSF abstract:</p>
<p>Chromophoric dissolved organic matter (CDOM) is a small but important fraction of the marine carbon pool that interacts with solar radiation and thus affects many photochemical and biological processes in the ocean. Despite its importance, the chemical basis for the formation of oceanic CDOM remains unclear. CDOM may be formed from two possible sources: 1) heterotrophic bacterial transformations of primary productivity (plankton-derived), or 2) terrestrially-derived. This project will examine the role of phytoplankton as a source of CDOM in the ocean by utilizing a powerful, new technique to measure particulate organic matter absorbance and fluorescence, discrete chemical measurements of probable precursors to planktonic CDOM, and enzymatic assays. Results of this research will provide new insights into the origin and production of planktonic CDOM and its transformation by heterotrophic bacteria. This research on CDOM will be shared broadly through a module at a North Carolina Aquarium, and streaming live feeds of shipboard activities to elementary school classrooms.</p>
<p>Terrestrial and oceanic dissolved organic matter (DOM) differ in their chemical composition. Laboratory and open-ocean observations suggest that bacterial transformation of phytoplankton DOM produces humic-like CDOM signals that are visually similar to those in terrestrial CDOM. However, prior studies of oceanic CDOM using absorbance and fluorescence fit an electronic interaction (EI) model of intramolecular charge transfer (CT) reactions between donor and acceptor molecules common to partially-oxidized terrestrial molecules found in humic substances. This project will test the hypothesis that phytoplankton and bacteria provide a source of donors and acceptors that are microbially-transformed and linked, enabling CT contacts between them and creating oceanic CDOM. To address this, researchers will systematically study phytoplankton growth, including marine snow formation. A new technique for measuring base-extracted POM (BEPOM) absorbance and fluorescence will be used to incorporate planktonic CDOM results into the EI model, and supplemented with measurements of its probable chemical precursors. These experiments will improve understanding of how the production of CDOM in the ocean is linked to the optics and chemistry of planktonic CDOM formation. Determining the time course and extent of phytoplankton POM and DOM transformation by heterotrophic bacteria during the same phytoplankton growth experiments will provide an in-depth understanding as to how bacterial transformation of marine snow-associated planktonic organic matter drives CDOM production throughout the ocean.</p>
PlankDOM
largerWorkCitation
project
eng; USA
oceans
-69.63
-69.63
34.65
34.65
2016-11-15
2017-01-16
Northern Atlantic Ocean, 34.65 N, 69.63 W
0
BCO-DMO catalogue of parameters from Dissolved organic matter (DOM) and base-extracted particulate organic matter (BEPOM) collected from a plankton senescence experiment from water samples offshore of North Carolina
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/773804.rdf
Name: sample_id
Units: unitless
Description: Sample ID
http://lod.bco-dmo.org/id/dataset-parameter/773805.rdf
Name: sample_date
Units: unitless
Description: Date sample measured
http://lod.bco-dmo.org/id/dataset-parameter/773806.rdf
Name: days
Units: unitless
Description: Days of incubation in day-month-year
http://lod.bco-dmo.org/id/dataset-parameter/773807.rdf
Name: growth
Units: unitless
Description: Time point of experiment
http://lod.bco-dmo.org/id/dataset-parameter/773808.rdf
Name: label_time_rep
Units: unitless
Description: Extra sample information
http://lod.bco-dmo.org/id/dataset-parameter/773809.rdf
Name: bottle_nr
Units: unitless
Description: Incubation bottle number
http://lod.bco-dmo.org/id/dataset-parameter/773810.rdf
Name: raw_invivo_flu
Units: arbitrary
Description: Raw in vivo fluorescence
http://lod.bco-dmo.org/id/dataset-parameter/773811.rdf
Name: bact_abund
Units: cells per mL
Description: Bacteria Abundance
http://lod.bco-dmo.org/id/dataset-parameter/773812.rdf
Name: doc
Units: micromoles per Liter (umol/L)
Description: dissolved organic carbon
http://lod.bco-dmo.org/id/dataset-parameter/773813.rdf
Name: dom_b
Units: quinine sulfate units
Description: DOM fluorescence peak B
http://lod.bco-dmo.org/id/dataset-parameter/773814.rdf
Name: dom_t
Units: quinine sulfate units
Description: DOM fluorescence peak T
http://lod.bco-dmo.org/id/dataset-parameter/773815.rdf
Name: dom_a
Units: quinine sulfate units
Description: DOM fluorescence peak A
http://lod.bco-dmo.org/id/dataset-parameter/773816.rdf
Name: dom_c
Units: quinine sulfate units
Description: DOM fluorescence peak C
http://lod.bco-dmo.org/id/dataset-parameter/773817.rdf
Name: dom_m
Units: quinine sulfate units
Description: DOM fluorescence peak M
http://lod.bco-dmo.org/id/dataset-parameter/773818.rdf
Name: dom_n
Units: quinine sulfate units
Description: DOM fluorescence peak N
http://lod.bco-dmo.org/id/dataset-parameter/773819.rdf
Name: dom_bix
Units: unitless
Description: Biological index
http://lod.bco-dmo.org/id/dataset-parameter/773820.rdf
Name: dom_hix
Units: unitless
Description: Humificaiton index
http://lod.bco-dmo.org/id/dataset-parameter/773821.rdf
Name: dom_a254
Units: inverse meters
Description: DOM absorption coefficient at 254 nm
http://lod.bco-dmo.org/id/dataset-parameter/773822.rdf
Name: dom_a300
Units: inverse meters
Description: DOM absorption coefficient at 300 nm
http://lod.bco-dmo.org/id/dataset-parameter/773823.rdf
Name: dom_a320
Units: inverse meters
Description: DOM absorption coefficient at 320 nm
http://lod.bco-dmo.org/id/dataset-parameter/773824.rdf
Name: dom_slope
Units: inverse micrometer
Description: Slope of DOM absorption from 300 to 650 nm
http://lod.bco-dmo.org/id/dataset-parameter/773825.rdf
Name: dom_S275_295
Units: inverse nanometer
Description: Slope of DOM absorption from 275 to 295 nm
http://lod.bco-dmo.org/id/dataset-parameter/773826.rdf
Name: dom_S350_400
Units: inverse nanometer
Description: Slope of DOM absorption from 350 to 400 nm
http://lod.bco-dmo.org/id/dataset-parameter/773827.rdf
Name: dom_SR
Units: unitless
Description: Ratio of S275-295 to S350-400
http://lod.bco-dmo.org/id/dataset-parameter/773828.rdf
Name: BEPOC
Units: micromoles per Liter (umol/L)
Description: base-extracted POC concentration
http://lod.bco-dmo.org/id/dataset-parameter/773829.rdf
Name: bepom_b
Units: quinine sulfate units
Description: BEPOM fluorescence peak B
http://lod.bco-dmo.org/id/dataset-parameter/773830.rdf
Name: bepom_t
Units: quinine sulfate units
Description: BEPOM fluorescence peak T
http://lod.bco-dmo.org/id/dataset-parameter/773831.rdf
Name: bepom_a
Units: quinine sulfate units
Description: BEPOM fluorescence peak A
http://lod.bco-dmo.org/id/dataset-parameter/773832.rdf
Name: bepom_c
Units: quinine sulfate units
Description: BEPOM fluorescence peak C
http://lod.bco-dmo.org/id/dataset-parameter/773833.rdf
Name: bepom_m
Units: quinine sulfate units
Description: BEPOM fluorescence peak M
http://lod.bco-dmo.org/id/dataset-parameter/773834.rdf
Name: bepom_n
Units: quinine sulfate units
Description: BEPOM fluorescence peak N
http://lod.bco-dmo.org/id/dataset-parameter/773835.rdf
Name: bepom_bix
Units: unitless
Description: Biological index
http://lod.bco-dmo.org/id/dataset-parameter/773836.rdf
Name: bepom_hix
Units: unitless
Description: Humificaiton index
http://lod.bco-dmo.org/id/dataset-parameter/773837.rdf
Name: bepom_a254
Units: inverse meters
Description: BEPOM absorption coefficient at 254 nm
http://lod.bco-dmo.org/id/dataset-parameter/773838.rdf
Name: bepom_a300
Units: inverse meters
Description: BEPOM absorption coefficient at 300 nm
http://lod.bco-dmo.org/id/dataset-parameter/773839.rdf
Name: bepom_a320
Units: inverse meters
Description: BEPOM absorption coefficient at 320 nm
http://lod.bco-dmo.org/id/dataset-parameter/773840.rdf
Name: bepom_slope
Units: inverse micrometer
Description: Slope of BEPOM absorption from 300 to 650 nm
http://lod.bco-dmo.org/id/dataset-parameter/773841.rdf
Name: bepom_S275_295
Units: inverse nanometer
Description: Slope of BEPOM absorption from 275 to 295 nm
http://lod.bco-dmo.org/id/dataset-parameter/773842.rdf
Name: bepom_S350_400
Units: inverse nanometer
Description: Slope of BEPOM absorption from 350 to 400 nm
http://lod.bco-dmo.org/id/dataset-parameter/773843.rdf
Name: bepom_SR
Units: unitless
Description: Ratio of S275-295 to S350-400
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
7808
https://darchive.mblwhoilibrary.org/bitstream/1912/24380/1/dataset-773802_plankdom-na1__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.773802.1
download
onLine
dataset
<p>Inoculated bottles and seawater controls (medium without cells) were grown on a Wheaton roller apparatus rotating at ~1 rpm (Kinsey et al. 2018; Osburn et al. 2019) and maintained at 19 °C with a 12:12 light:dark cycle at ~90 μEs m−2 s−1 under cool-white fluorescent light in a growth incubator (Percival Scientific, Iowa). The algal assemblages reached stationary phase within ~20 days with cell densities at approximately 30,000 cells mL−1 with an average specific growth rate of 0.5. Changes in cell densities (mL−1) were based on microscopical cell counts (Olympus BX53) to monitor algal growth after preservation with acid Lugol's solution (5%) and settling varied volumes depending on growth phase. The remaining bottles were placed in the dark for 60 days of degradation to simulate transport of POM from surface waters to the mesopelagic ocean.&nbsp;</p>
<p>Sample aliquots were gently vacuum filtered through pre-combusted (450 °C, minimum 6 h) GF/F filters to collect particles for base extraction. The filtrate was collected in polycarbonate bottles for optical measurements and in pre-combusted borosilicate vials for DOC analysis. POM collected on GF/F filters was base-extracted with 0.1 M sodium hydroxide (NaOH) as described in Kinsey et al. (2018). DOC and base-extracted particulate organic carbon (from BEPOM solutions) were prepared and analyzed using an OI Analytical 1030D TOC analyzer as described in Kinsey et al. (2018). Limit of detection of this measurement was 0.11 mg C L-1; precision on standards (including the Hansell Deep Sea Reference material) was ± 0.04 mg C L−1.</p>
<p>Sodium borohydride (NaBH4) was used to reduce carbonyl groups (aldehydes, ketones) to their corresponding alcohols (Schendorf et al., 2016). CDOM and BEPOM samples from stationary and degradation stages were treated with 25-mass excess of NaBH4 (i.e., 15 mol borohydride per mole C per sample), using a basified 1M NaBH4 stock solution, and sparged with ultra-high purity argon gas for 24 h. Following reduction, samples were neutralized to their original pH and analyzed for absorbance and fluorescence as described below. For comparison, 2 mg C L−1 and 4 mg C L−1 samples of both SRFA (Lot 1R101F) and PLFA (Lot 1R109F) were prepared in MilliQ water. Optical measurements were taken before and after NaBH4 reduction for all samples.</p>
<p>Absorbance and fluorescence was measured from 200 to 800 nm on a Horiba Aqualog fluorescence spectrophotometer in 1 cm quartz cells (Starna Cells, Inc.). MilliQ water or a neutralized NaOH solution was used as a blank for initial DOM and BEPOM optical measurements, respectively. MilliQ water treated with NaBH4 was used as a blank following NaBH4 reduction. After blank subtraction, absorbance values (Aλ) were then converted to Napierian absorption coefficients (aλ) (Green and Blough, 1994).</p>
Specified by the Principal Investigator(s)
<p>Excel used for spreadsheets; Matlab (v 2016 to 2018) is used to process absorbance and fluorescence results and data and to conduct statistical testing using in-house scripts. SigmaPlot is used for data visualization.</p>
<p>BCO-DMO Processing Notes:<br />
-&nbsp;added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions</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
OI Analytical Aurora 1030 W Total Organic Carbon (TOC) Analyzer
OI Analytical Aurora 1030 W Total Organic Carbon (TOC) Analyzer
PI Supplied Instrument Name: OI Analytical Aurora 1030 W Total Organic Carbon (TOC) Analyzer PI Supplied Instrument Description:OI Analytical Aurora 1030 W Total Organic Carbon (TOC) Analyzer: DOC & DIC. Calibrated with stock solutions of sodium bicarbonate (DIC) and caffeine (DOC). A certified reference material (CRM) for DIC is analyzed regularly as a check standard. Instrument Name: Total Organic Carbon Analyzer Instrument Short Name:TOC analyzer Instrument Description: A unit that accurately determines the carbon concentrations of organic compounds typically by detecting and measuring its combustion product (CO2). See description document at: http://bcodata.whoi.edu/LaurentianGreatLakes_Chemistry/bs116.pdf Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
Horiba Aqualog Fluorescence Spectrometer
Horiba Aqualog Fluorescence Spectrometer
PI Supplied Instrument Name: Horiba Aqualog Fluorescence Spectrometer PI Supplied Instrument Description:Horiba Aqualog Fluorescence Spectrometer, absorbance and fluorescence. Calibrated with quinine sulfate solution after normalization to instrument’s water Raman peak. Fluorescence corrected for water blank, inner filtering effects. Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/