http://lod.bco-dmo.org/id/dataset/964684
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
2025-06-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Size fractionated Amino Acid data collected in the Sargasso Sea during BIOS-SCOPE cruises AE2114 and AE2123 in August and November 2021
2025-06-13
publication
2025-06-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-06-16
publication
https://doi.org/10.26008/1912/bco-dmo.964684.1
Craig A. Carlson
University of California-Santa Barbara
principalInvestigator
Hilary G. Close
University of Miami Rosenstiel School of Marine and Atmospheric Science
principalInvestigator
Chance English
University of California-Santa Barbara
principalInvestigator
Lillian Henderson
University of Miami Rosenstiel School of Marine and Atmospheric Science
principalInvestigator
Kimberly Popendorf
University of Miami Rosenstiel School of Marine and Atmospheric Science
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: Henderson, L., English, C., Jeng, D., Popendorf, K., Carlson, C. A., Close, H. G. (2025) Size fractionated Amino Acid data collected in the Sargasso Sea during BIOS-SCOPE cruises AE2114 and AE2123 in August and November 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.964684.1 [access date]
BIOSSCOPE Pump Amino Acid data Dataset Description: Methods and Sampling: <p>Samples were collected during August 2021 and November 2021 at or near the BATS site (31°40’ N, 64°10’ W) or at Hydrostation S (32°10’ N, 64°30’ W) on R/V Atlantic Explorer cruises AE2114 and AE2123.</p>
<p>Size-fractionated particle samples were collected using McLane WTS-LV <em>in-situ</em> pumps (4 L min<sup>-1 </sup>maximum pumping rate; McLane Research Laboratories, Inc.) during all sampling periods. Five to eight depths were sampled between the surface and 200&nbsp;meters during each cruise. Most pumps were dual-flow, collecting water through two filter holders simultaneously for geochemical and taxonomic analyses, as described by Henderson et al. (2024) and Comstock et al. (2024). Each filter holder was a vertical-intake (McLane) or mini-MULVFS style and contained four 142&nbsp;mm diameter filter tiers equipped as follows (from top to bottom) for the geochemical analyses reported here: [1] 20&nbsp;μm Nitex filter, [2] 6&nbsp;μm Nitex filter (5&nbsp;μm polyester filter), [3] two stacked 1.2&nbsp;μm glass fiber filters (GF/C), [4] two stacked 0.3&nbsp;μm glass fiber filters (GF75). A 150&nbsp;μm Nitex backing filter was placed beneath the filter(s) of interest on the first three tiers of all filter holders to ensure filter structural integrity. Nitex filters were acid-and methanol-washed before use, and glass fiber filters were pre‑combusted (450°C) for 5 hours. After pump recovery, filter holders were drained with a weak vacuum to remove excess seawater. Filters were photographed, removed and folded with clean forceps, stored in combusted foil, and transported and stored at ‑80°C. Flow meters were placed in-line on each flow path of the pumps, and exact filtered volumes for each flow path were determined; flow rates through filter stacks used for organic analyses averaged &lt;3 Liters per minutes (L/min). We collected dip blanks – filters that did not have any water pumped through them, but were submerged in natural seawater – along with our samples.</p>
<p><em><strong>Processing of large particle (&gt;20&nbsp;µm) samples</strong></em><br />
Samples were stored at ‑80°C until processing. Once in the lab, particles collected on 20&nbsp;µm Nitex filters were rinsed off the filters onto 47-mm diameter, pre-combusted (450°C, for 5&nbsp;hr) glass fiber filters with a nominal pore size of 0.7&nbsp;μm (GF/F) using 0.2&nbsp;µm-filtered seawater and combusted glass filter towers. Briefly, particles were rinsed from the Nitex filters using an acid-clean squirt bottle to spray across the filter. The Nitex mesh was then sonicated for three minutes in an acid-clean polypropylene Nalgene bottle with more filtered seawater. After sonication, this water was poured into the filter tower. The process was repeated three times, with all filtered seawater being drained from the filter tower with gentle vacuum after each rinse and sonication onto the same GF/F filter. Samples were then freeze-dried and inspected under a dissecting microscope to visually characterize the particles and remove intact zooplankton swimmers or contaminant fibers, which were both rare in the samples.</p>
<p><em><strong>Analysis of individual amino acids</strong></em><br />
Freeze-dried filters of the 0.3&nbsp;µm, 1.2&nbsp;µm, and 20&nbsp;µm size fractions were quantitatively split radially by weight for analysis of amino acid content for selected samples from August and November 2021.</p>
<p>For amino acid analysis, one filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections). Filter splits were hydrolyzed (20&nbsp;h, 110°C) using trace metal grade 6&nbsp;N hydrochloric acid. Hydrolysate was separated from filter material using combusted glass syringes with glass wool in the tip and syringe-tip 0.2&nbsp;μm polyethersulfone filters. Samples were neutralized by evaporating acid under nitrogen (N<sub>2</sub>),&nbsp;reconstituted in 0.1&nbsp;N hydrochloric acid, and purified via cation exchange chromatography. Notably, we found that cation exchange chromatography was crucial in achieving acceptable yields; trial samples analyzed without undergoing this purification step resulted in yields much lower than expected and much lower than when analyzed after the purification procedure, likely due to chromatographic interference from compound(s) that were effectively removed via the cation exchange procedure. Samples were aliquoted into individual 2&nbsp;mL HPLC vials, and known quantities of the synthetic amino acid aminoadipic acid were added as an internal standard to confirm accurate analysis. Samples were then dried under N<sub>2</sub>, reconstituted in 60/40 ultrapure water/methanol (v/v), and derivatized with <em>o</em>‑phthaldialdehyde and 2‑mercaptoethanol 2 minutes before injection for analysis via reverse‑phase high performance liquid chromatography (HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250&nbsp;nm, emission 410&nbsp;nm). The mobile phase was as follows: eluent A was 50 mmol&nbsp;L<sup>-1</sup> sodium acetate (HPLC‑grade; adjusted to pH 5.7), and eluent B was 100% methanol (HPLC‑grade). The stationary phase was a C18 column (Kinetex<sup>TM</sup> EVO-C18, 5&nbsp;µm, 100 Å, 4.6x250&nbsp;mm) with a C18 guard column (EVO-C18 ULTRA cartridge, 4.6&nbsp;mm) at 20°C. The flow rate was constant at 0.9&nbsp;mL min<sup>-1</sup> and the elution gradient of eluent B added to eluent A was as follows:</p>
<ul>
<li>-12 min to 0&nbsp;min: 5% eluent B</li>
<li>4&nbsp;min: 23% eluent B</li>
<li>8 min: 29% eluent B</li>
<li>24 min: 44% eluent B</li>
<li>37 to 44 min: 60% eluent B</li>
<li>52 min: 77% eluent B</li>
<li>57 to 62 min: 100% eluent B</li>
</ul>
<p>A standard curve was analyzed alongside samples during each run. The standard used was a mixed amino acid standard solution initially prepared in 0.1&nbsp;N hydrochloric acid. We measured the following amino acids: alanine, arginine, aspartic acid, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, threonine, tyrosine, valine, γ-aminobutyric acid, and β-alanine. The standard also included cysteine and proline, though these amino acids are not detectable with the OPA derivatization method. The standard was prepared from the Pierce amino acid calibration standard H with the addition of non-protein forming amino acids γ-aminobutyric acid and β-alanine. The standard solution was prepared to a concentration of 92&nbsp;μmol&nbsp;L<sup>-1</sup> for all amino acids except for γ-aminobutyric acid and β-alanine, which were prepared to concentrations of 30 and 34&nbsp;μmol L<sup>-1</sup>, respectively. The standard solution was aliquoted by weight to exact concentrations targeting a range of 0.2&nbsp;to 50&nbsp;μmol L<sup>-1</sup> for the protein-forming amino acids. As with the samples, standards were aliquoted directly into individual 2&nbsp;mL HPLC vials, supplemented with known quantities of aminoadipic acid as an internal standard, dried under N<sub>2</sub>, and reconstituted in 60/40 ultrapure water/methanol (v/v). The effect of cation exchange chromatography on measured amino acid yields in the standard was determined by subjecting two aliquots of the standard mixture to the procedure; average yields for each amino acid were 87-98% with the exception of arginine (40%) and lysine (71%). Yields were consistent for each amino acid across the duplicate standard aliquots. Sample concentrations were corrected assuming a yield of 40% for arginine, 71% for lysine, and 91% (average) for all other amino acids. Sample peak areas were converted to molar quantities using the calibration from the standard curve. Blanks of ultrapure water and full process blanks were analyzed alongside samples to check for any background amino acid content in reagents or contamination. Full process blanks consisted of dip blank filter splits that were processed exactly as sample filter splits. Seawater particulate amino acid concentrations (nmol&nbsp;L<sup>‑1</sup>) were calculated based on the original volume of seawater filtered through the portion of sample analyzed during each run (material extracted from 0.7 to 10.5&nbsp;L of seawater injected for a single run). We report concentrations here as (1) total amino acid carbon as a proportion of POC, where carbon from individual amino acids was calculated (via the molecular formula for each monomer), summed, and divided by the total POC concentration in that particle size fraction, and (2) individual amino acids as mol%, where the concentrations (in nmol&nbsp;L<sup>-1</sup>) of individual amino acids were each divided by the total amino acid concentration in that sample (sum of individual concentrations in nmol&nbsp;L<sup>‑1</sup>).</p>
Funding provided by Simons Foundation (Simons) Award Number: 409923
completed
Craig A. Carlson
University of California-Santa Barbara
(805) 893-2541
University of California Department of Ecology, Evolution and Marine Biology
Santa Barbara
CA
93106-6150
USA
craig_carlson@ucsb.edu
pointOfContact
Hilary G. Close
University of Miami Rosenstiel School of Marine and Atmospheric Science
305-421-4306 ext. 54306
46000 Rickenbacker Causeway
Miami
FL
33149
USA
hclose@miami.edu
pointOfContact
Chance English
University of California-Santa Barbara
cje@ucsb.edu
pointOfContact
Lillian Henderson
University of Miami Rosenstiel School of Marine and Atmospheric Science
4600 Rickenbacker Causeway
Miami
FL
33149-1031
USA
lillian.henderson@earth.miami.edu
pointOfContact
Kimberly Popendorf
University of Miami Rosenstiel School of Marine and Atmospheric Science
305-421-4328
4600 Rickenbacker Causeway
Miami
FL
33149
USA
kpopendorf@rsmas.miami.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Cruise
Latitude
Longitude
Date
Size_fraction
Filter_type
Depth
Asp
Asp_sd
Glu
Glu_sd
HisSer
HisSer_sd
Arg
Arg_sd
Thr
Thr_sd
Gly
Gly_sd
Bala
Bala_sd
Tyr
Tyr_sd
Ala
Ala_sd
GABA
GABA_sd
Met
Met_sd
Val
Val_sd
Phe
Phe_sd
Ile
Ile_sd
Leu
Leu_sd
Lys
Lys_sd
(HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250 nm, emission 410 nm).
flow meter
McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.)
dissecting microscope
sonicator
theme
None, User defined
sample identification
Cruise identfier
latitude
longitude
date
sample fraction (includes size fractions)
filter_size
depth
amino acid concentration
standard deviation
featureType
BCO-DMO Standard Parameters
Agilent 1100 G1321A FLD Detector
Flow Meter
McLane Large Volume Pumping System WTS-LV
Microscope - Optical
ultrasonic cell disrupter (sonicator)
instrument
BCO-DMO Standard Instruments
AE2114
AE2123
service
Deployment Activity
North Atlantic Subtropical Gyre - Bermuda Atlantic Time Series (BATS) and Hydrostation S site
North Atlantic Subtropical Gyre - Bermuda Atlantic Time Series (BATS) site
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.
Bermuda Institute of Ocean Sciences Simons Collaboration on Ocean Processes and Ecology
http://scope.bios.edu/
Bermuda Institute of Ocean Sciences Simons Collaboration on Ocean Processes and Ecology
<p>The aim of BIOS-SCOPE is to expand knowledge about the BATS ecosystem and achieve a better understanding of ocean food web sources, sinks and transformations of DOM. Advances in knowledge and technology now poise us to investigate the specific mechanisms of DOM incorporation, oxidation and transformation by zooplankton and the distinct microbial plankton communities that have been discovered at BATS.</p>
<p>The overarching goal of the BIOS-SCOPE is to form and foster collaborations of cross disciplinary science that utilize a broad suite of genomic, chemical, ecological, and biogeochemical approaches to evaluate microbial process, structure and function on various scales. These scales will range from organism-compound and organism-organism interactions to large biogeochemical patterns on the ecosystem scale. For this purpose we have assembled a cross-disciplinary team including microbial oceanographers (Carlson and Giovannoni), a chemical oceanographer (Kujawinski), biological oceanographer / zooplankton ecologists (Maas and Blanco-Bercial) and microbial bioinformatician (Temperton) with the expertise and technical acuity that are needed to study complex interactions between food web processes, microbes and DOM quantity and quality in the oligotrophic ocean. This scientific team has a vision of harnessing this potential to produce new discoveries that provide a mechanistic understanding of the carbon cycle and explain the many emergent phenomenon that have yet to be understood.</p>
<p>For additional details:</p>
<ul>
<li><em><strong>BIOS-SCOPE Narrative</strong>: <br />
<a href="https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/BIOS-SCOPE_Narrative_FINAL.pdf">https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/BIOS-SCOPE_Narrative_FINAL.pdf</a></em></li>
<li><em><strong>Physical Framework</strong>:<br />
<a href="https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/Physical_Framework.pdf">https://datadocs.bco-dmo.org/docs/302/BIOSSCOPE/data_docs/Physical_Framework.pdf</a></em></li>
</ul>
<p>BIOSSCOPE I: November 1st, 2015 through October 31st, 2020<br />
Current: November 1st, 2020 to October 31st, 2025</p>
BIOSSCOPE
largerWorkCitation
project
eng; USA
oceans
North Atlantic Subtropical Gyre - Bermuda Atlantic Time Series (BATS) and Hydrostation S site; North Atlantic Subtropical Gyre - Bermuda Atlantic Time Series (BATS) site
-64.5
-64.08
30.75
32.17
2021-08-05
2021-11-13
North Atlantic Subtropical Gyre, Bermuda Atlantic Time Series (BATS) site
0
BCO-DMO catalogue of parameters from Size fractionated Amino Acid data collected in the Sargasso Sea during BIOS-SCOPE cruises AE2114 and AE2123 in August and November 2021
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/964997.rdf
Name: Sample_ID
Units: unitless
Description: <p>Internal sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/964998.rdf
Name: Cruise
Units: unitless
Description: <p>BIOSSCOPE cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/964999.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/965000.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/965001.rdf
Name: Date
Units: units
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/965002.rdf
Name: Size_fraction
Units: micrometers (um)
Description: <p>Particle size range for water fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/965003.rdf
Name: Filter_type
Units: unitless
Description: <p>Filter type used for particle fraction (Nitex, GF/C ,GF75)</p>
http://lod.bco-dmo.org/id/dataset-parameter/965004.rdf
Name: Depth
Units: meters (m)
Description: <p>Water column depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/965005.rdf
Name: Asp
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Aspartic Acid. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965006.rdf
Name: Asp_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Aspartic Acid concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965007.rdf
Name: Glu
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Glutamic Acid. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965008.rdf
Name: Glu_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Glutamic Acid concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965009.rdf
Name: HisSer
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Histidine+Serine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965010.rdf
Name: HisSer_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Histidine+Serine amino acid concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965011.rdf
Name: Arg
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Arginine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965012.rdf
Name: Arg_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Arginine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965013.rdf
Name: Thr
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Threonine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965014.rdf
Name: Thr_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Threonine concenctration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965015.rdf
Name: Gly
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Glycine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965016.rdf
Name: Gly_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Glycine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965017.rdf
Name: Bala
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Beta-alanine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965018.rdf
Name: Bala_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Beta-alanine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965019.rdf
Name: Tyr
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Tyrosine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965020.rdf
Name: Tyr_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Tyrosine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965021.rdf
Name: Ala
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Alanine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965022.rdf
Name: Ala_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Alanine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965023.rdf
Name: GABA
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Gamma-aminobutyric acid. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965024.rdf
Name: GABA_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Gamma-aminobutyric acid concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965025.rdf
Name: Met
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Methionine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965026.rdf
Name: Met_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Methionine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965027.rdf
Name: Val
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Valine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965028.rdf
Name: Val_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Valine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965029.rdf
Name: Phe
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Phenylalanine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965030.rdf
Name: Phe_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Phenylalanine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965031.rdf
Name: Ile
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Isoleucine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965032.rdf
Name: Ile_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Isoleucine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965033.rdf
Name: Leu
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Leucine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965034.rdf
Name: Leu_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Leucine concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/965035.rdf
Name: Lys
Units: nanomoles carbon per liter
Description: <p>average amino acid concentration: Lysine. One filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections).</p>
http://lod.bco-dmo.org/id/dataset-parameter/965036.rdf
Name: Lys_sd
Units: nanomoles carbon per liter
Description: <p>standard deviation of Lysine concentration</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
7379
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/e210124a-3428-4b6a-9afe-4b7371008409/content
download
https://doi.org/10.26008/1912/bco-dmo.964684.1
download
onLine
dataset
<p>Samples were collected during August 2021 and November 2021 at or near the BATS site (31°40’ N, 64°10’ W) or at Hydrostation S (32°10’ N, 64°30’ W) on R/V Atlantic Explorer cruises AE2114 and AE2123.</p>
<p>Size-fractionated particle samples were collected using McLane WTS-LV <em>in-situ</em> pumps (4 L min<sup>-1 </sup>maximum pumping rate; McLane Research Laboratories, Inc.) during all sampling periods. Five to eight depths were sampled between the surface and 200&nbsp;meters during each cruise. Most pumps were dual-flow, collecting water through two filter holders simultaneously for geochemical and taxonomic analyses, as described by Henderson et al. (2024) and Comstock et al. (2024). Each filter holder was a vertical-intake (McLane) or mini-MULVFS style and contained four 142&nbsp;mm diameter filter tiers equipped as follows (from top to bottom) for the geochemical analyses reported here: [1] 20&nbsp;μm Nitex filter, [2] 6&nbsp;μm Nitex filter (5&nbsp;μm polyester filter), [3] two stacked 1.2&nbsp;μm glass fiber filters (GF/C), [4] two stacked 0.3&nbsp;μm glass fiber filters (GF75). A 150&nbsp;μm Nitex backing filter was placed beneath the filter(s) of interest on the first three tiers of all filter holders to ensure filter structural integrity. Nitex filters were acid-and methanol-washed before use, and glass fiber filters were pre‑combusted (450°C) for 5 hours. After pump recovery, filter holders were drained with a weak vacuum to remove excess seawater. Filters were photographed, removed and folded with clean forceps, stored in combusted foil, and transported and stored at ‑80°C. Flow meters were placed in-line on each flow path of the pumps, and exact filtered volumes for each flow path were determined; flow rates through filter stacks used for organic analyses averaged &lt;3 Liters per minutes (L/min). We collected dip blanks – filters that did not have any water pumped through them, but were submerged in natural seawater – along with our samples.</p>
<p><em><strong>Processing of large particle (&gt;20&nbsp;µm) samples</strong></em><br />
Samples were stored at ‑80°C until processing. Once in the lab, particles collected on 20&nbsp;µm Nitex filters were rinsed off the filters onto 47-mm diameter, pre-combusted (450°C, for 5&nbsp;hr) glass fiber filters with a nominal pore size of 0.7&nbsp;μm (GF/F) using 0.2&nbsp;µm-filtered seawater and combusted glass filter towers. Briefly, particles were rinsed from the Nitex filters using an acid-clean squirt bottle to spray across the filter. The Nitex mesh was then sonicated for three minutes in an acid-clean polypropylene Nalgene bottle with more filtered seawater. After sonication, this water was poured into the filter tower. The process was repeated three times, with all filtered seawater being drained from the filter tower with gentle vacuum after each rinse and sonication onto the same GF/F filter. Samples were then freeze-dried and inspected under a dissecting microscope to visually characterize the particles and remove intact zooplankton swimmers or contaminant fibers, which were both rare in the samples.</p>
<p><em><strong>Analysis of individual amino acids</strong></em><br />
Freeze-dried filters of the 0.3&nbsp;µm, 1.2&nbsp;µm, and 20&nbsp;µm size fractions were quantitatively split radially by weight for analysis of amino acid content for selected samples from August and November 2021.</p>
<p>For amino acid analysis, one filter split was prepared per sample, and three aliquots from the final prepared solution were analyzed (triplicate injections). Filter splits were hydrolyzed (20&nbsp;h, 110°C) using trace metal grade 6&nbsp;N hydrochloric acid. Hydrolysate was separated from filter material using combusted glass syringes with glass wool in the tip and syringe-tip 0.2&nbsp;μm polyethersulfone filters. Samples were neutralized by evaporating acid under nitrogen (N<sub>2</sub>),&nbsp;reconstituted in 0.1&nbsp;N hydrochloric acid, and purified via cation exchange chromatography. Notably, we found that cation exchange chromatography was crucial in achieving acceptable yields; trial samples analyzed without undergoing this purification step resulted in yields much lower than expected and much lower than when analyzed after the purification procedure, likely due to chromatographic interference from compound(s) that were effectively removed via the cation exchange procedure. Samples were aliquoted into individual 2&nbsp;mL HPLC vials, and known quantities of the synthetic amino acid aminoadipic acid were added as an internal standard to confirm accurate analysis. Samples were then dried under N<sub>2</sub>, reconstituted in 60/40 ultrapure water/methanol (v/v), and derivatized with <em>o</em>‑phthaldialdehyde and 2‑mercaptoethanol 2 minutes before injection for analysis via reverse‑phase high performance liquid chromatography (HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250&nbsp;nm, emission 410&nbsp;nm). The mobile phase was as follows: eluent A was 50 mmol&nbsp;L<sup>-1</sup> sodium acetate (HPLC‑grade; adjusted to pH 5.7), and eluent B was 100% methanol (HPLC‑grade). The stationary phase was a C18 column (Kinetex<sup>TM</sup> EVO-C18, 5&nbsp;µm, 100 Å, 4.6x250&nbsp;mm) with a C18 guard column (EVO-C18 ULTRA cartridge, 4.6&nbsp;mm) at 20°C. The flow rate was constant at 0.9&nbsp;mL min<sup>-1</sup> and the elution gradient of eluent B added to eluent A was as follows:</p>
<ul>
<li>-12 min to 0&nbsp;min: 5% eluent B</li>
<li>4&nbsp;min: 23% eluent B</li>
<li>8 min: 29% eluent B</li>
<li>24 min: 44% eluent B</li>
<li>37 to 44 min: 60% eluent B</li>
<li>52 min: 77% eluent B</li>
<li>57 to 62 min: 100% eluent B</li>
</ul>
<p>A standard curve was analyzed alongside samples during each run. The standard used was a mixed amino acid standard solution initially prepared in 0.1&nbsp;N hydrochloric acid. We measured the following amino acids: alanine, arginine, aspartic acid, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, threonine, tyrosine, valine, γ-aminobutyric acid, and β-alanine. The standard also included cysteine and proline, though these amino acids are not detectable with the OPA derivatization method. The standard was prepared from the Pierce amino acid calibration standard H with the addition of non-protein forming amino acids γ-aminobutyric acid and β-alanine. The standard solution was prepared to a concentration of 92&nbsp;μmol&nbsp;L<sup>-1</sup> for all amino acids except for γ-aminobutyric acid and β-alanine, which were prepared to concentrations of 30 and 34&nbsp;μmol L<sup>-1</sup>, respectively. The standard solution was aliquoted by weight to exact concentrations targeting a range of 0.2&nbsp;to 50&nbsp;μmol L<sup>-1</sup> for the protein-forming amino acids. As with the samples, standards were aliquoted directly into individual 2&nbsp;mL HPLC vials, supplemented with known quantities of aminoadipic acid as an internal standard, dried under N<sub>2</sub>, and reconstituted in 60/40 ultrapure water/methanol (v/v). The effect of cation exchange chromatography on measured amino acid yields in the standard was determined by subjecting two aliquots of the standard mixture to the procedure; average yields for each amino acid were 87-98% with the exception of arginine (40%) and lysine (71%). Yields were consistent for each amino acid across the duplicate standard aliquots. Sample concentrations were corrected assuming a yield of 40% for arginine, 71% for lysine, and 91% (average) for all other amino acids. Sample peak areas were converted to molar quantities using the calibration from the standard curve. Blanks of ultrapure water and full process blanks were analyzed alongside samples to check for any background amino acid content in reagents or contamination. Full process blanks consisted of dip blank filter splits that were processed exactly as sample filter splits. Seawater particulate amino acid concentrations (nmol&nbsp;L<sup>‑1</sup>) were calculated based on the original volume of seawater filtered through the portion of sample analyzed during each run (material extracted from 0.7 to 10.5&nbsp;L of seawater injected for a single run). We report concentrations here as (1) total amino acid carbon as a proportion of POC, where carbon from individual amino acids was calculated (via the molecular formula for each monomer), summed, and divided by the total POC concentration in that particle size fraction, and (2) individual amino acids as mol%, where the concentrations (in nmol&nbsp;L<sup>-1</sup>) of individual amino acids were each divided by the total amino acid concentration in that sample (sum of individual concentrations in nmol&nbsp;L<sup>‑1</sup>).</p>
Specified by the Principal Investigator(s)
- Imported data from source file "SizeFrac_AminoAcids_BIOSSCOPE_2021.xlsx" into the BCO-DMO data system.
- Modified parameter (column) names to conform with BCO-DMO naming conventions.
- Converted latitude and longitude columns to decimal degrees
- Changed date format to ISO format of yyyy-mm-dd
- Moved standard deviation values to be adjacent to the associated amino acid values
- Rounded values according to submitter's indicated precision
Specified by BCO-DMO Data Managers
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7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
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02543
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info@bco-dmo.org
http://www.bco-dmo.org
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For questions regarding this resource, please contact BCO-DMO via the email address provided.
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(HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250 nm, emission 410 nm).
(HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250 nm, emission 410 nm).
PI Supplied Instrument Name: (HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250 nm, emission 410 nm). PI Supplied Instrument Description:Samples were injected for analysis via reverse‑phase high performance liquid chromatography (HPLC, Agilent 1100) with fluorescence detection (Agilent G1321A FLD; excitation 250 nm, emission 410 nm). Instrument Name: Agilent 1100 G1321A FLD Detector Instrument Short Name:Agilent fluorescence detector Instrument Description: The Agilent 1100 G1321A FLD Detector is a high-performance fluorescence detector designed for precise and sensitive analysis in HPLC applications. Featuring advanced optical design and variable wavelength settings, this detector enhances fluorescence detection for a wide range of compounds, improving sensitivity and selectivity. Its robust design ensures reliable performance, while seamless integration with Agilent 1100 HPLC systems makes it an excellent choice for laboratories requiring high-quality fluorescence detection.
flow meter
flow meter
PI Supplied Instrument Name: flow meter PI Supplied Instrument Description:Flow meters were placed in-line on each flow path of the pumps, and exact filtered volumes for each flow path were determined. Instrument Name: Flow Meter Instrument Short Name:Flow Meter Instrument Description: General term for a sensor that quantifies the rate at which fluids (e.g. water or air) pass through sensor packages, instruments, or sampling devices. A flow meter may be mechanical, optical, electromagnetic, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/388/
McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.)
McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.)
PI Supplied Instrument Name: McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.) PI Supplied Instrument Description:Size-fractionated particle samples were collected using McLane WTS-LV in-situ pumps (4 L min-1 maximum pumping rate; McLane Research Laboratories, Inc.) during all sampling periods. Instrument Name: McLane Large Volume Pumping System WTS-LV Instrument Short Name:WTS-LV Instrument Description: The WTS-LV is a Water Transfer System (WTS) Large Volume (LV) pumping instrument designed and manufactured by McLane Research Labs (Falmouth, MA, USA). It is a large-volume, single-event sampler that collects suspended and dissolved particulate samples in situ.
Ambient water is drawn through a modular filter holder onto a 142-millimeter (mm) membrane without passing through the pump. The standard two-tier filter holder provides prefiltering and size fractioning. Collection targets include chlorophyll maximum, particulate trace metals, and phytoplankton. It features different flow rates and filter porosity to support a range of specimen collection. Sampling can be programmed to start at a scheduled time or begin with a countdown delay. It also features a dynamic pump speed algorithm that adjusts flow to protect the sample as material accumulates on the filter. Several pump options range from 0.5 to 30 liters per minute, with a max volume of 2,500 to 36,000 liters depending on the pump and battery pack used. The standard model is depth rated to 5,500 meters, with a deeper 7,000-meter option available. The operating temperature is -4 to 35 degrees Celsius.
The WTS-LV is available in four different configurations: Standard, Upright, Bore Hole, and Dual Filter Sampler. The high-capacity upright WTS-LV model provides three times the battery life of the standard model. The Bore-Hole WTS-LV is designed to fit through a narrow opening such as a 30-centimeter borehole. The dual filter WTS-LV features two vertical intake 142 mm filter holders to allow simultaneous filtering using two different porosities.
dissecting microscope
dissecting microscope
PI Supplied Instrument Name: dissecting microscope PI Supplied Instrument Description:Samples were inspected under a dissecting microscope to visually characterize the particles and remove intact zooplankton swimmers or contaminant fibers, which were both rare in the samples. Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
sonicator
sonicator
PI Supplied Instrument Name: sonicator PI Supplied Instrument Description:The mesh filter was sonicated for three minutes in an acid-clean polypropylene Nalgene bottle with filtered seawater. Instrument Name: ultrasonic cell disrupter (sonicator) Instrument Short Name: Instrument Description: Instrument that applies sound energy to agitate particles in a sample.
Cruise: AE2114
AE2114
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2114
Craig A. Carlson
University of California-Santa Barbara
Cruise: AE2123
AE2123
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2123
Craig A. Carlson
University of California-Santa Barbara
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel