http://lod.bco-dmo.org/id/dataset/982454
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
2025-08-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Nitrogen compound-specific isotope values of amino acids for each gelatinous zooplankton sample and the sample's estimated trophic position from R/V Sally Ride and R/V Roger Revelle cruises in the southern California Current Ecosystem from 2020-2023
2025-08-13
publication
2025-08-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-08-26
publication
https://doi.org/10.26008/1912/bco-dmo.982454.1
C. Anela Choy
University of California-San Diego Scripps
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: Chavarry, J., Choy, C. A. (2025) Nitrogen compound-specific isotope values of amino acids for each gelatinous zooplankton sample and the sample's estimated trophic position from R/V Sally Ride and R/V Roger Revelle cruises in the southern California Current Ecosystem from 2020-2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-08-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.982454.1 [access date]
CSIA of gelatinous zooplankton Dataset Description: Methods and Sampling: <p>Gelatinous zooplankton were collected on four research cruises between 2020 and 2023 at seven stations representing four nearshore and escarpment, and two offshore regions within the Southern California Bight. We conducted depth‑discrete sampling of gelatinous zooplankton using a 10-square-meter (m²) Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) equipped with five depth-discrete nets (mesh sizes 5-millimeter (mm), Wiebe et al., 1985). The 10 m² MOCNESS was towed obliquely as the ship traveled at a speed between 1 to 2 knots, with depth-discrete collections occurring on the upcast. Sampling stations and depth intervals varied across stations and cruises, but there were typically two depth intervals sampled within the upper 500 meters (m)&nbsp;and larger depth intervals below 500 m. The maximum depth of sampling increased from 1,250 m nearshore to 3,000 m offshore, corresponding with the deepening of the water column.&nbsp;<br />
<br />
Upon recovery, samples were stored in chilled seawater and kept at 5 degrees Celsius (°C) until processing. All sample processing was performed on ice to preserve body condition. Gelatinous zooplankton were identified to the most specific taxonomic level using published keys. The concentration of carbon and/or nitrogen can be low in gelatinous individuals (Lüskow et al., 2021), so we pooled multiple gelatinous individuals from the same taxonomic groups into a single sample, while standardizing size ranges. 561 samples of gelatinous zooplankton representing 13 taxonomic groups were chosen for bulk tissue stable carbon and nitrogen isotope analysis. A subset of twenty samples from seven gelatinous genera were chosen for nitrogen compound-specific isotope analysis of amino acids (CSIA-AA): <em>Pyrosoma atlanticum</em>, <em>Beroe cucumis</em>, <em>Hormiphora</em> spp., <em>Periphylla periphylla</em>, <em>Atolla vanhoeffeni</em>, <em>Aegina</em> spp., and <em>Pantachogon</em> spp. Taxa were selected for CSIA-AA because they represented a range in hypothesized feeding guilds, were found across a range of depth habitats (0 to&nbsp;1,025 m), and were abundant in our sampling region. To constrain possible spatiotemporal variability in baseline δ15N&nbsp;values, all the samples selected for CSIA-AA were limited to a daytime collection event at the escarpment in August 2021.</p>
<p>Gelatinous zooplankton were briefly thawed to remove visible gut contents using forceps and a scalpel, which were cleaned with ethanol between samples. Both gelatinous zooplankton and mesozooplankton samples were then lyophilized and homogenized in Whirl‑Paks. To ensure sufficient sample mass for stable isotope analysis, samples often contained multiple individuals from the same net, taxonomic group, and size class. The number of individuals per sample was typically fewer than 100, with a larger number of individuals pooled for some samples of <em>Pantachogon</em> spp. and <em>Hormiphora</em> spp.</p>
<p>Dried, homogenized tissues were packaged into tin capsules (1.5 to&nbsp;4 milligrams (mg) per sample) for bulk tissue stable isotope analyses, which were conducted at the University of Hawaii at Manoa and the University of California Merced. Briefly, samples were run on a Costech 4010 Elemental Combustion System coupled to either a ThermoScientific DELTA V Advantage, ThermoScientific DELTA V+, or a ThermoFinnigan DeltaPlus XP isotope ratio mass spectrometer through a ThermoScientific Conflo IV interface. Stable isotope values are reported in the standard per mille notation (‰), compared to the standards atmospheric N₂ and Vienna Pee Dee Belemnite for nitrogen and carbon, respectively. To ensure accuracy and instrument precision, both labs used a combination of international reference materials (from the United States Geological Survey or the National Institute of Standards and Technology) and in‑house reference materials (squid or tuna) with known δ15N and δ13C values. Based on analyzed reference materials, sample reproducibility was ± 0.2‰ for samples run at the University of Hawaii at Manoa, and sample reproducibility was ± 0.4‰ for samples run at the University of California Merced.</p>
<p>Samples were processed for CSIA-AA at the Laboratory for Marine Organic and Isotope Geochemistry at the University of Miami following the methods of Popp et al. (2007), Hannides et al. (2013), and Wojtal et al. (2023). Briefly, ∼50 mg of each dried sample was hydrolyzed, purified, and derivatized. Derivatives were then injected into a Thermo Trace 1310 gas chromatograph with a BPX5 column (50 m x 0.32 mm, 1.0 micrometer (μm) film thickness), fed into a combined oxidation/reduction reactor (Thermo Isolink II, 1000°C), and passed through a liquid nitrogen cold trap and into a Thermo Conflo IV and MAT 253 isotope ratio mass spectrometer. Three separate laboratory mixtures with known isotope ratios were used to correct δ15N values of gelatinous zooplankton samples and to ensure instrument accuracy and precision. Reliable data for each sample in comparison to standards were obtained from triplicate injections where possible but replicate injections for eight samples.</p>
<p>We used five approaches to estimate the trophic position of samples run for CSIA‑AA. The first approach, TP<sub>diet</sub>, was based on published diet studies, including <em>in situ</em> observations and gut content analyses. The second approach used δ15N&nbsp;values of bulk tissues to estimate the consumer trophic position (TP<sub>bulk</sub>) following the methods outlined in Post (2002). This estimate is based on the δ15N<sub>bulk</sub> values of gelatinous zooplankton, the trophic discrimination factor (TDF), and the δ15N value and trophic position of the isotopic baseline. Limited studies suggest that the TDF of gelatinous zooplankton may be lower than 3.4‰ (e.g., Schaub et al., 2021; Stukel et al., 2024; Tilves et al., 2018). We thus used a range in TDF (2.4 – 4.4‰; TP<sub>bulk-TDF-2.4</sub> and TP<sub>bulk-TDF-4.4</sub>) based on the reported standard deviation in TDF of 1‰ (Post, 2002). The third approach utilized published diet data along with δ15N values of bulk tissues to estimate trophic position (TP<sub>diet-bulk</sub>). We used known information about animal diet to designate a more accurate TDF. The fourth and fifth approaches for estimating trophic position relied on CSIA-AA following methods outlined in Chikaraishi et al. (2009) (TP<sub>AA</sub>). Briefly, phenylalanine was designated as a 'source'&nbsp;amino acid (after Chikaraishi et al., 2009; McMahon &amp; McCarthy 2016; Nielsen et al., 2015). We estimated TP<sub>AA</sub> two different ways by considering two 'trophic'&nbsp;amino acids, glutamic acid (TP<sub>Glu</sub>) and alanine (TP<sub>Ala</sub>). Glutamic acid is commonly used as the 'trophic'&nbsp;amino acid in food web studies (e.g., Nielsen et al., 2015; McMahon &amp; McCarthy 2016). However, we expected microbial cycling to be prominent within southern California Current Ecosystem food webs and subsequently designated alanine as another 'trophic'&nbsp;amino acid to capture these microbial contributions (after Décima et al., 2017).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2048210 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2048210
completed
C. Anela Choy
University of California-San Diego Scripps
808-822-3020
Scripps Institution of Oceanography 9500 Gilman Drive, MC 0218
La Jolla
CA
92093
USA
anela@ucsd.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
specimen_number
best_taxonomic_ID
tow
net
Date_UTC
year
month
day
latitude
longitude
hypothesized_diet
TP_glu
TP_glu_SD
TP_ala
TP_ala_SD
TP_bulk_TDF_2_4
TP_bulk_TDF_4_4
TP_diet_bulk
TP_diet
Alanine
Aspartic_Acid
Glutamic_Acid
Glycine
Isoleucine
Leucine
Lysine
Phenylalanine
Proline
Serine
Threonine
Valine
Alanine_SD
Aspartic_Acid_SD
Glutamic_Acid_SD
Glycine_SD
Isoleucine_SD
Leucine_SD
Lysine_SD
Phenylalanine_SD
Proline_SD
Serine_SD
Threonine_SD
Valine_SD
Thermo Isolink II
ThermoScientific Conflo IV interface
Costech 4010 Elemental Combustion System
Thermo Trace 1310 gas chromatograph
MAT 253 isotope ratio mass spectrometer
ThermoFinnigan Deltaplus XP isotope ratio mass spectrometer
10 m2 Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS)
Marel M2400 motion compensating scale
ThermoScientific DELTA V Advantage isotope ratio mass spectrometer
ThermoScientific DELTA V+ isotope ratio mass spectrometer
theme
None, User defined
sample identification
taxon
tow
net
date
year
month of year
day of month
latitude
longitude
sample description
d15N measured in biota
featureType
BCO-DMO Standard Parameters
Continuous Flow Interface for Mass Spectrometers
Continuous Flow Interface for Mass Spectrometers
Costech International Elemental Combustion System (ECS) 4010
Gas Chromatograph
Isotope-ratio Mass Spectrometer
Isotope-ratio Mass Spectrometer
MOCNESS
scale or balance
Thermo Fisher Scientific DELTA V Advantage isotope ratio mass spectrometer
Thermo Fisher Scientific DELTA V Plus isotope ratio mass spectrometer
instrument
BCO-DMO Standard Instruments
SR2007
SR2212
SR2323
RR2104
service
Deployment Activity
Southern California Current Ecosystem
Eastern Tropical and Subtropical Pacific Ocean
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.
Resolving vertical trophic linkages between surface and deep pelagic food webs
https://osprey.bco-dmo.org/project/853408
Resolving vertical trophic linkages between surface and deep pelagic food webs
<p><em>NSF Award Abstract:</em><br />
This CAREER award is advancing our understanding of connections between surface and deep water ocean food webs, which in turn has important implications for carbon cycling in the ocean. Although marine ecosystems deeper than 200 m encompass Earth’s largest single habitat, the food web relationships of deep-sea organisms are poorly resolved. The investigator is evaluating active transport by fishes, squids, crustaceans, and gelatinous animals that move organic matter from the more productive surface into deeper waters through feeding and diel vertical migration. She is using a combination of data on abundance and distribution of species with measurements of stable isotope biomarkers to understand trophic relationships and connect community composition and migratory behavior with food-web processes in the southern California Current ecosystem. The investigator is from a group traditionally underrepresented in science, and she has designed a comprehensive educational plan to train a more diverse, inclusive generation of seagoing biological oceanographers through hands-on field and research experiences. In addition to providing support for graduate and undergraduate students to participate directly in this research, the investigator is creating a novel and cohesive undergraduate curriculum involving a seagoing laboratory course to teach interdisciplinary field methods to conduct research on pelagic ecosystems and a seminar course highlighting Native and Indigenous knowledge alongside more traditional oceanographic research. The overall goal is to broaden participation in science by combining hands-on interdisciplinary research, mentoring, and expanding networks of minority and majority scientists.</p>
<p>This study centers around Vinogradov’s “ladder of migrations” as a conceptual framework, with the goal of understanding cumulative downward transport of organisms and organic matter to the deep ocean by overlapping vertical migrations and feeding. It is focusing on the role of micronekton, defined as ~2-20 cm fishes, cephalopods, crustaceans, and gelatinous animals, as active transporters of surface-derived organic matter across epipelagic, mesopelagic, and upper-bathypelagic layers in the southern California Current Ecosystem. One research cruise is sampling deep pelagic micronekton communities comprehensively and systematically and complements long-term data collected in the surface waters of this ecosystem. Depth-discrete MOCNESS tows are sampling organisms to assess micronekton abundance, biomass, and extent of diel vertical migrations to understand how relative compositions of taxa drive vertical connectivity. Analysis of bulk carbon and nitrogen stable isotopes and compound-specific isotopic analyses of amino acids (AA-CSIA) in organism tissue are providing quantitative assessments of deep-pelagic food webs and measuring the relative strength and composition of trophic linkages between surface and deeper water assemblages across distinct environmental gradients.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
<p>This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2).</p>
DeepSeaWebs
largerWorkCitation
project
eng; USA
oceans
Southern California Current Ecosystem; Eastern Tropical and Subtropical Pacific Ocean
-120.33
-120.21
32.4
32.56
2021-06-24
2021-06-25
Southern California Current
0
BCO-DMO catalogue of parameters from Nitrogen compound-specific isotope values of amino acids for each gelatinous zooplankton sample and the sample's estimated trophic position from R/V Sally Ride and R/V Roger Revelle cruises in the southern California Current Ecosystem from 2020-2023
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/983439.rdf
Name: specimen_number
Units: unitless
Description: <p>sample identifier that can be used to link to sample metadata in the related bulk tissue stable isotope dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/983440.rdf
Name: best_taxonomic_ID
Units: unitless
Description: <p>the finest taxonomic level the gelatinous zooplankton were identified to</p>
http://lod.bco-dmo.org/id/dataset-parameter/983441.rdf
Name: tow
Units: unitless
Description: <p>the tow number when the sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/983442.rdf
Name: net
Units: unitless
Description: <p>the net number when the sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/983443.rdf
Name: Date_UTC
Units: unitless
Description: <p>date the sample was collected (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983444.rdf
Name: year
Units: unitless
Description: <p>the year the sample was collected (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983445.rdf
Name: month
Units: unitless
Description: <p>the month the sample was collected (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983446.rdf
Name: day
Units: unitless
Description: <p>the day the sample was collected (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/983447.rdf
Name: latitude
Units: decimal degrees
Description: <p>the latitude of where the sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/983448.rdf
Name: longitude
Units: decimal degrees
Description: <p>the longitude of where the sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/983449.rdf
Name: hypothesized_diet
Units: unitless
Description: <p>the hypothesized primary diet of the gelatinous zooplankton taxonomic group, based on published diet data</p>
http://lod.bco-dmo.org/id/dataset-parameter/983450.rdf
Name: TP_glu
Units: unitless
Description: <p>The estimated trophic position of the sample, based on nitrogen compound-specific isotope analysis of amino acids and the 'trophic' amino acid glutamic acid</p>
http://lod.bco-dmo.org/id/dataset-parameter/983451.rdf
Name: TP_glu_SD
Units: unitless
Description: <p>The trophic position uncertainty of TP_glu based on propagation of errors</p>
http://lod.bco-dmo.org/id/dataset-parameter/983452.rdf
Name: TP_ala
Units: unitless
Description: <p>The estimated trophic position of the sample, based on nitrogen compound-specific isotope analysis of amino acids and the 'trophic' amino acid alanine</p>
http://lod.bco-dmo.org/id/dataset-parameter/983453.rdf
Name: TP_ala_SD
Units: unitless
Description: <p>The trophic position uncertainty of TP_ala based on propagation of errors</p>
http://lod.bco-dmo.org/id/dataset-parameter/983454.rdf
Name: TP_bulk_TDF_2_4
Units: unitless
Description: <p>The estimated trophic position of the sample based on bulk tissue stable nitrogen isotope analysis and a trophic discrimination factor of 2.4‰</p>
http://lod.bco-dmo.org/id/dataset-parameter/983455.rdf
Name: TP_bulk_TDF_4_4
Units: unitless
Description: <p>The estimated trophic position of the sample based on bulk tissue stable nitrogen isotope analysis and a trophic discrimination factor of 4.4‰</p>
http://lod.bco-dmo.org/id/dataset-parameter/983456.rdf
Name: TP_diet_bulk
Units: unitless
Description: <p>The estimated trophic position of the sample based on bulk tissue stable nitrogen isotope analysis and a trophic discrimination factor that is dependent on the taxonomic group's hypothesized diet</p>
http://lod.bco-dmo.org/id/dataset-parameter/983457.rdf
Name: TP_diet
Units: unitless
Description: <p>The estimated trophic position of the sample based on the taxonomic group's hypothesized diet</p>
http://lod.bco-dmo.org/id/dataset-parameter/983458.rdf
Name: Alanine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of alanine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983459.rdf
Name: Aspartic_Acid
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of aspartic acid for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983460.rdf
Name: Glutamic_Acid
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of glutamic acid for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983461.rdf
Name: Glycine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of glycine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983462.rdf
Name: Isoleucine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of isoleucine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983463.rdf
Name: Leucine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of leucine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983464.rdf
Name: Lysine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of lysine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983465.rdf
Name: Phenylalanine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of phenylalanine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983466.rdf
Name: Proline
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of proline for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983467.rdf
Name: Serine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of serine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983468.rdf
Name: Threonine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of threonine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983469.rdf
Name: Valine
Units: parts per thousand
Description: <p>The mean nitrogen stable isotope value of valine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983470.rdf
Name: Alanine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of alanine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983471.rdf
Name: Aspartic_Acid_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of aspartic acid for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983472.rdf
Name: Glutamic_Acid_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of glutamic acid for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983473.rdf
Name: Glycine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of glycine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983474.rdf
Name: Isoleucine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of isoleucine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983475.rdf
Name: Leucine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of leucine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983476.rdf
Name: Lysine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of lysine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983477.rdf
Name: Phenylalanine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of phenylalanine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983478.rdf
Name: Proline_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of proline for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983479.rdf
Name: Serine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of serine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983480.rdf
Name: Threonine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of threonine for samples run in replicate/triplicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/983481.rdf
Name: Valine_SD
Units: parts per thousand
Description: <p>The standard deviation of the nitrogen stable isotope value of valine for samples run in replicate/triplicate</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
4596
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/da528c48-3756-4f22-87e2-6e679ef55bc9/content
download
https://doi.org/10.26008/1912/bco-dmo.982454.1
download
onLine
dataset
<p>Gelatinous zooplankton were collected on four research cruises between 2020 and 2023 at seven stations representing four nearshore and escarpment, and two offshore regions within the Southern California Bight. We conducted depth‑discrete sampling of gelatinous zooplankton using a 10-square-meter (m²) Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) equipped with five depth-discrete nets (mesh sizes 5-millimeter (mm), Wiebe et al., 1985). The 10 m² MOCNESS was towed obliquely as the ship traveled at a speed between 1 to 2 knots, with depth-discrete collections occurring on the upcast. Sampling stations and depth intervals varied across stations and cruises, but there were typically two depth intervals sampled within the upper 500 meters (m)&nbsp;and larger depth intervals below 500 m. The maximum depth of sampling increased from 1,250 m nearshore to 3,000 m offshore, corresponding with the deepening of the water column.&nbsp;<br />
<br />
Upon recovery, samples were stored in chilled seawater and kept at 5 degrees Celsius (°C) until processing. All sample processing was performed on ice to preserve body condition. Gelatinous zooplankton were identified to the most specific taxonomic level using published keys. The concentration of carbon and/or nitrogen can be low in gelatinous individuals (Lüskow et al., 2021), so we pooled multiple gelatinous individuals from the same taxonomic groups into a single sample, while standardizing size ranges. 561 samples of gelatinous zooplankton representing 13 taxonomic groups were chosen for bulk tissue stable carbon and nitrogen isotope analysis. A subset of twenty samples from seven gelatinous genera were chosen for nitrogen compound-specific isotope analysis of amino acids (CSIA-AA): <em>Pyrosoma atlanticum</em>, <em>Beroe cucumis</em>, <em>Hormiphora</em> spp., <em>Periphylla periphylla</em>, <em>Atolla vanhoeffeni</em>, <em>Aegina</em> spp., and <em>Pantachogon</em> spp. Taxa were selected for CSIA-AA because they represented a range in hypothesized feeding guilds, were found across a range of depth habitats (0 to&nbsp;1,025 m), and were abundant in our sampling region. To constrain possible spatiotemporal variability in baseline δ15N&nbsp;values, all the samples selected for CSIA-AA were limited to a daytime collection event at the escarpment in August 2021.</p>
<p>Gelatinous zooplankton were briefly thawed to remove visible gut contents using forceps and a scalpel, which were cleaned with ethanol between samples. Both gelatinous zooplankton and mesozooplankton samples were then lyophilized and homogenized in Whirl‑Paks. To ensure sufficient sample mass for stable isotope analysis, samples often contained multiple individuals from the same net, taxonomic group, and size class. The number of individuals per sample was typically fewer than 100, with a larger number of individuals pooled for some samples of <em>Pantachogon</em> spp. and <em>Hormiphora</em> spp.</p>
<p>Dried, homogenized tissues were packaged into tin capsules (1.5 to&nbsp;4 milligrams (mg) per sample) for bulk tissue stable isotope analyses, which were conducted at the University of Hawaii at Manoa and the University of California Merced. Briefly, samples were run on a Costech 4010 Elemental Combustion System coupled to either a ThermoScientific DELTA V Advantage, ThermoScientific DELTA V+, or a ThermoFinnigan DeltaPlus XP isotope ratio mass spectrometer through a ThermoScientific Conflo IV interface. Stable isotope values are reported in the standard per mille notation (‰), compared to the standards atmospheric N₂ and Vienna Pee Dee Belemnite for nitrogen and carbon, respectively. To ensure accuracy and instrument precision, both labs used a combination of international reference materials (from the United States Geological Survey or the National Institute of Standards and Technology) and in‑house reference materials (squid or tuna) with known δ15N and δ13C values. Based on analyzed reference materials, sample reproducibility was ± 0.2‰ for samples run at the University of Hawaii at Manoa, and sample reproducibility was ± 0.4‰ for samples run at the University of California Merced.</p>
<p>Samples were processed for CSIA-AA at the Laboratory for Marine Organic and Isotope Geochemistry at the University of Miami following the methods of Popp et al. (2007), Hannides et al. (2013), and Wojtal et al. (2023). Briefly, ∼50 mg of each dried sample was hydrolyzed, purified, and derivatized. Derivatives were then injected into a Thermo Trace 1310 gas chromatograph with a BPX5 column (50 m x 0.32 mm, 1.0 micrometer (μm) film thickness), fed into a combined oxidation/reduction reactor (Thermo Isolink II, 1000°C), and passed through a liquid nitrogen cold trap and into a Thermo Conflo IV and MAT 253 isotope ratio mass spectrometer. Three separate laboratory mixtures with known isotope ratios were used to correct δ15N values of gelatinous zooplankton samples and to ensure instrument accuracy and precision. Reliable data for each sample in comparison to standards were obtained from triplicate injections where possible but replicate injections for eight samples.</p>
<p>We used five approaches to estimate the trophic position of samples run for CSIA‑AA. The first approach, TP<sub>diet</sub>, was based on published diet studies, including <em>in situ</em> observations and gut content analyses. The second approach used δ15N&nbsp;values of bulk tissues to estimate the consumer trophic position (TP<sub>bulk</sub>) following the methods outlined in Post (2002). This estimate is based on the δ15N<sub>bulk</sub> values of gelatinous zooplankton, the trophic discrimination factor (TDF), and the δ15N value and trophic position of the isotopic baseline. Limited studies suggest that the TDF of gelatinous zooplankton may be lower than 3.4‰ (e.g., Schaub et al., 2021; Stukel et al., 2024; Tilves et al., 2018). We thus used a range in TDF (2.4 – 4.4‰; TP<sub>bulk-TDF-2.4</sub> and TP<sub>bulk-TDF-4.4</sub>) based on the reported standard deviation in TDF of 1‰ (Post, 2002). The third approach utilized published diet data along with δ15N values of bulk tissues to estimate trophic position (TP<sub>diet-bulk</sub>). We used known information about animal diet to designate a more accurate TDF. The fourth and fifth approaches for estimating trophic position relied on CSIA-AA following methods outlined in Chikaraishi et al. (2009) (TP<sub>AA</sub>). Briefly, phenylalanine was designated as a 'source'&nbsp;amino acid (after Chikaraishi et al., 2009; McMahon &amp; McCarthy 2016; Nielsen et al., 2015). We estimated TP<sub>AA</sub> two different ways by considering two 'trophic'&nbsp;amino acids, glutamic acid (TP<sub>Glu</sub>) and alanine (TP<sub>Ala</sub>). Glutamic acid is commonly used as the 'trophic'&nbsp;amino acid in food web studies (e.g., Nielsen et al., 2015; McMahon &amp; McCarthy 2016). However, we expected microbial cycling to be prominent within southern California Current Ecosystem food webs and subsequently designated alanine as another 'trophic'&nbsp;amino acid to capture these microbial contributions (after Décima et al., 2017).</p>
Specified by the Principal Investigator(s)
- Imported original file "gelatinous_zooplankton_csia_aa.csv" into the BCO-DMO system.
- Created Date_UTC column in YYYY-MM-DD format.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved final file as "982454_v1_csia_gelatinous_zooplankton.csv".
Specified by BCO-DMO Data Managers
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7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
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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.
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Thermo Isolink II
Thermo Isolink II
PI Supplied Instrument Name: Thermo Isolink II PI Supplied Instrument Description:used for the determination of nitrogen compound-specific stable isotope ratios from amino acids Instrument Name: Continuous Flow Interface for Mass Spectrometers Instrument Short Name: Instrument Description: A Continuous Flow Interface connects solid and liquid sample preparation devices to instruments that measure isotopic composition. It allows the introduction of the sample and also reference and carrier gases.
Examples: Finnigan MATConFlo II, ThermoScientific ConFlo IV, and Picarro Caddy.
Note: This is NOT an analyzer
ThermoScientific Conflo IV interface
ThermoScientific Conflo IV interface
PI Supplied Instrument Name: ThermoScientific Conflo IV interface PI Supplied Instrument Description:used for the determination of stable isotope ratios of carbon and nitrogen from bulk tissues Instrument Name: Continuous Flow Interface for Mass Spectrometers Instrument Short Name: Instrument Description: A Continuous Flow Interface connects solid and liquid sample preparation devices to instruments that measure isotopic composition. It allows the introduction of the sample and also reference and carrier gases.
Examples: Finnigan MATConFlo II, ThermoScientific ConFlo IV, and Picarro Caddy.
Note: This is NOT an analyzer
Costech 4010 Elemental Combustion System
Costech 4010 Elemental Combustion System
PI Supplied Instrument Name: Costech 4010 Elemental Combustion System PI Supplied Instrument Description:used for the determination of stable isotope ratios of carbon and nitrogen from bulk tissues Instrument Name: Costech International Elemental Combustion System (ECS) 4010 Instrument Short Name:Costech ECS 4010 Instrument Description: The ECS 4010 Nitrogen / Protein Analyzer is an elemental combustion analyser for CHNSO elemental analysis and Nitrogen / Protein determination. The GC oven and separation column have a temperature range of 30-110 degC, with control of +/- 0.1 degC.
Thermo Trace 1310 gas chromatograph
Thermo Trace 1310 gas chromatograph
PI Supplied Instrument Name: Thermo Trace 1310 gas chromatograph PI Supplied Instrument Description:used for the determination of nitrogen compound-specific stable isotope ratios from amino acids Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
MAT 253 isotope ratio mass spectrometer
MAT 253 isotope ratio mass spectrometer
PI Supplied Instrument Name: MAT 253 isotope ratio mass spectrometer PI Supplied Instrument Description:used for the determination of nitrogen compound-specific stable isotope ratios from amino acids Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
ThermoFinnigan Deltaplus XP isotope ratio mass spectrometer
ThermoFinnigan Deltaplus XP isotope ratio mass spectrometer
PI Supplied Instrument Name: ThermoFinnigan Deltaplus XP isotope ratio mass spectrometer PI Supplied Instrument Description:used for the determination of stable isotope ratios of carbon and nitrogen from bulk tissues Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
10 m2 Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS)
10 m2 Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS)
PI Supplied Instrument Name: 10 m2 Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) PI Supplied Instrument Description:used to collect gelatinous zooplankton at sea Instrument Name: MOCNESS Instrument Short Name:MOCNESS Instrument Description: The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974). (from MOCNESS manual) Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
Marel M2400 motion compensating scale
Marel M2400 motion compensating scale
PI Supplied Instrument Name: Marel M2400 motion compensating scale PI Supplied Instrument Description:used to weigh gelatinous zooplankton at sea Instrument Name: scale or balance Instrument Short Name: Instrument Description: Devices that determine the mass or weight of a sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/
ThermoScientific DELTA V Advantage isotope ratio mass spectrometer
ThermoScientific DELTA V Advantage isotope ratio mass spectrometer
PI Supplied Instrument Name: ThermoScientific DELTA V Advantage isotope ratio mass spectrometer PI Supplied Instrument Description:used for the determination of stable isotope ratios of carbon and nitrogen from bulk tissues Instrument Name: Thermo Fisher Scientific DELTA V Advantage isotope ratio mass spectrometer Instrument Short Name:Delta V Advantage Instrument Description: The Thermo Scientific DELTA V Advantage is an isotope ratio mass spectrometer designed to measure isotopic, elemental, and molecular ratios of organic and inorganic compounds. The DELTA V Advantage is the standard model of the DELTA V series of isotope ratio mass spectrometers, which can be upgraded to the DELTA V Plus. The DELTA V Advantage can be operated in Continuous Flow or Dual Inlet mode. The standard collector configuration is the Universal Triple Collector. H2 collectors with online hydrogen capability are optional. The DELTA V Advantage is controlled by an automated, integrated Isodat software suite. A magnet, whose pole faces determine the free flight space for the ions, eliminates the traditional flight tube. The magnet is designed for fast mass switching which is further supported by a fast jump control between consecutive measurements of multiple gases within one run. The sample gas is introduced at ground potential, eliminating the need for insulation of the flow path, ensuring 100 percent transfer into the ion source. The amplifiers register ion beams up to 50 V. The DELTA V Advantage has a sensitivity of 1200 molecules per ion (M/I) in Dual Inlet mode and 1500 M/I in Continuous Flow mode. It has a system stability of < 10 ppm and an effective magnetic detection radius of 191 nm. It has a mass range of 1 - 80 Dalton at 3 kV.
ThermoScientific DELTA V+ isotope ratio mass spectrometer
ThermoScientific DELTA V+ isotope ratio mass spectrometer
PI Supplied Instrument Name: ThermoScientific DELTA V+ isotope ratio mass spectrometer PI Supplied Instrument Description:used for the determination of stable isotope ratios of carbon and nitrogen from bulk tissues Instrument Name: Thermo Fisher Scientific DELTA V Plus isotope ratio mass spectrometer Instrument Short Name:Delta V Plus IRMS Instrument Description: The Thermo Scientific DELTA V Plus is an isotope ratio mass spectrometer designed to measure isotopic, elemental and molecular ratios of organic and inorganic compounds. The DELTA V Plus is an enhanced model of the DELTA V series of isotope ratio mass spectrometers, which can be upgraded from the DELTA V Advantage. The DELTA V Plus can be operated in Continuous Flow or Dual Inlet mode and can accommodate up to 10 collectors, ensuring flexibility to cover many applications. The DELTA V Plus is controlled by an automated, integrated Isodat software suite. A magnet, whose pole faces determine the free flight space for the ions, eliminates the traditional flight tube. The magnet is designed for fast mass switching which is further supported by a fast jump control between consecutive measurements of multiple gases within one run. The sample gas is introduced at ground potential, eliminating the need for insulation of the flow path, ensuring 100 percent transfer into the ion source. The amplifiers register ion beams up to 50 V. The DELTA V Plus has refined optics, enabling greater ion transmission than the DELTA V Advantage. It has a sensitivity of 800 molecules per ion (M/I) in Dual Inlet mode and 1100 M/I in Continuous Flow mode. It has a system stability of < 10 ppm and an effective magnetic detection radius of 191 nm. It has a mass range of 1 - 96 Dalton at 3 kV.
Cruise: SR2007
SR2007
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR2007
C. Anela Choy
University of California-San Diego Scripps
Cruise: SR2212
SR2212
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR2212
C. Anela Choy
University of California-San Diego Scripps
Cruise: SR2323
SR2323
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR2323
C. Anela Choy
University of California-San Diego Scripps
Cruise: RR2104
RR2104
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
RR2104
C. Anela Choy
University of California-San Diego
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel