http://lod.bco-dmo.org/id/dataset/1008909
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
2026-10-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Particle-associated microbial respiration from RESPIRE sediment trap deployments during R/V Atlantis cruise AT50-10 in the Eastern Tropical Pacific in May 2023 and R/V Sally Ride cruise SR1919 in the Santa Barbara Basin in Dec 2019
2026-10-02
publication
2026-10-02
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-10-13
publication
https://doi.org/10.26008/1912/bco-dmo.1008909.1
Alyson E. Santoro
University of California-Santa Barbara
principalInvestigator
Nicola L. Paul
University of California-Santa Barbara
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: Paul, N. L., Santoro, A. E. (2026) Particle-associated microbial respiration from RESPIRE sediment trap deployments during R/V Atlantis cruise AT50-10 in the Eastern Tropical Pacific in May 2023 and R/V Sally Ride cruise SR1919 in the Santa Barbara Basin in Dec 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-10-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.1008909.1 [access date]
RESPIRE POM measurements Dataset Description: Methods and Sampling: <p><strong>Sediment trap deployments and sample collection</strong></p>
<p>REspiration on Sinking Particles In the subsuRface ocEan (RESPIRE) particle collection and incubation systems (Boyd et al., 2015; Bressac et al., 2024) were deployed on a drifting, surface-tethered trap (STT) array at each station for 2-3 days at depths between 80-225 m. RESPIRE traps were filled with 0.2 µm-filtered seawater collected from a CTD cast 2-3 hours prior to deployment. Upon recovery, overlying seawater in RESPIRE traps was siphoned off immediately after recovery, remaining RESPIRE water was collected for bacterial production, dissolved organic carbon (DOC), and cell count measurements, and remaining sample water was passed through a rotary wet splitter and divided into equal fractions. All trap samples were passed through screens to remove zooplankton “swimmers”. Split fractions of the sample water were then vacuum filtered onto pre-combusted 25mm GF/F (Whatman, Maidstone, Kent, United Kingdom) or quartz (Whatman) filters for CHN analyses. Samples collected for DNA were vacuum-filtered onto 25 mm or 47 mm 0.2 µm pore size polyethersulfone filters (Pall Supor, Port Washington, New York, USA), flash-frozen, then stored at -80°C until further processing in the lab. Filters for cell counts and CHN analyses were stored at -20°C and -80°C respectively until further processing in a shore-based lab.</p>
<p><strong>Dissolved and total organic carbon measurements</strong></p>
<p>Prior to each deployment, the 0.2 µm-filtered seawater used to fill RESPIRE traps prior to deployment was sampled for DOC and used as the DOC<sub>initial</sub> timepoint. After recovery, particle-containing water was collected from RESPIRE traps for DOC or total organic carbon (TOC) determination (DOC<sub>final</sub> or TOC<sub>final</sub>). Combusted 40 mL glass vials with Teflon-lined caps were used for sample collection. For DOC samples, water was filtered into the vial using a 0.2 µm filter to a volume of ~30 mL and was acidified with 50 µL of DOC-free 4 N hydrochloric acid (Stephens et al., 2020). TOC samples were collected following the same protocol but without 0.2 µm filtration. All samples were stored at 4°C until measurements could be made in a shore-based lab. DOC and TOC concentrations were measured via the high temperature combustion method using modified Shimadzu TOC-V or TOC-L analyzers following Halewood et al. (2022).</p>
<p><strong>DAPI staining and cell enumeration on particles</strong></p>
<p>Particle-containing fluid (~15mL) from RESPIRE traps were collected and fixed with 0.405 mL of formalin for the purposes of DAPI staining and cell enumeration. Samples were vacuum filtered onto 25 mm, 0.2 µm poresize polycarbonate filters (Pall Supor). Five mL were pipetted into the filtration tower and filtered using vacuum filtration until ~0.5 mL remained above the filter. 0.5 mL DAPI solution (5 µg/mL) was added to the sample, and the filtration tower was covered with foil and left to stain for 3 min. After 3 min, the remaining sample was filtered. The filtered sample was removed from the filtration tower and mounted on a labeled glass microscope slide using a drop of immersion oil between the slide and filter and another drop between the filter and cover slip. Filters were stored at -20°C until imaging and counting on-shore. Epifluorescence microscopy (63X objective, Zeiss Axio Observer 7 Inverted microscope, Carl Zeiss Microscopy, LLC, White Plains, NY, USA) was used to take 12 digital images across different parts of each sample filter.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924512 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924512
completed
Alyson E. Santoro
University of California-Santa Barbara
805-893-5318
2155 Marine Biotech Lab
Santa Barbara
CA
93106
USA
asantoro@ucsb.edu
pointOfContact
Nicola L. Paul
University of California-Santa Barbara
nicolapaul@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Station
Latitude
Longitude
Deployment
Deploy_date_UTC
Recovery_date_UTC
Depth
Deployment_length
Particle_collection_period
RESPIRE_O2_drawdown
RESPIRE_O2_drawdown_sd
Respiratory_quotient
RESPIRE_C_utilization
RESPIRE_C_utilization_sd
Avg_POC_final
Avg_POC_final_sd
DOC_initial
DOC_initial_sd
DOC_final
DOC_final_sd
C_specific_respiration
C_specific_respiration_uncertainty
POC_flux
POC_flux_uncertainty
RESPIRE_cell_conc
RESPIRE_cell_conc_uncertainty
Aanderaa oxygen optode (Aanderaa 4831 series)
CTD
Exeter Analytical Elemental Analyzer
Zeiss Axio Observer 7 Inverted microscope
Shimadzu TOC Analyzer
theme
None, User defined
Cruise identifier
station
latitude
longitude
deployment number
date begin
date end
depth
days
respiration rate
standard deviation
ratio
No BCO-DMO term
particulate organic Carbon (POC)
dissolved organic Carbon
cell_concentration
featureType
BCO-DMO Standard Parameters
Aanderaa 4831 oxygen optode
CTD - profiler
Elemental Analyzer
Inverted Microscope
Total Organic Carbon Analyzer
instrument
BCO-DMO Standard Instruments
AT50-10
SR1919
service
Deployment Activity
Eastern Tropical and Subtropical Pacific Ocean
Santa Barbara Basin
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.
Collaborative Research: Underexplored Connections between Nitrogen and Trace Metal Cycling in Oxygen Minimum Zones Mediated by Metalloenzyme Inventories
https://osprey.bco-dmo.org/project/806565
Collaborative Research: Underexplored Connections between Nitrogen and Trace Metal Cycling in Oxygen Minimum Zones Mediated by Metalloenzyme Inventories
<p><em>NSF abstract:</em><br />
Though scarce and largely insoluble, trace metals are key components of sophisticated enzymes (protein molecules that speed up biochemical reactions) involved in biogeochemical cycles in the dark ocean (below 1000m). For example, metalloenzymes are involved in nearly every reaction in the nitrogen cycle. Yet, despite direct connections between trace metal and nitrogen cycles, the relationship between trace metal distributions and biological nitrogen cycling processes in the dark ocean have rarely been explored, likely due to the technical challenges associated with their study. Availability of the autonomous underwater vehicle (AUV) Clio, a sampling platform capable of collecting high-resolution vertical profile samples for biochemical and microbial measurements by large volume filtration of microbial particulate material, has overcome this challenge. Thus, this research project plans an interdisciplinary chemistry, biology, and engineering effort to test the hypothesis that certain chemical reactions, such as nitrite oxidation, could become limited by metal availability within the upper mesopelagic and that trace metal demands for nitrite-oxidizing bacteria may be increased under low oxygen conditions. Broader impacts of this study include the continued development and application of the Clio Biogeochemical AUV as a community resource by developing and testing its high-resolution and adaptive sampling capabilities. In addition, metaproteomic data will be deposited into the recently launched Ocean Protein Portal to allow oceanographers and the metals in biology community to examine the distribution of proteins and metalloenzymes in the ocean. Undergraduate students will be supported by this project at all three institutions, with an effort to recruit minority students. The proposed research will also be synergistic with the goals of early community-building efforts for a potential global scale microbial biogeochemistry program modeled after the success of the GEOTRACES program, provisionally called "Biogeoscapes: Ocean metabolism and nutrient cycles on a changing planet".</p>
<p>The proposed research project will test the following three hypotheses: (1) the microbial metalloenzyme distribution of the mesopelagic is spatially dynamic in response to environmental gradients in oxygen and trace metals, (2) nitrite oxidation in the Eastern Tropical Pacific Ocean can be limited by iron availability in the upper mesopelagic through an inability to complete biosynthesis of the microbial protein nitrite oxidoreductase, and (3) nitrite-oxidizing bacteria increase their metalloenzyme requirements at low oxygen, impacting the distribution of both dissolved and particulate metals within oxygen minimum zones. One of the challenges to characterizing the biogeochemistry of the mesopelagic ocean is an inability to effectively sample it. As a sampling platform, we will use the novel biogeochemical AUV Clio that enables high-resolution vertical profile samples for biochemical and microbial measurements by large volume filtration of microbial particulate material on a research expedition in the Eastern Tropical Pacific Ocean. Specific research activities will be orchestrated to test the hypotheses. Hypothesis 1 will be explored by comparison of hydrographic, microbial distributions, dissolved and particulate metal data, and metaproteomic results with profile samples collected by Clio. Hypothesis 2 will be tested by incubation experiments using 15NO2- oxidation rates on Clio-collected incubation samples. Hypothesis 3 will be tested by dividing targeted nitrite oxidoreductase protein copies by qPCR (quantitative polymerase chain reaction)-based nitrite oxidizing bacteria abundance (NOB) to determine if cellular copy number varies with oxygen distributions, and by metalloproteomic analyses of NOB cultures. The demonstration of trace metal limitation of remineralization processes, not just primary production, would transform our understanding of the role of metals in biogeochemical cycling and provide new ways with which to interpret sectional data of dissolved and particulate trace metal distributions in the ocean. The idea that oxygen may play a previously underappreciated role in controlling trace metals due not just to metals' physical chemistry, but also from changing biological demand, will improve our ability to predict trace metal distributions in the face of decreasing ocean oxygen content.</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>
CliOMZ
largerWorkCitation
project
eng; USA
biota
oceans
Eastern Tropical and Subtropical Pacific Ocean; Santa Barbara Basin
-119.96605
-89.99734
-10.003051
34.30868333
2019-12-15
2023-05-30
Eastern Tropical Pacific
0
BCO-DMO catalogue of parameters from Particle-associated microbial respiration from RESPIRE sediment trap deployments during R/V Atlantis cruise AT50-10 in the Eastern Tropical Pacific in May 2023 and R/V Sally Ride cruise SR1919 in the Santa Barbara Basin in Dec 2019
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/1009019.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise name from which sampling took place.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009020.rdf
Name: Station
Units: unitless
Description: <p>Station number of specified cruise.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009021.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Sampling latitude in decimal degrees; a positive value indicates a northern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009023.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling longitude in decimal degrees; a negative value indicates a western coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009025.rdf
Name: Deployment
Units: unitless
Description: <p>Deployment number for the surface-tethered sediment trap array during the specified cruise.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009026.rdf
Name: Deploy_date_UTC
Units: unitless
Description: <p>Date of sediment trap array deployment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009027.rdf
Name: Recovery_date_UTC
Units: unitless
Description: <p>Date of sediment trap array recovery.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009028.rdf
Name: Depth
Units: meters (m)
Description: <p>Deployment depth of RESPIRE sediment trap.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009030.rdf
Name: Deployment_length
Units: days (d)
Description: <p>Length sediment trap array was deployed for</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009031.rdf
Name: Particle_collection_period
Units: days (d)
Description: <p>Length of time RESPIRE traps collected particles for prior to incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009032.rdf
Name: RESPIRE_O2_drawdown
Units: millimoles of oxygen per meter cubed per day (mmol O2 /m^3/d)
Description: <p>Rate of oxygen drawdown measured in RESPIRE trap incubations.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009033.rdf
Name: RESPIRE_O2_drawdown_sd
Units: millimoles of oxygen per meter cubed per day (mmol O2 /m^3/d)
Description: <p>Standard deviation of rate of oxygen drawdown measured in RESPIRE trap incubations.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009034.rdf
Name: Respiratory_quotient
Units: unitless
Description: <p>Respiratory quotient used to convert rates from oxygen to carbon units</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009035.rdf
Name: RESPIRE_C_utilization
Units: millimoles of carbon per meter cubed per day (mmol C/m^3/d)
Description: <p>Rate of carbon utilization calculated for RESPIRE trap incubations.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009036.rdf
Name: RESPIRE_C_utilization_sd
Units: millimoles of carbon per meter cubed per day (mmol C/m^3/d)
Description: <p>Standard deviation of the rate of carbon utilization calculated for RESPIRE trap incubations</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009037.rdf
Name: Avg_POC_final
Units: millimoles of carbon (mmol C)
Description: <p>Amount of POC at the end of RESPIRE trap incubations averaged from triplicate CHN measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009038.rdf
Name: Avg_POC_final_sd
Units: millimoles of carbon (mmol C)
Description: <p>Standard deviation of the average amount of POC at the end of RESPIRE trap incubations.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009039.rdf
Name: DOC_initial
Units: micromoles per liter (µmol/L)
Description: <p>Concentration of dissolved organic carbon prior to RESPIRE trap deployment. Measured from the filtered seawater that fills the RESPIRE trap prior to deployment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009040.rdf
Name: DOC_initial_sd
Units: micromoles per liter (µmol/L)
Description: <p>Standard deviation of the concentration of duplicate or triplicate dissolved organic carbon samples taken prior to RESPIRE trap deployment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009041.rdf
Name: DOC_final
Units: micromoles per liter (µmol/L)
Description: <p>Concentration of dissolved organic carbon after RESPIRE trap recovery. Estimated by subtracting the concentration of particulate organic carbon from the concentration of total organic carbon, where total organic carbon samples were taken.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009042.rdf
Name: DOC_final_sd
Units: micromoles per liter (µmol/L)
Description: <p>Standard deviation of the concentration of dissolved organic carbon from duplicate or triplicate samples taken after RESPIRE trap recovery.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009043.rdf
Name: C_specific_respiration
Units: per day (d^-1)
Description: <p>Carbon-specific respiration rate from RESPIRE trap incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009044.rdf
Name: C_specific_respiration_uncertainty
Units: per day (d^-1)
Description: <p>Propagated uncertainty for carbon-specific respiration rate from RESPIRE trap incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009045.rdf
Name: POC_flux
Units: millimoles of carbon per meter squared per day (mmol C/m^2/d)
Description: <p>Particulate organic carbon fluxes back-calculated from RESPIRE trap measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009046.rdf
Name: POC_flux_uncertainty
Units: millimoles of carbon per meter squared per day (mmol C/m^2/d)
Description: <p>Uncertainty associated with calculation of particulate organic carbon fluxes</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009047.rdf
Name: RESPIRE_cell_conc
Units: cells per liter (cells/L)
Description: <p>Concentration of cells in RESPIRE trap incubation chamber</p>
http://lod.bco-dmo.org/id/dataset-parameter/1009048.rdf
Name: RESPIRE_cell_conc_uncertainty
Units: cells per liter (cells/L)
Description: <p>Uncertainty associated with the calculation of the concentration of cells in the RESPIRE trap incubation chamber</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
https://doi.org/10.26008/1912/bco-dmo.1008909.1
download
onLine
dataset
<p><strong>Sediment trap deployments and sample collection</strong></p>
<p>REspiration on Sinking Particles In the subsuRface ocEan (RESPIRE) particle collection and incubation systems (Boyd et al., 2015; Bressac et al., 2024) were deployed on a drifting, surface-tethered trap (STT) array at each station for 2-3 days at depths between 80-225 m. RESPIRE traps were filled with 0.2 µm-filtered seawater collected from a CTD cast 2-3 hours prior to deployment. Upon recovery, overlying seawater in RESPIRE traps was siphoned off immediately after recovery, remaining RESPIRE water was collected for bacterial production, dissolved organic carbon (DOC), and cell count measurements, and remaining sample water was passed through a rotary wet splitter and divided into equal fractions. All trap samples were passed through screens to remove zooplankton “swimmers”. Split fractions of the sample water were then vacuum filtered onto pre-combusted 25mm GF/F (Whatman, Maidstone, Kent, United Kingdom) or quartz (Whatman) filters for CHN analyses. Samples collected for DNA were vacuum-filtered onto 25 mm or 47 mm 0.2 µm pore size polyethersulfone filters (Pall Supor, Port Washington, New York, USA), flash-frozen, then stored at -80°C until further processing in the lab. Filters for cell counts and CHN analyses were stored at -20°C and -80°C respectively until further processing in a shore-based lab.</p>
<p><strong>Dissolved and total organic carbon measurements</strong></p>
<p>Prior to each deployment, the 0.2 µm-filtered seawater used to fill RESPIRE traps prior to deployment was sampled for DOC and used as the DOC<sub>initial</sub> timepoint. After recovery, particle-containing water was collected from RESPIRE traps for DOC or total organic carbon (TOC) determination (DOC<sub>final</sub> or TOC<sub>final</sub>). Combusted 40 mL glass vials with Teflon-lined caps were used for sample collection. For DOC samples, water was filtered into the vial using a 0.2 µm filter to a volume of ~30 mL and was acidified with 50 µL of DOC-free 4 N hydrochloric acid (Stephens et al., 2020). TOC samples were collected following the same protocol but without 0.2 µm filtration. All samples were stored at 4°C until measurements could be made in a shore-based lab. DOC and TOC concentrations were measured via the high temperature combustion method using modified Shimadzu TOC-V or TOC-L analyzers following Halewood et al. (2022).</p>
<p><strong>DAPI staining and cell enumeration on particles</strong></p>
<p>Particle-containing fluid (~15mL) from RESPIRE traps were collected and fixed with 0.405 mL of formalin for the purposes of DAPI staining and cell enumeration. Samples were vacuum filtered onto 25 mm, 0.2 µm poresize polycarbonate filters (Pall Supor). Five mL were pipetted into the filtration tower and filtered using vacuum filtration until ~0.5 mL remained above the filter. 0.5 mL DAPI solution (5 µg/mL) was added to the sample, and the filtration tower was covered with foil and left to stain for 3 min. After 3 min, the remaining sample was filtered. The filtered sample was removed from the filtration tower and mounted on a labeled glass microscope slide using a drop of immersion oil between the slide and filter and another drop between the filter and cover slip. Filters were stored at -20°C until imaging and counting on-shore. Epifluorescence microscopy (63X objective, Zeiss Axio Observer 7 Inverted microscope, Carl Zeiss Microscopy, LLC, White Plains, NY, USA) was used to take 12 digital images across different parts of each sample filter.</p>
Specified by the Principal Investigator(s)
<p><strong>RESPIRE trap mechanism and respiration rate calculations</strong></p>
<p>The RESPIRE particle collection and incubation apparatus is designed to non-intrusively intercept sinking particles, deposit them into an incubation chamber containing 0.2 µm-filtered seawater from depth and incubate the particles <em>in situ</em> (Boyd et al., 2015; Bressac et al., 2024). Particle collection phases for the RESPIRE trap deployments in this study ranged from 0.5 to 1 d with the following incubation phases lasting 0.5 to 1.5 d. An oxygen optode (Aanderaa 4831 series) within the RESPIRE incubation chamber measured oxygen concentration every five minutes. Dissolved oxygen concentrations were corrected for pressure, salinity, and temperature (if temperature varied notably over the course of the incubation; AT5010 deployment 3) according to the Aanderaa Operating Manual and Thierry et al. (2018). The change in oxygen over the incubation phase time was determined from these measurements for the volume of the RESPIRE incubation chamber. A respiratory quotient (RQ), the incubation length (<em>t<sub>inc</sub></em>), and the volume of the RESPIRE incubation chamber (<em>V<sub>RES</sub></em>, 1.45 L) were used to convert the oxygen-based remineralization rate (<em>O<sub>2,cons</sub></em>) to units of carbon (<strong>Equation 1</strong>). Here, we define RQ to be the molar drawdown of dioxygen to carbon (O<sub>2</sub>:C). We selected an RQ of 1.1 (L. A. Anderson, 1995) for our calculations. End-point POC measurements (<em>POC<sub>final</sub></em>), the change in DOC over the course of the incubation (<em>delta DOC</em>), and the rate of oxygen consumption (<em>O<sub>2,cons</sub></em>) were used to back-calculate the starting concentration of POC (<em>POC<sub>initial</sub></em>) at the beginning of the RESPIRE incubation phase (<strong>Equation 1</strong>). For deployments where TOC samples were taken, DOC concentrations were calculated by subtracting the POC concentration (after RESPIRE incubation) from the <em>TOC<sub>final</sub></em> concentration (SR1919, AT5010). The change in dissolved organic carbon (DOC) concentration over the course of RESPIRE incubations was measured from two timepoints—an initial (before particle collection) and final (recovered RESPIRE water minus the measured POC concentration). The calculated amount of <em>POC<sub>initial</sub></em> (mmol C) was divided by the length of the collection period (<em>t<sub>col</sub></em>) and the area of the RESPIRE trap (<em>A<sub>RES</sub></em>, 0.014 m<sup>2</sup>) to estimate POC fluxes (<strong>Equation 2</strong>). Carbon remineralization rates were normalized to mean POC concentration (<em>[POC]<sub>avg</sub></em>) of the incubation chamber to achieve carbon-specific (C-specific) remineralization rates (<em>R<sub>norm</sub></em>; <strong>Equation 3</strong>). Uncertainties related to sample splitting, averaging sample replicates, and linear regressions were propagated through all calculations.<br />
&nbsp;</p>
<p class="rteindent1">Equation 1: <em>POC<sub>initial </sub></em>= <em>POC<sub>final&nbsp;</sub></em>+ <em>deltaDOC</em> + (<em>O<sub>2,cons </sub></em>/ <em>RQ</em> * <em>t<sub>inc</sub></em> * <em>V<sub>RES</sub></em>)</p>
<p class="rteindent1">&nbsp;</p>
<p class="rteindent1">Equation 2: POC flux = <em>POC<sub>initial</sub></em> / (<em>t<sub>col</sub></em> * <em>A<sub>RES</sub></em>)</p>
<p class="rteindent1">&nbsp;</p>
<p class="rteindent1">Equation 3: <em>R<sub>norm</sub></em> = (<em>O<sub>2,cons</sub></em> / <em>RQ</em>) / <em>[POC]<sub>avg</sub></em></p>
<p>&nbsp;</p>
<p><strong>DAPI staining and cell enumeration on particles</strong></p>
<p>Epifluorescence microscopy images were analyzed using CellProfiler (v4.2.8). Images were converted to grayscale as needed (Relative weight of each channel: Red = 0, Green = 0.8, Blue = 1.0) and images were analyzed sample by sample. If background intensity values were high, an illumination correction was applied to the image using a median filter smoothing method. Cells were identified based on intensity relative to the background intensity which was specific to each sample. The image with the most and least number of cells were removed from analysis and the cell counts for the remaining 10 images were averaged for each sample. Cell concentration in the RESPIRE incubation chamber was back-calculated from cell counts using the area imaged, the area of the filter, the volume of sample filtered, and the volume of the RESPIRE incubation chamber (1.45 L). Cell counts were converted to cell carbon using a carbon conversion factor of 20 fg C cell<sup>-1</sup> (Ducklow, 2000).</p>
Specified by the Principal Investigator(s)
This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability.
CURATION ACTIONS PERFORMED ON DATA
- Loaded BCO-DMO_AT5010_SR1919_2026-05-19.csv, using filename as resource name, with header row 1 and row 2 skipped; set missing value markers to "", "nd", and "NA"
- Output file as 1008909_v1_respire_rates_at5010_sr1919.csv
CURATION ACTIONS PERFORMED ON METADATA
- BCO-DMO's standard metadata entry and text formatting steps were performed. See: https://www.bco-dmo.org/how-to/standard-curation-edits
ISSUES POTENTIALLY IMPACTING REUSE
- N/A
Specified by BCO-DMO Data Managers
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
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Aanderaa oxygen optode (Aanderaa 4831 series)
Aanderaa oxygen optode (Aanderaa 4831 series)
PI Supplied Instrument Name: Aanderaa oxygen optode (Aanderaa 4831 series) PI Supplied Instrument Description:RESPIRE particle collection and incubation systems (custom build) with Aanderaa oxygen optode (Aanderaa 4831 series): Sinking particles were collected and incubated using RESPIRE trap particle collection and incubation systems and oxygen drawdown rates were determined from oxygen measurements using the Aanderaa oxygen optode located within the RESPIRE trap incubation chamber. Instrument Name: Aanderaa 4831 oxygen optode Instrument Short Name:AA optode 4831 Instrument Description: A dissolved oxygen sensor which provides analogue (0-5V) and digital output (RS-232) to third party data loggers, gliders and floats. Measurement based on the ability of selected substances to act as dynamic fluorescence quenchers. The fluorescent indicator is a special platinum porphyrin complex embedded in a gas permeable foil that is exposed to the surrounding water. In this standard model, a black optical isolation coating protects the complex from sunlight and fluorescent particles in the water. This sensing foil is attached to a window providing optical access for the measuring system from inside a watertight housing. The foil is excited by modulated blue light, and the phase of a returned red light is measured. For improved stability the 4831 optode also performs areference phase reading by use of a red LED that does not produce fluorescence in the foil. This model is fitted with a standard sensing foil. By linearizing and temperature compensating, with an incorporated temperature sensor, the absolute O2 concentration can be determined. Accuracy +/- 1.5% or 2uM; precision +/- 0.2 uM.
CTD
CTD
PI Supplied Instrument Name: CTD PI Supplied Instrument Description:RESPIRE traps were filled with 0.2 µm-filtered seawater collected from a CTD cast 2-3 hours prior to deployment. Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Exeter Analytical Elemental Analyzer
Exeter Analytical Elemental Analyzer
PI Supplied Instrument Name: Exeter Analytical Elemental Analyzer PI Supplied Instrument Description:Exeter Analytical Elemental Analyzer (Model: CEC 440HA): GF/F filters were analyzed for CHN on an Exeter Analytical Elemental Analyzer at the Marine Science Institute at UC Santa Barbara. Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
Zeiss Axio Observer 7 Inverted microscope
Zeiss Axio Observer 7 Inverted microscope
PI Supplied Instrument Name: Zeiss Axio Observer 7 Inverted microscope PI Supplied Instrument Description:Zeiss Axio Observer 7 Inverted microscope: DAPI-stained filters were imaged using a Zeiss Axio Observer 7 Inverted microscope at 63X objective. Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Shimadzu TOC Analyzer
Shimadzu TOC Analyzer
PI Supplied Instrument Name: Shimadzu TOC Analyzer PI Supplied Instrument Description:Shimadzu TOC Analyzer: DOC and TOC samples were analyzed via the high temperature combustion method using modified Shimadzu TOC-V or TOC-L analyzers following Halewood et al. (2022). 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/
Cruise: AT50-10
AT50-10
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT50-10
Mak A. Saito
Woods Hole Oceanographic Institution
https://www.rvdata.us/search/cruise/AT50-10
Report describing AT50-10
Cruise: SR1919
SR1919
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR1919
Alyson E. Santoro
University of California-Santa Barbara
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel