http://lod.bco-dmo.org/id/dataset/994607
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
2026-03-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Physiological measurements from an iron incubation experiment using upwelled waters in the California Current System during the PUPCYCLE II cruise in May and June 2023
2026-08-12
publication
2026-08-12
revision
BCO-DMO Linked Data URI
2026-08-12
creation
http://lod.bco-dmo.org/id/dataset/994607
Adrian Marchetti
University of North Carolina at Chapel Hill
principalInvestigator
Natalie Cohen
University of Georgia
principalInvestigator
Astrid Schnetzer
North Carolina State University
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: Speciale, E., Lim, P., Jeong, Y., Cook, C., Cohen, N., McClure, W., Schnetzer, A., Marchetti, A. (2026) Physiological measurements from an iron incubation experiment using upwelled waters in the California Current System during the PUPCYCLE II cruise in May and June 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/994607 [access date]
Physiology from iron incubation experiments PUPCYCLE II Dataset Description: <p>This dataset is one of many generated from an iron incubation experiment conducted as part of the PUPCYCLE II cruise in May and June 2023. The different analyses are listed here, with links to other datasets from this study in the Related Datasets section.</p>
<p>Analyses&nbsp;include:</p>
<ul>
<li><strong>Physiology (this dataset 994607)</strong>
<ul>
<li><strong>Dissolved inorganic nutrients (nitrate, phosphate, silicic acid)</strong></li>
<li><strong>Size-fractionated chlorophyll a</strong></li>
<li><strong>Size-fractionated isotope uptake rates (nitrate and DIC)</strong></li>
<li><strong>Flow cytometry</strong></li>
<li><strong>FlowCAM analysis</strong></li>
<li><strong>FLP experiments for mixotroph cell-specific grazing rates</strong></li>
</ul>
</li>
<li>RNA taxonomy data for normalized reads (dataset 1003525)</li>
<li>Differential expression for +Fe versus DFB treatments at T1 and T2: Pfam
<ul>
<li>Mixotroph Pfam (dataset 1004659)</li>
<li>Diatom Pfam (dataset 1004674)</li>
</ul>
</li>
<li>Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG gene&nbsp;(dataset 1004689)</li>
<li>Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG pathways (this dataset 1004704)</li>
<li>Dissolved iron concentrations (dataset 1004007)</li>
</ul>
<p>See Related Datasets section below for links to above mentioned datasets.</p> Methods and Sampling: <p>Data collection took place on the R/V Sally Ride from May 29th to June 10th, 2023. To simulate upwelling conditions under different iron treatments, an onboard incubation experiment was conducted. Seawater for the incubation experiment was collected within the northern CCS, off the southern coast of Oregon at 43°02'42.7"N, 124°33'07.2"W. The collected seawater was deemed as freshly upwelled water and taken from a depth of 55 meters – which corresponds to a depth slightly below the euphotic zone receiving less than 1% irradiance – using trace-metal clean techniques on May 30th, 2023, 13:30 GMT. The seawater was pumped and homogenized using trace metal clean techniques, then transferred into a total of thirty 20 L low-density polyethylene cubitainers. Three cubitainers were immediately harvested for the initial timepoint (T0). The remaining twenty-seven cubitainers were assigned treatments: nine were unamended (labeled Ctrl), nine were amended with 5 nM FeCl<sub>2</sub> (labeled +Fe), and nine were amended with 200 nM desferrioxamine B, a strong iron chelator that inhibits dissolved iron uptake (labeled DFB). The cubitainers were placed in an on-deck incubator covered with two layers of neutral-density screening to simulate 26% of incident irradiance and supplied with flow-through surface seawater to maintain ambient surface temperature. Three cubitainers from each treatment were harvested for each of the three subsequent timepoints: 48 hours (T1), 168 hours (T2), and 264 hours (T3) after incubation.</p>
<p><strong>Dissolved inorganic nutrients. </strong>Dissolved inorganic nutrient measurements were collected by filtering 30 mL of seawater through a GF/F filter into an acid-rinsed polypropylene scintillation vial. The filtrate was immediately frozen and then sent to Wetland Biogeochemistry Analytic Services at Louisiana State University and analyzed via their OI Analytical Flow Solutions IV auto analyzer for nitrate + nitrite, nitrite, phosphate (PO<sub>4</sub><sup>3-</sup>), and silicic acid (Si(OH)<sub>4</sub>). Detection limits were 0.09 μM for nitrate + nitrite, 0.02 μM for PO<sub>4</sub><sup>3-</sup>, and 0.02 μM for Si(OH)<sub>4</sub>. Nitrate (NO<sub>3</sub><sup>-</sup>) concentrations were derived by subtracting the concentration of nitrite<sup> </sup>from nitrate + nitrite. NO<sub>3</sub><sup>-</sup> concentrations were also used in calculations for NO<sub>3</sub><sup>-</sup> uptake rates.</p>
<p><strong>Size-fractionated chlorophyll a. </strong>Chlorophyll <em>a</em> (chl <em>a</em>) measurements were collected by gravity filtering 250 mL of seawater through 5 μm Isopore membrane filters (47 mm) to collect large cells (≥ 5 μm), then vacuum filtering the remaining seawater onto GF/F (25 mm) filters under 100 mmHg of vacuum pressure to collect small cells (&lt; 5 μm). Filters were then rinsed with filtered seawater and stored at -20℃. Chl <em>a</em> was extracted on the ship using 90% acetone solution at -20℃ for 24 hours, then measured on a 10-AU fluorometer (Turner Designs, San Jose, CA) using the acidification method (Parsons et al., 1984).&nbsp;</p>
<p><strong>Size-fractionated isotope uptake rates. </strong>Isotope uptake rates of dissolved inorganic carbon (DIC) and NO<sub>3</sub><sup>-</sup> were assessed by collecting seawater into 1 L polycarbonate bottles (filled to the top, resulting in a total volume of 1.09 L). Each bottle was immediately spiked with NaH<sup>13</sup>CO<sub>3</sub> and Na<sup>15</sup>NO<sub>3</sub>, with spiking concentrations varying depending on the ambient DIC and NO<sub>3</sub><sup>-</sup> concentrations. The ambient DIC concentrations were estimated at 2000 μM based on literature values (Fassbender et al., 2011), while the NO<sub>3</sub><sup>-</sup> ambient concentrations were estimated using the Submersible Ultraviolet Nitrate Analyzer (SUNA) (Johnson &amp; Coletti, 2002). These estimates resulted in adding 200 μM of <sup>13</sup>C to every sample as well as 2, 2, 0.50, and 0.20 μM of <sup>15</sup>N at T0, T1, T2, and T3 respectively, to achieve approximate additions of 10% of the ambient DIC and NO<sub>3</sub><sup>-</sup> concentrations.</p>
<p>Samples were then placed in the ship incubator for 6 hours, simulated under 25% of incident irradiance. After incubation, the seawater from each bottle was gravity filtered onto 5 μm Isopore membrane filters (47 mm) to collect large cells and vacuum filtered onto pre-combusted (450℃ for 5 hours) GF/F filters to collect small cells. Large cells were then rinsed off the Isopore filter using 0.2 mm filtered seawater and vacuum filtered onto pre-combusted (450℃ for 5 hours) GF/F filters. The standard filtering volume was 1.09 L, but due to accumulation of biomass hindering filtering at the later timepoints, all samples in T2 and T3 had a filtering volume of 0.5 L. Filters were stored in small petri dishes at -20℃ until lab preparation.</p>
<p>To prepare for lab analysis, filters were dried at 60℃ for 24 hours, encapsulated in tin, and pelletized. Pelletized samples were sent to the UC Davis Stable Isotope Facility, where they were analyzed for particulate organic carbon (POC), particulate organic nitrogen (PON), and atom percentages of <sup>13</sup>C and <sup>15</sup>N using an isotope ratio mass spectrometer (EA-IRMS).&nbsp;POC and PON concentrations (μM) were calculated by dividing the mass of POC/PON (μg) by the respective atomic mass of carbon and nitrogen over the volume filtered. Absolute uptake rates (⍴) of DIC and NO<sub>3</sub><sup>- </sup>were calculated using the constant transport model and biomass-normalized uptake rates (<em>V</em>) of DIC and NO<sub>3</sub><sup>-</sup> were calculated using the specific uptake model; these calculations utilize actual dissolved NO<sub>3</sub><sup>- </sup>concentrations (Dugdale and Wilkerson, 1986).</p>
<p><strong>Flow Cytometry. </strong>Flow cytometry was performed on a Guava easyCyte HT flow cytometer live on the cruise. The Guava easyCyte HT was outfitted with a blue 488 nm laser. Gain settings were forward scatter (FSC) 4, side scatter (SSC) 1, green fluorescence 2.95, yellow fluorescence 98.7, and red fluorescence 4. Communities of interest were gated based on community recommendations (Thyssen et al., 2022). <em>Synechococcus</em> were detected based on high yellow fluorescence and low FSC, picoeukaryotes (~1-3 µm) were detected based on medium yellow and red fluorescence, and nanoeukaryotes (~3-20 µm) were detected based on high red fluorescence. Samples for bacteria abundance were preserved with 0.25% glutaraldehyde and frozen at -80 ºC. Samples were then stained SYBR Green I (Thermo Fisher; 10,000x stock) diluted to a final concentration of 1x and measured on the Guava EasyCyte HT flow cytometer.</p>
<p><strong>FlowCAM Analysis. </strong>FlowCAM imaging was performed for T2 samples of the iron incubation experiment based on the protocol provided by Pierce et al. 2023 using a Portable Series FlowCam connected to a peristaltic pump. A 10x FlowCell objective was used on autoimage mode for samples preserved in Lugols. The sets of images produced were analyzed using the Yokogawa Fluid Imaging VisualSpreadsheet software. Any images not containing particles (such as bubbles or blurry images) and/or less than 15 µm were deleted from the dataset. For each sample, the first 300 identifiable diatom cells were counted and categorized based on cell morphology and assigned to taxa at the genus level when possible. Final categories included: <em>Asterionellopsis</em> spp., <em>Chaetoceros</em> spp., <em>Pseudo-nitzschia</em> spp., other centric diatoms, and other pennate diatoms. To calculate concentrations of each diatom taxonomy within each sample (cells/L), the following equation was used:</p>
<p>(# of cells counted * image factor) / volume run&nbsp;through FlowCAM</p>
<p>The image factor was determined by taking the total number of images for the sample (after quality control) divided the number of images counted for all taxonomy. The volume processed through the FlowCAM was 25 mL for all samples.</p>
<p><strong>FLP Experiments for Mixotroph Grazing. </strong>Fluorescently labeled particle (FLP) incubations were performed and analyzed for the iron incubation experiment based on the protocol provided and used by Cook et al. (2025). 500 mL of seawater was pre-screened through 200 µm mesh to remove mesozooplankton. Fluorescently labeled surrogate microspheres (0.5 µm diameter, Fluoresbrite, Polysciences) were spiked into the volume at concentrations of 10^<sup>5</sup> particles mL<sup>-1</sup>. Immediately after surrogate prey addition, a time zero (T<sub>initial</sub>) sample was taken and preserved. For preservation, 10-30 mL were fixed with 4% glutaraldehyde, incubated at 4 ºC for 30 minutes, filtered onto 3 µm polycarbonate filters, mounted using DAPI Vectashield (Vector Laboratories), and frozen at -20 ºC. Incubations were carried out for one hour in a clear plexiglass flow-through incubator with mesh bags emulating <em>in situ </em>light availability. After an hour incubation, another sample (T<sub>final</sub>) was taken and preserved in the same manner as T<sub>initial</sub>.&nbsp;</p>
<p>FLP incubation analysis was performed using an Olympus CKX53 inverted microscope at 400x total magnification. The field-of-view counting method with a calibrated reticle was used. At least 300 chloroplast-containing cells were enumerated on every slide to ensure statistical reliability. Cell specific grazing rate (CSGR, bacteria mixotroph<sup>-1</sup> hr<sup>-1</sup>), was calculated using the following equation:</p>
<p>CSGR = (((C<sub>ingested </sub>/ C<sub>photo</sub>)<sub>Tfinal</sub> - (C<sub>ingested </sub>/ C<sub>photo</sub>)<sub>Tinitial</sub>) / t) * (C<sub>bacteria</sub> / C<sub>FLP</sub>)</p>
<p>C<sub>ingested</sub> is the count of ingested beads divided by the count of all pigmented phototrophic cells (C<sub>photo</sub>), with T<sub>initial</sub> values subtracted from T<sub>final</sub> values to account for non-ingestion adsorption. Values were divided by time of incubation in hours (t) then multiplied by the Bacteria:FLP ratio. C<sub>bacteria</sub> is the natural concentration of heterotrophic bacteria measured via flow cytometry and C<sub>FLP</sub> is the concentration of FLPs spiked into the sample (10<sup>5</sup> particles mL<sup>-1</sup>).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1751805 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1751805
completed
Adrian Marchetti
University of North Carolina at Chapel Hill
919-843-3473
123 South Rd.
Chapel Hill
NC
27514
USA
amarchet@email.unc.edu
pointOfContact
Natalie Cohen
University of Georgia
919-519-8297
10 Ocean Science Circle
Savannah
GA
31411
USA
cohen@uga.edu
pointOfContact
Astrid Schnetzer
North Carolina State University
919-515-7837
2800 Faucette Drive 4148 Jordan Hall
Raleigh
NC
27695
USA
aschnet@ncsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Q_Number
Timepoint
Treatment
Replicate
Timepoint_Hours
ISO_DateTime_UTC
Nitrate
Phosphate
Silicic_Acid
Chla_Large
Chla_Small
PON_Large
PON_Small
pNO3_Large
pNO3_Small
VNO3_Large
VNO3_Small
POC_Large
POC_Small
pDIC_Large
pDIC_Small
VDIC_Large
VDIC_Small
Nanoeuks_R1
Synec_R1
Picoeuks_R1
Nanoeuks_R2
Synec_R2
Picoeuks_R2
Bacteria
Asterionellopsis
Chaetoceros
Pseudonitzschia
Other_Centrics
Other_Pennates
Bacteria_FLP_Ratio
Cell_Specific_Grazing_Rate
Latitude
Longitude
Guava easyCyte HT flow cytometer
Olympus CKX53 inverted microscope
EA-IRMS
Niskin bottle
OI Analytical Flow Solutions IV auto analyzer
Submersible Ultraviolet Nitrate Analyzer (SUNA)
10-AU fluorometer (Turner Designs, San Jose, CA)
Yokogawa Portable Series FlowCam
theme
None, User defined
sample identification
time_point
treatment
replicate
ISO_DateTime_UTC
Nitrate
phosphate
Silicic acid
chlorophyll a
particulate organic nitrogen
pNO3 absolute uptake rate
VNO3 specific nitrate uptake rate (normalized to biomass)
particulate organic Carbon (POC)
pDIC absolute uptake rate
VDIC specific uptake rate
nano eukaryotic phytoplankton
synechococcus abundance
pico_euks
bacterial abundance
diatom abundance
ratio
rate_measurements
latitude
longitude
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Inverted Microscope
Isotope-ratio Mass Spectrometer
Niskin bottle
Nutrient Autoanalyzer
Satlantic Submersible Ultraviolet Nitrate Analyser
Turner Designs Fluorometer 10-AU
Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system
instrument
BCO-DMO Standard Instruments
SR2311
service
Deployment Activity
California Current System
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.
CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans
https://osprey.bco-dmo.org/project/768006
CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans
<p><em>NSF Award Abstract:</em><br />
Upwelling zones are hotspots of photosynthesis that are very dynamic in space and time. Microscopic algae, known as phytoplankton, bloom when deep, nutrient-rich waters are upwelled into sunlit surface layers of the ocean, providing nourishment that supports productive food webs and draws down carbon dioxide (CO2) from the atmosphere to the deep ocean. Photosynthetic microbes in these regions must constantly adapt to changes in their chemical and physical environments. For example, subsurface populations respond to changes in light as they approach the surface. When upwelled waters move offshore, cells sink out of the illuminated zone, establishing seed populations that remain inactive until the next upwelling event. This process is called the upwelling conveyor belt cycle (UCBC). How phytoplankton respond to these changes in environmental conditions and how they may influence their nutrient requirements remains unknown. With future ocean changes predicted to alter seawater chemistry, including ocean acidification and decreased iron availability, some phytoplankton groups may be more vulnerable than others. Accompanying educational activities provide learning experiences to enhance understanding and awareness of marine microbes. The development of a research hub at UNC aims to provide infrastructure and support for scientists and students conducting research on environmental genomics. A laboratory component for an upper-level undergraduate course focused on marine phytoplankton is being developed. Educational outreach activities to broader communities include creation of a lesson plan on phytoplankton in upwelling zones and a virtual research cruise experience for middle-school students, as well as a hands-on lab activity for a local museum focused on marine phytoplankton and the important roles they play in shaping our planet.</p>
<p>The project examines how phytoplankton respond at the molecular and physiological level to the different UCBC stages, which seed populations (i.e., surface versus subsurface) contribute most to phytoplankton blooms during upwelling events of varying intensity, how phytoplankton elemental compositions are altered throughout UCBC stages, and how future predicted ocean conditions will affect the phytoplankton responses to UCBC conditions. This project contains both laboratory and fieldwork. In the laboratory, phytoplankton isolates recently obtained from upwelling regions are exposed to simulated UCBC conditions to examine changes in gene expression, growth and photosynthetic characteristics and elemental composition. Cultures are subjected to both current and future ocean conditions, including reduced iron availability and higher CO2. In the field, research cruises within upwelling regions study the dynamics of natural phytoplankton communities (both surface and subsurface) experiencing upwelling and relaxation and within simulated upwelling incubation experiments. Knowledge of how phytoplankton are affected by UCBC conditions at an integrated molecular, physiological and elemental level under both current and future scenarios is imperative for the proper conservation and management of these critically important ecosystems.</p>
Upwelled Phytoplankton Dynamics
largerWorkCitation
project
eng; USA
biota
oceans
California Current System
-124.552
-124.552
43.045194
43.045194
2023-05-29
2023-06-10
California Upwelling Zone
0
BCO-DMO catalogue of parameters from Physiological measurements from an iron incubation experiment using upwelled waters in the California Current System during the PUPCYCLE II cruise in May and June 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/1004335.rdf
Name: Sample_ID
Units: unitless
Description: <p>Full name of sample indicating timepoint, treatment, and replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004336.rdf
Name: Q_Number
Units: unitless
Description: <p>Q number identification for each sample (used for sequences)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004337.rdf
Name: Timepoint
Units: unitless
Description: <p>Timepoint identification (T0, T1, T2, or T3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004338.rdf
Name: Treatment
Units: unitless
Description: <p>Treatment identification (Ctrl, +Fe, or DFB)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004339.rdf
Name: Replicate
Units: unitless
Description: <p>Replicate identification (A, B, or C)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004340.rdf
Name: Timepoint_Hours
Units: hours
Description: <p>Measured time at which each sample was collected during experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004341.rdf
Name: ISO_DateTime_UTC
Units: datetime
Description: <p>Month, day, year and time at which each sample was collected in GMT</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004343.rdf
Name: Nitrate
Units: micromolar (uM)
Description: <p>Dissolved nutrient concentration of nitrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004344.rdf
Name: Phosphate
Units: micromolar (uM)
Description: <p>Dissolved nutrient concentration of phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004345.rdf
Name: Silicic_Acid
Units: micromolar (uM)
Description: <p>Dissolved nutrient concentration of silicic acid</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004346.rdf
Name: Chla_Large
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll a concentration of large (>= 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004347.rdf
Name: Chla_Small
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll a concentration of small (< 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004348.rdf
Name: PON_Large
Units: micromolar (uM)
Description: <p>Particulate organic nitrogen concentration of large (>= 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004349.rdf
Name: PON_Small
Units: micromolar (uM)
Description: <p>Particulate organic nitrogen concentration of small ( < 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004350.rdf
Name: pNO3_Large
Units: micromoles per liter per hour (umol/ (L*hr))
Description: <p>Absolute uptake rate of nitrate from the large (>= 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004351.rdf
Name: pNO3_Small
Units: micromoles per liter per hour (umol/ (L*hr))
Description: <p>Absolute uptake rate of nitrate from the small (< 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004352.rdf
Name: VNO3_Large
Units: per hour (1/hr)
Description: <p>Biomass-normalized uptake rate of nitrate from the large (>= 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004353.rdf
Name: VNO3_Small
Units: per hour (1/hr)
Description: <p>Biomass-normalized uptake rate of nitrate from the small (< 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004354.rdf
Name: POC_Large
Units: micromolar (uM)
Description: <p>Particulate organic carbon concentration of large (>= 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004355.rdf
Name: POC_Small
Units: micromolar (uM)
Description: <p>Particulate organic carbon concentration of small (< 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004356.rdf
Name: pDIC_Large
Units: micromoles per liter per hour (umol/ (L*hr))
Description: <p>Absolute uptake rate of dissolved inorganic carbon (DIC) from the large (>= 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004357.rdf
Name: pDIC_Small
Units: micromoles per liter per hour (umol/ (L*hr))
Description: <p>Absolute uptake rate of dissolved inorganic carbon (DIC) from the small (< 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004358.rdf
Name: VDIC_Large
Units: per hour (1/hr)
Description: <p>Biomass-normalized uptake rate of dissolved inorganic carbon (DIC) from the large (>= 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004359.rdf
Name: VDIC_Small
Units: per hour (1/hr)
Description: <p>Biomass-normalized uptake rate of dissolved inorganic carbon (DIC) from the small (< 5 microns) size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004360.rdf
Name: Nanoeuks_R1
Units: cells per milliliter (cells/mL)
Description: <p>Nanoeukaryote concentration of first replicate using flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004361.rdf
Name: Synec_R1
Units: cells per milliliter (cells/mL)
Description: <p>Synechococcus concentration of first replicate using flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004362.rdf
Name: Picoeuks_R1
Units: cells per milliliter (cells/mL)
Description: <p>Picoeukaryote concentration of first replicate using flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004363.rdf
Name: Nanoeuks_R2
Units: cells per milliliter (cells/mL)
Description: <p>Nanoeukaryote concentration of second replicate using flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004364.rdf
Name: Synec_R2
Units: cells per milliliter (cells/mL)
Description: <p>Synechococcus concentration of second replicate using flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004365.rdf
Name: Picoeuks_R2
Units: cells per milliliter (cells/mL)
Description: <p>Picoeukaryote concentration of second replicate using flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004366.rdf
Name: Bacteria
Units: cells per milliliter (cells/mL)
Description: <p>Bacteria concentration using flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004367.rdf
Name: Asterionellopsis
Units: cells per liter (cells/L)
Description: <p>Asterionellopsis concentration from FlowCAM imaging</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004368.rdf
Name: Chaetoceros
Units: cells per liter (cells/L)
Description: <p>Chaetoceros concentration from FlowCAM imaging</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004369.rdf
Name: Pseudonitzschia
Units: cells per liter (cells/L)
Description: <p>Pseudo-nitzschia concentration from FlowCAM imaging</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004370.rdf
Name: Other_Centrics
Units: cells per liter (cells/L)
Description: <p>Other unidentified centric diatom concentrations from FlowCAM imaging</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004371.rdf
Name: Other_Pennates
Units: cells per liter (cells/L)
Description: <p>Other unidentified pennate diatom concentrations from FlowCAM imaging</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004372.rdf
Name: Bacteria_FLP_Ratio
Units: unitless
Description: <p>Bacteria concentration (based on flow cytometry) to fluorescently labelled particle concentration (always 10^5 particles/mL) ratio</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004373.rdf
Name: Cell_Specific_Grazing_Rate
Units: bacteria cells per hour (bacteria cells/hr)
Description: <p>Cell specific grazing rates of mixotrophs calculated using FLP incubation results</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004941.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling station</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004943.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling station</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
7317
https://datadocs.bco-dmo.org/file/nGE8o5XiGARNE4/994607_v1_physiology_pupcycle2.csv
994607_v1_physiology_pupcycle2.csv
Physiological measurements from an iron incubation experiment using upwelled waters sampled in the California Current System (CCS) during the PUPCYCLE II cruise in 2023. Primary data file for dataset ID 994607, version 1
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https://osprey.bco-dmo.org/dataset/994607/data/download
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<p>Data collection took place on the R/V Sally Ride from May 29th to June 10th, 2023. To simulate upwelling conditions under different iron treatments, an onboard incubation experiment was conducted. Seawater for the incubation experiment was collected within the northern CCS, off the southern coast of Oregon at 43°02'42.7"N, 124°33'07.2"W. The collected seawater was deemed as freshly upwelled water and taken from a depth of 55 meters – which corresponds to a depth slightly below the euphotic zone receiving less than 1% irradiance – using trace-metal clean techniques on May 30th, 2023, 13:30 GMT. The seawater was pumped and homogenized using trace metal clean techniques, then transferred into a total of thirty 20 L low-density polyethylene cubitainers. Three cubitainers were immediately harvested for the initial timepoint (T0). The remaining twenty-seven cubitainers were assigned treatments: nine were unamended (labeled Ctrl), nine were amended with 5 nM FeCl<sub>2</sub> (labeled +Fe), and nine were amended with 200 nM desferrioxamine B, a strong iron chelator that inhibits dissolved iron uptake (labeled DFB). The cubitainers were placed in an on-deck incubator covered with two layers of neutral-density screening to simulate 26% of incident irradiance and supplied with flow-through surface seawater to maintain ambient surface temperature. Three cubitainers from each treatment were harvested for each of the three subsequent timepoints: 48 hours (T1), 168 hours (T2), and 264 hours (T3) after incubation.</p>
<p><strong>Dissolved inorganic nutrients. </strong>Dissolved inorganic nutrient measurements were collected by filtering 30 mL of seawater through a GF/F filter into an acid-rinsed polypropylene scintillation vial. The filtrate was immediately frozen and then sent to Wetland Biogeochemistry Analytic Services at Louisiana State University and analyzed via their OI Analytical Flow Solutions IV auto analyzer for nitrate + nitrite, nitrite, phosphate (PO<sub>4</sub><sup>3-</sup>), and silicic acid (Si(OH)<sub>4</sub>). Detection limits were 0.09 μM for nitrate + nitrite, 0.02 μM for PO<sub>4</sub><sup>3-</sup>, and 0.02 μM for Si(OH)<sub>4</sub>. Nitrate (NO<sub>3</sub><sup>-</sup>) concentrations were derived by subtracting the concentration of nitrite<sup> </sup>from nitrate + nitrite. NO<sub>3</sub><sup>-</sup> concentrations were also used in calculations for NO<sub>3</sub><sup>-</sup> uptake rates.</p>
<p><strong>Size-fractionated chlorophyll a. </strong>Chlorophyll <em>a</em> (chl <em>a</em>) measurements were collected by gravity filtering 250 mL of seawater through 5 μm Isopore membrane filters (47 mm) to collect large cells (≥ 5 μm), then vacuum filtering the remaining seawater onto GF/F (25 mm) filters under 100 mmHg of vacuum pressure to collect small cells (&lt; 5 μm). Filters were then rinsed with filtered seawater and stored at -20℃. Chl <em>a</em> was extracted on the ship using 90% acetone solution at -20℃ for 24 hours, then measured on a 10-AU fluorometer (Turner Designs, San Jose, CA) using the acidification method (Parsons et al., 1984).&nbsp;</p>
<p><strong>Size-fractionated isotope uptake rates. </strong>Isotope uptake rates of dissolved inorganic carbon (DIC) and NO<sub>3</sub><sup>-</sup> were assessed by collecting seawater into 1 L polycarbonate bottles (filled to the top, resulting in a total volume of 1.09 L). Each bottle was immediately spiked with NaH<sup>13</sup>CO<sub>3</sub> and Na<sup>15</sup>NO<sub>3</sub>, with spiking concentrations varying depending on the ambient DIC and NO<sub>3</sub><sup>-</sup> concentrations. The ambient DIC concentrations were estimated at 2000 μM based on literature values (Fassbender et al., 2011), while the NO<sub>3</sub><sup>-</sup> ambient concentrations were estimated using the Submersible Ultraviolet Nitrate Analyzer (SUNA) (Johnson &amp; Coletti, 2002). These estimates resulted in adding 200 μM of <sup>13</sup>C to every sample as well as 2, 2, 0.50, and 0.20 μM of <sup>15</sup>N at T0, T1, T2, and T3 respectively, to achieve approximate additions of 10% of the ambient DIC and NO<sub>3</sub><sup>-</sup> concentrations.</p>
<p>Samples were then placed in the ship incubator for 6 hours, simulated under 25% of incident irradiance. After incubation, the seawater from each bottle was gravity filtered onto 5 μm Isopore membrane filters (47 mm) to collect large cells and vacuum filtered onto pre-combusted (450℃ for 5 hours) GF/F filters to collect small cells. Large cells were then rinsed off the Isopore filter using 0.2 mm filtered seawater and vacuum filtered onto pre-combusted (450℃ for 5 hours) GF/F filters. The standard filtering volume was 1.09 L, but due to accumulation of biomass hindering filtering at the later timepoints, all samples in T2 and T3 had a filtering volume of 0.5 L. Filters were stored in small petri dishes at -20℃ until lab preparation.</p>
<p>To prepare for lab analysis, filters were dried at 60℃ for 24 hours, encapsulated in tin, and pelletized. Pelletized samples were sent to the UC Davis Stable Isotope Facility, where they were analyzed for particulate organic carbon (POC), particulate organic nitrogen (PON), and atom percentages of <sup>13</sup>C and <sup>15</sup>N using an isotope ratio mass spectrometer (EA-IRMS).&nbsp;POC and PON concentrations (μM) were calculated by dividing the mass of POC/PON (μg) by the respective atomic mass of carbon and nitrogen over the volume filtered. Absolute uptake rates (⍴) of DIC and NO<sub>3</sub><sup>- </sup>were calculated using the constant transport model and biomass-normalized uptake rates (<em>V</em>) of DIC and NO<sub>3</sub><sup>-</sup> were calculated using the specific uptake model; these calculations utilize actual dissolved NO<sub>3</sub><sup>- </sup>concentrations (Dugdale and Wilkerson, 1986).</p>
<p><strong>Flow Cytometry. </strong>Flow cytometry was performed on a Guava easyCyte HT flow cytometer live on the cruise. The Guava easyCyte HT was outfitted with a blue 488 nm laser. Gain settings were forward scatter (FSC) 4, side scatter (SSC) 1, green fluorescence 2.95, yellow fluorescence 98.7, and red fluorescence 4. Communities of interest were gated based on community recommendations (Thyssen et al., 2022). <em>Synechococcus</em> were detected based on high yellow fluorescence and low FSC, picoeukaryotes (~1-3 µm) were detected based on medium yellow and red fluorescence, and nanoeukaryotes (~3-20 µm) were detected based on high red fluorescence. Samples for bacteria abundance were preserved with 0.25% glutaraldehyde and frozen at -80 ºC. Samples were then stained SYBR Green I (Thermo Fisher; 10,000x stock) diluted to a final concentration of 1x and measured on the Guava EasyCyte HT flow cytometer.</p>
<p><strong>FlowCAM Analysis. </strong>FlowCAM imaging was performed for T2 samples of the iron incubation experiment based on the protocol provided by Pierce et al. 2023 using a Portable Series FlowCam connected to a peristaltic pump. A 10x FlowCell objective was used on autoimage mode for samples preserved in Lugols. The sets of images produced were analyzed using the Yokogawa Fluid Imaging VisualSpreadsheet software. Any images not containing particles (such as bubbles or blurry images) and/or less than 15 µm were deleted from the dataset. For each sample, the first 300 identifiable diatom cells were counted and categorized based on cell morphology and assigned to taxa at the genus level when possible. Final categories included: <em>Asterionellopsis</em> spp., <em>Chaetoceros</em> spp., <em>Pseudo-nitzschia</em> spp., other centric diatoms, and other pennate diatoms. To calculate concentrations of each diatom taxonomy within each sample (cells/L), the following equation was used:</p>
<p>(# of cells counted * image factor) / volume run&nbsp;through FlowCAM</p>
<p>The image factor was determined by taking the total number of images for the sample (after quality control) divided the number of images counted for all taxonomy. The volume processed through the FlowCAM was 25 mL for all samples.</p>
<p><strong>FLP Experiments for Mixotroph Grazing. </strong>Fluorescently labeled particle (FLP) incubations were performed and analyzed for the iron incubation experiment based on the protocol provided and used by Cook et al. (2025). 500 mL of seawater was pre-screened through 200 µm mesh to remove mesozooplankton. Fluorescently labeled surrogate microspheres (0.5 µm diameter, Fluoresbrite, Polysciences) were spiked into the volume at concentrations of 10^<sup>5</sup> particles mL<sup>-1</sup>. Immediately after surrogate prey addition, a time zero (T<sub>initial</sub>) sample was taken and preserved. For preservation, 10-30 mL were fixed with 4% glutaraldehyde, incubated at 4 ºC for 30 minutes, filtered onto 3 µm polycarbonate filters, mounted using DAPI Vectashield (Vector Laboratories), and frozen at -20 ºC. Incubations were carried out for one hour in a clear plexiglass flow-through incubator with mesh bags emulating <em>in situ </em>light availability. After an hour incubation, another sample (T<sub>final</sub>) was taken and preserved in the same manner as T<sub>initial</sub>.&nbsp;</p>
<p>FLP incubation analysis was performed using an Olympus CKX53 inverted microscope at 400x total magnification. The field-of-view counting method with a calibrated reticle was used. At least 300 chloroplast-containing cells were enumerated on every slide to ensure statistical reliability. Cell specific grazing rate (CSGR, bacteria mixotroph<sup>-1</sup> hr<sup>-1</sup>), was calculated using the following equation:</p>
<p>CSGR = (((C<sub>ingested </sub>/ C<sub>photo</sub>)<sub>Tfinal</sub> - (C<sub>ingested </sub>/ C<sub>photo</sub>)<sub>Tinitial</sub>) / t) * (C<sub>bacteria</sub> / C<sub>FLP</sub>)</p>
<p>C<sub>ingested</sub> is the count of ingested beads divided by the count of all pigmented phototrophic cells (C<sub>photo</sub>), with T<sub>initial</sub> values subtracted from T<sub>final</sub> values to account for non-ingestion adsorption. Values were divided by time of incubation in hours (t) then multiplied by the Bacteria:FLP ratio. C<sub>bacteria</sub> is the natural concentration of heterotrophic bacteria measured via flow cytometry and C<sub>FLP</sub> is the concentration of FLPs spiked into the sample (10<sup>5</sup> particles mL<sup>-1</sup>).&nbsp;</p>
Specified by the Principal Investigator(s)
<p>The Yokogawa Fluid Imaging VisualSpreadsheet software was used to analyze FlowCAM samples. Excel and R v4.3.2 were used to input sample information and calculations.&nbsp;</p>
Specified by the Principal Investigator(s)
CURATION ACTIONS PERFORMED ON DATA
- Imported source file "BCO_DMO_PUPCYCLEII_Physiology.csv" with NA as missing data identifier replaced with empty cells.
- Converted the Datetime column into ISO 8601 DateTime format
- Added columns for latitude and longitude of sampling station
- Set data types as string for the first 5 columns, set time point hours as integer, date as datetime, and all others as numeric
- Exported the final file as "994607_v1_physiology_pupcycle2.csv"
CURATION ACTIONS PERFORMED ON METADATA
- Added summary for the broader study showing connections between this dataset and related datasets
- Changed in-line citations to have format of (author, year) replacing number references.
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
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
Guava easyCyte HT flow cytometer
Guava easyCyte HT flow cytometer
PI Supplied Instrument Name: Guava easyCyte HT flow cytometer PI Supplied Instrument Description:During the cruise, flow cytometry was performed on a Guava easyCyte HT flow cytometer outfitted with a blue 488 nm laser. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. Description from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Olympus CKX53 inverted microscope
Olympus CKX53 inverted microscope
PI Supplied Instrument Name: Olympus CKX53 inverted microscope PI Supplied Instrument Description:FLP incubation analysis was performed using an Olympus CKX53 inverted microscope at 400x total magnification. The field-of-view counting method with a calibrated reticle was used. 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/
EA-IRMS
EA-IRMS
PI Supplied Instrument Name: EA-IRMS PI Supplied Instrument Description:Pelletized samples were sent to the UC Davis Stable Isotope Facility, where they were analyzed for particulate organic carbon (POC), particulate organic nitrogen (PON), and atom percentages of 13C and 15N using an isotope ratio mass spectrometer (EA-IRMS).
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/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Freshly upwelled seawater was collected from approximately 55 meters depth using Niskin bottles Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
OI Analytical Flow Solutions IV auto analyzer
OI Analytical Flow Solutions IV auto analyzer
PI Supplied Instrument Name: OI Analytical Flow Solutions IV auto analyzer PI Supplied Instrument Description:The filtrate was immediately frozen and then sent to Wetland Biogeochemistry Analytic Services at Louisiana State University and analyzed via their OI Analytical Flow Solutions IV auto analyzer for nitrate + nitrite, nitrite, phosphate (PO43-), and silicic acid (Si(OH)4). Instrument Name: Nutrient Autoanalyzer Instrument Short Name:Nutrient Autoanalyzer Instrument Description: Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
Submersible Ultraviolet Nitrate Analyzer (SUNA)
Submersible Ultraviolet Nitrate Analyzer (SUNA)
PI Supplied Instrument Name: Submersible Ultraviolet Nitrate Analyzer (SUNA) PI Supplied Instrument Description:The NO3- ambient concentrations were estimated using the Submersible Ultraviolet Nitrate Analyzer (SUNA). Instrument Name: Satlantic Submersible Ultraviolet Nitrate Analyser Instrument Short Name:SUNA Instrument Description: The Submersible Ultraviolet Nitrate Analyser (SUNA) uses ultraviolet absorption spectroscopy to measure in-situ dissolved nitrate. It is a chemical-free method that allows real-time and continuous nitrate concentration measurements in a variety of environments. It has a 1 cm path length, 190 - 370 nm wavelength range and a depth rating of 100 m.
10-AU fluorometer (Turner Designs, San Jose, CA)
10-AU fluorometer (Turner Designs, San Jose, CA)
PI Supplied Instrument Name: 10-AU fluorometer (Turner Designs, San Jose, CA) PI Supplied Instrument Description:Chl a was extracted on the ship using 90% acetone solution at -20℃ for 24 hours, then measured on a 10-AU fluorometer (Turner Designs, San Jose, CA) using the acidification method. Instrument Name: Turner Designs Fluorometer 10-AU Instrument Short Name:Turner Fluorometer 10-AU Instrument Description: The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/
Yokogawa Portable Series FlowCam
Yokogawa Portable Series FlowCam
PI Supplied Instrument Name: Yokogawa Portable Series FlowCam PI Supplied Instrument Description:FlowCAM imaging was performed for T2 samples of the iron incubation experiment using a Portable Series FlowCam connected to a peristaltic pump. Instrument Name: Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system Instrument Short Name:FlowCAM Instrument Description: Imaging cytometers are automated instruments that quantify properties of single cells, one cell at a time. They combine some aspects of flow cytometry with particle imaging capabilities in an automated device to classify small particles, including phytoplankton and protozoa. They can measure a variety of properties: cell size, cell granularity, cell aspect ratio, equivalent spherical diameter (ESD) and area-based diameter (ABD) [to estimate bio-volume, which is used to estimate cell carbon biomass]. Particle images are digitally recorded and sorted into different classes according to training libraries using a support vector machine (supervised learning methods). The instruments particle-size is calibrated using different sizes of latex beads.
The FlowCam VS series are automated imaging-in-flow instruments that generate high-resolution digital images for measuring size and shape of microscopic particles. The sample introduced in the system is attracted by a peristaltic or a syringe pump into a flow cell (or flow chamber) with known dimensions, located in front of a microscope objective which is connected to a camera video. The benchtop model is ideally suited to a typical laboratory environment with applications in oceanographic research, municipal water, biopharmaceutical formulations, chemicals, oil and gas, biofuels, and many other markets. FlowCam VS is available in four models, from the imaging-only VS-I (i.e. without excitation wavelength or fluorescence emission wavelengths) to the top-of-the-line VS-IV with two channels of fluorescence measurement and scatter triggering capabilities. The instrument can measure particles between 2µm and 2mm; can analyse in vivo or fixed samples; has a flow rate between 0.005 ml/minute and 250 ml/minute (dependant upon magnification, flow cell depth, camera frame rate, efficiency desired, etc.). It can produce either 8-bit Grayscale (Monochrome Camera) or 24-bit Colour (Colour Camera) images, depending on the model.
Cruise: SR2311
SR2311
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR2311
Adrian Marchetti
University of North Carolina at Chapel Hill
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel