http://lod.bco-dmo.org/id/dataset/887787
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
2023-01-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
FlowCAM enumeration of phytoplankton classes from samples taken during R/V Endeavor cruise EN616 in July 2018
2023-01-27
publication
2023-01-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-03-09
publication
https://doi.org/10.26008/1912/bco-dmo.887787.1
William M. Balch
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Stephen D. Archer
Bigelow Laboratory for Ocean Sciences
principalInvestigator
David T. Drapeau
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Jelena Godrijan
Bigelow Laboratory for Ocean Sciences
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: Balch, W. M., Archer, S. D., Drapeau, D. T., Godrijan, J. (2023) FlowCAM enumeration of phytoplankton classes from samples taken during R/V Endeavor cruise EN616 in July 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-01-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.887787.1 [access date]
Dataset Description: <p>This dataset is part of a larger study with the following goals:</p>
<ul>
<li><strong>Goal #1</strong>: measure the mixotrophic uptake and assimilation of 14C-acetate, 14C-mannitol and 14C-glycerol as a carbon source by natural assemblages of coccolithophores and compare it to their autotrophic uptake and assimilation of DIC. These three organics were chosen due to their high potential for significant osmotrophy by coccolithophores as seen in previous culture studies (Godrijan et al. (2020) and BCO-DMO dataset:&nbsp;<a href="https://www.bco-dmo.org/dataset/858771" style="margin: 0px; padding: 0px; border: 0px; font: inherit; vertical-align: baseline; text-decoration-line: none; color: rgb(0, 102, 153);">https://www.bco-dmo.org/dataset/858771</a>).&nbsp;The design of these experiments used radiochemical and single cell/flow cytometer methods to distinguish osmotrophy of coccolithophores from that by other naturally-occurring microalgae.</li>
<li><strong>Goal #2</strong>: test for the fixation of 14C-labeled organics into both POC and PIC fractions in natural populations of coccolithophores, in order to examine the potential role of coccolithophore osmotrophy in the&nbsp;biological carbon pump and alkalinity carbon pump paradigms.</li>
</ul> Methods and Sampling: <p><strong>At sea collections</strong><br />
Nine stations were visited during R/V Endeavor&nbsp;EN616 cruise in the northwest Atlantic.&nbsp;&nbsp;<br />
At eight depths, three 10L Niskin samples were taken for discrete measurements of:</p>
<p>1. Chlorophyll, nutrients including nitrate, nitrite, ammonium, phosphate, and silicate&nbsp;<br />
2.&nbsp;Particulate organic carbon (POC) plus particulate organic nitrogen (PON)&nbsp;<br />
3.&nbsp;Particulate inorganic carbon (PIC)<br />
4.&nbsp;Biogenic silica<br />
5. Birefringence counts of coccolithophores (done ashore)&nbsp;<br />
6. Shipboard Yokogawa Fluid Imaging Technologies FlowCam imaging cytometer, in order to enumerate the major microalgal classes and estimate the particle size distribution function</p>
<p>Measurements 1 to 4 are part of BCO-DMO dataset 837074 (See&nbsp;<a href="https://www.bco-dmo.org/dataset/837074" style="margin: 0px; padding: 0px; border: 0px; font: inherit; vertical-align: baseline; text-decoration-line: none; color: rgb(0, 102, 153);">https://www.bco-dmo.org/dataset/837074</a>, and the Related Datasets section below).<br />
Measurement 5 of birefringence counts data is BCO-DMO dataset 887863 (See&nbsp;<a href="https://www.bco-dmo.org/dataset/887863" style="margin: 0px; padding: 0px; border: 0px; font: inherit; vertical-align: baseline; text-decoration-line: none; color: rgb(0, 102, 153);">https://www.bco-dmo.org/dataset/887863</a>, and the Related Datasets section below).<br />
Measurement 6 is flow cytometer data presented in <strong>this </strong>dataset.&nbsp;</p>
<p><strong>FlowCAM enumeration of various phytoplankton classes</strong><br />
A Yokogowa FlowCAM imaging cytometer was used to enumerate different classes of phytoplankton.&nbsp; The instrument was keyed on particle backscattering and fluorescence properties.&nbsp; Samples were first filtered through 100um Nitex mesh to make sure the 100um diameter flow chamber did not clog.&nbsp; The instrument was run with a 10X objective in order to reliably count particles bigger than 4-5um diameter. Samples were processed according to Poulton and Martin (2010).</p>
<p>Concentrations (per mL), percent contribution with respect to total particles, and biomass are presented.&nbsp; Carbon biomass was determined&nbsp;based on the Menden-Deuer &amp; Lessard (2000) method.&nbsp;&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1635748 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1635748
completed
William M. Balch
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive
East Boothbay
ME
04544
USA
bbalch@bigelow.org
pointOfContact
Stephen D. Archer
Bigelow Laboratory for Ocean Sciences
207-350-0791
60 Bigelow Drive
East Boothbay
ME
04554
USA
sarcher@bigelow.org
pointOfContact
David T. Drapeau
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive
East Boothbay
ME
04544
USA
ddrapeau@bigelow.org
pointOfContact
Jelena Godrijan
Bigelow Laboratory for Ocean Sciences
+385-1-456-1148
Ruder Boskovic Institute Bijenicka cesta 54
10000 Zagreb
Croatia
jelena.godrijan@irb.hr
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Station
Type
Longitude
Latitude
Depth
ISO_DateTime_UTC
Gear
Balch_Sample_num
ParticleSizeDistFunc_Slope_5um
StdErr_of_PDFslope
Y_int_of_PDFslope
R2_of_PDFslope
F_statistic_of_PDFslope
Total
Small_0_to_4um
Round_4_to_12um
Ovoid_4_to_12um
Dinoflagellates
Ciliates
Diatoms
Silicoflagellates
Other_Cells
Pct_Small_0_to_4um
Pct_Round_4_to_12um
Pct_Ovoid_4_to_12um
Pct_Dinoflagellates
Pct_Ciliates
Pct_Diatoms
Pct_Silicoflagellates
Pct_Other_Cells
Total_C_biomass
Small_C_biomass
Round_C_biomass
Ovoid_C_biomass
Dinoflagellates_C_biomass
Ciliates_C_biomass
Diatoms_C_biomass
Silicoflagellates_C_biomass
Other_Cells_C_biomass
Yokogowa FlowCAM imaging cytometer
theme
None, User defined
Cruise identfier
station
sample type
longitude
latitude
depth
ISO_DateTime_UTC
sampling_method
sample identification
No BCO-DMO term
standard error
correlation coefficient
F statistic
cell_concentration
relative abundance
biomass_C
featureType
BCO-DMO Standard Parameters
Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system
instrument
BCO-DMO Standard Instruments
EN616
service
Deployment Activity
Gulf of Maine and North West Atlantic
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.
Coccolithophore Mixotrophy
https://osprey.bco-dmo.org/project/648016
Coccolithophore Mixotrophy
<p><strong>NSF Award Abstract</strong><br />
Coccolithophores are single-cell algae that are covered with limestone (calcite) plates called coccoliths. They may make up most of the phytoplankton biomass in the oceans. Coccolithophores are generally considered to be autotrophs, meaning that they use photosynthesis to fix carbon into both soft plant tissue and hard minerogenic calcite, using sunlight as an energy source ("autotrophic"). However, there is an increasing body of evidence that coccolithophores are "mixotrophic", meaning that they can fix carbon from photosynthesis as well as grow in darkness by engulfing small organic particles plus taking up other simple carbon molecules from seawater. The extent to which Coccolithophores engage in mixotrophy can influence the transfer of carbon into the deep sea. This work is fundamentally directed at quantifying coccolithophore mixotrophy -- the ability to use dissolved and reduce carbon compounds for energy -- using lab and field experiments plus clarifying its relevance to ocean biology and chemistry. This work will generate broader impacts in three areas: 1) Undergraduate training: Two REU undergraduates will be trained during the project. The student in the second year will participate in the research cruise. 2) Café Scientifique program: This work will be presented in Bigelow Laboratory’s Café Scientifique program. These are free public gatherings where the public is invited to join in a conversation about the latest ideas and issues in ocean science and technology. 3) Digital E-Book: We propose to make a digital E-book to specifically highlight and explain mixotrophy within coccolithophores. Images of mixotrophic coccolithophores would be the primary visual elements of the book. The E-book will be publicly available and distributed to our educational affiliate, Colby College. The goal of the book is to further communicate the intricacies of the microbial world, food web dynamics, plus their relationship to the global carbon cycle, to inspire interest, education, and curiosity about these amazing life forms.</p>
<p>Coccolithophores can significantly affect the draw-down of atmospheric CO2 and they can transfer CO2 from the surface ocean and sequester it in the deep sea via two carbon pump mechanisms: (1) The "alkalinity pump" (also known as the calcium carbonate pump), where coccolithophores in the surface ocean take up dissolved inorganic carbon (DIC; primarily a form called bicarbonate, a major constituent of ocean alkalinity). They convert half to CO2, which is either fixed as plant biomass or released as the gas, and half is synthesized into their mineral coccoliths. Thus, coccolithophore calcification can actually increase surface CO2 on short time scales (i.e. weeks). However, over months to years, coccoliths sink below thousands of meters, where they dissolve and release bicarbonate back into deep water. Thus, sinking coccoliths essentially "pump" bicarbonate alkalinity from surface to deep waters, where that carbon remains isolated in the abyssal depths for thousands of years. (2) The "biological pump", where the ballasting effect of the dense limestone coccoliths speeds the sinking of organic, soft-tissue debris (particulate organic carbon or POC), essentially "pumping" this soft carbon tissue to depth. The biological pump ultimately decreases surface CO<sub>2</sub>. The soft-tissue and alkalinity pumps reinforce each other in maintaining a vertical gradient in DIC (more down deep than at the surface) but they oppose each other in terms of the air-sea exchange of CO<sub>2</sub>. Thus, the net effect of coccolithophores on atmospheric CO2 depends on the balance of their CO<sub>2</sub>-raising effect associated with the alkalinity pump and their CO2-lowering effect associated with the soft-tissue biological pump. It is virtually always assumed that coccolith particulate inorganic carbon (PIC) originates exclusively from dissolved inorganic carbon (DIC, as bicarbonate), not dissolved organic carbon (DOC). The goal of this proposal is to describe a) the potential uptake and assimilation of an array of DOC compounds by coccolithophores, b) the rates of uptake, and potential incorporation of DOC by coccolithophores into PIC coccoliths, which, if true, would represent a major shift in the alkalinity pump paradigm. This work is fundamentally directed at quantifying coccolithophore mixotrophy using lab and field experiments plus clarifying its relevance to ocean biology and chemistry. There have been a number of technological advances to address this issue, all of which will be applied in this work. The investigators will: (a) screen coccolithophore cultures for the uptake and assimilation of a large array of DOC molecules, (b) perform tracer experiments with specific DOC molecules in order to examine uptake at environmentally-realistic concentrations, (c) measure fixation of DOC into organic tissue, separately from that fixed into PIC coccoliths, (d) separate coccolithophores from other phytoplankton and bacteria using flow cytometry and e) distinguish the modes of nutrition in these sorted coccolithophore cells. This work will fundamentally advance the state of knowledge of coccolithophore mixotrophy in the sea and address the balance of carbon that coccolithophores derived from autotrophic versus heterotrophic sources.</p>
Cocco-Mix
largerWorkCitation
project
eng; USA
biota
oceans
Gulf of Maine and North West Atlantic
-72.92708
-66.51748
36.98572
43.71835
2018-07-05
2018-07-13
Partially lab-based, with field sites in Gulf of Maine and NW Atlantic between the Gulf of Maine and Bermuda
0
BCO-DMO catalogue of parameters from FlowCAM enumeration of phytoplankton classes from samples taken during R/V Endeavor cruise EN616 in July 2018
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/890787.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/890788.rdf
Name: Station
Units: unitless
Description: <p>Station number for EN616 cruise for water sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/890789.rdf
Name: Type
Units: unitless
Description: <p>Type of sample. B = discrete bottle sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/890790.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of water sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/890791.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of water sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/890792.rdf
Name: Depth
Units: meters
Description: <p>Depth of water sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/890793.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/890794.rdf
Name: Gear
Units: unitless
Description: <p>Gear used to collect the water and coccolithophore samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/890795.rdf
Name: Balch_Sample_num
Units: unitless
Description: <p>Consecutive unique numbers assigned to each water sample for all analyses done for a given station</p>
http://lod.bco-dmo.org/id/dataset-parameter/890796.rdf
Name: ParticleSizeDistFunc_Slope_5um
Units: unitless
Description: <p>PDF Slope logABD>0.75 (only particles >5um); Particle size Distribution Function slope of the plot of log cell abundance (particles per mL) versus Area Based Diameter (micrometers) calculated for particles of >= 5 micrometers diameter using a Yokogowa FlowCAM. Area Based Diameter (ABD) is defined as the diameter measured by the number of grey scale pixels of the binary image converted to a circle with the same number of pixels.</p>
http://lod.bco-dmo.org/id/dataset-parameter/890797.rdf
Name: StdErr_of_PDFslope
Units: unitless
Description: <p>Std Err of PDF Slope logABD>0.75 (for particles >5um); Standard error of the above particle size distribution slope for only particles of 5 micrometers diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/890798.rdf
Name: Y_int_of_PDFslope
Units: unitless
Description: <p>Y-int of PDF Slope logABD>0.75 (only particles >5um); the Y intercept of above PDF for only particles of 5um diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/890799.rdf
Name: R2_of_PDFslope
Units: unitless
Description: <p>R2of PDF Slope logABD>0.75; squared correlation coefficient of above PDF for only particles of >= 5um diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/890800.rdf
Name: F_statistic_of_PDFslope
Units: unitless
Description: <p>F-statistic of PDF Slope logABD>0.75 (only particles >5um); the F statistic of the above PDF for only particles of >=5um diameter or larger using a Yokogowa FlowCAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/890801.rdf
Name: Total
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of total particles measured by Yokogowa measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890802.rdf
Name: Small_0_to_4um
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of small particles with diameters of 0 to 4 micrometers measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890803.rdf
Name: Round_4_to_12um
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of round particles with diameters of 4 to 12 micrometers measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890804.rdf
Name: Ovoid_4_to_12um
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of ovoid particles with long axis of 4 to 12 micrometers measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890805.rdf
Name: Dinoflagellates
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of dinoflagellates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890806.rdf
Name: Ciliates
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of ciliates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890807.rdf
Name: Diatoms
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of pennate and centric diatoms measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890808.rdf
Name: Silicoflagellates
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of silicoflagellates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890809.rdf
Name: Other_Cells
Units: cells per milliliter (cells/mL)
Description: <p>Concentration of unidentified other particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890810.rdf
Name: Pct_Small_0_to_4um
Units: percent
Description: <p>Percent of total particles contributed by small (0-4 um) particles as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890811.rdf
Name: Pct_Round_4_to_12um
Units: percent
Description: <p>Percent of total particles contributed by round (4-12 um diameters) particles as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890812.rdf
Name: Pct_Ovoid_4_to_12um
Units: percent
Description: <p>Percent of total particles contributed by ovoid (long axis 4-12 um) particles as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890813.rdf
Name: Pct_Dinoflagellates
Units: percent
Description: <p>Percent of total particles contributed by dinoflagellates as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890814.rdf
Name: Pct_Ciliates
Units: percent
Description: <p>Percent of total particles contributed by ciliates as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890815.rdf
Name: Pct_Diatoms
Units: percent
Description: <p>Percent of total particles contributed by diatoms as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890816.rdf
Name: Pct_Silicoflagellates
Units: percent
Description: <p>Percent of total particles contributed by silicoflagellates as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890817.rdf
Name: Pct_Other_Cells
Units: percent
Description: <p>Percent of total particles contributed by unidentified other particles as measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890818.rdf
Name: Total_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Total carbon biomass (based on Menden-Deuer and Lessard, 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890819.rdf
Name: Small_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for small (0-4 um) particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890820.rdf
Name: Round_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for round-(4-12 um) particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890821.rdf
Name: Ovoid_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for ovoid (4-12 um long axis) particles measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890822.rdf
Name: Dinoflagellates_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for dinoflagellates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890823.rdf
Name: Ciliates_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for ciliates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890824.rdf
Name: Diatoms_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for the sum of pennate and centric diatoms measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890825.rdf
Name: Silicoflagellates_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for silicoflagellates measured by Yokogowa FlowCAM imaging cytometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/890826.rdf
Name: Other_Cells_C_biomass
Units: micrograms per liter (ug/L)
Description: <p>Carbon biomass (based on Menden-Deuer and Lessard, 2000) for unidentified other particles measured by Yokogowa FlowCAM imaging cytometer</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
23958
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a1425ff7-f4e1-50ec-9f8d-f8758a206940/content
download
https://doi.org/10.26008/1912/bco-dmo.887787.1
download
onLine
dataset
<p><strong>At sea collections</strong><br />
Nine stations were visited during R/V Endeavor&nbsp;EN616 cruise in the northwest Atlantic.&nbsp;&nbsp;<br />
At eight depths, three 10L Niskin samples were taken for discrete measurements of:</p>
<p>1. Chlorophyll, nutrients including nitrate, nitrite, ammonium, phosphate, and silicate&nbsp;<br />
2.&nbsp;Particulate organic carbon (POC) plus particulate organic nitrogen (PON)&nbsp;<br />
3.&nbsp;Particulate inorganic carbon (PIC)<br />
4.&nbsp;Biogenic silica<br />
5. Birefringence counts of coccolithophores (done ashore)&nbsp;<br />
6. Shipboard Yokogawa Fluid Imaging Technologies FlowCam imaging cytometer, in order to enumerate the major microalgal classes and estimate the particle size distribution function</p>
<p>Measurements 1 to 4 are part of BCO-DMO dataset 837074 (See&nbsp;<a href="https://www.bco-dmo.org/dataset/837074" style="margin: 0px; padding: 0px; border: 0px; font: inherit; vertical-align: baseline; text-decoration-line: none; color: rgb(0, 102, 153);">https://www.bco-dmo.org/dataset/837074</a>, and the Related Datasets section below).<br />
Measurement 5 of birefringence counts data is BCO-DMO dataset 887863 (See&nbsp;<a href="https://www.bco-dmo.org/dataset/887863" style="margin: 0px; padding: 0px; border: 0px; font: inherit; vertical-align: baseline; text-decoration-line: none; color: rgb(0, 102, 153);">https://www.bco-dmo.org/dataset/887863</a>, and the Related Datasets section below).<br />
Measurement 6 is flow cytometer data presented in <strong>this </strong>dataset.&nbsp;</p>
<p><strong>FlowCAM enumeration of various phytoplankton classes</strong><br />
A Yokogowa FlowCAM imaging cytometer was used to enumerate different classes of phytoplankton.&nbsp; The instrument was keyed on particle backscattering and fluorescence properties.&nbsp; Samples were first filtered through 100um Nitex mesh to make sure the 100um diameter flow chamber did not clog.&nbsp; The instrument was run with a 10X objective in order to reliably count particles bigger than 4-5um diameter. Samples were processed according to Poulton and Martin (2010).</p>
<p>Concentrations (per mL), percent contribution with respect to total particles, and biomass are presented.&nbsp; Carbon biomass was determined&nbsp;based on the Menden-Deuer &amp; Lessard (2000) method.&nbsp;&nbsp;</p>
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Specified by the Principal Investigator(s)
<p><strong>BCO-DMO processing</strong><br />
- Data is from columns P through AT on the original source file titled "EN616_master_datasheet_bottle_and_discrete_organics_updated_ccc_BCODMO.csv"<br />
- FlowCAM cytometry data extracted from combined "master datasheet" into a separate file called "Flow_cytometer_EN616.csv"<br />
- Modified parameter (column) names to conform with BCO-DMO naming conventions.&nbsp;<br />
- Converted date format to ISO Date 8601 format<br />
- Missing data identifier of -999 was removed to keep value from being mistaken for true data</p>
Specified by the Principal Investigator(s)
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7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
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Yokogowa FlowCAM imaging cytometer
Yokogowa FlowCAM imaging cytometer
PI Supplied Instrument Name: Yokogowa FlowCAM imaging cytometer PI Supplied Instrument Description:Particles were measured by Yokogowa FlowCAM imaging cytometer. 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. 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: EN616
EN616
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN616
William M. Balch
Bigelow Laboratory for Ocean Sciences
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel