http://lod.bco-dmo.org/id/dataset/887863
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
2023-01-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coccolithophore counts from polarized microscopy birefringence measurements of samples collected in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018
2023-02-05
publication
2023-02-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-03-03
publication
https://doi.org/10.26008/1912/bco-dmo.887863.1
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) Coccolithophore counts from polarized microscopy birefringence measurements of samples collected in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-02-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.887863.1 [access date]
Dataset Description: <p>This dataset is part of a larger study with the following goals:</p>
<ul>
<li>&nbsp;<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). 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 dir="ltr">Inherent optical properties of coccolithophores can be used for estimating particulate inorganic carbon (PIC) distributions in the water column. Polarized microscopy&nbsp;was used to determine the concentration of coccolithophores and detached coccoliths in samples collected&nbsp;in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018.&nbsp; Water samples were collected using CTD casts&nbsp;from nine stations encompassing New England Shelf, Slope, and Sargasso Sea waters.&nbsp;</p>
<p dir="ltr">At eight depths, three 10L Niskin samples were taken for discrete measurements of:</p>
<p dir="ltr">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 dir="ltr">Measurements 1 to 4 are part of BCO-DMO dataset 837074 (See&nbsp;https://www.bco-dmo.org/dataset/837074, and the Related Datasets section below).<br />
Measurement 5 of birefringence counts data is detailed here on this dataset page<br />
Measurement 6 is BCO-DMO dataset 887787.&nbsp; (See https://www.bco-dmo.org/dataset/887787, and the Related Datasets section below)</p>
<p dir="ltr">Quantitative light microscope counts of birefringent coccolithophores and detached coccoliths were also required for determining their concentration in the field incubation sample. A volume of 200mL was filtered onto 0.4μm-pore size, 25mm diameter polycarbonate filter then processed according to Balch &amp; Utgoff (2009).</p>
<p dir="ltr">&nbsp;</p>
<div>&nbsp;</div>
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
Singlet_Lith
Doublet_Lith
Triplet_Lith
Quadruplet_Lith
Total_Lith
Cell_plus_Aggregates
Quantitative light microscope (Olympus BH-2 microscope equipped with polarization optics)
Niskin bottle
theme
None, User defined
Cruise identfier
station
sample type
longitude
latitude
depth
ISO_DateTime_UTC
sampling_method
sample identification
number
featureType
BCO-DMO Standard Parameters
Microscope - Optical
Niskin bottle
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 Coccolithophore counts from polarized microscopy birefringence measurements of samples collected in the Northwest Atlantic 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/890578.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/890579.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/890580.rdf
Name: Type
Units: unitless
Description: <p>Type of sample. B = discrete bottle sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/890581.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of water sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/890582.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of water sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/890583.rdf
Name: Depth
Units: meters
Description: <p>Depth of water sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/890584.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/890585.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/890586.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/890587.rdf
Name: Singlet_Lith
Units: particles per milliliter (particles/mL)
Description: <p>Concentration of birefringent particles under polarized light microscope that show one cross-polarized point of light per particle</p>
http://lod.bco-dmo.org/id/dataset-parameter/890588.rdf
Name: Doublet_Lith
Units: particles per milliliter (particles/mL)
Description: <p>Concentration of birefringent particles under polarized light microscope that show two cross-polarized points of light per particle</p>
http://lod.bco-dmo.org/id/dataset-parameter/890589.rdf
Name: Triplet_Lith
Units: particles per milliliter (particles/mL)
Description: <p>Concentration of birefringent particles under polarized light microscope that show three cross-polarized points of light per particle</p>
http://lod.bco-dmo.org/id/dataset-parameter/890590.rdf
Name: Quadruplet_Lith
Units: particles per milliliter (particles/mL)
Description: <p>Concentration of birefringent particles under polarized light microscope that show four cross-polarized points of light per particle</p>
http://lod.bco-dmo.org/id/dataset-parameter/890591.rdf
Name: Total_Lith
Units: particles per milliliter (particles/mL)
Description: <p>Concentration of all birefringent particles under polarized light microscope that show single, double, triple, or quadruple cross-polarized points of light per particle</p>
http://lod.bco-dmo.org/id/dataset-parameter/890592.rdf
Name: Cell_plus_Aggregates
Units: particles per milliliter (particles/mL)
Description: <p>Concentration of plated coccolithophores, empty coccospheres, and coccolith aggregates enumerated by image-analysis software (CCC) that was used to analyze all polarized microscope samples</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
8225
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/93c0a21f-3d6e-5d59-b73d-b4b84c852e42/content
download
https://doi.org/10.26008/1912/bco-dmo.887863.1
download
onLine
dataset
<p dir="ltr">Inherent optical properties of coccolithophores can be used for estimating particulate inorganic carbon (PIC) distributions in the water column. Polarized microscopy&nbsp;was used to determine the concentration of coccolithophores and detached coccoliths in samples collected&nbsp;in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018.&nbsp; Water samples were collected using CTD casts&nbsp;from nine stations encompassing New England Shelf, Slope, and Sargasso Sea waters.&nbsp;</p>
<p dir="ltr">At eight depths, three 10L Niskin samples were taken for discrete measurements of:</p>
<p dir="ltr">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 dir="ltr">Measurements 1 to 4 are part of BCO-DMO dataset 837074 (See&nbsp;https://www.bco-dmo.org/dataset/837074, and the Related Datasets section below).<br />
Measurement 5 of birefringence counts data is detailed here on this dataset page<br />
Measurement 6 is BCO-DMO dataset 887787.&nbsp; (See https://www.bco-dmo.org/dataset/887787, and the Related Datasets section below)</p>
<p dir="ltr">Quantitative light microscope counts of birefringent coccolithophores and detached coccoliths were also required for determining their concentration in the field incubation sample. A volume of 200mL was filtered onto 0.4μm-pore size, 25mm diameter polycarbonate filter then processed according to Balch &amp; Utgoff (2009).</p>
<p dir="ltr">&nbsp;</p>
<div>&nbsp;</div>
Specified by the Principal Investigator(s)
<p>The "CCC algorithm" (Count Coccolithophores and Coccoliths) from Balch &amp; Utgoff (2009) was implemented.&nbsp; The CCC algorithm takes advantage of the distinct birefringence patterns of coccoliths to&nbsp;analyze polarized microscope images for individual coccoliths as well as plated coccolithophores.&nbsp;</p>
<p>CCC analysis involves the following steps:</p>
<ul>
<li>Quantification (and elimination) of background light scattering in the image.</li>
<li>Estimation of the birefringence of non-PIC particles in the image (which typically are more diffuse than PIC particles, with lower contrast).</li>
<li>Enumeration of free coccoliths in the image (clusters of bright, birefringent pixels, arranged in distinctive patterns within a prescribed proximity of each other).</li>
<li>Partioning of the remaining birefringence patterns into (a) plated coccolithophores (having coccoliths, arranged in spherical patterns with known diameters of plated coccolithophore cells and within a specific proximity of each other) or (b) randomly shaped coccolith aggregates (statistically distinct from spherical coccolithophore cells)</li>
</ul>
<p><strong>BCO-DMO processing</strong><br />
- Data is from columns I through O on the original source file called "EN616_master_datasheet_bottle_and_discrete_organics_updated_ccc_BCODMO.csv"&nbsp;<br />
- Birefringence data extracted from combined "master datasheet" into a separate file called "birefringence_EN616.csv"<br />
-&nbsp;Modified parameter (column) names to conform with BCO-DMO naming conventions.&nbsp;<br />
- Converted date format&nbsp;to ISO Date 8601 format</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
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
Quantitative light microscope (Olympus BH-2 microscope equipped with polarization optics)
Quantitative light microscope (Olympus BH-2 microscope equipped with polarization optics)
PI Supplied Instrument Name: Quantitative light microscope (Olympus BH-2 microscope equipped with polarization optics) PI Supplied Instrument Description:Quantitative light microscope (Olympus BH-2 microscope equipped with polarization optics) was used to determine counts of coccolithophores and detached coccoliths. Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:At eight depths, three 10L Niskin bottle samples were taken 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/
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