Dataset: Coccolithophore birefringence from polarized microscopy

Name: Coccolithophore counts from polarized microscopy birefringence measurements of samples collected in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018
Published: 2023-02-05
Keywords: Coccolithophore, birefringence, polarized microscopy, phytoplankton enumeration, coccoliths, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.887863.1

Spatial Extent: N:43.71835 E:-66.51748 S:36.98572 W:-72.92708

Temporal Extent: 2018-07-05 - 2018-07-13

Project:

Coccolithophore Mixotrophy (Cocco-Mix)

Principal Investigator:

William M. Balch (Bigelow Laboratory for Ocean Sciences)

Co-Principal Investigator:

Stephen D. Archer (Bigelow Laboratory for Ocean Sciences)

David T. Drapeau (Bigelow Laboratory for Ocean Sciences)

Jelena Godrijan (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-02-05

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Coccolithophore counts from polarized microscopy birefringence measurements of samples collected in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018

Abstract:

This dataset presents polarized microscopy-derived concentration data for coccolithophores and detached coccoliths in samples collected from stations in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018. Counts are based on image analysis of dark-field, cross-polarized views of filtered particulate matter. These counts take advantage of the birefringence property of calcium carbonate (particulate inorganic carbon) that it rotates the plane of linearly polarized incident light by 90 degrees. Incident light directed upwards, towards the microscope slide, is polarized 90 degrees with a linear polarizer. Particles are viewed from above the slide, through a second, linear polarizer filter held between the microscope stage and the camera which only accepts light that is polarized orthogonal to the lower polarizer. Calcium carbonate particles in the beam appear as bright dots of light. Image analysis software then analyzes the pattern of birefringence and enumerates only those particles with size and shape of coccolithophores or detached coccoliths.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-02-05	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.887863.1	2023-03-03

Description

This dataset is part of a larger study with the following goals:

Goal #1: 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.
Goal #2: 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 biological carbon pump and alkalinity carbon pump paradigms.

Methods & Sampling

Inherent optical properties of coccolithophores can be used for estimating particulate inorganic carbon (PIC) distributions in the water column. Polarized microscopy was used to determine the concentration of coccolithophores and detached coccoliths in samples collected in the Northwest Atlantic during R/V Endeavor cruise EN616 in July 2018. Water samples were collected using CTD casts from nine stations encompassing New England Shelf, Slope, and Sargasso Sea waters.

At eight depths, three 10L Niskin samples were taken for discrete measurements of:

1. Chlorophyll, nutrients including nitrate, nitrite, ammonium, phosphate, and silicate
2. Particulate organic carbon (POC) plus particulate organic nitrogen (PON)
3. Particulate inorganic carbon (PIC)
4. Biogenic silica
5. Birefringence counts of coccolithophores (done ashore)
6. Shipboard Yokogawa Fluid Imaging Technologies FlowCam imaging cytometer, in order to enumerate the major microalgal classes and estimate the particle size distribution function

Measurements 1 to 4 are part of BCO-DMO dataset 837074 (See https://www.bco-dmo.org/dataset/837074, and the Related Datasets section below).
Measurement 5 of birefringence counts data is detailed here on this dataset page
Measurement 6 is BCO-DMO dataset 887787. (See https://www.bco-dmo.org/dataset/887787, and the Related Datasets section below)

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 & Utgoff (2009).

Data Processing Description

The "CCC algorithm" (Count Coccolithophores and Coccoliths) from Balch & Utgoff (2009) was implemented. The CCC algorithm takes advantage of the distinct birefringence patterns of coccoliths to analyze polarized microscope images for individual coccoliths as well as plated coccolithophores.

CCC analysis involves the following steps:

Quantification (and elimination) of background light scattering in the image.
Estimation of the birefringence of non-PIC particles in the image (which typically are more diffuse than PIC particles, with lower contrast).
Enumeration of free coccoliths in the image (clusters of bright, birefringent pixels, arranged in distinctive patterns within a prescribed proximity of each other).
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)

BCO-DMO processing
- Data is from columns I through O on the original source file called "EN616_master_datasheet_bottle_and_discrete_organics_updated_ccc_BCODMO.csv"
- Birefringence data extracted from combined "master datasheet" into a separate file called "birefringence_EN616.csv"
- Modified parameter (column) names to conform with BCO-DMO naming conventions.
- Converted date format to ISO Date 8601 format

Data Files

File
birefringence_en616.csv (Comma Separated Values (.csv), 8.03 KB) MD5:81d19d91289fb8206e159a4fd293b2dc Polarized microscopy birefringence data of coccolithophores sampled during cruise EN616.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635748

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
EN616	Cocco-Mix	2018-07-03	R/V Endeavor	William M. Balch (Chief Scientist)	data info

Instruments

Microscope - Optical

Supplied Name: Quantitative light microscope (Olympus BH-2 microscope equipped with polarization optics)

Supplied Description:

Quantitative light microscope (Olympus BH-2 microscope equipped with polarization optics) was used to determine counts of coccolithophores and detached coccoliths.

Instrument Type

Generic Name: Microscope - Optical

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

Generic 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".

Niskin bottle

Supplied Description:

At eight depths, three 10L Niskin bottle samples were taken

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise identification	unitless	cruise_id
Station	Station number for EN616 cruise for water sample collection	unitless	station
Type	Type of sample. B = discrete bottle sample	unitless	sample_type
Longitude	Longitude of water sample collection	decimal degrees	lon
Latitude	Latitude of water sample collection	decimal degrees	lat
Depth	Depth of water sample	meters	depth
ISO_DateTime_UTC	Date and time of sample collection Format: %Y-%m-%dT%H:%M:%SZ	unitless	ISO_DateTime_UTC
Gear	Gear used to collect the water and coccolithophore samples	unitless	sampling_method
Balch_Sample_num	Consecutive unique numbers assigned to each water sample for all analyses done for a given station	unitless	sample
Singlet_Lith	Concentration of birefringent particles under polarized light microscope that show one cross-polarized point of light per particle	particles per milliliter (particles/mL)	number
Doublet_Lith	Concentration of birefringent particles under polarized light microscope that show two cross-polarized points of light per particle	particles per milliliter (particles/mL)	number
Triplet_Lith	Concentration of birefringent particles under polarized light microscope that show three cross-polarized points of light per particle	particles per milliliter (particles/mL)	number
Quadruplet_Lith	Concentration of birefringent particles under polarized light microscope that show four cross-polarized points of light per particle	particles per milliliter (particles/mL)	number
Total_Lith	Concentration of all birefringent particles under polarized light microscope that show single, double, triple, or quadruple cross-polarized points of light per particle	particles per milliliter (particles/mL)	number
Cell_plus_Aggregates	Concentration of plated coccolithophores, empty coccospheres, and coccolith aggregates enumerated by image-analysis software (CCC) that was used to analyze all polarized microscope samples	particles per milliliter (particles/mL)	number

Database

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Dataset: Coccolithophore birefringence from polarized microscopy