Dataset: Phytoplankton Orientation - 4 Diatom Species

Name: Orientation and growth of colonies of four diatom species (Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis) in Couette flow
Published: 2021-11-04
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.864069.1

Spatial Extent: N:27.53428 E:-80.35547 S:27.53428 W:-80.35547

Temporal Extent: 2020-03-23 - 2021-06-26

Project:

Collaborative Research: Orientation of elongate diatoms as a strategy for light harvesting (Phytoplankton Orientation)

Principal Investigator:

James Sullivan (Florida Atlantic University, FAU-HBOI)

Co-Principal Investigator:

Malcolm McFarland (Florida Atlantic University, FAU-HBOI)

Aditya Nayak (Florida Atlantic University, FAU-HBOI)

Melissa Omand (University of Rhode Island, URI-GSO)

Jan Rines (University of Rhode Island, URI-GSO)

Contact:

Aditya Nayak (Florida Atlantic University, FAU-HBOI)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-11-04

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Orientation and growth of colonies of four diatom species (Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis) in Couette flow

Abstract:

This dataset includes data on the orientation and growth of colonies of four diatom species (Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis) in Couette flow. Experiments were conducted at Harbor Branch Oceanographic Institute in Fort Pierce, FL, USA from March 2020 to June 2021. Data are provided from all replicates and summary data (means) are provided as a Supplemental File.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date PID Issued
2021-11-04	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.864069.1	2021-11-16

Methods & Sampling

Uni-algal cultures of the colonial diatoms Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis were grown in 2 separate Couette chambers under controlled shear conditions for up to 24 days. The Couette chambers (40 cm height) consisted of an inner rotating cylinder (12.7 cm radius) and an outer stationary cylinder (14.92 cm radius). A laminar flow chamber rotated at 0.5 rpm and a turbulent flow chamber rotated at 13 rpm. The gap between the cylinders was filled with 8 L of sterile L1 medium (Guillard and Hargraves 1993). Experiments took place in a temperature and light controlled walk-in incubator at 20° C with a 12:12 hour light:dark cycle. Light was provided by cool white fluorescent lamps producing 33 µmol photons m⁻² s⁻¹ at the center of each chamber.

Digital holograms through the entire height of each Couette chamber (40 cm) were acquired at ~1 day intervals during each experiment. Each hologram imaged 19.25 mL of water. The total volume imaged and analyzed on each day and for each chamber was ~1.5 L.

A custom digital holographic microscope (DHM) was constructed to image particles within the Couette chambers. Coherent illumination was provided by a green (532 nm) nanosecond pulsed laser. The incident beam was directed upward through the bottom of the chamber and images were acquired by a CCD camera (4896 x 3264 pixels) positioned above the chamber looking downward through the illuminated volume. An objective lens in front of the camera increased magnification and positioned the hologram image plane at the water surface. Hologram resolution was 1.74 µm/pixel.

Data Processing Description

Data Processing:
Holograms were numerically reconstructed in Matlab (version 2019a) using the Kirchoff-Fresnel convolution kernel (Katz and Sheng 2010) at 1 mm intervals throughout the height of the chamber. Reconstructed images were combined to produce a single extended depth of field (EDF) image for each hologram. These EDF images were segmented with a fixed threshold and particle measurements were obtained through automated region analysis in Matlab. See Nayak et al. 2018 for further details.

BCO-DMO Processing:
- concatenated data from separate Excel files into one dataset;
- created the "Replicate" and "Species" columns;
- renamed fields to conform with BCO-DMO naming conventions;
- changed Date to YYYY-MM-DD format;
- concatenated each of the Summary data files into one dataset (see Supplemental Files).

Data Files

File
phyto_orientation_diatoms.csv (Comma Separated Values (.csv), 36.36 MB) MD5:9dffebef8a83a19a5ee47895d60538e9 Primary data file for dataset ID 864069

Supplemental Files

File

Summary Data
filename: summary_data.csv

(Comma Separated Values (.csv), 25.84 KB)
MD5:458049382731212353d75c485aa31679

Summary data from Couette flow experiments of four diatom species (Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis). Associated with dataset https://www.bco-dmo.org/dataset/864069.

Column names, descriptions, and units:

Species = species names

Replicate = replicate number

Date = date; format: YYYY-MM-DD

No_of_colony_0_5_rpm = number of colonies analyzed; from the laminar flow chamber rotating at 0.5 rpm (count)

Total_Volume_0_5_rpm = volume analzyed; from the laminar flow chamber rotating at 0.5 rpm (milliliters (mL))

Mean_Orientation_0_5_rpm = mean colony angle from direction of flow; from the laminar flow chamber rotating at 0.5 rpm (degrees)

Mean_Major_Axis_Length_0_5_rpm = mean colony length; from the laminar flow chamber rotating at 0.5 rpm (micrometers (um))

Mean_Aspect_Ratio_0_5_rpm = mean ratio of colony length to width; from the laminar flow chamber rotating at 0.5 rpm

No_of_colony_13_rpm = number of colonies analyzed; from the laminar flow chamber rotating at 13 rpm (count)

Total_Volume_13_rpm = volume analzyed; from the laminar flow chamber rotating at 13 rpm (milliliters (mL))

Mean_Orientation_13_rpm = mean colony angle from direction of flow; from the laminar flow chamber rotating at 13 rpm (degrees)

Mean_Major_Axis_Length_13_rpm = mean colony length; from the laminar flow chamber rotating at 13 rpm (micrometers (um))

Mean_Aspect_Ratio_13_rpm = mean ratio of colony length to width; from the laminar flow chamber rotating at 13 rpm

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1657332

Deployments

None available yet

Instruments

Digital inline holographic microscope

Supplied Name: digital holographic microscope (DHM)

Supplied Description:

Instrument Type

Generic Name: Digital inline holographic microscope

Acronym: DIHM

Generic Description:

A Digital Inline Holographic Microscope (DIHM) uses coherent (laser) light and a digital camera to image objects with micrometer scale resolution. A portion of the light scattered by illuminated objects interferes with incident light in a predictable manner. The resulting interference patterns projected onto a two-dimensional plane (i.e. digital camera sensor) are recorded as holograms. These digital holograms are then numerically reconstructed to produce an in-focus image at a given distance from the recording plane. A relatively large illuminated volume (>100 mL) can be reconstructed in this manner to produce a single image with an extended depth of field.

Taylor-Couette system

Supplied Name: Couette chamber

Supplied Description:

Instrument Type

Generic Name: Taylor-Couette system

Generic Description:

An apparatus composed of two vertically oriented, coaxial cylinders separated by a gap that contains seawater. During operation, the outer cylinder rotates at a prescribed speed causing relative motion between the cylinders and thereby shearing the seawater between them.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Species	name of species	unitless	species
Replicate	replicate number	unitless	replicate
Date	date of analysis; format: YYYY-MM-DD Format: %Y-%m-%d	unitless	date
Orientation_0_5_rpm	colony angle from direction of flow; from the laminar flow chamber rotating at 0.5 rpm	degrees	no_bcodmo_term
Major_Axis_Length_0_5_rpm	colony length; from the laminar flow chamber rotating at 0.5 rpm	micrometers	length
Aspect_Ratio_0_5_rpm	ratio of colony length to width; from the laminar flow chamber rotating at 0.5 rpm	unitless (ratio)	ratio
Orientation_13rpm	colony angle from direction of flow; from the laminar flow chamber rotating at 13 rpm	degrees	no_bcodmo_term
Major_Axis_Length_13_rpm	colony length; from the laminar flow chamber rotating at 13 rpm	micrometers	length
Aspect_Ratio_13_rpm	ratio of colony length to width; from the laminar flow chamber rotating at 13 rpm	unitless (ratio)	ratio

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Dataset: Phytoplankton Orientation - 4 Diatom Species