Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Supplemental Files
• Related Publications
• Parameters
• Instruments
• Project Information
• Funding

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:
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).

NSF Award Abstract:
Phytoplankton have an intimate connection to the hydrodynamic environment in which they live.

Previous studies have examined the role that turbulence and shear play in nutrient uptake, patch/layer formation, and predator-prey encounters, but the role of phytoplankton orientation to increase light capture (and ultimately primary production) has been largely overlooked. Compelling evidence of persistent horizontal orientation of chain-forming diatoms, obtained from novel in situ holographic imaging, has led to a hypothesis that in regions of strong stratification, shear flows will lead to systematic horizontal orientation of elongate phytoplankton forms that maximizes their cross-sectional area (and light capture) in the ambient downwelling light field. It has also been suggested that variations in phytoplankton size and shape are fundamental traits conferring selective competitive advantages in certain hydrodynamic environments, thus modifying/mediating community composition. The interdisciplinary research of this project crosses three scientific disciplines (biology, optics and fluid dynamics) and will advance our understanding of the function of diverse forms of phytoplankton, their interactions with fluid flows, and the resultant impacts on the optics of the environment. The project will support a number of undergraduate and graduate students, and post-doctoral researchers.

This project combines analysis of previously collected field data with laboratory experiments and modeling. For the field data analysis, phytoplankton orientation is quantified from in situ holographic images of the undisturbed water column along with concurrent high resolution measurements of critical physical (turbulence/shear/stratification) and optical parameters collected from a ship-based holographic bio-physics profiler. In the laboratory, the orientation response of different phytoplankton species and morphologies is evaluated in custom built shear tanks under controlled laminar and turbulent conditions to confirm that elongate forms can orient in certain hydrodynamic environments to maximize light capture. In addition, controlled growth/physiology experiments in various shear tank treatments will explore the effects of orientation on growth, photosynthetic parameters and productivity. Lastly, the project results will be incorporated into a global analysis of observed and modeled physical, bio-optical and ecologically-relevant parameters, to quantify the relevance of this phenomenon to primary production and the carbon cycle.