http://lod.bco-dmo.org/id/dataset/864069 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 2021-11-01 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Orientation and growth of colonies of four diatom species (Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis) in Couette flow 2021-11-04 publication 2021-11-04 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2021-11-16 publication https://doi.org/10.26008/1912/bco-dmo.864069.1 James Sullivan Florida Atlantic University HBOI principalInvestigator Malcolm McFarland Florida Atlantic University HBOI principalInvestigator Aditya Nayak Florida Atlantic University HBOI principalInvestigator Melissa Omand University of Rhode Island principalInvestigator Jan Rines University of Rhode Island 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: Sullivan, J., McFarland, M., Nayak, A., Omand, M., Rines, J. (2021) Orientation and growth of colonies of four diatom species (Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis) in Couette flow. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-11-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.864069.1 [access date] Phytoplankton Orientation - 4 Diatom Species Dataset Description: Methods and Sampling: &lt;p&gt;Uni-algal cultures of the colonial diatoms &lt;em&gt;Stephanopyxis turris&lt;/em&gt;, &lt;em&gt;Pseudo-nitzschia&lt;/em&gt; sp., &lt;em&gt;Skeletonema&lt;/em&gt; sp., and &lt;em&gt;Odontella sinensis&lt;/em&gt; 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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657332 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657332 completed James Sullivan Florida Atlantic University HBOI 772-242-2445 Florida Atlantic University - Harbor Branch Oceanographic Institute 5600 US 1 North Fort Pierce FL 34946 USA jsullivan@fau.edu pointOfContact Malcolm McFarland Florida Atlantic University HBOI 772-242-2234 Florida Atlantic University - Harbor Branch Oceanographic Institute 5600 US 1 North Fort Pierce FL 34946 USA mmcfarland@fau.edu pointOfContact Aditya Nayak Florida Atlantic University HBOI 772-242-6427 Florida Atlantic University - Harbor Branch Oceanographic Institute 5600 US 1 North Fort Pierce FL 34946 USA anayak@fau.edu pointOfContact Melissa Omand University of Rhode Island 401-874-6610 215 S Ferry Rd Narrangsett RI 02882-1197 USA momand@uri.edu pointOfContact Jan Rines University of Rhode Island 401-874-6691 Graduate School of Oceanography South Ferry Road Narragansett RI 02882 USA jrines@uri.edu pointOfContact asNeeded Dataset Version: 1 Unknown Species Replicate Date Orientation_0_5_rpm Major_Axis_Length_0_5_rpm Aspect_Ratio_0_5_rpm Orientation_13rpm Major_Axis_Length_13_rpm Aspect_Ratio_13_rpm digital holographic microscope (DHM) Couette chamber theme None, User defined species scientific name (binomial) replicate date No BCO-DMO term length ratio featureType BCO-DMO Standard Parameters Digital inline holographic microscope Taylor-Couette system instrument BCO-DMO Standard Instruments 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. Collaborative Research: Orientation of elongate diatoms as a strategy for light harvesting https://osprey.bco-dmo.org/project/686802 Collaborative Research: Orientation of elongate diatoms as a strategy for light harvesting <p><em>NSF Award Abstract:</em><br /> Phytoplankton have an intimate connection to the hydrodynamic environment in which they live.</p> <p>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.</p> <p>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.</p> Phytoplankton Orientation largerWorkCitation project eng; USA oceans -80.35547 -80.35547 27.53428 27.53428 2020-03-23 2021-06-26 Laboratory based experiments conducted at FAU-HBOI and URI 0 BCO-DMO catalogue of parameters from Orientation and growth of colonies of four diatom species (Stephanopyxis turris, Pseudo-nitzschia sp., Skeletonema sp., and Odontella sinensis) in Couette flow 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/864122.rdf Name: Species Units: unitless Description: <p>name of species</p> http://lod.bco-dmo.org/id/dataset-parameter/864123.rdf Name: Replicate Units: unitless Description: <p>replicate number</p> http://lod.bco-dmo.org/id/dataset-parameter/864124.rdf Name: Date Units: unitless Description: <p>date of analysis; format: YYYY-MM-DD</p> http://lod.bco-dmo.org/id/dataset-parameter/864125.rdf Name: Orientation_0_5_rpm Units: degrees Description: <p>colony angle from direction of flow; from the laminar flow chamber rotating at 0.5 rpm</p> http://lod.bco-dmo.org/id/dataset-parameter/864126.rdf Name: Major_Axis_Length_0_5_rpm Units: micrometers Description: <p>colony length; from the laminar flow chamber rotating at 0.5 rpm</p> http://lod.bco-dmo.org/id/dataset-parameter/864127.rdf Name: Aspect_Ratio_0_5_rpm Units: unitless (ratio) Description: <p>ratio of colony length to width; from the laminar flow chamber rotating at 0.5 rpm</p> http://lod.bco-dmo.org/id/dataset-parameter/864128.rdf Name: Orientation_13rpm Units: degrees Description: <p>colony angle from direction of flow; from the laminar flow chamber rotating at 13 rpm</p> http://lod.bco-dmo.org/id/dataset-parameter/864129.rdf Name: Major_Axis_Length_13_rpm Units: micrometers Description: <p>colony length; from the laminar flow chamber rotating at 13 rpm</p> http://lod.bco-dmo.org/id/dataset-parameter/864130.rdf Name: Aspect_Ratio_13_rpm Units: unitless (ratio) Description: <p>ratio of colony length to width; from the laminar flow chamber rotating at 13 rpm</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 38130696 https://darchive.mblwhoilibrary.org/bitstream/1912/27762/1/dataset-864069_phytoplankton-orientation-4-diatom-species__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.864069.1 download onLine dataset &lt;p&gt;Uni-algal cultures of the colonial diatoms &lt;em&gt;Stephanopyxis turris&lt;/em&gt;, &lt;em&gt;Pseudo-nitzschia&lt;/em&gt; sp., &lt;em&gt;Skeletonema&lt;/em&gt; sp., and &lt;em&gt;Odontella sinensis&lt;/em&gt; 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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;Data Processing:&lt;/strong&gt;&lt;br /&gt; 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.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing:&lt;/strong&gt;&lt;br /&gt; - concatenated data from separate Excel files into one dataset;&lt;br /&gt; - created the &quot;Replicate&quot; and &quot;Species&quot;&amp;nbsp;columns;&lt;br /&gt; - renamed fields to conform with BCO-DMO naming conventions;&lt;br /&gt; - changed Date to YYYY-MM-DD format;&lt;br /&gt; - concatenated each of the Summary data files into one dataset (see Supplemental Files).&lt;/p&gt; 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 digital holographic microscope (DHM) digital holographic microscope (DHM) PI Supplied Instrument Name: digital holographic microscope (DHM) Instrument Name: Digital inline holographic microscope Instrument Short Name:DIHM Instrument 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.  Couette chamber Couette chamber PI Supplied Instrument Name: Couette chamber Instrument Name: Taylor-Couette system Instrument Short Name: Instrument 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.