Tail beat frequency in the appendicularian Oikopleura dioica during particle tracking experiments comprised of three temperature treatments conducted in December 2015

Website: https://www.bco-dmo.org/dataset/897617
Data Type: experimental
Version: 1
Version Date: 2023-06-15

Project
» Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey (Gelatinous Grazer Feeding)
ContributorsAffiliationRole
Gemmell, Brad J.University of South Florida (USF)Principal Investigator
Sutherland, Kelly RakowUniversity of OregonPrincipal Investigator, Contact
Conley, Keats R.University of OregonScientist
Hiebert, Terra C.University of OregonScientist
von Dassow, GeorgeUniversity of OregonScientist
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
These data include tail beat kinematics measurements and particle tracking from the appendicularian Oikopleura dioica during experiments conducted in December 2015 at the Sars Centre for Marine Molecular Biology in Bergen, Norway. The experiments comprised three temperature treatments. The data were collected from high-speed video frames. This dataset includes measurements of tail beat frequency. Tail beat kinematic measurements were used to describe how O. dioica drives flow across food concentrating filters and how it is affected by temperature.


Coverage

Temporal Extent: 2015-12-05 - 2015-12-10

Dataset Description

The primary data file for this dataset, "897617_tailbeat_counts.csv", contains data on all replicates for each video. The supplemental file, "897617_tailbeat_averages_and_frequency.csv", contains the averages for each video including the average tail beat frequency for each video. The videos are attached as Supplemental Files (there is one .zip folder for each temperature treatment).


Methods & Sampling

All experimental animals were obtained from the appendicularian culture facility at the Sars Centre for Marine Molecular Biology in Bergen, Norway in December 2015. Oikopleura dioica were filmed individually following Gemmell et al. (2014). Images were recorded using an Edgertronic high-speed camera (1280 × 1024-pixel resolution, 500 frames per second) with brightfield illumination from a fiber optic light source, or a Photron FastCam Mini Ux100 (1280x1024, 125-1000 frames per second) with darkfield illumination from a tilting mirror base. The filming vessel was positioned on a manually adjustable stage between the light source and the camera. A long working-distance microscope objective (4x or 40x) was mounted to an adjustable-height optics clamp positioned between the filming vessel and the camera. Videos were converted to image stacks in QuickTime Pro. Day 1 animals were filmed in a 50-milliliter glass cuvette in treatments comprising 3 temperatures: 5° Celsius, 15° Celsius, and 25° Celsius.


Data Processing Description

Data Processing:
Tail beat kinematics were measured in ImageJ. Five tail beats were recorded per individual, with a single tail beat measured as one complete wave cycle.

BCO-DMO Processing:
- removed "-" as a missing data value (missing/null values are blank/empty in the final .csv files);
- rounded the Frames, Time, and Frequency columns to 3 decimal places;
- separated the original data file into two resources: one with the averages and frequencies and one with the counts;
- renamed fields for both resources to comply with BCO-DMO naming conventions;
- bundled the videos into 3 .zip files (see Supplemental Files).


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Data Files

File
897617_tailbeat_counts.csv
(Comma Separated Values (.csv), 5.24 KB)
MD5:68dc5af742bdaaacdd51034ecb6f9120
Primary data file for dataset ID 897617.

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Supplemental Files

File
15C.zip
(ZIP Archive (ZIP), 1.94 GB)
MD5:5ee628c77dd3b5079923bb2d4004a5dc
This .zip contains 17 .mov video files from the 15 degrees Celsius treatments. See the file inventory (Appendicularian_Video_Inventory.csv) for a description of each file.
25C.zip
(ZIP Archive (ZIP), 2.01 GB)
MD5:02928e5f9fd97b1f5f73cd4dc8f5e6c4
This .zip contains 16 .mov video files from the 25 degrees Celsius treatments. See the file inventory (Appendicularian_Video_Inventory.csv) for a description of each file.
5C.zip
(ZIP Archive (ZIP), 2.49 GB)
MD5:6888cc317e68626484f97c5fd5a53df6
This .zip contains 20 .mov video files from the 5 degrees Celsius treatments. See the file inventory (Appendicularian_Video_Inventory.csv) for a description of each file.
897617_tailbeat_averages_and_frequency.csv
(Comma Separated Values (.csv), 1.40 KB)
MD5:c628f83fc1c752a5f14a1c44cc196070
Supplemental file for dataset ID 897617. This file contains the average frame number and time for each video, as well as tail beat frequency.

Column descriptions:
(column_name,definition,units,type)
Temperature,"Temperature treatment (5°C, 15°C, or 25°C)",degrees Celsius,Float
Video,Video identifier,unitless,String
Frames_Avg,Average frame number of all replicates for the video,unitless,Float
Time_Avg,Average time of all replicates for the video,seconds per beat,Float
Frequency,Tail beat frequency calculated as 500/(Frames_Avg),beats per second,Float
Appendicularian_Video_Inventory.csv
(Comma Separated Values (.csv), 2.77 KB)
MD5:3984ad11c2e6a3e4373883742f6988ad
Inventory/description of video files contained in the three .zip files - one for each temperature treatment. This inventory was originally provided as an Excel file and was converted to .csv by BCO-DMO.

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Related Publications

Gemmell, B. J., Jiang, H., & Buskey, E. J. (2014). A new approach to micro-scale particle image velocimetry (µPIV) for quantifying flows around free-swimming zooplankton. Journal of Plankton Research, 36(5), 1396–1401. https://doi.org/10.1093/plankt/fbu067
Methods
Hiebert, TC, Gemmell, BJ, von Dassow, G, Conley, KR, & Sutherland, KR. (Under Review). The hydrodynamics and kinematics of the appendicularian tail underpin peristaltic pumping.
Results

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Related Datasets

IsRelatedTo
Gemmell, B. J., Sutherland, K. R., Conley, K. R., Hiebert, T. C., von Dassow, G. (2023) Filter area measurements from Oikopleura dioica tail beat kinematics and particle tracking experiments conducted in December 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-15 doi:10.26008/1912/bco-dmo.897665.1 [view at BCO-DMO]
Gemmell, B. J., Sutherland, K. R., Conley, K. R., Hiebert, T. C., von Dassow, G. (2023) Inlet particle speeds from 5 high-speed video frames at 3 temperature treatments from Oikopleura dioica particle tracking experiments conducted in December 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-15 doi:10.26008/1912/bco-dmo.897682.1 [view at BCO-DMO]
Gemmell, B. J., Sutherland, K. R., Conley, K. R., Hiebert, T. C., von Dassow, G. (2023) Tail wave amplitude from 5 high-speed video frames at 3 temperatures from Oikopleura dioica particle tracking experiments conducted in December 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-22 doi:10.26008/1912/bco-dmo.897825.1 [view at BCO-DMO]

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Parameters

ParameterDescriptionUnits
Temperature

Temperature treatment (5°C, 15°C, or 25°C)

degrees Celsius
Video

Video identifier. This number is the last 5 digits of the .mov file names. The .mov files are provided in the attached .zip folders as Supplemental Files. The number following the dash represents the animal number. For example, "75974-1" is the identifier for animal 1 in the .mov file ending in 75974, which is in the 5C.zip folder (5C contains movies from the 5 degrees C temperature treatment.)

unitless
Tailbeat

Tailbeat replicate number

unitless
Frames

Video frame number for replicate tail beat

unitless
Time

Time for replicate tail beat

seconds per beat


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Instruments

Dataset-specific Instrument Name
Edgertronic high-speed camera
Generic Instrument Name
Camera
Generic Instrument Description
All types of photographic equipment including stills, video, film and digital systems.

Dataset-specific Instrument Name
Photron FastCam Mini Ux100
Generic Instrument Name
Camera
Generic Instrument Description
All types of photographic equipment including stills, video, film and digital systems.


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Project Information

Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey (Gelatinous Grazer Feeding)

Coverage: North Pacific Subtropical Gyre, at a field site 3 nautical miles offshore of Kona, Hawai’i (19.710746 N, 22.75 W) & Sars Centre for Marine Molecular Biology in Bergen, Norway


NSF Award Abstract:
The oceans are dominated by microscopic plants and animals (microorganisms) that are at the base of the food web and drive energy and carbon cycles on global scales. Soft jellylike animals called gelatinous grazers specialize in feeding on microorganisms using nets made out of mucus. Gelatinous grazers are abundant in the ocean and have high feeding rates on microorganisms so could have a very strong influence on the abundance and diversity of microorganisms and could change how oceanic food webs are currently understood. However, gelatinous grazers are very fragile and patchy in their distributions so it has been difficult to determine the magnitude and dynamics of these important predator-prey relationships on a meaningful scale using traditional approaches, thus they have typically been disregarded in food web studies. Learning more about the predator-prey relationship between gelatinous grazers and microorganisms will improve understanding of the structure, mechanics, and dynamics of the ocean's food web, which is a critical economic and ecosystem resource on Earth. This project is determining grazing rates by gelatinous animals on microbes to inform food web models. The project also trains students to communicate, disseminate, and interpret scientific findings. These broader impacts goals will be attained through partnerships at the University of Oregon (Applied Scientific Communication) and Portland State University (Advanced Technical Writing), training of 1 PhD student, 2 undergraduates, and 4 science communication interns, and development of a week-long workshop and establish student mentorship relationships towards production of communication products.

The project integrates laboratory and oceanographic approaches to address several specific aspects of the predator-prey relationship between gelatinous grazers and ocean microorganisms. Five distinct types of gelatinous grazers, each with different feeding morphologies and life history, will be studied in an oceanographic setting with an abundant and diverse natural microbial population. These target organisms include pelagic tunicates (salps, appendicularians, doliolods and pyrosomes) and thecosome pteropods. The approach quantifies: 1) grazing rates in the natural ocean environment, 2) particle selectivity with a focus on size and shape and, 3) the morphological and hydrodynamic properties of feeding that underlie the measured grazing rates and particle selection. The project uses a variety of techniques including sampling via SCUBA diving, laboratory experiments, high speed/high resolution videography, flow cytometry, and DNA sequencing techniques.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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