Data from: The effect of external flow on 3D orientation of a microscopic sessile suspension feeder, Vorticella convallaria
Data files
Jul 16, 2024 version files 5.51 MB
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Flow_channel_laser_cutter_outlines.cdr
416.44 KB
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Flow_channel_laser_cutter_outlines.pdf
1.25 MB
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README.md
4.37 KB
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Vorticella_matlab_datafiles.zip
636.88 KB
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VorticellaData.xlsx
3.21 MB
Abstract
Vorticella convallaria are microscopic sessile suspension feeders that live attached to substrates in aquatic environments. They feed using a self‐generated current and help maintain the health of aquatic ecosystems and wastewater treatment facilities by consuming bacteria and detritus. Their environmental impact is mediated by their feeding rate. In ambient flow, feeding rates are highly dependent on an individual's orientation relative to the substrate and the flow. Here, we investigate how this orientation is impacted by flow speed. Furthermore, we examined whether individuals actively avoid orientations unfavorable for feeding. We exposed individuals to unidirectional laminar flow at shear rates of 0, 0.5, 1.0, and 1.5 s−1, and recorded their 3D orientation using a custom biplanar microscope. We determined that V. convallaria orientation became progressively tilted downstream as the shear rate increased, but individuals were still able to actively reorient. Additionally, at higher shear rates, individuals spent a larger fraction of their time in orientations with reduced feeding rates. Our shear rates correspond to freestream flows on the scale of mm s−1 to cm s−1 in natural environments.
These data consist of:
1) Matlab data files (.mat), which are raw data of angle vs. time for the cell body and stalk of 15 individuals. Details of the data files are described below.
2) plot_vorticella_angle_data.ipynb is a Python notebook that illustrates how to use the Matlab data files in Python if desired.
3) R code to do the statistical analyses described in our paper. This code contains further comments with details of each analysis.
4) Vorticella_data.xlsx. An Excel file that contains all data used in the R code in a format suitable for use with this code. Details of this data file are described below.
5) Flow channel laser cutter outlines.cdr and Flow channel laser cutter outlines.pdf. These files are to-scale outlines of the laser cut pieces used to make the flow chamber used in our experiments. The cored draw (.cdr) file can be used directly with many laser cutter to cut the needed shapes.
Description of Matlab raw data:
The file name gives the vorticella individual identifier and the flow shear rate in inverse seconds as “vort###shear###.mat”
These Matlab files contain the following variables:
- t: the time in seconds
- bphi: The body phi angle in degrees (azimuthal angle).
- btheta: The body phi angle (polar angle).
- sphi: The stalk phi angle in degrees (azimuthal angle).
- stheta: The stalk theta angle (polar angle).
The format of the data is such that plot(t,bphi) will make a vector plot of the body phi as a function of time.
The plot_piv_data.ipynb notebook will also import the Matlab data files and plot a vector plot of the velocity fields.
Description of Excel data:
This Excel file has the following labeled columns:
- indiv_num: A number that identifies each individual organism. These numbers match the numbers referenced in Böttger et al.
- vort_num: A number that identifies each individual organism. These numbers match the matlab file names.
- shear: The shear rate that the organism was exposed to
- order: The order of exposure (i.e 1 means exposed to this shear rate first).
- time_min: The time point of this data (in minute)
- bodyphi: The phi angle of the cell body
- bodytheta: The theta angle of the cell body
- stalkphi: The phi angle of the stalk
- stalktheta: The theta angle of the stalk
- peristome_height_mm: The height of the peristome above the surface in mm.
- stalk_length_mm: The length of the stalk in mm
- peristome_dia_avg_mm: The diameter of the peristome in mm averaged over several measurements for each individual.
- frscaled: The scaled feeding rate for each organism at each time point. These are scaled by the feeding rate_vert column and this scaling is described further in Böttger et al. Data were filtered to remove outliers which represent times when Vorticella were contracting. At these time points this column contains no data. The Excel file is optimized to work with the R code. Modifying the empty cells may disrupt the code intended for file analysis.
- frscaledmean: The mean value of the scaled feeding rate (previous column) for each individual at each shear rate.
- inrecirc: Whether the organism is predicted to be at an orientation that leads to recirculation in the flow through the organisms feeding rate. The value 0 means not predicted to be in an orientation with recirculation at that time, 1 means predicted to be in an orientation with recirculation at that time.
- fracinrecirc: The fraction of time this individual at that flow speed spends in orientations predicted to lead to recirculation.
- feedingrate_vert: The predicted feeding rate for this individual at this flow speed when oriented vertically in m^3/s.
Description of individual identifier number:
Both the matlab and excel data use identifier number for individual organisms. These match between the matlab and excel and correspond to the individuals referenced in Böttger et al as follows:
Individual 1: 020
Individual 2: 013
Individual 3: 015
Individual 4: 007
Individual 5: 009
Individual 6: 010
Individual 7: 017
Individual 8: 018
Individual 9: 021
Individual 10: 022
Individual 11: 024
Individual 12: 025
Individual 13: 027
Individual 14: 032
Individual 15: 033
Please see details in the methods section of T. Böttger, B. Klaassen van Oorschot, and R. E. Pepper, “The effect of external flow on 3D orientation of a microscopic sessile suspension feeder, Vorticella convallaria,” Annals of the New York Academy of Sciences, doi: 10.1111/nyas.15170.