Abstract:

The motion of bacteria near gas, fluid, and solid interfaces is investigated in the Complex Flow Lab of the Mechanical Engineering department of Purdue University. Experimental data were captured using an inverted microscope and processed to find the individual trajectories of Escherichia coli cells within the imaging domain. Numerical simulations were conducted using the super-computing clusters at Purdue. Using MATLAB software, the numerical results investigated the distribution of bacteria near gas, liquid, and solid surfaces. Both experimental and simulated data were collected in 2018 and 2019 to study the attraction of motile bacteria to liquid and gas interfaces. The dataset contains the data needed to re-create figures in the accompanying manuscript, as well as trajectories and distributions of E. coli 437. This dataset supports the publication: Ahmadzadegan, A., Wang, S., Vlachos, P. P., & Ardekani, A. M. (2019). Hydrodynamic attraction of bacteria to gas and liquid interfaces. Physical Review E, 100(6). doi:10.1103/physreve.100.062605

Suggested Citation:

Adib Ahmadzadegan, Shiyan Wang, Pavlos P. Vlachos, Arezoo M. Ardekani. 2020. Dataset for: Hydrodynamic attraction of bacteria to gas and liquid interfaces. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/WGAQQWN8

Publications:

Ahmadzadegan, A., Wang, S., Vlachos, P. P., & Ardekani, A. M. (2019). Hydrodynamic attraction of bacteria to gas and liquid interfaces. Physical Review E, 100(6). doi:10.1103/physreve.100.062605

Purpose:

The data were acquired to study how hydrodynamic interactions affect the distribution of bacteria near gas-liquid and liquid-liquid interfaces. The study was carried out with a motivation to analyze the differences between microorganism motion near clean and contaminated interfaces. This is particularly relevant in the context of microbial bio-degradation of hydrocarbons.

Data Parameters and Units:

Experiments: The data include .mat files with location of bacteria cells in space and time; vertical profiles of cell distribution near the interfaces are provided over a set time period, and cell trajectories are followed within a single layer above the solid interface. Bacteria locations are provided in pixels and velocities in pixels per frame. The conversion of pixels and frame rate are provided. Fluid viscosities varied from to 0 to ~ 50mpa.s. Bacteria concentration is set to OD of 0.2. The bacteria of interest is E. coli 437 non-chemotaxis non-tumbling bacteria. Numerical Simulations: Location, speed, and rotation of bacteria cells in space and time are provided in .dat files. Bacteria locations are reported in microns and velocities in microns per second. Fluid viscosities are varied from 0 to ~50 mpa.s. Bacteria concentration is 1000 per simulation domain. Please note that the numerous 'readme.txt' files included within the dataset describe in detail the dataset parameters and units.

Methods:

A 500 microns deep microscopy chamber was mounted to a glass microscope coverslip, filled with a cell solution, and topped by three different oils of various viscosity ratios to the cell suspension (mineral oil, soybean oil, and dodecane), as well as a gaseous (CO2) and solid interface. Cell distribution was imaged in vertical layers at the top and bottom interfaces of the cell suspension. Four replicates were measured for each viscosity ratio.

Instruments:

Nikon Ti-e microscope, 20x objective lens, Zyla 5.5 megapixel camera.

Individual Files: