Abstract:

This dataset contains both time lapse and high speed micrographs of different bacterial isolates flowing past and aggregating on a stationary crude oil droplet in a microchannel including: Alcanivorax borkumensis (ATCC 700651), Marinobacter hydrocarbonoclasticus (ATCC 27132), and Pseudomonas sp. (ATCC 27259). Flow speeds are similar to the rising velocity of equivalent sized oil droplets rising due to buoyancy in the water column. Images are recorded using a Nikon Ti-E microscope with 20X objective and both an Andor DU-888 EMCCD (time lapse) and IDT NR4 CMOS (high speed) cameras.

Suggested Citation:

White, Andrew. 2020. Aggregation onto an oil droplet in a microchannel by different flowing suspensions of bacterial isolates. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-zex0-5e09

Purpose:

To examine the formation of aggregates around an oil droplet by environmentally relevant bacterial isolates (Alcanivorax borkumensis, Marinobacter hydrocarboniclasticus, and Pseudomonas species).

Data Parameters and Units:

Images are in tiff and videos are in nd2 format: Alcanivorax borkumensis; Marinobacter hydrocarboniclasticus; Pseudomonas species

Methods:

Three microfluidics experiments were performed using suspension of pure bacterial strains- Pseudomonas sp. P62; Alcanivorax borkumensis; Marinobacter hydrocarboniclasticus. The bacterial strains were grown in a flask containing 20 mL of nutrient broth (Difco) or marine broth (Difco) with shaking at 120 rpm at room temperature. The experiments were initiated using the culture at saturation growth (~4 days and OD600 > 1). The experiments were conducted using the new ecology-on-a-chip (eChip) microfluidic platform. The eChip is a platform that enables us to study microbial interactions with a rising droplet at ecologically relevant length and time scales. This method generates a micro-scale droplet in a microfluidic channel that allows suspended bacteria to naturally flow and interact with the droplet simulating a real environment. The eChip platform is composed of a polydimethyl siloxane (PDMS) microchannel bonded to a glass microscope slide, a reservoir flask (150 mL), two peristaltic pumps, and 3D rendering. These components are interconnected with tubing and fittings to create a close-loop microcosm environment. The microchannel was functionalized using layer-by-layer deposition to form a strongly hydrophilic surface. A crude oil droplet (~200 µm) (light Louisiana crude oil) was dispensed and pinned in the microfluidic channel and mounted on the stage of the microscope. The reservoir was filled with 50 mL seawater and the entire system was primed. The peristaltic pump was used to draw seawater from the reservoir and the culture loop into the microchannel, where it encounters the immobilized oil droplet. The interaction of the oil droplet with seawater and the formation of streamer was observed under the inverted microscope (Nikon-Ti-E) at 20x magnification equipped with a 1K × 1K EMCCD camera (Andor iXon) for time lapse imaging and a 1K × 1K CMOS high speed camera (IDT-NR4) for flow measurement over an area of 720 × 720 μm at resolutions of 0.7 μm. To capture events of streamer formation, phase contrast images were recorded at 2 fps over the first 8 hours and time-lapsed images were obtained every 30 seconds for the remainder of the X-day experiment.

Instruments:

Inverted microscope (Nikon-Ti-E); Andor DU-888 EMCCD (time lapse) and IDT NR4 CMOS (high speed) cameras

Individual Files: