Abstract:

In this experiment, optical microscopy was used to detect and screen oil-degrading bacteria via a novel technique. In the bottom surface of Petri dish prefilled with mineral salt medium, a 100µm crude-oil droplet was injected and attached. Microbes were pipetted into the Petri dish and the interactions between the bacteria and the oil drops were observed. The size of the oil drop decreased, and the perfectly spherical shaped oil drop became irregular as bacterial degradation of oil droplets proceeded. However, bacteria that cannot degrade oil did not change the size or shape of the oil drop. This dataset supports the publication: Zheng, M., Wang, W., & Papadopoulos, K. (2019). Direct visualization of oil degradation and biofilm formation for the screening of crude oil-degrading bacteria. Bioremediation Journal, 1–11. doi:10.1080/10889868.2019.1671795

Suggested Citation:

Mengyuan Zheng, Weiyao Wang, Kyriakos Papadopoulos. 2019. Dataset for: Direct visualization of oil degradation and biofilm formation for the screening of crude oil-degrading bacteria. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/S9EVQXM5

Publications:

Zheng, M., Wang, W., & Papadopoulos, K. (2019). Direct visualization of oil degradation and biofilm formation for the screening of crude oil-degrading bacteria. Bioremediation Journal, 1–11. doi:10.1080/10889868.2019.1671795

Purpose:

A microscope based assay was proposed to quickly identify crude oil degrading bacteria, the data are used to support the feasibility of the assay.

Data Parameters and Units:

This dataset contains a folder of videos, several JPG photos (Figures 4 A&B,5 A&B, and 6 A-I) and 2 Excel files (Figure 3 Affinity of bacteria towards crude oil.xlsx, Specifications for Figure 4, 5, 6.xlsx). Figures 4 A&B,5 A&B, and 6 A-I contain photographs of freshly deposited droplets while corresponding videos captured oil-degrading processes. The Excel file titled “Figure 3 Affinity of bacteria towards crude oil.xlsx” contains information regarding the results of the BATH test and headers such as the number of bacteria in the water phase, percentage of bacteria in the water phase, Average and SEM (standard error). Other headers are DO, VC (Vibrio coralliilyticus), PP (Pseudomonas putida) and OEB (oil-eating bacteria). The Excel file titled “Specifications for Figure 4, 5, 6.xlsx” contains the diameter of a freshly deposited droplet as seen in Figures 4-6 and associated duration of incubation. The headers are diameter (µm) and time (day). Note: All the file name with "Figure #" refers to the figures in the associated publication Zheng et al., 2019.

Methods:

A micropipette puller (Narishige, PB-7, Japan) was used to pull A 30 μl microcap® with an original length of 78 mm. Heating duration, times of pulling, pulling length and pulling speed can be used to control the diameter and length of the capillary (Liu and Papadopoulos, 1995). Processed SOB was used to fill the pulled capillary with a 1 ml syringe (BD, Franklin Lakes, NJ) mounted with a needle (0.5 mm × 40 mm, BD, Franklin Lakes, NJ). The size of the oil droplet was controlled by adjusting the nitrogen flow. Inverted microscope (IMT-2, Olympus) connected to a computer was used for data acquisition from a 35-mm Petri dish (Corning Incorporated, Corning, NY) and storage. Images were taken under 20X magnification. After 3 mL MB was pipetted into the Petri dish, a cover glass was immersed into the Petri dish and A 100 μm-diameter oil droplet was injected and placed on the immersed glass slide, by controlling the flow rate of nitrogen. Bacteria was then added at concentration of 1 × 10^9 cells/ml. optical video microscopy was used to capture oil degradation. using a digital camera (Imperx IPXVGA-210-L, FL) videos were taken at 24 frames per second. Image analysis was with software (XCAP® Std3.0, EPIX Inc, Buffalo Grove, IL).

Instruments:

Inverted microscope (IMT-2, Olympus) Micropipette puller (Narishige, PB-7, Japan) Nitrogen microinjection system (IM-200, Narishige, Japan) Spectrophotometer (OD600)

Provenance and Historical References:

Liu, Z., & Papadopoulos, K. D. (1995). Unidirectional motility of Escherichia coli in restrictive capillaries. Appl. Environ. Microbiol., 61(10), 3567-3572.

Individual Files: