Pseudomonas azotoformans strain NBRC

Pseudomonas azotoformans is an off-white, pinkish bacteria that has been found in Japanese unhulled rice (Nie, 2011). In Prince Edward County, this bacteria was collected from a Hampden-Sydney steam.



Nie ZJ, Hang BJ, Cai S, Xie XT, He J, Li SP. 2011. Degradation of cyhalofop-butyl (CtB) by Pseudomonas

azotoformans strain QDZ-1 and cloning of a novel gene encoding CyB-hydrolyzing esterase. J.

Agric. Food Chem; 55(11): 6040-6.

Date Collected: January 31, 2017

Methods for Isolation and Identification:

Soil was collected from the bottom of a stream near the campus of Hampden-Sydney (Figure 1).

It was mixed with 10 mL of sterile water and it was streaked onto a nutrient-rich agar plate using the

hockey method. An off-white, pinkish bacterial colony was chosen to have its DNA sequenced by PCR amplification and identified through the BLAST database on NCBI (Figure 2).

After the PCR was produced, a restriction enzyme, MSP 1, was used to digest the DNA and it was run through a gel. It was sent off for sequencing to identify the bacteria.

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Figure 1. Sample collection site

Screen Shot 2017-04-19 at 10.18.52 PMFigure 2. Colony selected for identification.


  • MSP1 digestion (Figure 3): A 2,000 bp product was amplified through the PCR method. One band was identified at approximately 250 bp after it was digested with MSP1.
  • Screen Shot 2017-04-19 at 9.26.07 PM

Figure 3. Result of MSP 1 digestion and PCR amplification test through Gel Electrophoresis

  • Sequence Analysis (Figure 4): 709 bases were produced in the PCR product to be analyzed. With this product, clear nucleotide base sequences were used from SnapGene Viewer to be used as the sequence for a targeted loci BLAST in the ncbi BLAST database. The chromatogram can be viewed: (TGCEHS2_PREMIX_JF7573_41). The BLAST data revealed that a 99% identity between the query and the potential microbe from base pairs 29-736. Within those base pairs, there were only 2 gaps between the two. The bacteria was identified as Pseudomonas azotoformans (Figure 4).

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Figure 4. NCBI Blast analysis of Pseudomonas azotoformans strain NBRC

Contributed by: Tatianna Griffin and Cecilie Elliott, BIOL 250-50 Spring 2017