Adam probes biofilm formation by Bacillus subtilis in his Summer Placement

Adam, who is a fourth year studying for a bachelor’s degree in microbiology at the University of Dundee, did his placement at the Division of Molecular Microbiology (MMB) in Nicola Stanley-Wall’s lab in the same university, working with post-doc Dr. Natalie Bamford.

He says:

Biofilms can be found throughout nature and understanding them is crucial in many different aspects. Biofilms can have great benefits for humans - for example, Bacillus subtilis is a soil-dwelling bacterium that forms symbiotic biofilms with plant roots. 

A better understanding of how these interactions take place could further agricultural practices and food security, and my work could assist in this field. On the flip side, bacteria forming biofilms can also have grave consequences for humans, as during infection bacteria forming biofilms can increase their drug tolerance, making antibiotics less effective and increasing the chances of long-lasting and invasive infection. 

Fully understanding the processes involved with bacterial biofilms can allow us to promote biofilms when it benefits us and disperse them when it doesn’t.

Biofilm formation

The broad topic I was investigating was the process of biofilm formation by a Gram-positive bacterium called Bacillus subtilis. Our hypothesis was that we could learn more about biofilm formation in the species by investigating isolates beyond the laboratory model strain normally investigated in vitro.

I studied how deleting two genes affected biofilm formation in the laboratory model strain and three soil isolates, as it was thought these soil isolates may make more use of the gene products under stress conditions.

I was personally involved in the experiments, under the supervision of Dr Natalie Bamford. I constructed deletion strains and other reporter strains to monitor the transcription of the genes I had deleted. 

I was successful with the strain construction, so I then tested the impact via physiological assays, growing the strains in liquid or solid media to form biofilms, and imaging using a stereoscope. 

I was tasked with creating a poster to show at a poster symposium with other summer school students at the University, in which I won runner-up for best poster. I also participated in an outreach event in the local community.

Interesting results

My findings are not definitive and further testing is needed to verify my results. However, I did gain some interesting results. We observed an effect on biofilm morphology in the soil isolates after the genes were deleted, hinting that the products may be being utilised by these bacteria, but not the laboratory strain. 

Within the reporter strains, there was only a very low level of transcription observed. However, this could be due to the bacterial cells only needing a low amount of the protein products, or it could be that the reporter is not working correctly. 

More biological repeats and further testing in a broader range of stress conditions would be needed to come to any kind of definitive conclusion.

As this bacterium often associates with plant roots, maybe the products involved in biofilm formation could be involved in certain conditions found around plant roots. If it is a response to stress such as nutrient deprivation, toxins, invading pathogens etc, then testing for this particular exopolysaccharide in the soil could be an early indication that something is going wrong in the soil of plants and could lead to preventative measures.

Next steps

Next, I am doing my honours project with Dr Daniel Neill’s lab studying Streptococcus pneumoniae, as I wanted to try to work with a human pathogen and do cross-disciplinary work with immunology as well.

My least favourite job in the lab was going through all the pictures of the bacterial biofilms and trying to collate them into figures. When all the biological and technical replicates were done of the different assays, I ended up with close to 1,000 pictures in total. 

I guess this was a case of suffering from success as I had lots of data to use for my poster, but it was still a bit of a pain to go through so many!

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