Author Archives: Amrutha Seshadri

Microbe vs. Microbe: My experience at CAZyme lab

It was the spring semester of my Masters programme at Stockholm University when I first contacted Lauren McKee to ask about a potential Masters thesis. From the very beginning, she was welcoming and talked with me at length about the possible projects that I could do for my thesis.  Following our meeting, I had a lecture on “Microbial interactions in the rhizosphere“ from Lauren. A particularly interesting concept to me was manipulating the behaviour of a biocontrol agent (BCA) to perform better in terms of increased growth or increased production of anti-pathogenic enzymes. This manipulation can be achieved by providing carbon sources specific to both the BCA and the plant pathogen. And that is where most commercial biocontrol formulations go wrong. Failing to understand how and what a BCA responds to leads to inefficiency. One of the important research themes at the CAZyme lab is to elucidate the molecular mechanism of nutrient-microbiota interactions: this will help us to create more effective and science-based solutions for sustainable agriculture. In this photo you can see me setting up one of the dozens of six-well agar plates I used during my thesis project!

I decided to work on a 3-week course project to familiarise myself with the ongoing work within Lauren’s group. In this project, I looked at the biocontrol properties of a gram-positive bacterium Bacillus subtilis natto against plant pathogenic oomycetes – Aphanomyces euteiches and Aphanomyces cochlioides – based on a previous thesis and publication from Anna Schönbichler, a former student in the group. During this period, I got to interact with CAZyme group members and other research groups within the Division. The best part is that it was a multicultural environment in the lab and it has been amazing getting to know people from many different backgrounds. 

Working with plant pathogens, in terms of plant protection, has always interested me and I believed that this would be a great opportunity for me. I started my year-long thesis in September 2020 and I worked on the topic “Assessment of Bacillus subtilis natto as a potential biocontrol agent against Aphanomyces euteiches,” which was a continuation of my earlier short project. For my thesis, I grew the bacterium in a variety of carbon sources that were representative of the cell-wall of the oomycete pathogen. This was done in order to gain an understanding of how the bacterium will respond when faced with the “real” pathogen. Following this, the enzymes and proteins produced by the bacterium in response to these carbon sources were analysed for cell wall-degrading activities and their ability to inhibit pathogen growth on an agar plate. This was really a fundamental investigation into bacterial biochemistry. Being a plant biologist, I wanted to understand the dynamics of the relationship between the host plant, pathogen, and biocontrol agent. For this, experiments using pea plants were conducted in growth chambers in a collaborator’s lab in Uppsala. It was found that there was some inhibition when a certain carbon source was used to manipulate B. subtilis natto. But, sufficient data was not produced to conclusively say that this bacterium could potentially be used as a BCA against this particular pathogen. Due to the natural variability in how plants grow, and how they respond to a pathogen, more replicates than I could study in my thesis would likely be required in order to generate statistically meaningful data. However, I believe that this project will serve as a blueprint for further experiments using B. subtilis in combination with other plant pathogens.

The research in Lauren’s group on biocontrol using soil bacteria is absolutely relevant for both the present and future world scenarios. I have to mention that the entire time I spent in the Division of Glycoscience with Lauren and other members was a fantastic learning phase. As a newbie researcher, I made mistakes (quite a few!), but I learnt from them and I couldn’t have asked for a better learning experience. I was able to work very independently within the group, so I figured out how to think ahead and manage my own time. Lauren was very encouraging and seldom lost her patience with me. Throughout my project, I learned better ways to communicate, plan, and truly understand the impact of science in everyday life. Scientific research is infinite, like human stupidity (sic). I have talked to other people working on biocontrol research and they tell me a similar story: there is always one small detail that is left to be discovered. I hope that future group members will continue with this project, avoid making the mistakes I made, optimise, and discover more and more.