Bachelor Research Project with Sofie the Bacterium: Tiny Microbe, Big Potential for Sustainable Dairy
On the seventh floor of the University of Groningen's biology building, everyone seems to be talking about "Sofie." But Sofie isn’t a student or a scientist—she’s a hydrogen-oxidizing bacterium at the heart of an exciting research project. As part of their Bachelor Research Project, Sara Khong and Eliza Zylstra have been working with Xanthobacter sp. SoF1, affectionately nicknamed Sofie, to explore how it might one day produce milk proteins from just CO₂ and hydrogen—paving the way for more sustainable food production. Now, they share their experiences in the second chapter of the Behind the HYDROCOW blog series!
In the corridors of the seventh floor of the biology building at the University of Groningen, you’ll hear many students and scientists walking around talking about Sofie. “Sofie this, Sofie that…” During our Bachelor Research Project, we’ve gotten to know Sofie pretty well. And no, Sofie isn’t our lab colleague, or our project supervisor, but rather a personified nickname for the bacterium that our lab works with. Xantobacter sp. SoF1, known as Sofie around here, is a species of non-model hydrogen-oxidising bacteria, whose only nutritional requirement is CO2 and H2. So, it can pretty much grow on thin air.
The HYDROCOW project aims to engineer this bacterium to make it produce the milk protein beta-lactoglobulin, for a more sustainable and circular food production. One of the challenges in getting SoF1 to produce beta-lactoglobulin is engineering a secretion system that can efficiently produce a large amount of the protein and release it into the medium. To secrete protein out of a cell, bacteria attach a small signal peptide to the protein destined for export. This signal is a bit like an address on a postcard, telling the cell’s machinery (i.e. the postman) how to process the protein and where to send it.
“But these seemingly meaningless clear liquids actually contain the crucial DNA parts needed to express the gene of interest in SoF1.”
For our Bachelor’s project, we are testing different secretion signals by inserting them into SoF1’s DNA, and checking whether they can effectively secrete a cellulase reporter protein. The first weeks of our project were spent behind our laptops, researching various articles related to the engineering of hydrogen-oxidizing bacteria. After having set up a plan for how we were going to conduct our project in the upcoming weeks, it was time to head into the lab for some hands-on action.
A typical day in the lab involves a lot of pipetting tiny droplets of what looks like water into different tubes. But these seemingly meaningless clear liquids actually contain the crucial DNA parts needed to express the gene of interest in SoF1. We patiently wait for shiny yellow colonies to grow on our petri-dishes, indicating to us that SoF1 is growing happily. Then we stain the plates red and cross our fingers in the hope to see protein secretion.
But plans don’t always go as expected. After presenting our preliminary results to our lab colleagues, we receive insightful and enriching feedback, enabling us to troubleshoot our protocols and overcome our challenges. In between intensive lab days and writing our thesis we have had the chance to attend interesting group discussions with other research groups from the university, broadening our knowledge within molecular microbiology. We have gotten to see what other scientists study, what challenges they face and what challenges they have overcome.
Time flies, and after four weeks in the lab our time here is almost over. Not only have we learned a lot about the role of signal peptides in secretion, but we have also gained a lot of valuable hands-on experience and developed our critical research skills. Working on the HYDROCOW project has been both fun and fulfilling, as we feel that our work has made an impactful contribution - albeit small - in paving the way towards more sustainable food production.
Sara Khong and Eliza Zylstra
Bachelor Students, University of Groningen