Periodic Reporting for period 1 - BactoBubble (Microscale investigation of key bacterial phenotypes enhancing collection by rising bubbles and aerial dispersal)
Reporting period: 2018-06-01 to 2020-05-31
First, we investigate whether microbial motility (or ability to swim) increases microbial collection by rising bubbles. Indeed motility sets microbes starkly apart from inert particles, likely promoting collection by increasing the likelihood of encountering bubbles, and also influencing attachment as swimming appendages modify the cell surface properties. Second, we investigate whether starvation of microbes increases microbial collection by rising bubbles. Starving bacteria modify their surface properties and size, which may make them ‘stickier’ and hence enhance collection by bubbles –this might promote dispersal and escape from nutrient poor areas. Aerosolisation could then represent an active stage in the life cycle and ecological dynamics of bacteria in oceans.
To investigate these hypotheses, this project’s goal is to develop a novel microfluidic flow channel containing a pinned bubble, and use advanced optical microscopy to quantify collection rates for a range of microbes on a single bubble in flow. By bringing together pioneering quantitative microscopy and characterisation of flow regimes and microbial surface properties, the proposed research will determine the role of key factors influencing microbial collection by bubbles and develop new mathematical models for microbial aerosolisation.
First, our investigation of the flow patterns of the interface revealed that the attached microbes do not accumulate at the downflow pole of the bubble, as fluid mechanical theory would predict. Instead, the attached microbes are constantly recirculated and distributed over the entire bubble surface. The absence of accumulation points makes the identification of individual cells more delicate: instead of imaging a restricted area at high magnification, knowing that cells located there are effectively attached, we had to image a complete hemisphere to obtain suitable statistics on cell attachment.
Moreover, we found that to distinguish between attached cells and cells flowing just above the bubble surface required the development of advanced image analysis techniques. We developed a novel focus-stacking pipeline for analyzing our fluorescence data, which reconstructs a flattened view of the bubble interface, thus enabling the accurate estimation of the number of attached cells.
Delays due to the COVID-19 pandemic prevented us from completing laboratory experiments investigating the role of microbial motility and starvation on microbial collection by rising bubbles. We plan to use our established techniques to finish testing these hypotheses and ultimately publish our results in peer-reviewed journals. A presentation of this technique at both the Gordon Research Conference and Seminar on Marine Microbes in 2020 was postponed due to the pandemic, and rescheduled to 2022.
A secondary goal of this project was to promote the fruitful interaction of modelling with experimental and field ocean microbial research. I therefore contributed to several projects, providing a theoretical support to experimental work. In particular, I contributed to a mathematical model of the carbon pump, that is the sinking of organic carbon particles in the ocean, which included the novel coupling of sinking speed with microbial degradation observed in the lab. I also provided the theoretical basis to a new quantification of bacterial motility in situ. Both contributions are part of upcoming publications.
This project also provided the opportunity for the principal investigator to train and supervise several BSc and MSc students, and develop and organize outreach events to introduce a young audience to the complexity of microbial life in lakes and oceans, thus more broadly contributing in the effort of scientific education and public outreach.