USING MICROFLUIDICS TO STUDY MAGNETOTACTIC BACTERIA by Saeed Rismani Yazdi A thesis submitted to the Department of Chemical Engineering In conformity with the requirements for the degree of Doctor of Philosophy Queen’s University Kingston, Ontario, Canada (September, 2019) Copyright © Saeed Rismani Yazdi, 2019 i Abstract The purpose of this thesis was to investigate the swimming behavior of magnetotactic bacteria 1) in flow conditions and 2) in porous media; and further 3) to exploit their unique characteristics towards bio-actuation of small droplets. Bacteria are found in every habitable niche on Earth. In their planktonic lifestyle they often inhabit dynamic environments where their motility is influenced by flow and the proximity to different surfaces. Recently, considerable interest has been demonstrated in the use of bacteria to perform complex tasks, such as carrying cargo for targeted drug delivery. Magnetotactic bacteria (MTB) found in both freshwater and marine environments can orient to, and swim along, the geomagnetic field lines, a behavior called magnetotaxis. While foraging in their native habitats, their ultimate swimming path originates from the competition between magnetotaxis and hydrodynamic influences related to flow and nearby surfaces. MTB have advantages over other bacteria as microbiorobots for controlled transport due to their motility and steerability. However, how MTB interact with complex environments in aquatic environments has remained poorly defined. Therefore, to better exploit the abilities of MTB for in vivo applications, understanding their behavior in relevant environments is crucial. By using microfluidics and microscopy techniques, I have demonstrated in this thesis that magnetotaxis enables directed motion of Magnetospirillum magneticum over long distances in flow conditions relevant to both aquatic environments and biomedical applications. These MTB can overcome higher flow velocities when directed to swim perpendicular to the flow as compared to upstream. In addition, I showed that magnetotaxis enables MTB to migrate effectively through both homogenous and heterogeneous porous micromodels, interacting with obstacles and overcoming tortuous flow fields. These results bring new insight into MTB navigation in environments similar to their natural habitats, and their potential in vivo applications as microbiorobots. Lastly, I have presented a biologically-driven magnetic actuation of droplets ii on a superhydrophobic surface using MTB. With magnetotaxis for navigation, it is possible to harness MTB to transport microdroplets, thus suggesting their potential for lab-on-a-chip applications. iii Co-Authorship Chapter 2 is co-authored with Dr. Reza Nosrati, Dr. Corey A. Stevens, Mr. David Vogel, Dr. Peter L. Davies, and Dr. Carlos Escobedo, and has been published as: Rismani Yazdi, S., Nosrati, R., Stevens, C.A., Vogel, D., Davies, P.L. and Escobedo, C., 2018. Magnetotaxis enables magnetotactic bacteria to navigate in flow. Small, 14(5), p.1702982. doi: 10.1002/smll.201702982. S.R.Y. designed, fabricated, and tested the microfluidic system, designed and conducted the experiments with magnetotactic bacteria in stagnant and flow conditions, performed microscopy imaging, collected and analyzed the data, prepared figures, and wrote the draft manuscript. R.N. helped with the E. coli experiments and drag analysis. C.A.S. maintained bacterial stocks and provided the bacterial cultures. D.V. helped with magnetotactic bacteria experiments and data analysis. C.E. and P.L.D. provided expertise. S.R.Y., R.N., C.A.S, P.L.D., and C.E. all contributed to the writing and editing of the paper. Chapter 3 is co-authored with Dr. Reza Nosrati, Dr. Corey A. Stevens, Mr. David Vogel, and Dr. Carlos Escobedo, and has been published as: Rismani Yazdi, S., Nosrati, R., Stevens, C.A., Vogel, D. and Escobedo, C., 2018. Migration of magnetotactic bacteria in porous media. Biomicrofluidics, 12(1), p.011101. doi: 10.1063/1.5024508. S.R.Y. designed and fabricated the microfluidic devices, designed and conducted the experiments, performed microscopy imaging, collected and analyzed the data, prepared figures iv and drafted the manuscript. R.N. helped with conducting flow simulations. C.A.S. provided the bacterial culture. D.V. helped with magnetotactic bacteria experiments and data analysis. C.E. provided expertise. S.R.Y., R.N., and C.E. contributed to the writing and editing of the paper. Chapter 4 is co-authored with Dr. Prashant Agrawal, Mr. Erick Morales, Dr. Corey A. Stevens, Dr. Laura Oropeza, Dr. Peter L. Davies, Dr. Carlos Escobedo, and Dr. Richard D. Oleschuk, and has been submitted as: Rismani Yazdi, S.,* Agrawal, P.,* Morales, E., Stevens, C. A., Oropeza, L., Davies, P. L., Oleschuk, R. D. and Escobedo, C., 2019. Facile actuation of aqueous droplets on a superhydrophobic surface using magnetotactic bacteria for digital microfluidics applications, Analytica Chimica Acta, doi.org/10.1016/j.aca.2019.08.020 [* Authors contributed equally]. S.R.Y. designed and fabricated the microfluidic device, prepared bacterial cultures, performed experiments, optical and transmission electron microscopy imaging, collected and analyzed data, prepared figures, and co-wrote the manuscript. P.A. contributed to the droplet actuation experiments, setup preparation, scanning electron microscopy imaging, data analysis, and the writing of the manuscript. E.M. helped with performing droplet actuation experiments and collecting data. C.A.S. provided the bacterial culture. S.R.Y., P.A., P.L.D., C.E., and R.D.O. conceived the project and revised and edited the manuscript. v Acknowledgements First and foremost, I would like to express my sincere gratitude to my current supervisors Prof. Peter L. Davies and Prof. Brian Amsden for their support and guidance throughout my PhD study. My deepest thanks go to both for accepting me as their student. Without their precious help, it would not be possible to finish this journey. I’m very grateful to Peter for his knowledge, advice, understanding, patience, and persistent help. I have learned a lot directly and indirectly from him and I feel honored to have had the chance to work under his supervision. I would like to extend my thanks to Dr. Carlos Escobedo for his support of my early PhD research. Great thanks to my thesis committee members who have agreed to evaluate my thesis and for their valuable suggestions and advice. I would like to thank Queen’s University, Department of Chemical Engineering, Department of Biomedical and Molecular Sciences, and funding agencies (NSERC) for providing resources for my study. Additionally, I am very grateful for the friendship of all of the members of Davies’ Lab, Botterell Hall 6th floor, and Chemical Engineering Department members at Queen’s University. Special thanks to Tyler for his friendship and willingness to talk and for the time he spent helping me in my research. I feel privileged that I have had the chance to work with all these amazing people. I will always be appreciative. Finally, I want to thank my parents, brothers, and most importantly my wife for their constant love, support, and encouragement along the way for my PhD and my life. Without their continuous support, none of my achievements would have been possible. Thank you for everything you have done for me. vi Table of Contents Abstract ............................................................................................................................................ ii Co-Authorship ................................................................................................................................ iv Acknowledgements ......................................................................................................................... vi List of Figures .................................................................................................................................. x List of Tables ................................................................................................................................. xii List of Abbreviations .................................................................................................................... xiii Chapter 1 Introduction ..................................................................................................................... 1 1.1 Interaction of bacteria and flow ............................................................................................. 1 1.2 Interaction of bacteria with surfaces ...................................................................................... 4 1.3 Living at a small scale ............................................................................................................ 5 1.4 Getting bacteria to perform specific tasks .............................................................................. 6 1.5 Magnetotactic bacteria ......................................................................................................... 12 1.6 Microfluidics ........................................................................................................................ 17 1.7 Microfluidics for microbial studies ...................................................................................... 18 1.8 Digital microfluidics ............................................................................................................ 20 1.9 Thesis Objectives ................................................................................................................