| Summary: | Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2015. === Cataloged from PDF version of thesis. === Includes bibliographical references. === Marine microbes play a fundamental role in driving ocean ecosystem dynamics and biogeochemistry. While their importance is global in scale, microbial processes unfold at the level of single cells and are intimately dependent on interactions between microorganisms, their neighbors, and the surrounding physical and chemical environment. Furthermore, traditional imaging techniques often provide frozen snapshots of the marine microbial world, yet microbial interactions are inherently dynamic, as for example in the case of motility, chemotaxis, and the encounter of microbes with viruses and animal hosts. These biological processes are frequently driven by physical mechanisms, and our understanding of them can benefit from a focus on the physical ecology of marine microbes. This is the approach pursued in this thesis, by directly applying dynamic imaging and microfluidics, which offer powerful new opportunities to study microbial processes in a time resolved manner and with exquisite environmental control. Through single-cell, live imaging of three fundamental marine microbial processes - motility, chemotaxis and viral adsorption - we demonstrate how capturing previously unseen biophysical processes in microbial ecology at their natural timescales can both shed light on unexplained mechanisms and provide robust quantifications of interaction rates. We first study a newly discovered nanoscale motility adaptation in the marine bacterium Vibrio alginolyticus using high-speed imaging. We found that marine bacteria can exploit a buckling instability of their flagellum to change direction during swimming, achieving the same functionality as multi-flagellated cells, but with the cost of synthesizing and operating only one flagellum. This finding not only reveals a new role of flexibility in prokaryotic flagella, but also highlights the exquisite motility adaptations of marine microbes to the resource-poor environment of the ocean. We then determine how this motility adaptation affects the cells' ability to climb chemical gradients ('chemotaxis'). We found that, counter- to current models, chemotaxis in V. alginolyticus is speed-dependent. Faster cells exhibited not only faster chemotactic migration, but also tighter accumulation around the resource peak. This result adds a new dimension to our understanding of bacterial chemotaxis pathways, by demonstrating that swimming speed can be an important and counter-intuitive control parameter in how marine microbes encounter and exploit chemical resources. Finally, we consider an encounter process that is motility-independent - that between a nonmotile host and a virus. Using the globally abundant marine cyanobacterium Prochlorococcus and a cyanobacterial virus ('cyanophage') as a model system, we directly imaged the encounter and adsorption dynamics of the virus and the host at the level of single cells, using dual-wavelength epifluorescent microscopy. By applying this non-invasive approach to quantify thousands of encounter events using automated image acquisition and analysis, we directly measured the rate at which viruses encounter and adsorb to hosts. We found that the probability of adsorption is considerably lower than was obtained with traditional, bulk measurement approaches, suggesting the need for a revision of viral infection dynamics in marine ecosystem models and opening the door for studies of microbial individuality in the context of viral infection. In summary, this thesis demonstrates that physical processes in microbial ecology, studied by means of new approaches including microfluidics and dynamic imaging at the single-cell scale, can contribute fundamental new insights into the ecology of marine microbes. === by Kwangmin Son. === Ph. D.
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