Joshua Tamayo

Bioengineering (BIOE)

Ph.D Dissertation Defense

Cell morphology and cell-fluid interactions affects colony strategy and propagation in Serratia marcescens swarms

Abstract
   Swarming is a multicellular mode of motility common to flagellated bacteria species which enables coordinated rapid surface translocation, expansion, and colonization. The swarming state displays multiple characteristics resembling active matter systems, most importantly intense and persistent long-ranged clusters and strong velocity fields with significant vorticity. Individual bacteria change phenotype to initiate this state, where the bacteria elongate and increase the number of flagella to increase speed. A key limitation of many studies is understanding the role of morphological change, as well as fluid hydrodynamics that cannot be decoupled from other factors in experiments. Studying these mechanisms is necessary to understand better the factors governing swarming and how the onset of swarming may be controlled.
   
   In this dissertation, I report on dilute & dense systems of the novel swarming species, Serratia marcescens and simulate their behavior in silico with a minimal, agent-based self-propelled rod (SPR) model. In dilute systems, I focus on the role of cell length and hydrodynamics on their collective motion and clustering ability while in dense systems, I report on the swarm front moving through movable, frictional domains of immotile (passive) bacteria. In dense systems, the active-passive interface between the two phases has a definable shape that constantly changes as the active swarm penetrates the passive region. The active region directly adjacent to the boundary consists of large, periodic vortices that continuously convect immotile cells away from the interface, allowing the active swarm to move into that territory. A simple, weak inclusion of hydrodynamics greatly benefits the ability of swarm clusters to remove passive rods and material, while neglecting hydrodynamics creates finger-like clusters that cannot move passive material as efficiently. Strong hydrodynamic interactions can destabilize large-scale structures, due to significant fluid and velocity gradients that depress and prevent persistent clustering. Increases in aspect ratio enhance overall cluster size and cluster persistence time. Finally, I conclude with a short method developed to image pre-swarming bacteria and discuss how statistics obtained from those images may further advance our knowledge of swarming.

Biography
   Joshua Tamayo is a Ph.D. candidate in Arvind Gopinath’s research group. Before joining the Bioengineering graduate program, he received his B.S. in Mechanical Engineering from UC Merced in 2018. While earning his bachelor's degree, he began research with Professor Arvind Gopinath which inspired him to continue his research in graduate school. Joshua’s research has focused on understanding and modeling how bacteria swarming initiates and how the unique features of swarms enable rapid surface motility. His work has been presented at several national conferences, including the annual meetings of the Biophysical Society and the American Institute of Chemical Engineers. Joshua has also been heavily involved in teaching and outreach with the Center for Cellular and Biomolecular Machines, garnering the scientific interest of visiting K-12 students from around the California Central Valley.