Envisioned applications of microswimmers often imply their use in complex environments that may present a variety of obstacles, confinement to pores, fluid flows, complex fluids, or other complications ( Bente et al., 2018 Felfoul et al., 2016b) compared to the motion in simple aqueous solutions that is typical under lab conditions ( Bennet et al., 2014 Lefèvre et al., 2014 Popp et al., 2014). Microswimmers and other self-propelled microscopic particles have received extensive attention in recent years, both directed toward the fundamental physical principles of their propulsion mechanisms and their rich collective behavior ( Bechinger et al., 2016 Ezhilan et al., 2015 Lauga and Powers, 2009), and toward their potential for environmental and biomedical applications including as drug carriers, infertility cures, bioremediation, or MRI imaging ( Bente et al., 2018 Felfoul et al., 2016a Felfoul et al., 2016b Ford and Harvey, 2007 Magdanz and Schmidt, 2014 Peyer et al., 2013b Pieper and Reineke, 2000 Schwarz et al., 2017 Sherwood et al., 2003 Timmis and Pieper, 1999). In this way, our work establishes a basis for the analysis and prediction of microswimmer motility in more complex environments. We also analyze the pronounced cell-to-cell heterogeneity, which makes single-cell tracking essential for an understanding of the motility patterns.

Combining these experimental observations with simulations using a variant of an active Brownian particle model, we explain the variety of trajectories by the interplay between the wall interactions and the magnetic torque. We trap single cells in micrometer-sized microfluidic chambers and track and analyze their motion, which shows a variety of different trajectories, depending on the chamber size and the strength of the magnetic field. In this work, we investigate magnetically steerable microswimmers, specifically magnetotactic bacteria, in strong spatial confinement and under the influence of an external magnetic field. The simple aqueous conditions typically studied in the lab differ strongly from those found in these environments and often exclude the effects of small volume confinement or the influence that external fields have on their motion. The same is true for microswimmers in envisioned biomedical applications. Swimming microorganisms often experience complex environments in their natural habitat.

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