  We investigate the effects of bacterial activity on the mixing and transport
properties of a passive scalar in time-periodic flows in experiments and in a
simple model. We focus on the interactions between swimming E. coli and the
Lagrangian Coherent Structures (LCSs) of the flow, which are computed from
experimentally measured velocity fields. Experiments show that such
interactions are non-trivial and can lead to transport barriers through which
the scalar flux is significantly reduced. Using the Poincar\'e map, we show
that these transport barriers coincide with the outermost members of elliptic
LCSs known as Lagrangian vortex boundaries. Numerical simulations further show
that elliptic LCSs can repel elongated swimmers and lead to swimmer depletion
within Lagrangian coherent vortices. A simple mechanism shows that such
depletion is due to the preferential alignment of elongated swimmers with the
tangents of elliptic LCSs. Our results provide insights into understanding the
transport of microorganisms in complex flows with dynamical topological
features from a Lagrangian viewpoint.
