  Concentrated suspensions of swimming microorganisms and other forms of active
matter are known to display complex, self-organized spatio-temporal patterns on
scales large compared to those of the individual motile units. Despite
intensive experimental and theoretical study, it has remained unclear the
extent to which the hydrodynamic flows generated by swimming cells, rather than
purely steric interactions between them, drive the self-organization. Here we
utilize the recent discovery of a spiral-vortex state in confined suspensions
of \textit{B. subtilis} to study this issue in detail. Those experiments showed
that if the radius of confinement in a thin cylindrical chamber is below a
critical value the suspension will spontaneously form a steady single-vortex
state encircled by a counter-rotating cell boundary layer, with spiral cell
orientation within the vortex. Left unclear, however, was the flagellar
orientation, and hence the cell swimming direction, within the spiral vortex.
Here, using a fast simulation method that captures oriented cell-cell and
cell-fluid interactions in a minimal model of discrete-particle systems, we
predict the striking, counterintuitive result that in the presence of
collectively-generated fluid motion the cells within the spiral vortex actually
swim upstream against those flows. This is then confirmed by new experiments
reported here, which include measurements of flagella bundle orientation and
cell tracking in the self-organized state. These results highlight the complex
interplay between cell orientation and hydrodynamic flows in concentrated
suspensions of microorganisms.
