Ensembles of magnetotactic bacteria are known to interact hydrodynamically and form swarms under the influence of external magnetic fields. We describe the synchronization of puller type magnetotactic bacteria in a rotating magnetic field by representing the bacteria as hydrodynamic force dipoles. Numerical simulations show that at moderate values of the hydrodynamic interaction parameter large ensembles of asynchronously rotating bacteria randomly eject propagating doublets of synchronized bacteria. We quantitatively analyze the dynamics of the doublets and show that an important role in the formation of these propagating structures is played by the parameters characterizing the possible trajectories of a single bacterium in a rotating magnetic field.