Summary: Particle methods are very convenient to compute transport equations in fluid mechanics as their computational cost is linear and they are not limited by convection stability conditions. To achieve large 3D computations the method must be coupled to efficient algorithms for velocity computations, including a good treatment of non-homogeneities and complex moving geometries. The Penalization method enables to consider moving bodies interaction by adding a term in the conservation of momentum equation. This work introduces a new computational algorithm to solve implicitly in the same step the Penalization term and the Laplace operators, since explicit computations are limited by stability issues, especially at low Reynolds number. This computational algorithm is based on the Sherman-Morrison-Woodbury formula coupled to a GMRES iterative method to reduce the computations to a sequence of Poisson problems: this allows to formulate a penalized Poisson equation as a large perturbation of a standard Poisson, by means of algebraic relations. A direct consequence is the possibility to use fast solvers based on Fast Fourier Transforms for this problem with good efficiency from both the computational and the memory consumption point of views, since these solvers are recursive and they do not perform any matrix assembling. The resulting fluid mechanics computations are very fast and they consume a small amount of memory, compared to a reference solver or a linear system resolution. The present applications focus mainly on a coupling between transport equation and 3D Stokes equations, for studying biological organisms motion in a highly viscous flows with variable viscosity.