Microbial transport is paramount in environmental and industrial sciences, whether they mediate essential biogeochemical processes in sediments or end up clogging diesel filters. To colonize these environments, they have developed various strategies to self-propel. This motion can be biased towards favorable niche, using their flagellar apparatus to orient their swimming directions. This talk will present some recent results concerning microbial motility in viscosity gradients and porous media flows. The consequences of these micro-scale phenomena on the large scale transport will be discussed.