Microbial ecology remains one of the fastest moving and exciting research areas in biology and ecology. In the past year, this has been highlighted by the quantity and quality of ecological sessions at the FEMS Microbiology Ecology, are reflected in the increasing numbers of papers submitted to the journal. This can lead to an increase in publication time, and we are grateful to our new publisher, Blackwell, for producing this ‘bumper issue’. During 2006, the impact factor and ranking of the journal increased. We published a Thematic Issue on Rhizosphere Microbiology and two further Thematic Issues are planned for 2007, on Microorganisms in Alpine and Polar Environments and on Ecological Theory and Microbial Ecology. We will also have the first of our Head-to-Head debates in the near future.