The future of single-cell environmental microbiology

One of the key objectives in environmental microbiology is to couple identity and function of microorganisms in soil, water, sediment or other ecosystems. The field has come a long way over the past decade, both with respect to ‘who is there?’ and to ‘what are they doing?’ The coupling between identification and activity, however, remains the weakest point. Existing approaches need to be further developed and combined. It is a dream to one day do experiments with prokaryotes the way that they are done with higher animals or plants, at the level of the individual organism. There are indeed already methods in use that enable this to a certain extent. These may be based on pulse‐chase experiments during which the microorganisms have been fed a radioactive or an isotopically heavy meal. Those cells that have taken up the substrate may subsequently be identified, e.g. by a combination of microautoradiography and fluorescence in situ hybridization (MAR‐FISH). MAR‐FISH has the advantage that the active substrate uptake can be related to cells. This is not the case with most methods that combine stable isotope tracers and the analysis of DNA, RNA or biomarkers. The fact that MAR uses radioactivity, however, limits its use to those elements that have a radioisotope with a suitable half‐life and excludes the study of other elements such as nitrogen