On page 2568 of this issue, Hatzenpichler and colleagues describe the application of BONCAT (bioorthogonal non-canonical amino acid tagging) (Hinz et al., 2013), a click-chemistry method originally developed to study protein synthesis and localization in neuronal cells, to pure-culture and environmental bacteria and archaea. Click chemistry and other bioorthogonal reactions have been intensively studied by chemists and some biologists for the past 15 years but have been little used as yet by environmental microbiologists. The authors show that click-chemistry amino acid analogues can be taken up by and detected in a range of pure-culture and environmental bacteria and archaea; that cells identified as translationally active by BONCAT are generally also metabolically active by the independent criterion of ammonia incorporation; and that production of proteins induced by an environmental change (heat shock) can be followed over time. BONCAT and other click-chemistry methods offer a promising route towards minimally invasive, cultivation-free investigations of the in situ enzymatic capabilities of microbes in diverse communities.