1. Stress is a major component of natural selection in soil ecosystems. The most prominent abiotic stress factors in the field are temperature extremes (heat, cold), dehydration (drought), high salinity and specific toxic compounds such as heavy metals. Organisms are able to deal with these stresses to a certain extent, which determines the limits of their ecological amplitudes. Functional genomic tools are now becoming available to study stress in ecologically relevant soil organisms. 2. Here we give an overview of transcriptomic studies aiming to elucidate how plants and soil invertebrates respond and adapt to a stressful environment. The picture emerging from signalling pathways and transcription factors identified in transcription profiling studies suggests that there is a large overlap of genomic responses to drought, salinity and cold; however, heat and heavy metals trigger different stress response pathways. 3. The heat shock response and the oxidative stress response seem to represent universal components of the environmental stress response (ESR). Furthermore, the commonality across plants and animals seems to be higher in effector genes than in transcriptional regulators. 4. Finally, adaptation to stress factors in soil seems to evolve through enhanced constitutive transcription of otherwise stress responsive genes both in plants and animals. © 2007 The Authors.