Microbes produce millions of organic compounds of low molecular weight--a world of very diverse chemical and biological ecology. We propose that, at the low concentrations likely to be found in the environment, the majority of these compounds play important roles in the modulation of metabolic function in natural microbial communities. The biological diversity is reflected by distinct target responses affecting a variety of transcription regulatory networks by different mechanisms. This provides the basis of chemical signalling processes in the microbial world and may well extend into many prokaryote-eukaryote interactions.