To characterise the physiological state of cells during adaptation to osmotic stress, we decompose the dynamic regulatory network of E. coli into subgraphs. We then compare the results of E. coli and Salmonella. Beside the sigma factor associated with stress, the response involves global regulators that modify nucleoid conformation which has been shown to be different in the two bacteria. In Salmonella, some genes involved in osmotic stress are also linked to virulence regulation. We conclude that decomposition of regulatory networks into subgraphs as a function of environmental conditions may be a useful representation of the physiological state of bacteria.