Prochlorococcus MED4 has, with a total of only 1,716 annotated protein-coding genes, the most compact genome of a free-living photoautotroph. Although light quality and quantity play an important role in regulating the growth rate of this organism in its natural habitat, the majority of known light-sensing proteins are absent from its genome. To explore the potential for light sensing in this phototroph, we measured its global gene expression pattern in response to different light qualities and quantities by using high-density Affymetrix microarrays. Though seven different conditions were tested, only blue light elicited a strong response. In addition, hierarchical clustering revealed that the responses to high white light and blue light were very similar and different from that of the lower-intensity white light, suggesting that the actual sensing of high light is mediated via a blue-light receptor. Bacterial cryptochromes seem to be good candidates for the blue-light sensors. The existence of a signaling pathway for the redox state of the photosynthetic electron transport chain was suggested by the presence of genes that responded similarly to red and blue light as well as genes that responded to the addition of DCMU [3-(3,4-dichlorophenyl)-1,1-N-N-dimethylurea], a specific inhibitor of photosystem II-mediated electron transport.The acclimation of plants and phototrophic microorganisms to the ambient light climate is crucial for survival. All photosynthetic organisms respond to changes in light, including changes in light quantity and quality, i.e., wavelength, by regulating their gene expression. Adaptations to light color detection involve red-light (RL)-, green-light (GL)-, and blue-light (BL)-absorbing receptors, such as phytochromes, cryptochromes, rhodopsins, and xanthopsins (16). Photoreceptors are common to both eukaryotes and prokaryotes, playing important roles in processes such as phototaxis, circadian regulation, and the regulation of flavonoid and alkaloid synthesis (13,17,50).Prochlorococcus is a marine oxyphotobacterium that thrives in the vast oligotrophic gyres of the open ocean between 40°N and 40°S. In these areas, it numerically dominates the phytoplankton, accounting for up to 50% of the total chlorophyll (40, 51). Light appears to have been one of the most important environmental factors driving the speciation and adaptation of Prochlorococcus (36). In the natural environment, Prochlorococcus cells occur from the water surface down to about 200 m (39), experiencing differences in light intensity of over 4 orders of magnitude and a strong spectral shift from white light (WL) to blue light with increasing depth. The ability to grow over this broad range of light intensities is attributed, in part, to the existence of distinct "ecotypes" that have different light optima for growth and different relative abundances with depth in the ocean (1, 9, 24, 53, 56) and constitute distinct phylogenetic clades (24,35,38,44,52).Little is known about photoreceptor-mediated light regulation in Prochloroco...