The whole-genome sequence of the endosymbiotic bacterium Azorhizobium caulinodans ORS571, which forms nitrogen-fixing nodules on the stems and roots of Sesbania rostrata, was recently determined. The sizes of the genome and symbiosis island are 5.4 Mb and 86.7 kb, respectively, and these sizes are the smallest among the sequenced rhizobia. In the present study, a whole-genome microarray of A. caulinodans was constructed, and transcriptomic analyses were performed on free-living cells grown in rich and minimal media and in bacteroids isolated from stem nodules. Transcriptional profiling showed that the genes involved in sulfur uptake and metabolism, acetone metabolism, and the biosynthesis of exopolysaccharide were highly expressed in bacteroids compared to the expression levels in free-living cells. Some mutants having Tn5 transposons within these genes with increased expression were obtained as nodule-deficient mutants in our previous study. A transcriptomic analysis was also performed on free-living cells grown in minimal medium supplemented with a flavonoid, naringenin, which is one of the most efficient inducers of A. caulinodans nod genes. Only 18 genes exhibited increased expression by the addition of naringenin, suggesting that the regulatory mechanism responding to the flavonoid could be simple in A. caulinodans. The combination of our genome-wide transcriptional profiling and our previous genome-wide mutagenesis study has revealed new aspects of nodule formation and maintenance.The symbiosis between rhizobia and legumes results in the formation of nitrogen-fixing nodules. The symbiotic interaction begins with the induction of bacterial nod genes by flavonoids secreted from the plant roots (8). The nod genes encode proteins that synthesize the nodulation (Nod) factor, which initiates many developmental changes, such as root hair curling and root cell division required for the formation of the nodule primordium in the host plant early during the nodulation process (8,24,50). Bacteria are entrapped in the curled root hair and subsequently infect the root hair through infection threads made of the plant cell wall. Upon release from the infection threads, bacteria invade the plant cell cytoplasm, where they differentiate into bacteroids and provide ammonium to the host plant by reducing atmospheric dinitrogen in exchange for carbon and amino acid compounds (16,49,53). It has been deduced that multiple stages exist in the establishment of nitrogen-fixing symbiosis. To identify novel genes involved in various stages of symbiosis, transcriptomic studies based on complete genome sequences were performed using Sinorhizobium (1, 2, 5, 9), Mesorhizobium (71), and Bradyrhizobium (10,42,54).Azorhizobium caulinodans ORS571 is a microsymbiont of Sesbania rostrata (18)(19)(20). Nitrogen-fixing nodules are formed by A. caulinodans on the stems as well as on the roots of S. rostrata. Stem nodules occur at the site of adventitious root primordia located on the stems after crack-entry invasion by A. caulinodans (70). During...