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c-di-GMP is a cellular second messenger that regulates diverse bacterial processes, including swimming, biofilm formation and virulence. However, in  Stenotrophomonas maltophilia , a nosocomial pathogen that frequently infects immunodeficient or immunoincompetent patients, the regulatory function of c-di-GMP remains unclear. Here we show that BsmR is a negative regulator of biofilm development that degrades c-di-GMP through its EAL domain. Increasing BsmR expression resulted in significant increase in bacterial swimming and decrease in cell aggregation. BsmR regulates the expression of at least 349 genes. Among them, 34 involved in flagellar assembly and a flagellar-assembly-related transcription factor ( fsnR ) are positively regulated. Although BsmR is a response regulator of the two-component signaling system, its role in biofilm formation depends on the expression level of its respective gene ( bsmR ), not on the protein’s phosphorylation level. A transcription factor, BsmT, whose coding gene is located in the same tetra-cistronic operon as  bsmR , was shown to directly bind to the promoter region of the operon and, through a positive regulatory loop, modulate  bsmR  transcription. Thus, our results revealed that the c-di-GMP signaling pathway controls biofilm formation and swimming in  S. maltophilia , suggesting c-di-GMP signaling as a target in the development of novel antibacterial agents to resist this pathogen.

BsmR degrades c-di-GMP to modulate biofilm formation of nosocomial pathogen Stenotrophomonas maltophilia