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Background   Burkholderia cenocepacia  belongs to a group of closely related organisms called the  B. cepacia  complex (Bcc) which are important opportunistic human pathogens.  B. cenocepacia  utilizes a mechanism of cell-cell communication called quorum sensing to control gene expression including genes involved in virulence. The  B. cenocepacia  quorum sensing network includes the CepIR and CciIR regulatory systems.    Results  Global gene expression profiles during growth in stationary phase were generated using microarrays of  B. cenocepacia cepR ,  cciR  and  cepRcciIR  mutants. This is the first time CciR was shown to be a global regulator of quorum sensing gene expression. CepR was primarily responsible for positive regulation of gene expression while CciR generally exerted negative gene regulation. Many of the genes that were regulated by both quorum sensing systems were reciprocally regulated by CepR and CciR. Microarray analysis of the  cepRcciIR  mutant suggested that CepR is positioned upstream of CciR in the quorum sensing hierarchy in  B. cenocepacia . A comparison of CepIR-regulated genes identified in previous studies and in the current study showed a substantial amount of overlap validating the microarray approach. Several novel quorum sensing-controlled genes were confirmed using qRT-PCR or promoter:: lux  fusions. CepR and CciR inversely regulated flagellar-associated genes, the nematocidal protein AidA and a large gene cluster on Chromosome 3. CepR and CciR also regulated genes required for iron transport, synthesis of extracellular enzymes and surface appendages, resistance to oxidative stress, and phage-related genes.    Conclusion  For the first time, the influence of CciIR on global gene regulation in  B. cenocepacia  has been elucidated. Novel genes under the control of the CepIR and CciIR quorum sensing systems in  B. cenocepacia  have been identified. The two quorum sensing systems exert reciprocal regulation of many genes likely enabling fine-tuned control of quorum sensing gene expression in  B. cenocepacia  strains carrying the cenocepacia island.

Reciprocal regulation by the CepIR and CciIR quorum sensing systems in Burkholderia cenocepacia