Transcriptome response to oxygen tension and light irradiation in Roseobacter denitrificans OCh114

Transcriptome profiles of an aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 grown under different oxygen tension and light irradiation conditions were determined by NimbleGen Prokaryotic Expression array (12x135K). R. denitrificans OCh114 was cultivated in glycerol medium without or with irradiation of near-infrared or blue light. For the aerobic or microaerobic conditions, the cells were grown in glass bottles with continuous bubbling of air or a gas mixture of 2% O2 and 98% N2, respectively. Total RNA was extracted when optical density at 600 nm (OD600) was 0.4-0.42. For the denitrification condition, the medium was supplemented with 20 mM NaNO3 and the cells were grown in side-armed Erlenmeyer flasks. The flasks were sealed with silicone plugs and butyl rubber septa and the headspaces of the flasks were replaced with argon. Total RNA was extracted when OD600 was 0.2-0.23. For the denitrification-shift condition, the medium was supplemented with 20 mM NaNO3 and the cells were grown in baffled Erlenmeyer flasks with rotary shaking at 200 rpm. When OD600 was 0.4, the cultures were moved to vials. After the vials were sealed with butyl rubber septa, the headspaces of the vials were replaced with argon. Total RNA was extracted after cultivation anaerobically for 3 hours. The experiment was performed in duplicate independent cultures.