Incubation of agar plates [edit]. Plates are incubated upside down to prevent drops of condensation collecting on the inoculated surface. Some plates are incubated at 37° C in a 5% CO 2 atmosphere: the temperature and conditions at which some of the body's bacteria will grow.Special incubators can maintain these conditions.ungi, and some bacteria (e.g. Yersinia sp.), should be incubated slightly cooler. This is usually 30 °C, and room air often is used. Yoghurt bacteria grow at much higher temperatures (typically ~45 °C). They are therefore particulally safe to use when teaching microbiology, especially to children.