Incubation is the time after inoculation and before the mycelium has fully colonized the substrate. This is the time at which the fungus has not yet consolidated its hold on the substrate. During this stage, the nutritious substrate is more susceptible to contamination. Most often, colonization of highly nutritious spawn substrates is completed in an enclosed sterile environment.
Growing mycelium should be kept in an ideal temperature range. For example, P. cubensis colonizes most rapidly between 75-80°F (24-27°C). Temperatures higher than this range may kill the mycelium and encourage growth of contaminants, and temperatures lower than this range may slow down colonization. While the mycelium is growing it will generate a considerable amount of heat and can suffer harm if it is placed in too high of a temperature. If the mycelium is growing from within a jar, the ambient air around the jar should not rise substantially above room temperature since the mycelium in the jar will be a few degrees warmer.
Until recently, it was commonly held that maintaining a higher ambient temperature was necessary to accelerate mycelium growth. Various incubation techniques such as the heat bomb incubator and tub-in-tub incubator were developed for this purpose. Unless the room where a set of jars are incubating is below 72°F or 22°C, an incubator should not be necessary. Even in cold rooms, simply placing the incubating jars on top of a large appliance like a refrigerator will provide sufficient heat.
A commonly held belief among growers is that mycelium will grow faster in total darkness. There is no data to support this premise; however, significant exposure to direct UV light from the sun can be detrimental. Light is a secondary trigger for initiating fruiting bodies. Artificial or ambient light is sufficient light for the incubation period.
Gas exchange occurs during incubation by exchanging air from within the substrate and external air. Natural temperature fluctuations between night time temperatures and day time temperatures will cause gasses to exchange. Mycelium produce carbon-dioxide and can stall if there is not sufficient gas exchange.