I realize all this seems rather moot, though is a still a question asked. Notwithstanding Dichromacy, sporadic appearance of these dark areas esp. in aged substrate jars is distinctly blue. Probably a lack of gas exchange over time. When in doubt, contamination evokes a feeling of uneasiness and alarm more than anything. Pay attention to your feelings aside from what you are looking at. In no instance ever agitate suspect grain jars.
The substrate is perfectly clean. There is no contamination. However, you should do something with it. NOTE: hydrate drying substrates with sterile clean water. Do not use tap water expecting to extend shelf life. At this stage of storage is a perfect time to make as much liquid culture as you'd like. Simply drop a few grains in your sweetened solution. LC does not store well with or without gas exchange and other preservative methods for long periods; imo best reserved for clone runs. Inoculate pasteurized substrate directly from syringe. Mix well and incubate.
I don't know that I agree with Stamet's contention, as I've experienced no evident loss of potency as a result of bruising, as to the contrary would rather seem, like extruding sap, or palpating a fruit for ripeness the best way to prime the fruit for ingestion.
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