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I had a casing of brown rice flour cased with coco coir and vermiculite. The first flush was fine, but my second flush I noticed some of the caps were rotting in some places. What kind of problem does this indicate.
That isn't something I would eat. As for the contamination, if indeed it is a contamination (and I think it is, but I need more info on your tek and material used), I thin it may be a Bacterial Blotch:
Yellow to brown lesions form on mushrooms. Typically, spotting occurs at or near the edge of mushroom caps. Blotch occurs when mushrooms remain wet for a period of 4 to 6 hours or longer after water has been applied. The bacterium is spread in air-borne soil particles. Controls include lowering humidity and watering with a 150 ppm chlorine solution (calcium hypochlorite products are used since sodium hypochlorite products may burn caps). If the mushroom stays wet, however, chlorine has little effect since the bacterial population reproduces at a rate that neutralizes the effect of the oxidizing agent. Shiitake caps are affected by a bacterial disease caused by Pseudomonas gladioli (Burkholderia gladioli). Sanitation is a critical component of control measures