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Someone I know recently injected 6 grain jars with 2 different strains on a millett substrate. The first time he/she was not happy with the results after pc'ing, so the jars (metal lids and all) were used in the 2nd attempt. Happy with the consistency of the grain (which was soaked 18 hours prior to pcing) the jars cooled over night, and were then injected. After a week of growth all seemed well, then on the same day someone I know noticed that on the bottom of all of the jars there was a rust color that had formed. Each jar had 3 areas of the color (which to my friends knowledge has not spread nor gotten any bigger). Each jar also had 3 innoculation holes punched into them, leading my friend to believe that it could be rust that resulted from the lids being cooked twice, since each rusty colored area is supposedly near the innoculation hole. My friend did not notice any odd smell in the jar that she/he took out of the inncubation chameber, and it does not have the characteristics of baccauilus (sp). Does this rust theory seem plausible? Could it be something else. Sorry no pics.
Yes, it's a common occurrence. When the lids get rusty, they drop the rust to the substrate, so your theory is probably correct. Don't worry too much about it but keep an eye on those spots and see how they evolve, as it could be something else.