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A verm layer is not needed in my opinion if you use the right equipment instead of using jars with innoculation holes in them use filter patch tops for your jars also if you use verm then you cannot shake them as recomended, one of the bennifits of using rye. As far as organic rye is concerned I am not 100% but I use only organic because I would think that the pecticedes and mostly FUNGICIDES that farmers use on non organic produce would have adverse reactions to the mycellium. Hope I could be a little help.
1) Yes. 2) You would be better off using half-full quart jars fitted with either a FP filter disc or an improvised filter lid as described in this thread. I use this method (except using birdseed instead of rye grain; same principle) and it works great for me. If you do decide to use a vermiculite layer (a method which I would advise against), you should definately use a Ramsey seal (using tin foil to hold the vermiculite), as I would imagine the vermiculite would easily fall through the spaces in between the kernels of grain if it were layered directly on top.
Isn't everyone glad the Shroomery is back up again?!
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