Treating the chicken run?

Feces accumulation does need to be controlled somehow. Left to accumulate, they will harbor parasites and bacteria. There are various ways to manage a run. Some of us install sand as long as the run can be kept dry. This allows for daily scooping of the run with a cat box implement. This is how I manage my run. All feces are continually removed over the course of the day every time I visit my chickens.

Others employ the deep litter method. This is a composting technique that allows the accumulated feces to be broken down my microbes in the litter. This requires good drainage and constant disruption of the material so it doesn't develop anaerobic conditions which can lead to deadly bacteria growing in the bottom level.

The method you choose depends on your drainage and your own lifestyle - how much time you choose to devote to it.
 
Sounds like a very good plan. The smell will tell you if this is working. A chicken run shouldn't have a smell that is overpowering. Conveniently, bacteria lets us know by their smell when they are getting out of hand and may becoming hazardous to everyone's health.
 
Wood chips, the kind you get free from tree service company trucks not the pine shavings you get in bales from feed supply stores, will help break down feces and keep things dry. A good 4-6 inches in the run works perfectly. Feces washes through to the ground below. Wood chips keep everything dry above. As chips deteriorate it acts as the “brown” portion of a compost pile which keeps odor down. It all drains through the chips creating rich soil below which you can use in your garden. Best time to harvest that soil and put it on your garden bed is fall. It will mellow and prepare your garden by springtime.
 

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