With my gardens I add chicken crap and horse manure. Those micro organisms live pretty deep in the soil. I doubt you did much harm to them. I put 20 trashcans of leaves on my main garden today. In 2 weeks it will look like 1 cans worth. As a side note a shovel of soil from the mountians will contain different benificial bacterias and fungus. Every 4-5 years 1 shovel is enough to start a good colony.