Types and influence factors of microbe which take part in the nitrification and denitrification processes are resumed. It is pointed out that benthonic animals in lakes increase the abundance of ammonia oxidizing bacteria in sediments and accelerate the denitrification process in sediments and overlying water. Meanwhile, the intestines of benthonic animals are also the room of denitrification and release N₂O. The structure and diversity of microbe community which take part in the nitrification and denitrification processes are studied. Molecular biology mechanism of nitrification and denitrification is stated. Impacts of benthonic animals on structure and function of microbe community which play role in the nitrification and denitrification processes were also explored.