Large numbers of microscopic life forms exist in Earth's water, such as glacier meltwater, seawater, sewage. Microorganisms, including archaea, bacteria, fungi and protists (protozoa and algae), dominate the ecological processes. Some of these microbes are key participants in biogeochemical processes which are of great importance to the entire ecosystem. Some microorganisms play an important role in the processes that control water quality, while some are crucially involved in pollution in the environment. Therefore, studying the diversity and community structure of microorganisms in water is crucial to protect the sources of water and develop sewage treatment.