One major natural role of micro organisms such as bacteria and protozoa is to help with the decomposition of organic material, and to act as a converter of organic waste found in bodies of water, into less harmful or polluting substances.
Both of these roles in nature make micro-organisms a vital part to the environment and the cycle of life.
Certain gasses such as carbon dioxide and nitrogen are also emitted by micro-organisms, another vital component to the balance of nature.