Microorganisms are responsible for the most biogeochemical cycles that shape the environment of earth and its oceans. So far, only part of these organisms has been well studied, especially those living on earth and more considered from an anthropogenic perspective, e.g causing human diseases or providing useful products and services. Further the inability to generate pure culture has hampered the possibility to study and understand the metabolic processes of many micro-organisms. Recently, advances in molecular biology and -omics technologies are offering new and more exciting perspectives and knowledge of the microbial world, such as to understand the biological communities and function relationships, to identify the diversity of the population; to monitor the effects of environmental factors on the community structures. This review will explore the development, application of the genomics technologies to the microbial biodiversity and microbial ecology monitoring.

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