Molecular microbiology methods for environmental diagnosis

To reduce the environmental footprint of human activities, the quality of environmental media such as water, soil and the atmosphere should be first assessed. Microorganisms are well suited for a such assessment because they respond fast to environmental changes, they have a huge taxonomic and genetic diversity, and they are actively involved in biogeochemical cycles. Here, we review microbiological methods that provide sensitive and robust indicators for environmental diagnosis. Methods include genomics, transcriptomics, proteomics and metabolomics to study the abundance, diversity, activity and functional potentials of indigenous microbial communities in various environmental matrices such as water, soil, air and waste. We describe the advancement, technical limits and sensitivity of each method. Examples of method application to farming, industrial and urban impact are presented. We rank the most advanced indicators according to their level of operability in the different environmental matrices based on a technology readiness level scale.