How to use molecular biology tools for the study of the anaerobic digestion process

Anaerobic digestion is used with success for the treatment of solid waste, urban and industrial effluents with a concomitant energy production. The process is robust and stable, but the complexity of the microbial community involved in the process is not yet fully comprehensive. Nowadays, the study of this complex ecosystem is facilitated by the availability of different molecular tools, but it is very important to choose the adequate tool to answer specific questions. The aim of this review is to describe different molecular techniques, indicate the questions that can be addressed by each technique, enumerate their limitations and give practical advices for their use. Examples of how the molecular tools have been used to address various questions in anaerobic digestion are presented. The key point now is to apply all this information to improve anaerobic digestion. The integration of concepts of microbial-ecology, environmental-engineering, modeling and bioinformatics is currently necessary.