Successful biogas production is based on stable or adaptable microbial community structure and activity which depends on type of substrate used and several physico-chemical conditions in the bioreactor. Monitoring those and the dynamics of microbiota is important for planning and optimizing the biogas process, avoiding critical points and reaching the maximum methane yield. Methanogens are extremely difficult to study with culture-based methods. Molecular methods for microbial community structure analysis in biogas reactors, which offer qualitative and quantitative information on bacterial and archaeal species and their microbial community changes, and causes for process instability are surveyed in this review. For comparative studies semi-quantitative, rapid and cheap techniques like T-RFLP, DGGE and TGGE are used. More laborious and expensive techniques with high-throughput like semi-quantitative FISH and DNA microarrays and also quantitative techniques like qPCR and sequencing are used for phylogenetic analysis. Technique type adequacy for certain study depends on what information is needed and on several advantages and disadvantages every technique possesses.
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