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Abstract
Anaerobic digestion (AD) is a complex biological process, and the microbial diversity and dynamics within the reactor needs to be understood and considered when process optimization is sought after. Microbial interactions such as competition, mutualism, antagonism and syntrophism affect the function and the survival of single species in the community; hence, they need to be understood for process improvement. Although the relationship between process performance and the microbial community structure is well established, changes in the community might occur without detectable changes in gas production and reactor performance. Recent molecular-based studies have highlighted the complexity of AD systems revealing the presence of several uncultivated species and the need for further research in this area. However, this information is still rarely used for process optimization. The integration of next generation sequencing technologies, such as 454-pyrosequencing, with other techniques, such as phospholipid-derived fatty acids analysis, can provide a holistic understanding of the microbial community. In addition, the in-depth phylogenetic resolution provided can aid environmental ecologists and engineers to better understand and optimize the AD process and consolidate the information collected to date.