Microbiomes in bioenergy production: From analysis to management

Currently, bioreactors exploiting natural microbial communities, that is, microbiomes, for bioenergy production are almost exclusively operated based on bulk parameters and empirical expert knowledge. The microbiome of these bioreactors often remains a black box, that is, its composition and function are only analyzed retrospectively (mostly in a case of failure). Here, on-time microbiome analysis can allow a proactive process management. However, today's sophisticated molecular ecology methods appear inaccessible for the routine analysis of reactor microbiomes in bioenergy production. This review analyzes the requirements of methods for routine microbiome diagnostics. Especially the ability of current molecular and cell based methods to derive structure-function-relationships, that is, correlations between the microbial community structure and dynamics and the reactor performance, are emphasized and key-criteria for routine on-site monitoring are defined. Finally, a critical assessment of selected methods for microbiome monitoring is performed focusing on (i) the production of biogas in anaerobic digesters and (ii) the production of the biofuel precursor n-butyrate.