This study analyzed dairy wastewater fermentation in convection- and microwave-heated hybrid reactors at loadings of 1 and 2 kg COD/(m3 d) and temperatures of 35 and 55 °C. The biomass was investigated at a molecular level to determine the links between the operational parameters of anaerobic digestion and methanogenic Archaea structure. The highest production of biogas with methane content of ca. 67% was noted in the mesophilic microwave-heated reactors. The production of methane-rich biogas and the overall diversity of Archaea was determined by Methanosarcinaceae presence. The temperature and the application of microwaves were the main factors explaining the variations in the methanogen community. At 35 °C, the microwave heating stimulated the growth of highly diverse methanogen assemblages, promoting Methanosarcina barkeri presence and excluding Methanosarcina harudinacea from the biomass. A temperature increase to 55 °C lowered Methanosarcinaceae abundance and induced a replacement of Methanoculleus palmolei by Methanosarcina thermophila.
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