Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO 2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.Methanogenic archaea (methanogens) are ubiquitously present in anaerobic environments, such as digestive tracts, paddy fields, and aquatic sediments, and play an important role in anaerobic degradation of organic matter and the global cycle of carbon 1, 2 . Additionally, they contribute to human society via their ability to produce methane gas in anaerobic digesters 3 . In methanogenic ecosystems, methane is produced via syntrophic associations between methanogens and anaerobic bacteria, including fermenters and syntrophs 4,5 . Fermenters and syntrophs degrade organic substances and produce acetate, formate, methanol, CO 2 , and H 2 , which serve as carbon and/or energy sources for acetoclastic, methylotrophic, and hydrogenotrophic methanogenesis 6,7 . Among them, acetate serves as the key intermediate metabolite, from which methane is produced by syntrophic acetate oxidation (SAO) coupled to hydrogenotrophic methanogenesis, in addition to acetoclastic methanogenesis [8][9][10] . Thus far, a number of microbes have been isolated from methanogenic microbial communities, and their genomic and metabolic features have been characterized [11][12][13][14] . Furthermore, recent metagenomic and metatranscriptomic studies have provided insights into uncultured members of methanogenic communities [15][16][17][18][19][20][21] . For example, Nobu et al. reported that anaerobic degradation of terephthalate in a methanogenic bioreactor was supported by complex synergistic networks comprised of many uncultivat...