Background: Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood. Findings: In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination. Conclusions: This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.

High nickel (Ni) availability during the Archean enabled the proliferation of Ni-dependent methanogens1,2, whose methane (CH4) emissions sustained a strong greenhouse effect that offset the reduced luminosity of the young Sun3. By the end of the Archean eon, a severe decline in Ni availability—a phenomenon known as the Nickel Famine (~2.7-2.5 Ga)—triggered a drop in methane production, contributing to global cooling, and a subsequent rise in atmospheric oxygen (O2)4,5. Intriguingly, despite Earth’s permanent decline in bioavailable Ni6,7, methanogens utilizing organic energy source such as acetate and methyl compounds remain pivotal agents in modern methane emissions and global carbon cycling8,9. Here, we demonstrated that organotrophic methanogens are inherently more tolerant to Ni scarcity, with less inhibitory impact on growth rates and methane production under Ni limitation. We attribute this resilience to a systematic metabolism retooling—replacement of ancestral [NiFe]-hydrogenase-based energy system with an electron transport chain (ETC), which underpins the advent of organotrophic methanogens. Divergence time estimations reveal that the emergence of organotrophic methanogenesis aligned with the Nickel Famine. This temporal correlation suggests that the profound metabolic innovation was triggered by the protracted decline in environmental Ni bioavailability. It marks a key evolutionary adaptation to a major geochemical shift, revealing how microbial metabolic flexibility regulates planetary processes, enabled methanogens to endure sustained Ni limitation, and explains the ~1.5 Gyr delay in further global glaciations.