Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment

Abstract

Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution, and ecological functions remains poorly constrained. Here, we present the largest dataset of Bathyarchaeia metagenome assembled genome to date and reclassify Bathyarchaeia into eight order-level units corresponding to the former subgroup system. Highly diversified and versatile carbon metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ~3.3 billion years, followed by three major diversifications at ~3.0, ~2.5, and ~1.8 to 1.7 billion years, likely driven by continental emergence, growth, and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ~300 million years perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary history of Bathyarchaeia potentially has been shaped by geological forces, which, in turn, affected Earth’s surface environment.

Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

“…In total, 367 metagenome-assembled genomes (MAGs) of Bathyarchaeia , including 78 high-quality MAGs (Extended Data Supplementary Table S1 ), were obtained from our previous results [ 9 , 50 ] and public databases. Phylogenetic analysis based on a concatenated alignment of an optimized set of 51 marker proteins (see Methods) yielded 7 major clades of Bathyarchaeia that mostly correspond to the orders in the latest taxonomy [ 51 ] ( Fig. 1A and Extended Data Supplementary Fig.…”

Effect of bioaugmentation on gas production and microbial community during anaerobic digestion in a low-temperature fixed-bed reactor

“…Previous reports suggest that Candidatus_Udaeobacter contains highly affinitive hydrogenases that can metabolize H 2 to provide energy for the respiratory chain under nutrient-limited conditions ( Greening et al, 2015 ; Willms et al, 2020 ). On the other hand, Bathyarchaeia are known for their autotrophic acetogenic metabolism capabilities ( Xie et al, 2022 ; Hou et al, 2023 ). This indicates that following the addition of Methanomicrobiaceae , which produce methane through H 2 and CO 2 metabolism pathways, the microbial community in the reaction system gradually shifts toward these pathways, while the proportion of microorganisms utilizing organic acids to produce methane decreases.…”

Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems

“…Reads were then mapped to an index of the phage marker genes, phage contigs, and prokaryote marker genes made with Minimap2 [ 54 ] (options: -x sr). CoverM [ 55 ] was then used for the mapping (coverm contig --min-read-percent-identity 95 -m covered_fraction rpkm count variance length --minimap2-reference-is-index --min-covered-fraction 0 --coupled) and retained with 50% gene covered or 20% of contig covered [ 56 ] (Supplementary Dataset 3 ). See Supplementary Dataset 4 for the number of each sequence type detected in at least one sample.…”