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.

Fig. 1.. The newly improved taxonomy and subgroup assignment of the class Bathyarchaeia.

(A) Phylogenomic affiliation of 304 representative Bathyarchaeia MAGs refined from publicly available databases and our laboratory datasets based on a concatenated alignment of 122-archaeal marker proteins implemented in GTDB-Tk by using IQ-TREE2 with LG+F+R10+C60 model and Shimodaira Hasegawa–like approximate likelihood ratio test with 1000 bootstrap replicates (bootstrap higher than 0.9 are shown with black dots). The colored background and outer rings denote the eight proposed orders of class Bathyarchaeia, and the inner black and gray rings represent the whole class Bathyarchaeia and phylum Thermoproteota, respectively. The number of MAGs used in the phylogenetic analysis is listed under the name for each taxonomic lineage. (B) Taxonomic assignment of subgroups for the representative Bathyarchaeia MAGs with 16S rRNA genes. The phylogenetic tree was constructed with subgroup-classified sequences from Zhou et al. (9) as a reference by using RaxML 8.2.12 (84) with -m GTRGAMMA -N autoMRE and 1000 bootstrap replicates (fig. S2).

Fig. 2.. Environmental and geographic distribution of the class Bathyarchaeia.

(A) Distribution of 304 representative Bathyarchaeia MAGs across different oceanic and terrestrial environments. The number of MAGs associated with each environment is indicated below the name. (B) Environmental distribution of Bathyarchaeia MAGs from the eight proposed orders. (C) Environmental distribution of a total of 2226 metagenomic samples with Bathyarchaeia (>1%) from diverse marine and terrestrial ecosystems based on Sandpiper v0.0.23 (https://sandpiper.qut.edu.au/). Geographic distribution of the metagenomes from hydrothermal sediment, soil, marine sediment, and hot spring sediment. Relative abundance of the eight Bathyarchaeia orders within each sample is indicated with the circle size.

Fig. 3.. Distinctive metabolic traits of the class Bathyarchaeia.

(A) Phylogenomic tree includes 86 high-quality representative Bathyarchaeia MAGs and was inferred by iQ-TREE2 with LG+F+R7+C20 model from 122 archaeal marker proteins implemented in GTDB-Tk (see Materials and Methods). Colors on branches indicate eight proposed Bathyarchaeia orders. The completeness of each metabolic pathway is defined by the ratio of marker genes identified in the complete gene repertoire for each MAG, while for many key genes or complexes, such as those involved in C1 compound metabolism, their presence and absence in each MAG are directly indicated by the percentage of completeness. Metabolic capabilities of carbohydrate degradation are evaluated by the gene numbers of different CAZymes identified in each MAG. The following metabolic pathways and key enzymes were used in the figure (table S7): archaeal PPP, archaeal pentose phosphate pathway; PRPP synthesis, phosphoribosyl pyrophosphate synthesis; TCA cycle, tricarboxylic acid cycle; PFOR complex, pyruvate:ferredoxin oxidoreductase complex; ack-pta, acetate kinase and phosphate acetyltransferase; ACSS, acetyl-CoA synthetase; rGlyP, reductive glycine pathway; GCS, glycine cleavage system; GlyA, glycine hydroxymethyltransferase; SdaA, l-serine dehydratase; fae, formaldehyde-activating enzyme; Cox complex, aerobic carbon-monoxide dehydrogenase; MttB, trimethylamine-corrinoid protein co-methyltransferase; MtmB, methylamine-corrinoid protein co-methyltransferase; MCR complex, methyl-coenzyme M reductase complex; AA, auxiliary activity; GH, glycoside hydrolase; CE, carbohydrate esterase. (B and C) Box plots show the average number of CAZyme and peptidase genes per 100 genes in one MAG for each Bathyarchaeia order, respectively. The stars indicate that the order has a significantly higher average genomic gene number in comparison with all other Bathyarchaeia orders (Wilcoxon test with Benjamini-Hochberg correction, P < 0.05).

Fig. 4.. Overall metabolic reconstruction of the class Bathyarchaeia.

The presence of specific pathways or enzymes in at least two MAGs from different samples for each Bathyarchaeia order is indicated by different colored parts in octagon. White color denotes that all enzymes of a specific pathway are absent in any MAGs of the order. The enzymes of the H₄-MPT pathway marked with white stars in brown background, including Fwd, Ftr, Mch, Mtd, Mer, and CODH/ACDS, indicate that they are present in all other MAGs in the order Houtuarculales, except for the special genus Houtuousia recovered from soil. In contrast, those marked with brown stars in white background represent that they are exclusively identified in the members of genus Houtuousia, but not in other Houtuarculales MAGs. The following metabolic pathways, key enzymes, and compounds were used in the figure (table S7): PPP, archaeal pentose phosphate pathway; TCA cycle, tricarboxylic acid cycle; PFOR, pyruvate:ferredoxin oxidoreductase complex; ack-pta, acetate kinase and phosphate acetyltransferase; ACSS, acetyl-CoA synthetase; rGlyP, reductive glycine pathway; GCS, glycine cleavage system; GlyA, glycine hydroxymethyltransferase; Sda, L-serine dehydratase; Fae, formaldehyde-activating enzyme; Cox, aerobic carbon-monoxide dehydrogenase; Fwd, formylmethanofuran dehydrogenase complex; Ftr, formylmethanofuran–tetrahydromethanopterin N-formyltransferase; Mch, methenyltetrahydromethanopterin cyclohydrolase; Mtd, methylenetetrahydromethanopterin dehydrogenase; Mer, coenzyme F₄₂₀-dependent 5,10-methenyltetrahydromethanopterin reductase; Fdh, formate dehydrogenase; Fhs, formate-tetrahydrofolate ligase; FolD, methylenetetrahydrofolate dehydrogenase (NADP⁺)/methenyltetrahydrofolate cyclohydrolase; MetF, methylenetetrahydrofolate reductase (NADPH); Cyt ox, cytochrome c oxidase; MttB; MtmB; MCR complex; ACR, alkyl-coenzyme M reductase complex; TMA, trimethylamine; MMA, monomethylamine; BCAA, branched-chain amino acids; ArOCH₃, methoxylated aromatic compounds; ATPase, adenosine triphosphatase; ADP, adenosine 5′-diphosphate; CODH/ACDS, anaerobic carbon-monoxide dehydrogenase/acetyl-CoA decarbonylase/synthase; PCW, plant cell wall.

Fig. 5.. Evolutionary history of the class Bathyarchaeia and timing correlations with major geological activities.

(A) Phylogenomic tree and estimated divergence times of the major Bathyarchaeia lineages. The whole tree was constructed on the basis of 259 Bathyarchaeia and 190 reference MAGs by the concatenated alignment of their SMC and 16 conserved proteins (fig. S9). Different color schemes represent the descendent lineages for eight Bathyarchaeia orders (the label of order Xuanwuarculales is removed as the only one MAG). The divergence ages of major nodes are numbered 0 to 13 and labeled with the posterior 95% CIs (flanking horizontal blue bar). The relative proportions of juvenile crust through time are represented as a brown bar chart in the top panel (60). The vertical pink, green, and yellow bands indicate the first subaerial continent exposed above the sea at 3.46 to 3.2 Ga ago (48), rapidly increasing subaerial landmass at ~2.5 Ga ago (62), and the global submarine volcanism intensively occurred at 1.88 to 1.7 Ga ago (64), respectively. (B) Evolutionary timeline of the Bathyarchaeia lignin-degrading lineage and contemporaneous Permo-Carboniferous coal peak. The tree is part of the whole phylogenomic tree of Bathyarchaeia, comprising nine MAGs from the genus Baizosediminiarchaeum. The four MAGs with pink background, which were specifically recovered from the lignin enrichment, are designated as the lignin-degrading Bathyarchaeia clade in this study. The MAGs labeled with the number “8” within the purple box are assigned to the previous subgroup 8. The top panel shows the burial flux of terrestrial organic sediments accumulated in North America through time (69) and contemporaneous key evolutionary time points for terrestrial plants (105), white rot fungi (68), and xylophagous beetles (70, 71).