Groundwater archaea reveal purifying selection and genomic plasticity in CO2-rich aquifer

Deep beneath a CO2-rich, acidic aquifer, one of the least-understood branches of the archaeal tree has now been brought into genomic focus. Researchers reconstructed three metagenome-assembled genomes of thaumarchaeotal Group 1.1c, a lineage within the family Gagatemarchaeaceae, from groundwater measured at pH 4.8, 7.6 degrees Celsius and microoxic conditions. The study, published in Environmental Microbiome on 16 September 2026, combined these new genomes with 33 publicly available Group 1.1c genomes to ask what this lineage does in groundwater microbiomes and how evolution has shaped its DNA.

The first surprise is numerical. Among 789 archaeal SSU rRNA gene assignments recovered from metagenomic reads at the site, 67.2 percent were classified as Group 1.1c. That makes this deeply branching, non-ammonia-oxidizing archaeal group a dominant component of the archaeal community in the sampled water, despite the fact that Group 1.1c has historically been detected mainly in acidic soils and subsurface habitats and remains poorly characterized in groundwater.

The three reconstructed metagenome-assembled genomes ranged from 85.3 to 97.5 percent complete, with contamination estimates between 0.07 and 3.28 percent. What was missing from them proved as informative as what was present. The groundwater genomes lacked amoABC, the gene set central to ammonia oxidation, the metabolic signature for which thaumarchaeotes are best known. They also lacked the canonical 3-hydroxypropionate/4-hydroxybutyrate carbon-fixation pathway, meaning these organisms do not appear equipped for the autotrophic carbon fixation typical of many ammonia-oxidizing relatives.

In place of those pathways, the genomes encoded genes associated with carbohydrate utilization, fatty-acid degradation and central heterotrophic metabolism. They carried an aa3-type cytochrome c oxidase, indicating aerobic respiratory potential, and superoxide dismutase, an enzyme linked to oxidative-stress management. Together, these gene repertoires are consistent with heterotrophic metabolism, aerobic respiratory potential and oxidative-stress management in a microoxic, acidic groundwater environment, although the authors note that the data do not demonstrate direct adaptation to those specific conditions.

Phylogenomic comparison across the expanded genome set resolved five subgroups, designated G1 through G5, which differed in their accessory-gene repertoires and in synonymous-site composition. The two G1 genomes, including representatives from the groundwater site, had lower genomic GC content and weaker codon-usage bias than genomes in subgroups G2 through G5. Source metadata attached to the public genomes showed that all four G2 genomes were recovered from groundwater, including the three CO2-rich groundwater genomes reconstructed in this study, while seven of nine G4 genomes originated from temperate grasslands. G1 and G5 were represented by soil- or peat-derived genomes, and G3 spanned peat, soil, sediment and groundwater sources.

Because environmental measurements were not harmonized across the public genomes, the researchers treated these habitat patterns descriptively rather than as evidence of habitat-specific ecotypes. The same caution applied to translation-related signals: fixed-coefficient tAI estimates were lowest in G1, but this pattern was not robust to coefficient optimization, and its interpretation was limited by the incompleteness, fragmentation and sparse tRNA recovery of the two available G1 genomes. It was therefore treated as descriptive rather than as evidence of translational adaptation.

The evolutionary analysis turned to how nucleotide changes accumulate across the lineage. A fitted recombination model indicated that recombination contributed less to nucleotide change than mutation, with a median r/m ratio of 0.264 and a central 95 percent range of 0.253 to 0.275 across 100 emsim draws. The model also inferred kilobase-scale importation tracts, showing that DNA exchange does occur within the lineage but at a rate that leaves point mutation as the dominant engine of sequence divergence.

To probe selective constraint, the team examined 208 one-to-one relaxed-core candidate genes, of which 135 passed alignment and taxon-coverage filters. All 135 had gene-wide dN/dS estimates below 1, with a median omega of 0.046, including the 14 genes that met both strict starting-value stability and no-saturation criteria. Values well below 1 indicate that nonsynonymous changes are far rarer than synonymous ones, a signature of broad purifying selection acting across the model-estimable portion of the relaxed core. In other words, the protein-coding machinery shared across the lineage has been strongly conserved, while accessory genes and synonymous-site composition have diversified alongside the deep splits between subgroups.

The authors conclude that Group 1.1c accounted for a large proportion of archaeal SSU rRNA gene assignments in the sampled groundwater and that the recovered genomes encode metabolic capacities consistent with heterotrophic metabolism, aerobic respiratory potential and oxidative-stress management. Gene-wide dN/dS estimates were consistent with broad purifying constraint across the model-estimable component of the relaxed core, whereas accessory-gene and synonymous-site variation accompanied deep lineage diversification. The study expands the genomic representation of groundwater Group 1.1c, but the researchers are explicit that these data do not demonstrate direct adaptation to acidic, microoxic or CO2-influenced conditions. What the work delivers is a clearer genomic baseline for a lineage that has long evaded cultivation and characterization, and a framework for testing, with harmonized environmental data, whether the subgroup patterns observed here reflect genuine ecological differentiation or simply the habitats in which these archaea happened to be sampled.

Subject of Research: Genomic analysis of a distinct thaumarchaeotal Group 1.1c lineage from CO2-rich groundwater

Article Title: Evolutionary constraints and genomic plasticity of a distinct thaumarchaeotal group 1.1c lineage from CO2-rich groundwater

Article References: Kim, M., Kim, S.-J., Ko, K.-S., Koh, D.-C., Kim, D.-H., Chae, G., Li, M., & Park, S.-J. (2026). Evolutionary constraints and genomic plasticity of a distinct thaumarchaeotal group 1.1c lineage from CO2-rich groundwater. Environmental Microbiome. https://doi.org/10.1186/s40793-026-00964-x

Image Credits: AI Generated

DOI: 10.1186/s40793-026-00964-x

Keywords: archaea, Thaumarchaeota, groundwater, metagenomics, CO2-rich aquifer, purifying selection, recombination, codon usage, Gagatemarchaeaceae, microbial evolution, heterotrophic metabolism, subsurface microbiome