Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere

Abstract

The exploration of Earth's terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage's evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.

Fig. 1

Phylogenetic associations of the Juan du Fuca Candidatus Hydrothermarchaeota. Black (100%) and white (99–80%) circles indicate nodes with high local support values. a Phylogenetic associations relative to other Ca. Hydrothermarchaeota. 16S rRNA genes sequences from this study are in bold, sequences from other studies are indicated with their accession numbers (Table S8). b Phylogenomic associations of Ca. Hydrothermarchaeota genomes among archaeal genomes publicly available in Integrated Microbial Genomes (IMG), National Center for Biotechnology Information (NCBI), and other repositories, using classifications suggested by the Genome Taxonomy Database [26] (Table S4). Tree represents the concatenation of 43 single copy marker proteins (Table S5)

Fig. 2

Metabolism interpretation of Candidatus Hydrothermarchaeota single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) from Juan de Fuca Ridge flank subsurface crustal aquifer, based on the genes present within all genomes collectively. Black labels represent metabolites, blue labels represent genes or gene subunits that are present within at least one of the genomes (for individual genomes see Figure S4), gray labels represent genes or subunits not found in the genomes studied. Two black arrows aligned in the same direction represent a pathway requiring multiple genes, all of which were found in at least one genome. Pathway abbreviations: WL Wood–Ljungdahl, RHP reductive hexulose-phosphate. Gene name abbreviations: cdhABCDE CO dehydrogenase/acetyl-CoA synthase (subunits alpha, A; epsilon, B; beta, C; delta, D; gamma, E), cooC CO dehydrogenase maturation factor, cooS carbon monoxide dehydrogenase catalytic subunit, fwdABCDEFG formylmethanofuran dehydrogenase (subunits A–G), ftr formylmethanofuran-tetrahydromethanopterin formyltransferase, mch methenyltetrahydromethanopterin cyclohydrolase, mtd methylenetetrahydromethanopterin dehydrogenase, mer methylenetetrahydromethanopterin reductase, mtrA tetrahydromethanopterin S-methyltransferase (subunit A), hdrBCD CoB–CoM heterodisulfide reductase (subunits B–D), fdo formate dehydrogenase, Fqo ferredoxin:NADP⁺ oxidoreductase, frhABG coenzyme F420-reducing hydrogenase (subunits ABG), pgm/pmm phosphomannomutase/phosphoglucomutase, gpi glucose-6-phosphate isomerase, fba fructose-bisphosphate aldolase, fbp D-fructose 1,6-bisphosphatase, gap glyceraldehyde 3-phosphate dehydrogenase, pgk phosphoglycerate kinase, pgm phosphoglycerate mutase, eno enolase, pk pyruvate kinase, porABGD pyruvate ferredoxin oxidoreductase (subunits A–D), acs acetyl-coenzyme A synthetase, apr dissimilatory adenylylsulfate reductase (subunits A, B), dsrAB sulfite reductase alpha (subunits, A, B), sat sulfate adenylyltransferase, NapADGH nitrate reductase (subunits ADGH). Biomolecule abbreviations: SO₄ sulfate, APS adenosine-5’-phosphate, SO₃ sulfite, S sulfide, NO₃⁻ nitrate, NO₂⁻ nitrite, MQ menaquinone, F420 coenzyme F420, MF methanofuran, MPT methanopterin, CoA/CoB/CoM coenzyme A/B/M, P phosphate

Fig. 3

Free energy yield (kJ mol^–1 e^–1) for sulfate reduction coupled to acetate, hydrogen, methane, or carbon monoxide (CO) oxidation (Table S19) at various electron donor concentrations, based on the in situ conditions of Juan de Fuca Ridge fluids (Table S18)

Fig. 4

The relative abundance of motility genes in publicly available marine-related genomes and metagenomes as defined by COG (Clusters of Orthologous Groups) annotations. a Relative abundance of motility genes in single-amplified genomes and metagenome-assembled genomes collected from various marine environments relative to their genome completeness (considering genomes that are at least 10% complete, Table S28): sediments (brown triangle), hydrothermal vents (purple circle), crustal aquifers (orange circles), and ocean water column samples (blue squares). Candidatus Hydrothermarchaeota genomes are highlighted as yellow diamonds. b The relative abundance of motility genes in metagenomes collected from various marine environments (Table S29). The box and whiskers represent the range of relative abundance as defined by quartiles