Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts

Abstract

Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H₂ oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.

Fig. 1. Community composition of the 18 global desert soils, classified using the universal single-copy ribosomal protein gene rplP retrieved from shotgun metagenomic reads.

The relative abundance of major bacterial and archaeal phyla residing in triplicate desert soils from Alexandra Fjord Highlands (AFH), Spitsbergen Svalbard (SS), Tibetan Plateau (TP), Mitchell Peninsula (MP), New Harbour (NH) and The Ridge (TR) are displayed; phyla with <2% relative abundance in all soil samples were grouped to the “Other” phyla. Actinobacteriota dominate all sites, particularly The Ridge (average 77.9%), TP (average 62.9%) and Mitchell Peninsula (average 45.2%). Photosynthetic Cyanobacteria are extremely scarce within NH, TP and The Ridge samples (<0.07%), with greater average abundances observed at Mitchell Peninsula (0.6%), SS (0.4%) and Alexandra Fjord Highlands (2.0%). Ca. Eremiobacterota and Ca. Dormibacterota dominate Mitchell Peninsula microbiomes (average 7.8% and 3.6%, respectively) and are present at lower levels within SS and Alexandra Fjord Highlands. Archaea are minor members of these ecosystems (average relative abundances; <0.2% within The Ridge, Mitchell Peninsula, NH; 2.6% within TP; 0.5% within SS; 1.2% within Alexandra Fjord Highlands).

Fig. 2. Heatmap displaying the abundance of key metabolic marker genes involved in carbon fixation and energy conservation, and their distribution throughout 18 metagenomes spanning six cold desert regions.

For each region, relative gene abundances were displayed for three metagenomes. Genes encoding the CBB cycle, energy metabolism, aerobic respiration, nitrogen cycling, and trace gas oxidation were widely distributed throughout all environments. Phototrophy genes were more abundant within Alexandra Fjord Highlands metagenomes than the other sites studied.

Fig. 3. Heatmap displaying key functional genes involved in microbial autotrophy and energy conservation, and their distribution throughout the 76 high-quality (>90% completeness, <5% contamination) and 154 medium-quality bins (50–90% completeness, 5–10% contamination) constructed.

Abundances are displayed relative to the total number of MAGs from each phylogenetic group. Genes encoding the CBB cycle, energy metabolism, respiration, and nitrogen cycling were widely distributed. Phototrophy genes were primarily limited to Cyanobacteria MAGs, whilst trace gas oxidation genes were widely distributed throughout 11 of the 18 phyla detected through MAG construction.

Fig. 4. Maximum likelihood phylogenetic tree of RuBisCO gene sequences focusing on form IE, pruned from a larger tree containing binned cold desert metagenomic assembled genomes (MAGs) and over 3000 published genomes.

Leaves are colored to represent phylum, while colored branches show RuBisCO form. The cold desert-site that each MAG was obtained from is shown in the outer ring. Genomes which additionally harbored high-affinity groups 1h [NiFe]-hydrogenase (hhyL), 1m [NiFe]-hydrogenase (hhmL), 1l [NiFe]-hydrogenase (hylL) and/or aerobic carbon monoxide dehydrogenase (coxL) with an active-site loop are indicated by outer triangles, colored red, green, pink, and blue, respectively. Bootstrap values >90% are depicted as filled circles on branches. Medium and high-quality MAGS constructed in this study are marked with gray circles. RuBisCO form IE is highly diverse, spanning 8 bacterial phyla (Actinobacteriota, Chloroflexota, Firmicutes, Verrucomicrobiota, Ca. Dormibacterota, Ca. Eremiobacterota, Acidobacteriota and Deinococcota) with multiple distinct clades observed. Most genomes containing RuBisCO form IE also contained high-affinity group 1 [NiFe]-hydrogenase and/or aerobic carbon monoxide dehydrogenase.

Fig. 5. The oxidation of atmospheric gases by surface soil microcosms from six cold deserts.

The oxidation of A hydrogen and B carbon monoxide are displayed. Values shown have been normalized against the starting concentration of each gas and are the mean of biological triplicates. The dashed line in A indicates atmospheric H₂ (530 p.p.b.v) and in B indicates atmospheric CO (90 p.p.b.v). Rapid high-affinity hydrogenase activity was observed across all sites (Average H₂ consumption; Mitchell Peninsula 421.4 nmol/mol/h/g, NH 42.6 nmol/mol/h/g, The Ridge 41.1 nmol/mol/h/g, TP 35.6 nmol/mol/h/g, Alexandra Fjord Highlands 21.6 nmol/mol/h/g, SS 9.4 nmol/mol/h/g), particularly within the Mitchell Peninsula microcosms, each of which consumed hydrogen to sub-atmospheric levels within 6 h of incubation. Carbon monoxide consumption was observed however, compared to hydrogen consumption, these rates were slower and varied greatly between samples within each site.

Fig. 6. Changes in ¹⁴CO₂ assimilation in soils from six cold deserts under differing abiotic conditions.

Increases in carbon assimilation under A hydrogen stimulation and B light exposure are displayed. Carbon assimilation by soil microcosms from all deserts were consistently stimulated by the addition of atmospherically relevant hydrogen concentrations (~10 p.p.m.v), with significant increases observed within microcosms from New Harbour (p = 0.013), Spitsbergen Svalbard (p = 0.033) and Alexandra Fjord Highlands (p = 0.031). Light exposure also led to a significant increase in carbon assimilation within soils from Spitsbergen Svalbard and Alexandra Fjord Highlands (p = 0.022 and 0.015, respectively), but did not significantly influence primary production across the other deserts. Normality was determined using Shapiro–Wilk tests. When the data were normally distributed, statistical significance was determined using a two-tailed paired t-test. Otherwise, a two-tailed Wilcoxon signed-rank test with a Bonferroni correction was implemented.