Chemolithoautotroph distributions across the subsurface of a convergent margin

Abstract

Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.

Fig. 1. General convergent margin geological structure and sample sites spanning the Costa Rican convergent margin.

Geological provinces (A) and sample sites (B) are colored by their province location: outer forearc (blue), forearc (orange), and arc (red). A The green arrow indicates the location of trench, black arrows show the direction of plate movements, blue arrows show fluids and degassing throughout subduction. B Green dotted line indicates the trench while gray dotted lines mark the depth of the 122 °C isotherm in 5 km increments, based on data for this region of Costa Rica from Harris and Wang 2010. Locations of volcanoes are shown with volcano icons. Dotted white line demarcates the plates emerging from the East Pacific Rise (EPR) and the Cocos Nazca Spreading center (CNS).

Fig. 2. Heatmap of metagenomic read recruitment to each MAG and hierarchical clustering based on Spearman rank correlations between MAGs (vertical clusters) and sample sites (horizontal clusters) shows the separation of MAGs into those found mostly in the forearc/arc, the outer forearc, or delocalized across geological provinces.

Entire heatmap is shown to the left, with numbers corresponding to clusters; and representative enlarged sections are shown to the right, with metabolic pathways for redox couples and carbon fixation pathways listed. Subsections were chosen based on inclusion of the key metabolisms and taxa that characterize province-specific clusters (clusters 1 and 3) and delocalized clusters (clusters 2, 4, and 5). Sulfur* and nitrogen* refer to the metabolic capability of metabolizing multiple oxidation states. The full heatmap in high resolution is in Supplementary Fig. S1.

Fig. 3. Average read abundance (GCPM) per site of MAGs with metabolic pathways for redox reactions and carbon fixation pathways.

A–C show the province-specific average read recruitment of MAGs with these metabolic pathways at all A outer forearc sites, B forearc sites, and C arc sites, after removing MAGs in the delocalized cluster, which are in panel D. Colors correspond to the top 10 most abundant classes for each province and the delocalized community. Panels B and C show top 9 and 8 most abundant classes, respectively, since MAGs lacking redox genes and carbon fixation pathways were in the top 10 most abundant classes. Bars represent the GCPM mean for MAGs at each province specific site.

Fig. 4. Nitrogen, sulfur, and hydrogen cycling pathways in MAGs with carbon fixation pathways from the outer forearc and the forearc/arc.

Arrow width corresponds to abundance of MAGs with that gene and dots show which CFP pathways were present in the MAGs that had that gene, with blue for WL, yellow for rTCA, and pink for CBB. Class names are listed from most to least abundant (top to bottom), and MAGs in the top 3 CFP-containing classes are in bold. Pink dashed box highlights sulfur-associated chemoautotrophic nitrogen reduction. Blue dashed box highlights hydrogenotrophic sulfur reduction. Gray dotted line with a question mark represents missing aprBA predictions for all sulfide-oxidizing MAGs.

Fig. 5. Transformation-based canonical correspondence analysis showing variables most closely correlated with MAG abundance distribution at each site and site distribution of each MAG (scaling = 2).

Distances between MAGs are chi-square distances. A 90° projection of a MAG marker on an environmental vector represents the maximum abundance of that MAG along that vector. Site markers are distributed around the weighted centroid of the MAGs. The model explains 36% of the total variation in community structure and the axes that are displayed contributed 62% of the total explained variation. The four MAGs with multiple carbon fixation pathways have those two colors overlain.

Fig. 6. Schematic cross-section (to scale) of the 3D distribution of subsurface microbial communities and their metabolisms across the Costa Rica convergent margin, showing a shallowing of potential habitable area from the outer forearc to the arc.

A subset of sites is shown. Crustal thickness, angle of subduction, and 122 °C isothermal depth are from Harris and Wang [3], while aquifer depth, location, and size are from Worzewski et al. [63]. Top 3 classes per province and their associated metabolisms are listed. Cell morphology displayed is based on morphologies of cultures from each class. Site colors follow those of Fig. 1.