Novel Microbial Groups Drive Productivity in an Archean Iron Formation

Abstract

Deep subsurface environments are decoupled from Earth's surface processes yet diverse, active, and abundant microbial communities thrive in these isolated environments. Microbes inhabiting the deep biosphere face unique challenges such as electron donor/acceptor limitations, pore space/fracture network limitations, and isolation from other microbes within the formation. Of the few systems that have been characterized, it is apparent that nutrient limitations likely facilitate diverse microbe-microbe interactions (i.e., syntrophic, symbiotic, or parasitic) and that these interactions drive biogeochemical cycling of major elements. Here we describe microbial communities living in low temperature, chemically reduced brines at the Soudan Underground Mine State Park, United States. The Soudan Iron mine intersects a massive hematite formation at the southern extent of the Canadian Shield. Fractured rock aquifer brines continuously flow from exploratory boreholes drilled circa 1960 and are enriched in deuterium compared to the global meteoric values, indicating brines have had little contact with surface derived waters, and continually degas low molecular weight hydrocarbons C₁-C₄. Microbial enrichments suggest that once brines exit the boreholes, oxidation of the hydrocarbons occur. Amplicon sequencing show these borehole communities are low in diversity and dominated by Firmicute and Proteobacteria phyla. From the metagenome assemblies, we recovered approximately thirty genomes with estimated completion over 50%. Analysis of genome taxonomy generally followed the amplicon data, and highlights that several of the genomes represent novel families and genera. Metabolic reconstruction shows two carbon-fixation pathways were dominant, the Wood-Ljungdahl (acetogenesis) and Calvin-Benson-Bassham (via RuBisCo), indicating that inorganic carbon likely enters into the microbial foodweb with differing carbon fractionation potentials. Interestingly, methanogenesis is likely driven by Methanolobus and suggests cycling of methylated compounds and not H₂/CO₂ or acetate. Furthermore, the abundance of sulfate in brines suggests cryptic sulfur cycling may occur, as we detect possible sulfate reducing and thiosulfate oxidizing microorganisms. Finally, a majority of the microorganisms identified contain genes that would allow them to participate in several element cycles, highlighting that in these deep isolated systems metabolic flexibility may be an important life history trait.

Keywords: archean; brines; geomicrobiology; metagenomics; methane; subsurface.

FIGURE 1

Overview and layout of the legacy boreholes sampled at the Soudan Underground Iron Mine.

FIGURE 2

Phylum and OTU_0.03 level diversity in borehole microbial communities. (A) Abundance of phyla recovered from pyroTag sequencing, (B) Individual OTU_0.03 abundance, and (C) Total coverage by phyla for 16S rRNA genes assembled from the shotgun metagenome raw reads.

FIGURE 3

Taxonomy and coverage of Metagenome Assembled Genomes (MAGs) recovered from Soudan metagenomes. Bars below one represents rare to nearly absent genotypes.

FIGURE 4

Potential routes for Trimethylamine (TMA) production and isotopic fractionation of methane. (A) MAGs containing genes for glycine betaine uptake, glycine betaine production, and glycine betaine conversion to trimethylamine (left to right). Colored boxes represent phyla association and WL and CBB inset indicate the presence of the Wood-Ljungdahl or Calvin-Benson-Bassham cycle. (B) Theoretical flow of carbon and the potential isotopic fractionations that would render the methane signature of Soudan.

FIGURE 5

Sulfur cycling genes detected in metagenome assembled genomes (MAGs). Sulfur biogeochemical cycling pathways (A) interpreted from genes detected in Soudan MAGs (B). Blue lines represent abiotic reactions.

FIGURE 6

Nitrogen cycling genes detected in metagenome assembled genomes (MAGs). Nitrogen biogeochemical cycling pathways (left) interpreted from genes detected in Soudan MAGs (Right). Blue lines represent abiotic reactions.

FIGURE 7

The dominance of genes for carbon (A), hydrogen (B), nitrogen (C), and sulfur (D) at each borehole. Gene coverage is based on the MAG coverage.