Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring

Abstract

Background: Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O₂), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L^-1) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars.

Results: Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination.

Conclusions: We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.

Keywords: Cryosphere; Metagenome-assembled genomes; Metagenomics; Metatranscriptomics; Saline spring; Sulfidic spring.

Fig. 1

A Relative abundance of orders in 16S rRNA gene amplicon sequencing and shotgun metagenomes and number of MAGs in each order. Shotgun metagenome relative abundance was determined by read mapping to SSU rRNA genes with phyloFlash. B Phylogenomic tree of the 57 high- and medium-quality MAGs with phylum, relative abundance in the metagenome (percentage of mapped metagenome reads), and relative transcript abundance (transcripts per million reads of genes in each MAG) indicated. The tree was constructed with the anvi’o Bacteria_71 set of single-copy genes for both bacterial and archaeal MAGs and midpoint-rooted. C Level of taxonomic novelty of the MAGs. The number of classified and unclassified genomes at each taxonomic level was determined according to its rank assignment and taxonomic placement by GTDB-tk

Fig. 2

Metabolic gene relative transcript abundance and distribution of transcripts by phylum. Relative transcript abundance by phylum is based on the presence of transcribed genes in MAGs and phylogenetic classification of unbinned genes in JGI. Complete phylogenetic distribution of depicted genes in MAGs is located in Table S8

Fig. 3

Total relative transcript abundance (tpm) of MAGs and unbinned genes in phyla or classes > 1% relative abundance. Error bars indicate standard deviation between metatranscriptome replicates. Unbinned genes were classified with the JGI Phylo Distribution function

Fig. 4

Pathway and gene presence in MAGs. Where applicable, “X” indicates presence of a complete pathway and “/” indicates a partial pathway. Heat map indicates square root of relative transcript abundance (transcripts per million reads) of genes in each MAG. A complete table of gene IDs and criteria for denoting the presence of a complete or partial pathway is located in Table S9; a corresponding table with tpm values is located in Table S10

Fig. 5

Genome content of key sulfur-cycling MAGs. Genes involved in oxidation reactions are in pink; reduction in green; disproportionation in blue. Yellow text indicates sulfur species putatively exchanged between S-oxidizing and S-reducing bacteria. Complete gene names and genome content are located in Table S10. Abbreviations are as follows: CBB, Calvin Benson Bassham cycle; NSR, NADH-dependent sulfur reductase; TCA, tricarboxylic acid cycle; WL, Wood-Ljungdahl pathway

Fig. 6

A Plot of canonical correspondence analysis (CCA) of 16S rRNA gene sequencing from GH and cold, saline, and sulfur-rich environments relating environmental variables to taxonomic composition of the samples (ANOVA F = 1.46 and p-value = 0.003 **). Circles represent total samples, “ + ” indicates individual taxa, “*” represents statistically significant environmental variables of p-value ≤ 0.05. Sample metadata can be found in Table S4. B Plot of canonical correspondence analysis (CCA) of 16S rRNA gene sequencing from GH and additional comparable environments relating temperature and salinity to taxonomic composition of the samples (ANOVA F = 1.001 and p-value = 0.476). Circles represent total samples, “ + ” indicates individual taxa, “***” represents statistically significant environmental variables of p-value ≤ 0.001. Sample metadata can be found in Table S4

Fig. 7

Model for a hypothetical sulfur-cycling microbial community similar to the GH microbial community in a theoretical Martian environment such as subsurface sulfate brines. Putative Martian sources of energy and carbon are indicated in red. SRBs refer to S-reducing bacteria and SOBs refers to S-oxidizing bacteria. The asterisk indicates phototrophic metabolism, which would be relevant only in very near-surface or surface environments on ancient Mars