Viable cyanobacteria in the deep continental subsurface

Abstract

Cyanobacteria are ecologically versatile microorganisms inhabiting most environments, ranging from marine systems to arid deserts. Although they possess several pathways for light-independent energy generation, until now their ecological range appeared to be restricted to environments with at least occasional exposure to sunlight. Here we present molecular, microscopic, and metagenomic evidence that cyanobacteria predominate in deep subsurface rock samples from the Iberian Pyrite Belt Mars analog (southwestern Spain). Metagenomics showed the potential for a hydrogen-based lithoautotrophic cyanobacterial metabolism. Collectively, our results suggest that they may play an important role as primary producers within the deep-Earth biosphere. Our description of this previously unknown ecological niche for cyanobacteria paves the way for models on their origin and evolution, as well as on their potential presence in current or primitive biospheres in other planetary bodies, and on the extant, primitive, and putative extraterrestrial biospheres.

Keywords: astrobiology; deep/dark biosphere; endolithic cyanobacteria; extreme environments; metagenomics.

Fig. 1.

Distribution of cyanobacteria and other microbial taxa in core samples from the Iberian Pyrite Belt deep subsurface. (A) Relative abundance of different cyanobacterial clades based on 16S rRNA amplicons (bars) and hydrogen concentrations (purple area) across the borehole samples. Hydrogen concentrations are shown relative to the sample with the highest hydrogen concentration. (B) Taxonomic composition of the metagenomic reads from samples 420 and 607.

Fig. 2.

Fluorescence micrographs (CARD-FISH) showing the presence of clusters of cyanobacterial cells attached to rock surfaces in deep subsurface samples. (A and E) Microbial DNA stained with DAPI (blue signal). (B and F) Hybridization signals with the specific cyanobacterial oligonucleotide probe CYA361 (red signal). (C and G) Merged image of DAPI and probe hybridization signals (blue and red, respectively). (D and H) Merged image of DAPI and probe hybridization together with the mineral matrix. The gray and white signal shows the host mineral. (Scale bars, 5 μm in all cases.)

Fig. 3.

Schematic representation of the photosynthetic, respiratory, and fermentative pathways detected in the cyanobacterial pangenomes of two deep subsurface metagenomes. Orange and blue squares indicate whether an enzyme was detected in sample 420 or sample 607, respectively. Enzymes detected in the metagenomic reads but not in the assemblies have their square marked with a diagonal hatching. Reactions dependent on light or oxygen, and thus unlikely to be active in anoxic deep subsurface environments, are marked with a red cross. Abbreviations: cyt b6f, cytochrome b₆f; cyt bd, cytochrome bd; Fd, ferredoxin; Hox, bidirectional hydrogenase; Hup, uptake hydrogenase; NDH, NDH-1 complex; NorB, quinol-dependent nitric oxide reductase; Ox, cytochrome c oxidase; PC, plastocyanin; PQ, plastoquinone; PSI, photosystem I; PSII, photosystem II; SDH, succinate dehydrogenase; TCA, tricarboxylic acid cycle.