Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
- Published
- Accepted
- Subject Areas
- Ecology, Genomics, Microbiology
- Keywords
- deep subsurface, microorganisms, Firmicutes, Juan de Fuca Ridge, chemoautotrophy, basement biosphere, sulfate reduction, sporulation
- Copyright
- © 2016 Jungbluth et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ Preprints 4:e2592v1 https://doi.org/10.7287/peerj.preprints.2592v1
Abstract
It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling Bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Analysis of mapping frequency of artificially-fragmented reads corresponding to the genomes the “Ca. Desulfopertinax cowenii” and “Ca. Desulforudis audaxviator”
Comparison of mapping frequency of artificially-fragmented 150 bp reads corresponding to the genomes the “Ca. Desulfopertinax cowenii” and “Ca. Desulforudis audaxviator” mapped to the opposite genome using a range of nucleotide similarity scores. Inset plot shows details between mapping similarity score of 95-100% and revealed a mapping similarity score of 96% restricted spurious matches to a frequency of 1%.
Phylogenetic analysis of “Ca. Desulfopertinax cowenii”, “Ca. Desulforudis audaxviator” and other closely related dsrA genes
Phylogenetic relationships between “Ca. Desulfopertinax cowenii”, “Ca. Desulforudis audaxviator”, and closely related dsrA genes. Black (100%), gray (≥80%), and white (≥50%) circles indicate nodes with bootstrap support, from 2000 replicates. The scale bar corresponds to 0.05 substitutions per nucleotide position.