Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
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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.
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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 PeerJ Preprints 4:e2592v1 https://doi.org/10.7287/peerj.preprints.2592v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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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.
Summary of metagenome sequence reads mapped to “Ca. Desulforudis audaxviator”, “Ca. D. audaxviator”-related scaffolds from IMG-M, and genomic bin A32 from metagenome U1362A
Metagenomes from the IMG database used in Figure 7A
Metagenomes with accessible raw reads from IMG, MG-RAST, and NCBI databases used in Figure 7B
Similarities in “Ca. Desulforudis audaxviator” and “Ca. D. audaxviator” by COG category with example genes
Genes in “Ca. D. cowenii” without homologs in “Ca. D. audaxviator” genome
Genes in “Ca. D. audaxviator” without homologs in “Ca. D. cowenii” genome
“Ca. Desulfopertinax cowenii” genome in GenBank format
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Sean P Jungbluth conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Tijana Glavina del Rio contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Susannah G Tringe contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Ramunas Stepanauskas contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Michael S Rappé conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
The genome sequences described here are accessible via IMG Genome ID 2615840622.
Data Deposition
The following information was supplied regarding data availability:
The raw sequence data used for this analysis are accessible via SRA accession numbers SRR3723048 (U1362A) and SRR3732688 (U1362B).
Funding
This research was supported by funding from National Science Foundation grants MCB06-04014 and OCE-1260723 (to MSR) and OCE-1136488 (to RS), the Center for Dark Energy Biosphere Investigations, a National Science Foundation-funded Science and Technology Center of Excellence (NSF award OCE-0939564), and from Department of Energy Joint Genome Institute Community Sequencing Award 987 (to RS). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
