Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

PeerJ. 2017 Apr 6:5:e3134. doi: 10.7717/peerj.3134. eCollection 2017.

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.

Keywords: Basement biosphere; Chemoautotrophy; Deep subsurface; Firmicutes; Genomic; Juan de Fuca Ridge; Metagenomic; Microorganisms; Sporulation; Sulfate reduction.

Associated data

  • figshare/10.6084/m9.figshare.4539149.v1

Grants and 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 US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US 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.