First investigation of the microbiology of the deepest layer of ocean crust

Abstract

The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes ("GeoChip"), producing further evidence of genomic potential for hydrocarbon degradation--genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere.

Figure 1. Maximum-likelihood phylogenetic tree of proteobacterial 16S rRNA gene sequences from Atlantis Massif samples.

The environments from which microorganisms originated from are color coded (see key). Branch points supported by all phylogenetic analyses (quartet puzzling support values ≥90%) are shown by •; branch points supported by most analyses, but with less confidence (quartet puzzling support values 50–89%) are shown by ○; branch points without circles are unresolved (quartet puzzling support values <50%). Sequences <1200 nucleotides in length were inserted using the ARB parsimony insertion tool and are indicated by *. This proteobacterial ML tree was constructed with 1,000 puzzling steps. Prochlorococcus marinus (NC_009976) served as the outgroup (not shown).

Figure 2. Carbon isotopes from Atlantis Massif samples.

Carbonate ∂13C isotopic values were measured at various depths over the 1400 mbsf interval. Faults are indicated by dashed lines. Samples collected for microbiological analyses are indicated by squares to the left of the graph of carbonate ∂13C isotopic values; unfilled squares indicate that ribosomal DNA was successfully amplified from a sample; solid squares indicate that no ribosomal DNA was amplified. Samples that were analyzed by microarray to assay for functional genes are denoted by *.

Figure 3. Map of the Altantis Massif showing the locations of the Integrated Ocean Drilling Program Expeditions 304 and 305, Hole 1309D (yellow circle) and the Lost City Hydrothermal Field (green circle).

Inset figure shows the location of the Atlantis Massif (yellow circle), where Hole 1309D and the Lost City Hydrothermal Field are located. Figure adapted from Blackman, D. K., J. A. Karson, D. S. Kelley, J. R. Cann, G. L. Früh-Green, J. S. Gee, S. D. Hurst, B. E. John, J. Morgan, S. L. Nooner, D. K. Ross, T. J. Schroeder and E. A. Williams (2002). “Geology of the Atlantis Massif (Mid-Atlantic Ridge, 30°N): Implications for the evolution of an ultramafic oceanic core complex.” Marine Geophysical Researches 23(5): 443–469.