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.

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin

“…With the exception of Armatimonadetes, all these taxa were detected from pyrosequencing in crude samples from 1827 to 1922 m CSF-A. The majority of the sequences had relatives recovered from environments with similar physical-chemical characteristics (Lin et al, 2006;Mason et al, 2010; that is, hot and reduced habitats) compared with the Canterbury subseafloor. Considering the 'ubiquity' of these taxa, one can hypothesize that they are generalist bacteria, which would have been maintained during progressive burial of sediments or by transportation through circulating fluids.…”

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“…Some microbiological results from Expedition 305 at Atlantis Massif are available to guide our efforts (Mason et al, 2010). Rocks were collected for molecular analyses from 400 to 1400 mbsf, and aerobic bacteria were cultured in variable lithologies (gabbro and olivine-bearing gabbro) with variable (10%-50%) alteration deeper than 1300 mbsf (temperature > 75°C).…”

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

“…Due to low yield, DNA isolated from the water samples was amplified using whole genome amplification. Although amplification of nanogram quantities of DNA with whole genome amplification has made it possible to study microbial communities in environments where the amount of microbial biomass would otherwise be limiting (for example, Mason et al, 2010), the technique can introduce bias in the distribution of the amplified DNA (Pinard et al, 2006). In order to minimize this bias, whole genome amplification was performed in replicate reactions and the metagenomic sequences were filtered for redundant sequences (Supplementary Table S6).…”