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Deep sub-seafloor prokaryotes stimulated at interfaces over geological time


The sub-seafloor biosphere is the largest prokaryotic habitat on Earth1 but also a habitat with the lowest metabolic rates2. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism2. Here we present results from two Pacific Ocean sites, margin and open ocean, both of which have deep, subsurface stimulation of prokaryotic processes associated with geochemical and/or sedimentary interfaces. At 90 m depth in the margin site, stimulation was such that prokaryote numbers were higher (about 13-fold) and activity rates higher than or similar to near-surface values. Analysis of high-molecular-mass DNA confirmed the presence of viable prokaryotes and showed changes in biodiversity with depth that were coupled to geochemistry, including a marked community change at the 90-m interface. At the open ocean site, increases in numbers of prokaryotes at depth were more restricted but also corresponded to increased activity; however, this time they were associated with repeating layers of diatom-rich sediments (about 9 Myr old). These results show that deep sedimentary prokaryotes can have high activity, have changing diversity associated with interfaces and are active over geological timescales.

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Figure 1: Biogeochemical process and prokaryotic biodiversity profiles at the Peru margin site (ODP 1229).
Figure 2: Prokaryotic biodiversity at the Peru margin site (ODP Leg 201, site 1229).
Figure 3: Biogeochemical processes and prokaryotic populations at the Pacific open ocean site (ODP 1226).


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We thank members of the Leg 201 cruise for assistance in obtaining and processing samples, and T. Daniell for assistance with DNA sequencing. This research used samples and data provided by the ODP. The ODP is sponsored by the US National Science Foundation (NSF) and participating countries under the management of Joint Oceanographic Institutions (JOI), Inc. We thank the European Union and the Natural Environment Research Council (Marine and Freshwater Microbial Biodiversity Programme) for supporting this research financially.

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Correspondence to R. John Parkes.

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Reprints and permissions information is available at The authors declare no competing financial interests.

Supplementary information

Supplementary Figures S1-S4

Figures showing rarefaction curves and phylogenetic trees of representative sequences from 12 prokaryotic gene libraries from Peru Margin site 1229 (ODP Leg 201) deep sub-seafloor sediment. (PDF 84 kb)

Supplementary Figure Legends S1-S4 (PDF 69 kb)

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Parkes, R., Webster, G., Cragg, B. et al. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436, 390–394 (2005).

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