Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria

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Abstract
Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes1,2,3. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of the ocean and by triggering the emission of methane, with consequences for the marine carbon cycle and even the global climate4,5,6. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms7,8, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth7. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program1,9. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown10,11. Here, using ribosomal RNA as a target for the technique known as catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH), we provide direct quantification of live cells as defined by the presence of ribosomes. We show that a large fraction of the sub-seafloor prokaryotes is alive, even in very old (16 million yr) and deep (> 400 m) sediments. All detectable living cells belong to the Bacteria and have turnover times of 0.25–22 yr, comparable to surface sediments.