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

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 prokaryotes. 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 climate. Despite the fact that only about 1% of the total marine primary production of organic carbon is available for deep-sea microorganisms, sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This estimation has been calculated from numerous microscopic cell counts in sediment cores of the Ocean Drilling Program. Because these counts cannot differentiate between dead and alive cells, the population size of living microorganisms is unknown. 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.

Prokaryotic community structure and heterotrophic production in a river-influenced coastal arctic ecosystem

“…Microbial production was estimated with shipboard incubations of water samples with 3 H-leucine, and the offshore gradients in cell concentration of major taxonomic groups were determined by epifluorescence microscopy. Our approach included the application of a recently described molecular probe technique, the catalyzed reporter deposition for fluorescence in situ hybridization assay (CARD-FISH) (Pernthaler et al 2002, Schippers et al 2005. This method gives a much brighter detection of cells than the regular FISH approach, with values comparable to the application of polynucleotide probes (Pernthaler et al 2002).…”

Bubble Transport Mechanism: Indications for a gas bubble-mediated inoculation of benthic methanotrophs into the water column

“…We hypothesize that the strong oxygen sensitivity of ANME organisms (Treude et al, 2005b) may not allow prolonged water-column survival time even if their exposure to oxygen during the runtime of the experiment and recovery of the water samples was relatively short with a maximum of 120 min. Consequently, the applied CARD-FISH technique would have failed to detect dead ANME-2 cells if present, because the targeted RNA quickly degenerates after cell death (Schippers et al, 2005).…”

Data report: total cell counts and qPCR abundance of Archaea and Bacteria in shallow subsurface marine sediments of North Pond: gravity cores collected during site survey cruise prior to IODP Expedition 336

“…Published assays for the quantification of the 16S rRNA gene copy numbers of Archaea (Takai and Horikoshi, 2000) and Bacteria (Nadkarni et al, 2002) were applied. 16S rRNA gene copy numbers were converted to cell numbers using conversion factors of 1.5 for Archaea and 4.1 for Bacteria, as previously done (Schippers et al, 2005).…”

“…Specific archaeal communities for sediments with different trophic states could be detected (Durbin and Teske, 2012). An open question is if Bacteria or Archaea dominate in oligotrophic sediments as previously discussed for eutrophic sediments based on quantitative polymerase chain reaction (qPCR) analysis (Schippers et al, 2005(Schippers et al, , 2012. Similar to oligotrophic Pacific sediments, oligotrophic (total organic carbon = ~0.15% ± 0.07%) and oxic sediments from the North Pond area in the 7 m.y.…”

“…It is mainly controlled by the content of organic carbon in the sediment as the microbial substrate (Parkes et al, 1994;D'Hondt et al, 2004;Schippers et al, 2005Schippers et al, , 2012Edwards et al, 2012;Kallmeyer et al, 2012;Lomstein et al, 2012;Hoehler and Jørgensen, 2013). Organic-lean, oligotrophic, and oxic sediments of the Pacific host oxygen-respiring prokaryotes (Røy et al, 2012).…”