Deep Subseafloor Microbial Communities

Abstract

Marine subsurface sediments cover approximately 70% of the Earth surface and harbour a remarkable population of microbial life that comprises one‐tenth of all living biota on Earth. Metabolic activity of the subseafloor microbes is generally extremely low due to low flux of nutrient and energy substrates in the habitats. However, the long‐term microbial activities play important ecological roles in biogeochemical cycles over geologic time scales. Most subseafloor bacteria and archaea are phylogenetically distinct from known isolates. Hence, the growth characteristics and metabolic activities of each species remain largely unknown.

Key concepts:

  • Significant microbial biomass is present in the deep subseafloor biosphere.

  • Metabolic activity of subseafloor microbes is extraordinary low.

  • Subseafloor microbes play important biogeochemical roles on geologic time scale.

  • Subseafloor microbial communities are mainly composed of uncultivated, hence uncharacterized components.

  • Ecologically significant microbial functions are expected from functional gene surveys and metagenomic analyses.

  • New analytical developments provide new insights into the nature of subseafloor life and the biosphere.

Keywords: deep subseafloor biosphere; phylogenetic diversity; functional genes; Archaea World; biogeochemical cycle

Figure 1.

Global microbial biomass in aquatic, soil and subsurface habitats. Data are from Whitman et al..

Figure 2.

Discrimination of cell‐derived SYBR Green I fluorescence from background signals using a computer‐based image analysis. (a) Spectrum pattern of cell‐derived fluorescence and nonspecific binding of SYBR Green I, so‐called SYBR‐SPAM (SYBR‐stainable particulate matter). When SYBR Green I binds to SYBR‐SPAM, fluorescent spectra shift to longer wavelengths (red line), whereas fluorescent spectra of cell‐derived SYBR‐I (blue line) do not shift or shift very little from the original spectrum of SYBR Green I. Green and orange shading areas show the wavelength range of 528/38, 617/73 (nm of centre wavelength/bandwidth) band‐pass filters, respectively. (b) to (c) Image analysis to distinguish cell‐derived SYBR Green I signals from SYBR‐SPAM in heat‐sterilized control sediments mixed with E. coli. Fluorescent microscopic images taken using band‐pass filters of 528/38 (b) and 617/73 (c). Relative intensity profiles of green/red fluorescence (d) resulted in only cell‐derived fluorescent signals without background fluorescence. Bars: 10 μm. Data are derived from Morono et al., with permission from Nature Publishing Group.

Figure 3.

Phylogenetic tree of the domains Archaea and Bacteria based on 16S rRNA gene sequences. The red and blue phyla represent archaeal and bacterial groups that include frequently detected 16S rRNA gene sequences from the deep subseafloor sediments, respectively. The subseafloor sediment samples are derived from Peru Margin (ODP Leg 201), Cascadia Margin (ODP Leg 204), Eastern Flank of the Juan de Fuca Ridge (IODP Exp. 301), Northwestern Pacific offshore the Shimokita Peninsula (JAMSTEC CK06‐06) and the Nankai Trough seismogenic zone (IODP Exp. 315 and 316). The sequence data were analysed with the ARB software package (Ludwig et al., ).

Figure 4.

Quantitative analysis of archaeal population in deep marine sediments. (a) Depth profile of total microbial intact polar lipids (IPLs) and the ratio of archaeal IPLs. (b) Archaeal 16S rRNA gene ratios of total microbial 16S rRNA genes evaluated by quantitative‐PCR and slot‐blot hybridization (SBH) analyses using a new DNA extraction method with physical destruction and multiple displacement amplification (MDA). Data are derived from Lipp et al., with permission from Nature Publishing Group.

Figure 5.

An example of a schematic flow chart of culture‐independent molecular ecological and biogeochemical approaches for understanding of eco‐physiological functions of the subseafloor ecosystem and subseafloor microbes.

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Inagaki, Fumio(Feb 2010) Deep Subseafloor Microbial Communities. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021894]