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.

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

“…The predominant bacterial 16S rRNA gene phylotypes observed in the inoculum sample were related to members of the phyla Chloroflexi, Planctomycetes and Actinobacteria, candidate phyla JS1 and NT-B2 and the class Alphaproteobacteria, which have been frequently detected as the predominant bacterial components in various subseafloor sediments (for example, Fry et al, 2008;Inagaki, 2010; Figure 2c and Supplementary Figure S7, Supplementary Table S4). During cultivation in the DHS reactor, the composition of bacterial rRNA gene phylotypes changed drastically.…”

“…Culture-independent molecular analyses have found a limited population of the known methanogenic Archaea (methanogens) groups in a variety of subseafloor sediments (see references in reviews by Fry et al (2008);Inagaki (2010)). On average, methanogens represent only 0.1% population of the total archaeal 16S rRNA gene pool in deep subseafloor sediments (Fry et al, 2008).…”

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“…Hence, the geologic and sedimentological characteristics represent crucial factors controlling habitability of the deep subsurface. Culture-independent molecular ecological surveys of 16S ribosomal ribonucleic acid (rRNA) gene fragments reveal that the microbial communities in continental margin sediments are predominantly composed of species lacking cultivated relatives, such as the bacterial members within the candidate division JS1, Chloroflexi, and Planctomycetes, as well as the archaeal members within the Deep-Sea Archaeal Group, the Miscellaneous Crenarchaeotic Group, and the South African Gold Mine Euryarchaeotic Group (e.g., Inagaki et al, 2003Inagaki et al, , 2006bInagaki and Nakagawa, 2008;Inagaki, 2010). The carbon isotopic analysis of intact polar lipids (IPLs) and fluorescence in situ hybridization (FISH)-stained cells suggest that sizeable populations of heterotrophic Archaea significantly contribute to microbial biomass in organic-rich sediments, even at the SMT zone where the occurrence of anaerobic oxidation of methane (AOM) mediated by methanotrophic archaea and sulfate-reducing bacteria takes place (Biddle et al, 2006).…”

Present and future of subsurface biosphere studies in lacustrine sediments through scientific drilling

“…These impacts include dissolution, alteration and precipitation of minerals and changes in redox conditions (Vaughan and Lloyd 2012). While ocean drilling programs (ODP and IODP) pioneered the study of the "deep biosphere" (e.g., D'Hondt et al 2002D'Hondt et al , 2004Hinrichs and Inagaki 2012;Horsfield et al 2006;Inagaki 2010;Lever et al 2013;Lomstein et al 2012;Røy et al 2012), lake sediments provide a range of characteristics worth investigating. First, they can represent a wider range of different chemical conditions (e.g., from alkaline to acidic, oxic to anoxic), and these differences can occur in short lateral distances.…”

“…Blue and red labels represent archaeal and bacterial phylogenetic groups frequently identified in subsea floor and subfloor lacustrine sediments, respectively. Branches labeled in green correspond to groups identified in both marine and lacustrine environments (modified from Inagaki 2010) 1 3 influence the precipitation of authigenic minerals such as framboidal pyrite (Fig. 2, 4).…”