Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.

International audienceA general review of the sub-seafloor biosphere is presented. This includes an update and assessment of prokary-otic cell distributions within marine sediments, current deepest 1922 m, and the impact of this on global sub-seafloor biomass estimates. These global estimates appear relatively robust to different calculation approaches and our updated estimate is 5.39 × 10 29 cells, taking into consideration new data from very low organic matter South Pacific Gyre sediments. This is higher than other recent estimates, which is justified as several sediments, such as gas hydrate deposits and oil reservoirs, can have elevated cell concentrations. The proposed relationship between elevated cell concentrations and Milankovitch Cycles in sequential diatom rich layers at some sites, demonstrates not only a dynamic deep biosphere, but also that the deep biosphere is an integral part of Earth System Processes over geological time scales. Cell depth distributions vary in different oceanographic provinces and this is also reflected in contrasting biodiversity. Despite this there are some clear common, sub-seafloor prokary-otes, for Bacteria these are the phyla Chloroflexi, Gammaproteobacteria, Planctomycetes and the candidate phylum JS1, and for Archaea uncultivated lineages within the phylum Crenarchaeota (Miscellaneous Crenarchaeotal Group and Marine Benthic Group B), Euryarchaeota (SAGMEG, Marine Benthic Group-D/Thermoplasmatales associated groups) and Thaumarchaeota (Marine Group I). In addition, spores, viruses and fungi have been detected, but their importance is not yet clear. Consistent with the direct demonstration of active prokaryotic cells, prokaryotes have been enriched and isolated from deep sediments and these reflect a subset of the total diversity, including spore formers that are rarely detected in DNA analyses. Activities are generally low in deep marine sediments (~10,000 times lower than in near-surface sediments), however, depth integrated activity calculations demonstrate that sub-surface sediments can be responsible for the majority of sediment activity (up to 90%), and hence, are biogeochemically important. Unlike near-surface sediments, competitive metabolisms can occur together and metabolism per cell can be 1000 times lower than in culture, and below the lowest known maintenance energies. Consistent with this, cell turnover times approach geological timescales (100–1000s of years). Prokaryotic necromass may be an important energy and carbon source, but this is largely produced in near-surface sediments as cell numbers rapidly decrease. However, this and deposited organic matter may be activated at depth as temperatures increase. At thermogenic temperatures methane and other hydrocarbons, plus H 2 , acetate and CO 2 may be produced and diffuse upwards to feed the base of the biosphere (e.g. Nankai Trough and Newfoundland Margin). Temperature activation of minerals may also result in oxidation of sulphides and the formation of electron acceptors, plus H 2 from low temperature (~55 °C) serpentenisation and water radiolysis. New mineral surface formation from fracturing, weathering and subduction etc. can also mechanochemically split water producing both substrates (H 2) and oxidants (O 2 and H 2 O 2) for prokaryotes. These and other biosphere:geosphere interactions may be important for sustaining a globally significant sub-seafloor biosphere

The ‘Atribacteria’ is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the ‘Atribacteria’ inclusive of OP9 and JS1. Additional conserved features within the ‘Atribacteria’ were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the ‘Atribacteria’ are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria , “ Bacteroidetes ,” “ Fusobacteria ,” Actinobacteria , and “ Firmicutes .” Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.