Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor

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Science  24 Jul 2015:
Vol. 349, Issue 6246, pp. 420-424
DOI: 10.1126/science.aaa6882
  • Fig. 1 Depth profiles of microbial cell counts and geochemical data at Site C0020.

    (A) Microbial cell concentrations, (B) δ13C and δD of methane, and (C) C1/C2 ratios and δ13C of CO2. (A) For cell concentrations in the deep subseafloor, raw data of fluorescence image-based cell counts (8), the most likely indigenous cell concentrations based on the probability-relationship set analysis (7), and the most conservative indigenous cell concentrations estimated based on the taxonomic classification (7) are shown (figs. S6 and S7 and table S1). The correction factor is the proportion of sequences estimated to be indigenous (table S1). The minimal quantification limit for raw cell counts was 1.43 × 102 cells cm−3 (i.e., the upper 95% confidence interval of the negative background). All δ13C and δD in (B) and (C) are in per mil versus the Vienna Pee Dee Belemnite (VPDB) and Standard Mean Ocean Water (SMOW) standards, respectively. The Δ13CH3D-T values in (B) designate the apparent equilibrium temperatures derived from measurements of 13CH3D, a clumped isotopologue of methane (table S2) in discrete formation fluid (FF) samples (6, 7). Temperature is based on the temperature gradient of 24°C km−1 determined by downhole logging (6).

  • Fig. 2 Geochemical and microbiological indications for methanogenic microbial communities in ~2-km-deep subseafloor coal beds at Site C0020.

    (A) A representative chromatogram of the diagnostic methanogen biomarker F430 (as methyl ester) and its epimers from a coal sample (core 18R-2, 1946 mbsf) (table S3). (B) to (D) Photomicrographs of microbial cells in an enrichment culture from ~2-km-deep coal-bed samples using a continuous-flow bioreactor with powdered coal as the major energy source (7). (B) Phase-contrast micrograph of microbial cells attached to mineral particles. (C) Fluorescent micrograph of the same field shown in (B) showing the growth of methanogens that produce autofluorescence derived from coenzyme F420. (D) Phase-contrast micrograph showing spherical spore-like particles, indicated by arrows. (E) to (G) NanoSIMS analysis of cells in the reactor enrichment culture incubated with 13C-labeled bicarbonate (7). (E) Fluorescent micrograph of SYBR Green I–stained cells. (F) and (G) NanoSIMS ion images of 13C/12C (F) and 12C (G). The color gradient indicates the relative abundance of 13C expressed as 13C/12C. The length of the bars is 10 μm.

  • Fig. 3 Taxonomic distribution of the most conservative indigenous bacterial communities in sediments at Site C0020.

    (A) Phylum-level taxonomic composition of bacterial 16S gene-tagged sequences (i.e., V1–V3 region) in shallow (sample numbers 1 to 5, 9.5 to 364 mbsf, from Chikyu cruise CK06-06) and deep (sample numbers 6 to 32, 1279.1 to 2458.8 mbsf, from IODP Expedition 337) subseafloor sediment samples (7). (B) Cluster and Bray-Curtis dissimilarity analyses of bacterial community structure based on the genus-level classification of the same sequence assemblages used in (A). Colored dots on the cluster tree represent the sedimentological characteristics of each sample horizon (6). The OTU-based analysis for the most likely indigenous bacterial communities in deep subseafloor sediment samples is shown in fig. S10.

Supplementary Materials

  • Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor

    F. Inagaki, K.-U. Hinrichs, Y. Kubo, M. W. Bowles, V. B. Heuer, W.-L. Hong, T. Hoshino, A. Ijiri, H. Imachi, M. Ito, M. Kaneko, M. A. Lever, Y.-S. Lin, B. A. Methé, S. Morita, Y. Morono, W. Tanikawa, M. Bihan, S. A. Bowden, M. Elvert, C. Glombitza, D. Gross, G. J. Harrington, T. Hori, K. Li, D. Limmer, C.-H. Liu, M. Murayama, N. Ohkouchi, S. Ono, Y.-S. Park, S. C. Phillips, X. Prieto-Mollar, M. Purkey, N. Riedinger, Y. Sanada, J. Sauvage, G. Snyder, R. Susilawati, Y. Takano, E. Tasumi, T. Terada, H. Tomaru, E. Trembath-Reichert, D. T. Wang, Y. Yamada

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S14
    • References (3283)
    Tables S1 to S7

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