phic South Pacific Gyre (IODP Expedition 329 Sites U1367, U1368 and U1370). Palaeogeogr. Palaeoclimatol. Palaeoecol. 419, 115–142 (2015).
Morono, Y., Terada, T., Kallmeyer, J. & Inagaki, F. An improved cell separation technique for marine subsurface sediments: applications for high-throughput analysis using flow cytometry and cell sorting. Environ. Microbiol. 15, 2841–2849 (2013).
Kallmeyer, J., Smith, D. C., Spivack, A. J. & D’Hondt, S. New cell extraction procedure applied to deep subsurface sediments. Limnol. Oceanogr. Meth. 6, 236–245 (2008).
Morono, Y. & Inagaki, F. Automatic slide-loarder fluorescence microscope for discriminative enumeration of subseafloor life. Sci. Drilling 9, 32–36 (2010).
Morono, Y., Terada, T., Masui, N., Inagaki, F., Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J. 3, 503–511 (2009).
Inagaki, F. et al. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 349, 420–424 (2015).
Gormanns, P., Reckow, S., Poczatek, J. C., Turck, C. W. & Lechene, C. Segmentation of multi-isotope imaging mass spectrometry data for semi-automatic detection of regions of interest. PLoS One 7, e30576 (2012).
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671 (2012).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676 (2012).
R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria, 2018).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, New York, 2016).
Wilke, C. O. Cowplot: Streamlined llot theme and plot annotations for ‘ggplot2’. R package version 0.9.3. https://CRAN.R-project.org/package=cowplot (2018).
Xiao, N. ggsci: Scientific journal and Sci-Fi themed color palettes for ‘ggplot2’. R package version 2.9. https://CRAN.R-project.org/package=ggsci (2018).
Wickham, H. scales: Scale functions for visualization. R package version 1.0.0. https://CRAN.R-project.org/package=scales (2018).
Kopf, H. S. From lakes to lungs: Assessing microbial activity in diverse environments. PhD thesis (California Institute of Technology, 2015).
Morono, Y., Terada, T., Hoshino, T. & Inagaki, F. A hot-alkaline DNA extraction method for deep subseafloor archaeal communities. Appl. Environ. Microbiol. 80, 1985–1994 (2014).
Morono, Y. et al. Assessment of capacity to capture DNA aerosols by clean filters for molecular biology experiments. Microbes Environ. 33, 222–226 (2018).
Hoshino, T. & Inagaki, F. Abundance and distribution of Archaea in the subseafloor sedimentary biosphere. ISME J. 13, 227–231 (2019).
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
Caporaso, J. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Meth. 7, 335–336 (2010).
Yilmaz, P. et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucl. Acids. Res. 42, D643–D648 (2014).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids. Res. 41, D590–D596 (2013).
Oksanen, J. et al. Package ‘vegan’. Community ecology package, R package version 2.5–2. https://CRAN.R-project.org/package=vegan (2018).
The samples used in this study were collected during IODP Expedition 329 by the JOIDES Re