Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).
Google Scholar
Merino, N. et al. Living at the extremes: extremophiles and the limits of life in a planetary context. Front. Microbiol. 10, 780 (2019).
Google Scholar
Colman, D. R. et al. Geobiological feedbacks and the evolution of thermoacidophiles. ISME J. 12, 225–236 (2018).
Google Scholar
Reveillaud, J. et al. Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise. Environ. Microbiol. 18, 1970–1987 (2016).
Google Scholar
Lau, M. C. Y. et al. An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers. Proc. Natl Acad. Sci. USA 113, 7927–7936 (2016).
Google Scholar
Momper, L., Jungbluth, S. P., Lee, M. D. & Amend, J. P. Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISME J. 11, 2319–2333 (2017).
Google Scholar
Brazelton, W. J. et al. Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PeerJ 5, e2945 (2017).
Google Scholar
Havig, J. R., Raymond, J., Meyer-Dombard, D. R., Zolotova, N. & Shock, E. L. Merging isotopes and community genomics in a siliceous sinter-depositing hot spring. J. Geophys. Res. Biogeosci. 116, G01005 (2011).
Google Scholar
Power, J. F. et al. Microbial biogeography of 925 geothermal springs in New Zealand. Nat. Commun. 9, 2876 (2018).
Google Scholar
Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111–5120 (2009).
Google Scholar
Kelemen, P. B. & Manning, C. E. Reevaluating carbon fluxes in subduction zones, what goes down, mostly comes up. Proc. Natl Acad. Sci. USA 112, E3997–E4006 (2015).
Google Scholar
Brovarone, A. V. et al. Subduction hides high-pressure sources of energy that may feed the deep subsurface biosphere. Nat. Commun. 11, 3880 (2020).
Google Scholar
Plümper, O. et al. Subduction zone forearc serpentinites as incubators for deep microbial life. Proc. Natl Acad. Sci. USA 114, 4324–4329 (2017).
Google Scholar
Syracuse, E. M. & Abers, G. A. Global compilation of variations in slab depth beneath arc volcanoes and implications. Geochem. Geophys. Geosyst. 7, Q05017 (2006).
Google Scholar
Shaw, A. M., Hilton, D. R., Fischer, T. P., Walker, J. A. & Alvarado, G. E. Contrasting He–C relationships in Nicaragua and Costa Rica: insights into C cycling through subduction zones. Earth Planet. Sci. Lett. 214, 499–513 (2003).
Google Scholar
Barry, P. H. et al. Forearc carbon sink reduces long-term volatile recycling into the mantle. Nature 568, 487–492 (2019).
Google Scholar
Arce-Rodríguez, A. et al. Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO2-rich hydrothermal spring located in Tenorio Volcano National Park, Costa Rica. Extremophiles 23, 177–187 (2019).
Google Scholar
Crespo-Medina, M. et al. Methane dynamics in a tropical serpentinizing environment: the Santa Elena ophiolite, Costa Rica. Front. Microbiol. 8, 916 (2017).
Google Scholar
Probst, A. J. & Moissl-Eichinger, C. “Altiarchaeales”: uncultivated Archaea from the subsurface. Life https://doi.org/10.3390/life5021381 (2015).
Giggenbach, W. F. Geothermal solute equilibria, derivation of Na-K-Mg-Ca geoindicators. Geochim. Cosmochim. Acta 52, 2749–2765 (1988).
Google Scholar
Giggenbach, W. F. & Soto, R. C. Isotopic and chemical composition of water and steam discharges from volcanic–magmatic–hydrothermal systems of the Guanacaste Geothermal Province, Costa Rica. Appl. Geochem. 7, 309–332 (1992).
Google Scholar
Rodríguez, A. & van Bergen, M. J. Superficial alteration mineralogy in active volcanic systems: an example of Poás volcano, Costa Rica. J. Volcanol. Geotherm. Res. 346, 54–80 (2017).
Google Scholar
Chan, C. S., Fakra, S. C., Emerson, D., Fleming, E. J. & Edwards, K. J. Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation. ISME J. 5, 717–727 (2011).
Google Scholar
Lücke, O. H. & Arroyo, I. G. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data. Solid Earth 6, 1169–1183 (2015).
Google Scholar
Protti, M., Gündel, F. & McNally, K. The geometry of the Wadati–Benioff zone under southern Central America and its tectonic significance: results from a high-resolution local seismographic network. Phys. Earth Planet. Inter. 84, 271–287 (1994).
Google Scholar
de Moor, J. M. et al. A new sulfur and carbon degassing inventory for the Southern Central American Volcanic Arc: the importance of accurate time-series data sets and possible tectonic processes responsible for temporal variations in arc-scale volatile emissions: new volatile budget for Central America. Geochem. Geophys. Geosyst. 18, 4437–4468 (2017).
Google Scholar
Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 359, 320–325 (2018).
Google Scholar
Kim, M. S., Jo, S. K., Roh, S. W. & Bae, J. W. Alishewanella agri sp. nov., isolated from landfill soil. Int. J. Syst. Evol. Microbiol. 60, 2199–2203 (2010).
Google Scholar
Chen, W. M. et al. Aquabacterium limnoticum sp. nov., isolated from a freshwater spring. Int. J. Syst. Evol. Microbiol. 62, 698–704 (2012).
Google Scholar
Garrity, G. M. & Bell, J. A. Bergey’s Manual of Systematics of Archaea and Bacteria (Bergey’s Manual Trust, 2015).
Hayashi, N. R., Ishida, T., Yokota, A., Kodama, T. & Igarashi, Y. Hydrogenophilus thermoluteolus gen. nov., sp. nov., a thermophilic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium. Int. J. Syst. Evol. Microbiol. 49, 783–786 (1999).
Google Scholar
Berg, I. A. et al. Autotrophic carbon fixation in archaea. Nat. Rev. Microbiol. 8, 447–460 (2010).
Google Scholar
Giovannelli, D. et al. Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans. eLife 6, e18990 (2017).
Google Scholar
Yokochi, R. et al. Noble gas radionuclides in Yellowstone geothermal gas emissions: a reconnaissance. Chem. Geol. 339, 43–51 (2013).
Google Scholar
Harris, R. N. & Wang, K. Thermal models of the Middle America Trench at the Nicoya Peninsula, Costa Rica. Geophys. Res. Lett. 29, 6-1–6-4 (2010).
Jelen, B. I., Giovannelli, D. & Falkowski, P. G. The role of microbial electron transfer in the coevolution of the biosphere and geosphere. Annu. Rev. Microbiol. 70, 45–62 (2016).
Google Scholar
Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive Earth’s biogeochemical cycles. Science 320, 1034–1039 (2008).
Google Scholar
Tassi, F. et al. The geothermal resource in the Guanacaste region (Costa Rica): new hints from the geochemistry of naturally discharging fluids. Front. Earth Sci. 6, 69 (2018).
Google Scholar
Tassi, F., Vaselli, O., Barboza, V., Fernandez, E. & Duarte, E. Fluid geochemistry and seismic activity in the period 1998–2002 at Turrialba Volcano (Costa Rica). Ann. Geophys. 47, 4 (2004).
Barry, P. H. et al. Helium, inorganic and organic carbon isotopes of fluids and gases across the Costa Rica convergent margin. Sci. Data https://doi.org/10.1038/s41597-019-0302-4 (2019).
Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A. & Reysenbach, A.-L. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl. Environ. Microbiol. 65, 4375–4384 (1999).
Google Scholar
Wright, J. J., Lee, S., Zaikova, E., Walsh, D. A. & Hallam, S. J. DNA extraction from 0.22 μm Sterivex filters and cesium chloride density gradient centrifugation. JOVE https://doi.org/10.3791/1352 (2009).
Teare, J. M. et al. Measurement of nucleic acid concentrations using the DyNA QuantTM and the GeneQuantTM. Biotechniques 22, 1170–1174 (1997).
Google Scholar
Simbolo, M. et al. DNA qualification workflow for next generation sequencing of histopathological samples. PLoS ONE 8, e62692 (2013).
Google Scholar
Giovannelli, D. et al. Diversity and distribution of prokaryotes within a shallow-water pockmark field. Front. Microbiol. 7, 941 (2016).
Google Scholar
Huse, S. M. et al. VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinformatics 15, 41 (2014).
Google Scholar
Huse, S. M. et al. Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. Microbiome 2, 5 (2014).
Google Scholar
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).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).
Google Scholar
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Google Scholar
Zhu, C. et al. Functional sequencing read annotation for high precision microbiome analysis. Nucleic Acids Res. 46, e23 (2018).
Google Scholar
R Core Team, R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2013).
McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
Google Scholar
vegan (CRAN, 2019).
Hamilton, N. E. & Ferry, M. ggtern: ternary diagrams using ggplot2. J. Stat. Softw. 87, 1–17 (2018).
Google Scholar
Stekhoven, D. J. & Buhlmann, P. MissForest—non-parametric missing value imputation for mixed-type data. Bioinformatics 28, 112–118 (2012).
Google Scholar
Genuer, R., Poggi, J.-M. & Tuleau-Malot, C. VSURF: an R package for variable selection using random forests. R J. 7, 1–19 (2015).
Google Scholar
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).
Sheik, C. S. et al. Identification and removal of contaminant sequences from ribosomal gene databases: lessons from the Census of Deep Life. Front. Microbiol. 9, 840 (2018).
Google Scholar
Sugimori, K. et al. Microbial life in the acid lake and hot springs of Poas Volcano, Costa Rica. In Proc. Colima Volcano International Meeting (2002).
Mcmurdie, P. J. & Holmes, S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 10, e1003531 (2014).
Google Scholar
Weiss, S. et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5, 27 (2017).
Google Scholar
Giovannelli, D. et al. Large-scale distribution and activity of prokaryotes in deep-sea surface sediments of the Mediterranean Sea and the adjacent Atlantic Ocean. PLoS ONE 8, e72996 (2013).
Holm, S. A simple sequentially rejective multiple test procedure. Scand. J. Stat. 6, 65–70 (1979).
Schruben, P. G. Geology and Resource Assessment of Costa Rica DDS-19-R (USGS, 1987).
Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012).
Google Scholar
Kurtz, Z. D. et al. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput. Biol. 11, e1004226 (2015).
Google Scholar
Schwager, E., Mallick, H., Ventz, S. & Huttenhower, C. A Bayesian method for detecting pairwise associations in compositional data. PLoS Comput. Biol. 13, e1005852 (2017).
Google Scholar
Zar, J. H. Significance testing of the spearman rank correlation coefficient. J. Am. Stat. Assoc. 67, 578–580 (1972).
Google Scholar
Csardi, G. & Nepusz, T. The igraph software package for complex network research. InterJournal 1695, 1–9 (2006).
Braun, S. et al. Microbial turnover times in the deep seabed studied by amino acid racemization modelling. Sci. Rep. 7, 5680 (2017).
Google Scholar
Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998).
Google Scholar
McMahon, S. & Parnell, J. Weighing the deep continental biosphere. FEMS Microbiol. Ecol. 87, 113–120 (2013).
Google Scholar
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