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Ahmed, B., Cao, B., McLean, J.S., Ica, T., Dohnalkova, A., Istanbullu, O., Paksoy, A., Fredrickson, J.K., and Beyenal, H., 2012. Fe(III) reduction and U(VI) immobilization by Paenibacillus sp. strain 300A, isolated from Hanford 300A subsurface sediments. Appl. Environ. Microbiol., 78(22):8001–8009. doi:10.1128/AEM.01844-12

Bach, W., and Edwards, K.J., 2003. Iron and sulfide oxidation within the basaltic ocean crust: implications for chemolithoautotrophic microbial biomass production. Geochim. Cosmochim. Acta, 67(20):3871–3887. doi:10.1016/S0016-7037(03)00304-1

Byrne-Bailey, K.G., Weber, K.A., Chair, A.H., Bose, S., Knox, T., Spanbauer, T.L., Chertkov, O., and Coates, J.D., 2010. Completed genome sequence of the anaerobic iron-oxidizing bacterium Acidovorax ebreus strain TPSY. J. Bacteriol., 192(5):1475–1476. doi:10.1128/​JB.01449-09

DeLong, E.F., 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. U. S. A., 89(12):5685–5689. doi:10.1073/​pnas.89.12.5685

Denkmann, K., Grein, F., Zigann, R., Siemen, A., Bergmann, J., van Helmont, S., Nicolai, A., Pereira, I.A.C., and Dahl, C., 2012. Thiosulfate dehydrogenase: a widespread unusual acidophilic c-type cytochrome. Environ. Microbiol., 14(10):2673–2688. doi:10.1111/​j.1462-2920.2012.02820.x

Expedition 336 Scientists, 2012a. Expedition 336 summary. In Edwards, K.J., Bach, W., Klaus, A., and the Expedition 336 Scientists, Proc. IODP, 336: Tokyo (Integrated Ocean Drilling Program Management International, Inc.). doi:10.2204/iodp.proc.336.101.2012

Expedition 336 Scientists, 2012b. Methods. In Edwards, K.J., Bach, W., Klaus, A., and the Expedition 336 Scientists, Proc. IODP, 336: Tokyo (Integrated Ocean Drilling Program Management International, Inc.). doi:10.2204/iodp.proc.336.102.2012

Fisher, A.T., Davis, E.E., Hutnak, M., Spiess, V., Zühlsdorff, L., Cherkaoui, A., Christiansen, L., Edwards, K., Macdonald, R., Villinger, H., Mottl, M.J., Wheat, C.G., and Becker, K., 2003. Hydrothermal recharge and discharge across 50 km guided by seamounts on a young ridge flank. Nature, 421(6923):618–621. doi:10.1038/nature01352

Han, S.K., Nedashkovskaya, O.I., Mikhailov, V.V., Kim, S.B., and Bae, K.S., 2003. Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int. J. Syst. Evol. Microbiol., 53(6):2061–2066. doi:10.1099/​ijs.0.02627-0

Hirayama, H., Fuse, H., Abe, M., Miyazaki, M., Nakamura, T., Nunoura, T., Furushima, Y., Yamamoto, H., and Takai, K., 2013. Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments. Int. J. Syst. Evol. Microbiol., 63(3):1073–1082. doi:10.1099/ijs.0.040568-0

Ivarsson, M., Bengtson, S., Belivanova, V., Stampanoni, M., Marone, F., and Tehler, A., 2012. Fossilized fungi in subseafloor Eocene basalts. Geology, 40(2):163–166. doi:10.1130/G32590.1

Kämpfer, P., Glaeser, S.P., and Busse, H.-J., 2013. Transfer of Bacillus schlegelii to a novel genus and proposal of Hydrogenibacillus schlegelii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol., 63(5):1723-1727. doi:10.1099/ijs.0.045146-0

Klenk, H.-P., Lapidus, A., Chertkov, O., Copeland, A., Del Rio, T.G., Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J.-F., Han, C., Bruce, D., Goodwin, L., Pitluck, S., Pati, A., Ivanova, N., Mavromatis, K., Daum, C., Chen, A., Palaniappan, K., Chang, Y., Land, M., Hauser, L., Jeffries, C.D., Detter, J.C., Rohde, M., Abt, B., Pukall, R., Göker, M., Bristow, J., Markowitz, V., Hugenholtz, P., and Eisen, J.A., 2011. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Stand. Genomic. Sci., 5(1):121–134. doi:10.4056/sigs.2144922

Lane, D.J., 1991. 16S/23S rRNA sequencing. In Stackebrandt, E., and Goodfellow, M. (Eds.), Nucleic Acid Techniques in Bacterial Systematics: New York (Wiley), 115–148.

Lever, M.A., Rouxel, O., Alt, J.C., Shimizu, N., Ono, S., Coggon, R.M., Shanks, W.C., III, Laphan, L., Elvert, M., Prieto-Mollar, X., Hinrichs, K.-U., Inagaki, F., and Teske, A., 2013. Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt. Science, 339(6125):1305–1308. doi:10.1126/science.1229240

Lysnes, K., Torsvik, T., Thorseth, I.H., and Pedersen, R.B., 2004. Microbial populations in ocean floor basalt: results from ODP Leg 187. In Pedersen, R.B., Christie, D.M., Miller, D.J. (Eds.), Proc. ODP, Sci. Results, 187: College Station, TX (Ocean Drilling Program), 1–27. doi:10.2973/

Mason, O.U., Nakagawa, T., Rosner, M., Van Nostrand, J.D., Zhou, J., Maruyama, A., Fisk, M.R., and Giovannoni, S.J., 2010. First investigation of the microbiology of the deepest layer of ocean crust. PLoS One, 5(11):e15399. doi:10.1371/journal.pone.0015399

McCarthy, M.D., Beaupré, S.R., Walker, B.D., Voparil, I., Guilderson, T.P., and Druffel, E.R.M., 2011. Chemosynthetic origin of 14C-depleted dissolved organic matter in a ridge-flank hydrothermal system. Nat. Geosci., 4(1):32–36. doi:10.1038/ngeo1015

Medlin, L., Elwood, H.J., Stickel, S., and Sogin, M.L., 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene, 71(2):491–499. doi:10.1016/​0378-1119(88)90066-2

Mijnendonckx, K., Provoost, A., Ott, C.M., Venkateswaran, K., Mahillon, J., Leys, N., and Van Houdt, R., 2013. Characterization of the survival ability of Cupriavidus metallidurans and Ralstonia pickettii from space-related environments. Microb. Ecol., 65(2):347–360. doi:10.1007/​s00248-012-0139-2

Nunoura, T., Oida, H., Miyazaki, J., Miyashita, A., Imachi, H., and Takai, K., 2008. Quantification of mcrA by fluorescent PCR in methanogenic and methanotrophic microbial communities. FEMS Microbiol. Ecol., 64(2):240–247. doi:10.1111/​j.1574-6941.2008.00451.x

Parkes, R.J., Cragg, B., Roussel, E., Webster, G., Weightman, A., and Sass, H., 2014. A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions. Mar. Geol., 352:409–425. doi:10.1016/​j.margeo.2014.02.009

Petri, R., Podgorsek, L., and Imhoff, J.F., 2001. Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria. FEMS Microbiol. Lett., 197(2):171–178. doi:10.1016/​S0378-1097(01)00111-2

Petrie, L., North, N.N., Dollhopf, S.L., Balkwill, D.L., and Kostka, J.E., 2003. Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI). Appl. Environ. Microbiol., 69(12):7467–7479. doi:10.1128/​AEM.69.12.7467-7479.2003

Puitika, T., Kasahara, Y., Miyoshi, N., Sato, Y., and Shimano, S., 2007. A taxon-specific oligonucleotide primer set for PCR-based detection of soil ciliate. Microbes Environ., 22(1):78–81. doi:10.1264/​jsme2.22.78

Rathsack, K., Stackebrandt, E., Reitner, J., and Schumann, G., 2009. Microorganisms isolated from deep sea low-temperature influenced oceanic crust basalts and sediment samples collected along the Mid-Atlantic Ridge. Geomicrobiol. J., 26(4):264–274. doi:10.1080/​01490450902892456

Ruibal, C., Platas, G., and Bills, G.F., 2008. High diversity and morphological convergence among melanised fungi from rock formations in the Central Mountain System of Spain. Persoonia, 21:93–110. doi:10.3767/003158508X371379

Schumann, G., Manz, W., Reitner, J., and Lustrino, M., 2004. Ancient fungal life in north Pacific Eocene oceanic crust. Geomicrobiol. J., 21(4):241–246. doi:10.1080/01490450490438748

Smith, A., Popa, R., Fisk, M., Nielsen, M., Wheat, C.G., Jannasch, H.W., Fisher, A.T., Becker, K., Sievert, S.M., and Flores, G., 2011. In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device. Geochem., Geophys., Geosyst., 12(6):Q06007. doi:10.1029/2010GC003424

Sorokin, D.Y., 2003. Oxidation of inorganic sulfur compounds by obligately organotrophic bacteria. Microbiology, 72(6):641–653. doi:10.1023/​B:MICI.0000008363.24128.e5

Sterflinger, K., De Baere, R., de Hoog, G.S., De Wachter, R., Krumbein, W.E., and Haase, G., 1997. Coniosporium perforans and C. apollinis, two new rock-inhabiting fungi isolated from marble in the Sanctuary of Delos (Cyclades, Greece). Antonie Van Leeuwenhoek, 72(4):349–363. doi:10.1023/A:1000570429688

Stevens, T.O., and McKinley, J.P., 1995. Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science, 270(5235):450–454. doi:10.1126/science.270.5235.450

Stevens, T.O., and McKinley, J.P., 2000. Abiotic controls on H2 production from basalt-water reactions and implications for aquifer biogeochemistry. Environ. Sci. Technol., 34(5):826–831. doi:10.1021/​es990583g

Takai, K., Inoue, A., and Horikoshi, K., 2002. Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system. Int. J. Syst. Evol. Microbiol., 52(4):1089–1095. doi:10.1099/​ijs.0.02106-0

Van Spanning, R.J.M., Stouthamer, A.H., Baker, S.C., and van Verseveld, H.W., 2005. Class I. Alphaproteobacteria, Order III. Rhodobacterales, Family 1. Rhodobacteraceae, Genus XII. Paracoccus. In Garrity, G.M., Brenner, D.J., Krieg, N.R., and Staley, J.T. (Eds.), Bergey’s Manual of Systematic Bacteriology (Vol. 2): The Proteobacteria (Part C): New York (Springer), 197–204.

Vandamme, P., and Coenye, T., 2004. Taxonomy of the genus Cupriavidus: a tale of lost and found. Int. J. Syst. Evol. Microbiol., 54(6):2285–2289. doi:10.1099/ijs.0.63247-0

White, T.J., Bruns, T., Lee, S., and Taylor, J.W., 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In Innis, M.A., Gelfand, D.H., Sninsky, J.J., and White, T.J. (Eds.), PCR Protocols: A Guide to Methods and Applications: London (Academic Press), 315–322. doi:10.1016/B978-0-12-372180-8.50042-1

Willems, A., Falsen, E., Pot, B., Jantzen, E., Hoste, B., Vandamme, P., Gillis, M., Kersters, K., and De Ley, J., 1990. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int. J. Syst. Bacteriol., 40(4):384–398. doi:10.1099/​00207713-40-4-384

Yabuuchi, E., and Kosako, Y., 2005. Class I. Alphaproteobacteria, Order IV. Sphingomonadales, Family I. Sphingomonadaceae, Genus I. Sphingomonas. In Garrity, G.M., Brenner, D.J., Krieg, N.R., and Staley, J.T. (Eds.), Bergey’s Manual of Systematic Bacteriology (Vol. 2): The Proteobacteria (Part C): New York (Springer), 234–258.