IODP

doi:10.2204/iodp.sp.337.2010

References

Alt, J.C., Kinoshita, H., Stokking, L.B., et al., 1993. Proc. ODP, Init. Repts., 148: College Station, TX (Ocean Drilling Program).
doi:10.2973/odp.proc.ir.148.1993

Aoike, K. (Ed.), 2007. CDEX Laboratory Operation Report: CK06-06 D/V Chikyu shakedown cruise offshore Shimokita: Yokohama (CDEX-JAMSTEC). http://sio7.jamstec.go.jp/JAMSTEC-exp-report/902/CK06-06_CR.pdf

Aoike, K., Nishi, H., Sakamoto, T., Iijima, K., Tsuchiya, M., Taira, A., Kuramoto, S., Masago, H., and the Shimokita Core Research Group, 2010. Paleoceanographic history of offshore Shimokita Peninsula for the past 800,000 years based on primary analyses on cores recovered by D/V Chikyu during the shakedown cruises. Fossils, 87:65–81. (in Japanese, with English abstract and figures)

Arndt, S., Brumsack, H.-J., and Wirtz, K.W., 2006. Cretaceous black shales as active bioreactors: a biogeochemical model for the deep biosphere encountered during ODP Leg 207 (Demerara Rise). Geochim. Cosmochim. Acta, 70(2):408–425. doi:10.1016/j.gca.2005.09.010

Biddle, J.F., Lipp, J.S., Lever, M.A., Lloyd, K.G., Sørensen, K.B., Anderson, R., Fredricks, H.F., Elvert, M., Kelly, T.J., Schrag, D.P., Sogin, M.L., Brenchley, J.E., Teske, A., House, C.H., and Hinrichs, K.-U., 2006. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci. U. S. A., 103(10):3846–3851. doi:10.1073/pnas.0600035103

Brown, C.J., Coates, J.D., and Schoonen, M.A.A., 1999. Localized sulfate-reducing zones in a coastal plain aquifer. Ground Water, 37(4):505–516. doi:10.1111/j.1745-6584.1999.tb01136.x

Colwell, F.S., Boyd, S., Delwiche, M.E., Reed, D.W., Phelps, T.J., and Newby, D.T., 2008. Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin. Appl. Environ. Microbiol., 74(11):3444–3452. doi:10.1128/AEM.02114-07

Cowen, J.P., Giovannoni, S.J., Kenig, F., Johnson, H.P., Butterfield, D., Rappé, M.S., Hutnak, M., and Lam, P., 2003. Fluids from aging ocean crust that support microbial life. Science, 299(5603):120–123. doi:10.1126/science.1075653

Detmers, J., Schulte, U., Strauss, H., and Kuever, J., 2001. Sulfate reduction at a lignite seam: microbial abundance and activity. Microb. Ecol.,42(3):238–247. doi:10.1007/s00248-001-1014-8

D'Hondt, S., Jørgensen, B.B., Miller, D.J., Batzke, A., Blake, R., Cragg, B.A., Cypionka, H., Dickens, G.R., Ferdelman, T., Hinrichs, K.-U., Holm, N.G., Mitterer, R., Spivack, A., Wang, G., Bekins, B., Engelen, B., Ford, K., Gettemy, G., Rutherford, S.D., Sass, H., Skilbeck, C.G., Aiello, I.W., Guerin, G., House, C.H., Inagaki, F., Meister, P., Naehr, T., Niitsuma, S., Parkes, R.J., Schippers, A., Smith, D.C., Teske, A., Wiegel, J., Naranjo Padillo, C., and Solis Acosta, J.L., 2004. Distributions of microbial activities in deep subseafloor sediments. Science, 306(5705):2216–2221. doi:10.1126/science.1101155

D'Hondt, S., Rutherford, S., and Spivack., A.J., 2002. Metabolic activity of the subsurface life in deep-sea sediments. Science, 295(5562):2067–2070. doi:10.1126/science.1064878

D'Hondt, S., Spivack, A.J., Pockalny, R., Ferdelman, T.G., Fischer, J.P., Kallmeyer, J., Abrams, L.J., Smith, D.C., Graham, D., Hasiuk, F., Schrum, H., and Stancine, A.M., 2009. Subseafloor sedimentary life in the South Pacific Gyre. Proc. Natl. Acad. Sci. U. S. A., 106(28):11651–11656. doi:10.1073/pnas.0811793106

Domitsu, H., Nishi, H., Uchida, J., Oda, M., Ogane, K., Taira, A., Aoike, K., and the Shimokita Microfossil Research Group, 2010. Age model of core sediments taken by D/V Chikyu during the shakedown cruises off Shimokita Peninsula. Fossils,87:47–64. (in Japanese, with English abstract and figures)

Dooley, J.J., Dahowski, R.T., Davidson, C.L., Wise, M.A., Gupta, N., Kim, S.H., and Malone, E.L., 2006. Carbon Dioxide Capture and Geological Storage: a Core Element of a Global Energy Technology Strategy to Address Climate Change. Technol. Rep.–Global Energy Technol. Strategy Program. http://tsa.pnl.gov/publications/pdf/
pnwd_3602_gtsp_css_report_2006.pdf

Engelen, B., Ziegelmüller, K., Wolf, L., Köpke, B., Gittel, A., Cypionka, H., Treude, T., Nakagawa, S., Inagaki, F., Lever, M.A., and Steinsbu, B.O., 2008. Fluids from the ocean crust support microbial activities within the deep biosphere. Geomicrobiol. J., 25(1):56–66. doi:10.1080/01490450701829006

Fry, J., Horsfield, B., Sykes, R., Cragg, B.A., Heywood, C., Kim, G.T., Mangelsdorf, K., Mildenhall, D.C., Rinna, J., Vieth, A., Zink, K.-G., Sass, H., Weightman, A.J., and Parkes, R.J., 2009. Prokaryotic populations and activities in an interbedded coal deposit, including a previously deeply buried section (1.6–2.3 km) above ~150 Ma basement rock. Geomicrobiol. J., 26(3):163–178. doi:10.1080/01490450902724832

Heuer, V.B., Pohlman, J.W., Torres, M.E., Elvert, M., and Hinrichs, K.-U., 2009. The stable carbon isotope biogeochemistry of acetate and other dissolved carbon species in deep subseafloor sediments at the northern Cascadia Margin. Geochim. Cosmochim. Acta, 73(11):3323–3336. doi:10.1016/j.gca.2009.03.001

Hinrichs, K.-U., Hayes, J.M., Bach, W., Spivack, A.J., Hmelo, L.R., Holm, N.G., Johnson, C.G., and Sylva, S.P., 2006. Biological formation of ethane and propane in the deep marine subsurface. Proc. Nat. Acad. Sci., U. S. A., 103(40):14684–14689. doi:10.1073/pnas.0606535103

House, C.H., Cragg, B.A., Teske, A., and the Leg 201 Scientific Party, 2003. Drilling contamination tests during ODP Leg 201 using chemical and particulate tracers. In D'Hondt, S.L., Jørgensen, B.B., Miller, D.J., et al., Proc. ODP, Init. Repts., 201: College Station, TX (Ocean Drilling Program), 1–19. doi:10.2973/odp.proc.ir.201.102.2003

House, K.Z., Schrag, D.P., Harvery, C.F., and Lackner, K.S., 2006. Permanent carbon dioxide storage in deep-sea sediments. Proc. Natl. Acad. Sci. U. S. A., 103(33):12291–12295. doi:10.1073/pnas.0605318103

Imachi, H., Aoi, K., Tasumi, E., Saito, Y., Yamanaka, Y., Saito, Y., Yamaguchi, T., Tomaru, H., Takeuchi, R., Morono, Y., Inagaki, F., and Takai, K., submitted. Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME J.

Inagaki, F., 2010. Deep subseafloor microbial communities. Encycl. Life Sci. doi:10.1002/9780470015902.a0021894

Inagaki, F., Kuypers, M.M.M., Tsunogai, U., Ishibashi, J.-I., Nakamura, K.-I., Treude, T., Ohkubo, S., Nakaseama, M., Gena, K., Chiba, H., Hirayama, H., Nunoura, T., Takai, K., Jørgensen, B.B., Horikoshi, K., and Boetius, A., 2006a. Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system. Proc. Natl. Acad. Sci. U.S.A., 103(38):14164–14169. doi:10.1073/pnas.0606083103

Inagaki, F., and Nakagawa, S., 2008. Spatial distribution of the subseafloor life: diversity and biogeography. In Dilek, Y., Furnes, H., and Muehlenbachs, K. (Eds.), Links Between Geological Processes, Microbial Activities and Evolution of Life Microbes and Geology. Mod. Approaches Solid Earth Sci., 4:135–158. doi:10.1007/978-1-4020-8306-8_4

Inagaki, F., Nunoura, T., Nakagawa, S., Teske, A., Lever, M., Lauer, A., Suzuki, M., Takai, K., Delwiche, M., Colwell, F.S., Nealson, K.H., Horikoshi, K., D'Hondt, S., and Jørgensen, B.B., 2006b. Biogeographical distribution and diversity of microbes in methane hydrate–bearing deep marine sediments on the Pacific Ocean margin. Proc. Natl. Acad. Sci. U. S. A., 103(8):2815–2820. doi:10.1073/pnas.0511033103

Inagaki, F., Suzuki, M., Takai, K., Oida, H., Sakamoto, T., Aoki, K., Nealson, K.H., and Horikoshi, K., 2003. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol., 69(12):7224–7235. doi:10.1128/AEM.69.12.7224-7235.2003

Japan Natural Gas Association and Japan Offshore Petroleum Development Association (Eds.), 1992. Oil and Gas Resources in Japan (revised ed.). Tokyo. (in Japanese)

Jones, D.M., Head, I.M., Gray, N.D., Adams, J.J., Rowan, A.K., Aitken, C.M., Bennett, B., Huang, H., Brown, A., Bowler, B.F.J., Oldenburg, T., Erdmann, M., and Larter, S.R., 2008a. Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature, (London, U. K.), 451(7175):176–180. doi:10.1038/nature06484

Jones, E.J.P., Voytek, M.A., Warwick, P.D., Corum, M.D., Cohn, A., Bunnell, J.E., Clark, A.C., and Orem W.H., 2008b. Bioassay for estimating the biogenic methane-generating potential of coal samples. Int. J. Coal Geol., 76(1–2):138–150. doi:10.1016/j.coal.2008.05.011

Kallmeyer, J., Smith, D.C., Spivack, A.J., and D'Hondt, S., 2008. New cell extraction procedure applied to deep subsurface sediments. Limnol. Oceanogr.: Methods, 6:236–245. http://www.aslo.org/lomethods/free/2008/0236.pdf

Kobayashi, T., Koide, O., Mori, K., Shimamura, S., Matsuura, T., Miura, T., Takaki, Y., Morono, Y., Nunoura, T., Imachi, H., Inagaki, F., Takai, K., and Horikoshi, K., 2008. Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles, 12(4):519–527. doi:10.1007/s00792-008-0157-7

Krüger, M., Beckmann, S., Engelen, B., Thielemann, T., Cramer, B., Schippers, A., and Cypionka, H., 2008. Microbial methane formation from hard coal and timber in an abandoned coal mine. Geomicrobiol. J., 25(6):315–321. doi:10.1080/01490450802258402

Krumholz, L.R., McKinley, J.P., Ulrich, G.A., and Suflita, J.M., 1997. Confined subsurface microbial communities in Cretaceous rock. Nature (London, U. K.), 386(6620):64–66. doi:10.1038/386064a0

Lever, M.A., Alperin, M., Engelen, B., Inagaki, F., Nakagawa, S., Steinsbu, B.O., Teske, A., and IODP Expedition Scientists, 2006. Trends in basalt and sediment core contamination during IODP Expedition 301. Geomicrobiol. J., 23(7):517–530. doi:10.1080/01490450600897245

Lever, M.A., Heuer, V.B., Morono, Y., Masui, N., Schmidt, F., Alperin, M.J., Inagaki, F., Hinrichs, K.-U., and Teske, A., 2010. Acetogenesis in deep subseafloor sediments of the Juan de Fuca Ridge flank: a synthesis of geochemical, thermodynamic, and gene-based evidence. Geomicrobiol. J., 27(2):183–211. doi:10.1080/01490450903456681

Lipp, J.S., Morono, Y., Inagaki, F., and Hinrichs K.-U., 2008. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature (London, U. K.), 454(7207):991–994. doi:10.1038/nature07174

Masui, N., Morono, Y., and Inagaki, F., 2008. Microbiological assessment of circulation mud fluids during the first operation of riser drilling by the deep-earth research vessel Chikyu. Geomicrobiol. J., 25(6):274–282. doi:10.1080/01490450802258154

Morono, Y., and Inagaki, F., 2010. Automatic slide-loader fluorescent microscope for discriminative enumeration of subseafloor life. Sci. Drill., 9:32–36. doi:10.2204/iodp.sd.9.06.2010

Morono, Y., Terada, T., Masui, N., and Inagaki, F., 2009. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J., 3(5):503–511. doi:10.1038/ismej.2009.1

Musat, N., Halm, H., Winterholler, B., Hoppe, P., Peduzzi, S., Hillion, F., Horreard, F., Amann, R., Jørgensen, B.B., and Kuypers, M.M.M., 2008. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc. Nat. Acad. Sci. U. S. A., 105(46):17861–17866. doi:10.1073/pnas.0809329105

Nakagawa, S., Inagaki, F., Suzuki, Y., Steinsbu, B.O., Lever, M.A., Takai, K., Engelen, B., Sako, Y., Wheat, C.G., Horikoshi, K., and Integrated Ocean Drilling Program Expedition 301 Scientists, 2006. Microbial community in black rust exposed to hot ridge-flank crustal fluids. Appl. Environ. Microbiol., 72(10):6789–6799. doi:10.1128/AEM.01238-06

Onstott, T.C., 2005. Impact of CO2 injections on deep subsurface microbial ecosystems and potential ramifications for the surface biosphere. In Thomas, D.C., and Benson, S.M. (Eds.), Carbon Dioxide Capture for Storage in Deep Geological Formations: the CO2 Capture Project, Vol. 2: London (Elsevier Ltd.), 1207–1239.

Orem, W.H., Voytek, M.A., Jones, E.J., Lerch, H.E., Bates, A.L., Corum, M.D., Warwick, P.D., and Clark, A.C., 2010. Organic intermediates in the anaerobic biodegradation of coal to methane under laboratory conditions. Org. Geochem., 41(9):997–1000. doi:10.1016/j.orggeochem.2010.03.005

Osawa, M., Nakanishi, S., Tanahashi, M., Oda, H., and Sasaki, A., 2002. Structure, tectonic evolution and gas exploration potential of offshore Sanriku and Hidaka provinces, Pacific Ocean, off northern Honshu and Hokkaido, Japan. J. Jpn. Assoc. Pet. Technol., 67(1):38–51. (in Japanese, with English abstract and figures)

Parkes, R.J., Cragg, B.A., Bale, S.J., Getliff, J.M., Goodman, K., Rochelle, P.A., Fry, J.C., Weightman, A.J., and Harvey, S.M., 1994. Deep bacterial biosphere in Pacific Ocean sediments. Nature (London, U. K.), 371(6496):410–413. doi:10.1038/371410a0

Parkes, R.J., Cragg, B.A., and Wellsbury, P., 2000. Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol. J., 8(1):11–28. doi:10.1007/PL00010971

Parkes, R.J., Webster, G., Cragg, B.A., Weightman, A.J., Newberry, C.J., Ferdelman, T.G., Kallmeyer, J., Jørgensen, B.B., Aiello, I.W., and Fry, J.C., 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature (London, U. K.), 436(7049):390–394. doi:10.1038/nature03796

Parkes, R.J., Wellsbury, P., Mather, I.D., Cobb, S.J., Cragg, B.A., Hornibrook, E.R.C., and Horsfield, B., 2007. Temperature activation of organic matter and minerals during burial has the potential to sustain the deep biosphere over geological timescales. Org. Geochem., 38(6):845–852. doi:10.1016/j.orggeochem.2006.12.011

Roussel, E.G., Cambon Bonavita, M.-A., Querellou, J., Cragg, B.A., Webster, G., Prieur, D., and Parkes, J.R., 2008. Extending the sub-sea-floor biosphere. Science, 320(5879):1046. doi:10.1126/science.1154545

Seno, T., Sakurai, T., and Stein, S., 1996. Can the Okhotsk plate be discriminated from the North American plate? J. Geophys. Res., [Solid Earth], 101(B5):11305–11315. doi:10.1029/96JB00532

Schmidt, F., Elvert, M., Koch, B.P., Witt, M., and Hinrichs, K.-U., 2009. Molecular characterization of dissolved organic matter in pore water in continental shelf sediments. Geochim. Cosmochim. Acta, 73(11):3337–3358. doi:10.1016/j.gca.2009.03.008

Schrag, D.P., 2009. Storage of carbon dioxide in offshore sediments. Science, 325(5948):1658–1659. doi:10.1126/science.1175750

Schultheiss, P., Holland, M., and Humphrey, G., 2009. Wireline coring and analysis under pressure: recent use and future developments of the HYACINTH system. Sci. Drill., 7:44–50. doi:10.2204/iodp.sd.7.07.2009

Shimizu, S., Akiyama, M., Naganuma, T., Fujioka, M., Nako, M., and Ishijima, Y., 2007. Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan. Geobiology, 5(4):423–433. doi:10.1111/j.1472-4669.2007.00123.x

Sivan, O., Schrag, D.P., and Murray, R.W., 2007. Rates of methanogenesis and methanotrophy in deep-sea sediments. Geobiology, 5(2):141–151. doi:10.1111/j.1472-4669.2007.00098.x

Smith, D.C., Spivack, A.J., Fisk, M.R., Haveman, S.A., and Staudigel, H., 2000. Tracer-based estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiol. J., 17(3):207–219. doi:10.1080/01490450050121170

Sørensen, K.B., and Teske, A., 2006. Stratified communities of active archaea in deep marinesubsurface sediments. Appl. Environ. Microbiol., 72(7):4596–4603. doi:10.1128/AEM.00562-06

Strapoc, D., Picardal, F.W., Turich, C., Schaperdoth, I., Macalady, J.L., Lipp, J.S., Lin, Y.-S., Ertefai, T.F., Schubotz, F., Hinrichs, K.-U., Mastalerz, M., and Schimmelmann, A., 2008. Methane-producing microbial community in a coal bed of the Illinois basin. Appl. Environ. Microbiol., 74(8):2424–2432. doi:10.1128/AEM.02341-07

Taira, A., and Curewitz, D. (Eds.), 2005. CDEX Technical Report (Vol. 2): Shimokita Area Site Survey: Northern Japan Trench Seismic Survey, Northern Honshu, Japan: Yokohama (CDEX-JAMSTEC)

Teske, A., and Sørensen, K.B., 2008. Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J., 2:3–18. doi:10.1038/ismej.2007.90

Tomaru, H., Fehn, U., Lu, Z., Takeuchi, R., Inagaki, F., Imachi, H., Kotani, R., Matsumoto, R., and Aoike, K., 2009. Dating of dissolved iodine in pore waters from the gas hydrate occurrence offshore Shimokita Peninsula, Japan: 129I results from D/V Chikyu shakedown cruise. Resour. Geol., 59(4):359–373. doi:10.1111/j.1751-3928.2009.00103.x

Wang, G., Spivack, A.J., Rutherford, S., Manor, U., and D'Hondt, S., 2008. Quantification of co-occurring reaction rates in deep subseafloor sediments. Geochim. Cosmochim. Acta, 72(14):3479–3488.
doi:10.1016/j.gca.2008.04.024

Wegener, G., Niemann, H., Elvert, M., Hinrichs, K.-U., and Boetius, A., 2008. Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane. Environ. Microbiol., 10(9):2287–2298. doi:10.1111/j.1462-2920.2008.01653.x

Whiticar, M.J., 1999. Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chem. Geol., 161(1–3):291–314.
doi:10.1016/S0009-2541(99)00092-3

Whitman, W.B., Coleman, D.C., and Wiebe, W.J., 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. U. S. A., 95(12):6578–6583. doi:10.1073/pnas.95.12.6578