Inagaki, F., and Nealson, K. H., 2006. The Paleome: letters from
ancient earth. In Neretin, L. N. (ed.), Past and Present Water
Column Anoxia. Dordrecht: Springer. NATO Science Series,
IV. Earth and Environmental Sciences, Vol. 64, pp. 21–39.
Inagaki, F., Takai, K., Komatsu, T., Kanamatsu, T., Fujiioka, K., and
Horikoshi, K., 2001. Archaeology of Archaea: geomicrobiological record of Pleistocene thermal events concealed in a
deep-sea subseafloor environment. Extremophiles, 5, 385–392.
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 costal subseafloor sediments from the Sea of Okhotsk. Applied and Environmental
Microbiology, 69, 7224–7235.
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. L., and Jørgensen, B. B., 2006.
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean
margin. Proceedings of the National Academy of Sciences of the
United States of America, 103, 2815–2820.
Itävaara, M., Nyyssönen, M., Kapanen, A., Nousiainen, A.,
Ahonen, L., and Kukkonen, I., 2011. Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield. FEMS Microbiology Ecology, 77,
295–309.
Jahnke, R. A., and Jackson, G. A., 1992. The spatial distribution of
sea floor oxygen consumption in the Atlantic and Pacific oceans.
In Rowe, G. T., and Pariente, V. (eds.), Deep-Sea Food Chains
and the Global Carbon Cycle. Dordrecht: Kluwer Academic,
pp. 295–308.
Jørgensen, B. B., 1982. Mineralization of organic matter in the sea
bed – the role of sulphate reduction. Nature, 296, 643–645.
Jørgensen, B. B., 2000. Bacteria and marine biogeochemistry. In
Schulz, H. D., and Zabel, M. (eds.), Marine Geochemistry. Berlin: Springer, pp. 173–207.
Jørgensen, B. B., and Boetius, A., 2007. Feast and famine – microbial life in the deep-sea bed. Nature Review Microbiology, 5,
770–783.
Jørgensen, B. B., and D’Hondt, S. L., 2006. A starving majority
deep beneath the seafloor. Science, 314, 932–934.
Jørgensen, B. B., D’Hondt, S. L., and Miller, D. J., 2006. Leg
201 synthesis: controls on microbial communities in deeply buried sediments. In Jørgensen, B. B., D’Hondt, S. L., Miller, D. J.
(eds.), Proceedings of ODP, Science Results, 201. Ocean Drilling Program, College Station. http://www-odp.tamu.edu/publications/201_SR/201sr.htm
Kallmeyer, J., Smith, D. C., D’Hondt, S. L., and Spivack, A. J.,
2008. New cell extraction procedure applied to deep subsurface
sediments. Limnology and Oceanography: Methods, 6,
236–245.
Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., and
D’Hondt, S., 2012. Global distribution of microbial abundance
and biomass in subseafloor sediment. Proceedings of the
National Academy of Sciences of the United States of America,
109, 16213–16216.
Kastner, M., Elderfield, H., Martin, J. B., Suess, E., Kvenvolden,
K. A., and Garrison, R. E., 1990. Diagenesis and interstitialwater chemistry at the Peruvian continental margin-major constituents and strontium isotopes. In Suess, E., von Huene, R.,
et al. (eds.), Proceedings of the ODP, Scienctific Results. Vol.
112, Chap. 25, pp. 413–440. http://www-odp.tamu.edu/publications/112_SR/112sr.htm
Kobayashi, T., Koide, O., Mori, K., Shimamura, S., Matsuura, T.,
Miura, T., et al., 2008. Phylogenetic and enzymatic diversity of
deep subseafloor aerobic microorganisms in organics- and
methane-rich
sediments
off
Shimokita
Peninsula.
Extremophiles, 12, 519–527.
Kubo, K., Lloyd, K., Biddle, J., Amann, R., Teske, A., and Knittel,
K., 2012. Archaea of the miscellaneous crenarchaeotal group are
abundant, diverse and widespread in marine sediments. ISME
Journal, 6, 1949–1965.
Lee, Y. J., Wagner, I. D., Brice, M. E., Kevbrin, V. V., Mills, G. L.,
Romanek, C. S., and Wiegel, J., 2005. Thermosediminibacter
oceani gen. nov., sp. nov. and Thermosediminibacter
litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru margin. Extremophiles, 9, 375–383.
Lever, M. A., 2013. Functional gene surveys from ocean drilling
expeditions – a review and perspective. FEMS Microbiology
Ecology, 84, 1–23.
Lever, M. A., Alperin, M., Engelen, B., Inagaki, F., Nakagawa, S.,
Steinsbu, B. O., Teske, A., and IODP Expedition 301 Scientists, 2006. Trends in basalt and sediment core contamination
during IODP Expedition 301. Geomicrobiology Journal, 23,
517–530.
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. Geomicrobiology Journal,
27, 183–211.
Lever, M. A., Rouxel, O., Alt, J. C., Shimizu, N., Ono, S., Coggon,
R. M., Shanks, W. C., III, Lapham, 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, 1305–1308.
Lin, L. H., Wang, P. L., Rumble, D., Lippmann-Pipke, J., Boice, E.,
Pratt, L. M., Sherwood Lollar, B., Brodie, E. L., Hazen, T. C.,
Andersen, G. L., DeSantis, T. Z., Moser, D. P., Kershaw, D.,
and Onstott, T. C., 2006. Long term sustainability of a high
energy, low diversity crustal biome. Science, 314, 479–482.
Lipp, J. S., Morono, Y., Inagaki, F., and Hinrichs, K. U., 2008. Significant contribution of archaea to extent biomass in marine subsurface sediments. Nature, 454, 991–994.
Lloyd, K. G., Schreiber, L., Petersen, D. G., Kjeldsen, K. U., Lever,
M. A., Steen, A. D., Stepanauskas, R., Richter, M., Kleindienst,
S., Lenk, S., Schramm, A., and Jørgensen, B. B., 2013a. Predominant archaea in marine sediments degrade detrital proteins.
Nature, 496, 215–218.
Lloyd, K. G., May, M. K., Kevorkian, R. T., and Steen, A. D.,
2013b. Meta-analysis of quantification methods shows that
Archaea and Bacteria have similar abundances in the
subseafloor. Applied and Environmental Microbiology, 79,
7790–7799.
Lockey, C., Otto, E., and Long, Z., 1998. Real-time fluorescence
detection of a single DNA molecule. BioTechniques, 24,
744–746.
Logemann, J., Graue, J., Köster, J., Engelen, B., Rullkötter, J., and
Cypionka, H., 2011. A laboratory experiment of intact polar lipid
degradation in sandy sediments. Biogeosciences Discussions, 8,
3289–3321.
Lomstein, B. A., Langerhuus, A. T., D’Hondt, S., Jørgensen, B. B.,
and Spivack, A. J., 2012. Endospore abundance, microbial
growth and necromass turnover in deep sub-seafloor sediment.
Nature, 484, 101–104.
Mascarelli, A. L., 2009. Low life. Nature, 459, 770–773.
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, e15399.
Mikucki, J. A., Liu, Y., Delwiche, M., Colwell, F. S., and Boone,
D. R., 2003. Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of
Methanoculleus submarines. sp. nov. Applied and Environmental Microbiology, 69, 3311–3316.
DEEP BIOSPHERE
153
ancient earth. In Neretin, L. N. (ed.), Past and Present Water
Column Anoxia. Dordrecht: Springer. NATO Science Series,
IV. Earth and Environmental Sciences, Vol. 64, pp. 21–39.
Inagaki, F., Takai, K., Komatsu, T., Kanamatsu, T., Fujiioka, K., and
Horikoshi, K., 2001. Archaeology of Archaea: geomicrobiological record of Pleistocene thermal events concealed in a
deep-sea subseafloor environment. Extremophiles, 5, 385–392.
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 costal subseafloor sediments from the Sea of Okhotsk. Applied and Environmental
Microbiology, 69, 7224–7235.
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. L., and Jørgensen, B. B., 2006.
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean
margin. Proceedings of the National Academy of Sciences of the
United States of America, 103, 2815–2820.
Itävaara, M., Nyyssönen, M., Kapanen, A., Nousiainen, A.,
Ahonen, L., and Kukkonen, I., 2011. Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield. FEMS Microbiology Ecology, 77,
295–309.
Jahnke, R. A., and Jackson, G. A., 1992. The spatial distribution of
sea floor oxygen consumption in the Atlantic and Pacific oceans.
In Rowe, G. T., and Pariente, V. (eds.), Deep-Sea Food Chains
and the Global Carbon Cycle. Dordrecht: Kluwer Academic,
pp. 295–308.
Jørgensen, B. B., 1982. Mineralization of organic matter in the sea
bed – the role of sulphate reduction. Nature, 296, 643–645.
Jørgensen, B. B., 2000. Bacteria and marine biogeochemistry. In
Schulz, H. D., and Zabel, M. (eds.), Marine Geochemistry. Berlin: Springer, pp. 173–207.
Jørgensen, B. B., and Boetius, A., 2007. Feast and famine – microbial life in the deep-sea bed. Nature Review Microbiology, 5,
770–783.
Jørgensen, B. B., and D’Hondt, S. L., 2006. A starving majority
deep beneath the seafloor. Science, 314, 932–934.
Jørgensen, B. B., D’Hondt, S. L., and Miller, D. J., 2006. Leg
201 synthesis: controls on microbial communities in deeply buried sediments. In Jørgensen, B. B., D’Hondt, S. L., Miller, D. J.
(eds.), Proceedings of ODP, Science Results, 201. Ocean Drilling Program, College Station. http://www-odp.tamu.edu/publications/201_SR/201sr.htm
Kallmeyer, J., Smith, D. C., D’Hondt, S. L., and Spivack, A. J.,
2008. New cell extraction procedure applied to deep subsurface
sediments. Limnology and Oceanography: Methods, 6,
236–245.
Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., and
D’Hondt, S., 2012. Global distribution of microbial abundance
and biomass in subseafloor sediment. Proceedings of the
National Academy of Sciences of the United States of America,
109, 16213–16216.
Kastner, M., Elderfield, H., Martin, J. B., Suess, E., Kvenvolden,
K. A., and Garrison, R. E., 1990. Diagenesis and interstitialwater chemistry at the Peruvian continental margin-major constituents and strontium isotopes. In Suess, E., von Huene, R.,
et al. (eds.), Proceedings of the ODP, Scienctific Results. Vol.
112, Chap. 25, pp. 413–440. http://www-odp.tamu.edu/publications/112_SR/112sr.htm
Kobayashi, T., Koide, O., Mori, K., Shimamura, S., Matsuura, T.,
Miura, T., et al., 2008. Phylogenetic and enzymatic diversity of
deep subseafloor aerobic microorganisms in organics- and
methane-rich
sediments
off
Shimokita
Peninsula.
Extremophiles, 12, 519–527.
Kubo, K., Lloyd, K., Biddle, J., Amann, R., Teske, A., and Knittel,
K., 2012. Archaea of the miscellaneous crenarchaeotal group are
abundant, diverse and widespread in marine sediments. ISME
Journal, 6, 1949–1965.
Lee, Y. J., Wagner, I. D., Brice, M. E., Kevbrin, V. V., Mills, G. L.,
Romanek, C. S., and Wiegel, J., 2005. Thermosediminibacter
oceani gen. nov., sp. nov. and Thermosediminibacter
litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru margin. Extremophiles, 9, 375–383.
Lever, M. A., 2013. Functional gene surveys from ocean drilling
expeditions – a review and perspective. FEMS Microbiology
Ecology, 84, 1–23.
Lever, M. A., Alperin, M., Engelen, B., Inagaki, F., Nakagawa, S.,
Steinsbu, B. O., Teske, A., and IODP Expedition 301 Scientists, 2006. Trends in basalt and sediment core contamination
during IODP Expedition 301. Geomicrobiology Journal, 23,
517–530.
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. Geomicrobiology Journal,
27, 183–211.
Lever, M. A., Rouxel, O., Alt, J. C., Shimizu, N., Ono, S., Coggon,
R. M., Shanks, W. C., III, Lapham, 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, 1305–1308.
Lin, L. H., Wang, P. L., Rumble, D., Lippmann-Pipke, J., Boice, E.,
Pratt, L. M., Sherwood Lollar, B., Brodie, E. L., Hazen, T. C.,
Andersen, G. L., DeSantis, T. Z., Moser, D. P., Kershaw, D.,
and Onstott, T. C., 2006. Long term sustainability of a high
energy, low diversity crustal biome. Science, 314, 479–482.
Lipp, J. S., Morono, Y., Inagaki, F., and Hinrichs, K. U., 2008. Significant contribution of archaea to extent biomass in marine subsurface sediments. Nature, 454, 991–994.
Lloyd, K. G., Schreiber, L., Petersen, D. G., Kjeldsen, K. U., Lever,
M. A., Steen, A. D., Stepanauskas, R., Richter, M., Kleindienst,
S., Lenk, S., Schramm, A., and Jørgensen, B. B., 2013a. Predominant archaea in marine sediments degrade detrital proteins.
Nature, 496, 215–218.
Lloyd, K. G., May, M. K., Kevorkian, R. T., and Steen, A. D.,
2013b. Meta-analysis of quantification methods shows that
Archaea and Bacteria have similar abundances in the
subseafloor. Applied and Environmental Microbiology, 79,
7790–7799.
Lockey, C., Otto, E., and Long, Z., 1998. Real-time fluorescence
detection of a single DNA molecule. BioTechniques, 24,
744–746.
Logemann, J., Graue, J., Köster, J., Engelen, B., Rullkötter, J., and
Cypionka, H., 2011. A laboratory experiment of intact polar lipid
degradation in sandy sediments. Biogeosciences Discussions, 8,
3289–3321.
Lomstein, B. A., Langerhuus, A. T., D’Hondt, S., Jørgensen, B. B.,
and Spivack, A. J., 2012. Endospore abundance, microbial
growth and necromass turnover in deep sub-seafloor sediment.
Nature, 484, 101–104.
Mascarelli, A. L., 2009. Low life. Nature, 459, 770–773.
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, e15399.
Mikucki, J. A., Liu, Y., Delwiche, M., Colwell, F. S., and Boone,
D. R., 2003. Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of
Methanoculleus submarines. sp. nov. Applied and Environmental Microbiology, 69, 3311–3316.
DEEP BIOSPHERE
153