Milucka, J., Ferdelman, T. G., Polerecky, L., Franzke, D., Wegener,
G., Schmid, M., Lieberwirth, I., Wagner, M., Widdel, F., and
Kuypers, M. M. M., 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature, 491, 541–546.
Morono, Y., Terada, T., Masui, N., and Inagaki, F., 2009. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME Journal, 3, 503–511.
Moser, D. P., Onstott, T. C., Fredrickson, J. K., Brockman, F. J.,
Balkwill, D. L., Drake, G. R., Pfiffner, S. M., White, D. C.,
Takai, K., Pratt, L. M., Fong, J., Sherwood Lollar, B., Slater,
G., Phelps, T. J., Spoelstra, N., Deflaun, M., Southam, G., Welty,
A. T., Baker, B. J., and Hoek, J., 2003. Temporal shifts in the
geochemistry and microbial community structure of an ultradeep
mine borehole following isolation. Geomicrobiology Journal,
20, 517–548.
Nunoura, T., Soffientino, B., Blazejak, A., Kakuta, J., Oida, H.,
Schippers, A., and Takai, K., 2009. Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of
Mexico continental slope (IODP Expedition 308). FEMS Microbiology Ecology, 69, 410–424.
Orcutt, B. N., Sylvan, J. B., Knab, N. J., and Edwards, K. J., 2011.
Microbial ecology of the dark ocean above at and below the seafloor. Microbiology and Molecular Biology Reviews, 75,
361–422.
Orcutt, B. N., LaRowe, D. E., Biddle, J. F., Colwell, F. S., Glazer,
B. T., Reese, B. K., Kirkpatrick, J. B., Lapham, L. L., Mills,
H. J., Sylvan, J. B., Wankel, S. D., and Wheat, C. G., 2013a.
Microbial activity in the marine deep biosphere: progress and
prospects. Frontiers in Microbiology, 4, 189.
Orcutt, B. N., Wheat, C. G., Rouxel, O., Hulme, S., Edwards, K. J.,
and Bach, W., 2013b. Oxygen consumption rates in subseafloor
basaltic crust derived from a reaction transport model. Nature
Communications, 4, 2539.
Orsi, W. D., Biddle, J. F., and Edgcomb, V., 2013a. Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across
marine subsurface provinces. PloS One, 8, e56335.
Orsi, W. D., Edgcomb, V., Christman, G. D., and Biddle, J. F.,
2013b. Gene expression in the deep biosphere. Nature, 499,
205–208.
Parkes, R. J., and Wellsbury, P., 2004. Deep biospheres. In Bull,
A. T. (ed.), Microbial Diversity and Bioprocessing. Washington,
DC: ASM press, pp. 120–129.
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, 371, 410–413.
Parkes, R. J., Cragg, B. A., and Wellsbury, P., 2000. Recent studies
on bacterial populations and processes in subseafloor sediments:
a review. Hydrogeology Journal, 8, 11–28.
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,
436, 390–394.
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. Organic Geochemistry, 38, 845–852.
Parkes, R. J., Sellek, G., Webster, G., Martin, D., Anders, E.,
Weightman, A. J., and Sass, H., 2009. Culturable prokaryotic
diversity of deep, gas hydrate sediments: first use of a continuous
high-pressure, anaerobic, enrichment and isolation system for
subseafloor sediments (DeepIsoBUG). Environmental Microbiology, 11, 3140–3153.
Parkes, R. J., Linnane, C. D., Webster, G., Sass, H., Weightman,
A. J., Hornibrook, E. R. C., and Horsfield, B., 2011. Prokaryotes
stimulate mineral H 2 formation for the deep biosphere and subsequent thermogenic activity. Geology, 39, 219–222.
Parkes, R. J., Cragg, B., Webster, G., Roussel, E. G., Weightman,
A. J., and Sass, H., 2014. A review of prokaryotic populations
and processes in sub-seafloor sediments, including biosphere:
geosphere interactions. Marine Geology, 352, 409–425.
Pedersen, K., 1993. The deep subterranean biosphere. Earth Science Reviews, 34, 243–260.
Pedersen, K., 1997. Microbial life in deep granitic rock. FEMS
Microbiology Review, 20, 399–414.
Ravenschlag, K., Sahm, K., Knoblauch, C., Jorgensen, B. B., and
Amann, R., 2000. Community structure, cellular rRNA content,
and activity of sulfate-reducing bacteria in marine Arctic sediments. Applied and Environmental Microbiology, 66,
3592–3602.
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson,
I. J., Cheng, J. F., Darling, A., et al., 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature,
499, 431–437.
Roussel, E. G., Bonavita, M. A. C., Querellou, J., Cragg, B. A.,
Webster, G., Prieur, D., and Parkes, R. J., 2008. Extending the
sub-sea-floor biosphere. Science, 320, 1046.
Roussel, E. G., Sauvadet, A. L., Chaduteau, C., Fouquet, Y.,
Charlou, J. L., Prieur, D., and Bonavita, M. A. C., 2009.
Archaeal communities associated with shallow to deep
subseafloor sediments of the New Caledonia Basin. Environmental Microbiology, 11, 2446–2462.
Røy, H., Kallmeyer, J., Adhikari, R. R., Pockalny, R., Jørgensen,
B. B., and D’Hondt, S., 2012. Aerobic microbial respiration in
86-million-year-old deep-sea red clay. Science, 336, 922–925.
Sahm, K., MacGregor, B. J., Jørgensen, B. B., and Stahl, D. A.,
1999. Sulfate-reduction and vertical distribution of sulphatereducing bacteria quantified by rRNA slot-blot hybridization in
a coastal marine sediment. Environmental Microbiology, 1,
65–74.
Santelli, C. M., Orcutt, B. H., Banning, E., Bach, W., Moyer, C. L.,
Sogin, M. L., Staudigel, H., and Edwards, K. J., 2008. Abundance and diversity of microbial life in ocean crust. Nature,
453, 653–657.
Santelli, C. M., Edgcomb, V. P., Bach, W., and Edwards, K. J., 2009.
The diversity and abundance of bacteria inhabiting seafloor lavas
positively correlate with rock alteration. Environmental Microbiology, 11, 86–98.
Schippers, A., and Neretin, L. N., 2006. Quantification of microbial
communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environmental Microbiology, 8, 1251–1260.
Schippers, A., Neretin, L. N., Kallmeyer, J., Ferdelman, T. G.,
Cragg, B. A., Parkes, R. J., and Jørgensen, B. B., 2005. Prokaryotic cells of the deep sub-seafloor biosphere identified as living
bacteria. Nature, 433, 861–864.
Schippers, A., Köweker, G., Höft, C., and Teichert, B., 2010. Quantification of microbial communities in three forearc
sediment basins off Sumatra. Geomicrobiology Journal, 27,
170–182.
Schippers, A., Kock, D., Höft, C., Köweker, G., and Siegert, M.,
2012. Quantification of microbial communities in subsurface
marine sediments of the Black Sea and off Namibia. Frontiers
in Microbiology, 3, 16.
Schouten, S., Middelburg, J. J., Hopmans, E. C., and Sinninghe
Damste, J. S., 2010. Fossilization and degradation of intact polar
lipids in deep subsurface sediments: a theoretical approach.
Geochimica et Cosmochimica Acta, 74, 3806–3814.
154
DEEP BIOSPHERE
G., Schmid, M., Lieberwirth, I., Wagner, M., Widdel, F., and
Kuypers, M. M. M., 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature, 491, 541–546.
Morono, Y., Terada, T., Masui, N., and Inagaki, F., 2009. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME Journal, 3, 503–511.
Moser, D. P., Onstott, T. C., Fredrickson, J. K., Brockman, F. J.,
Balkwill, D. L., Drake, G. R., Pfiffner, S. M., White, D. C.,
Takai, K., Pratt, L. M., Fong, J., Sherwood Lollar, B., Slater,
G., Phelps, T. J., Spoelstra, N., Deflaun, M., Southam, G., Welty,
A. T., Baker, B. J., and Hoek, J., 2003. Temporal shifts in the
geochemistry and microbial community structure of an ultradeep
mine borehole following isolation. Geomicrobiology Journal,
20, 517–548.
Nunoura, T., Soffientino, B., Blazejak, A., Kakuta, J., Oida, H.,
Schippers, A., and Takai, K., 2009. Subseafloor microbial communities associated with rapid turbidite deposition in the Gulf of
Mexico continental slope (IODP Expedition 308). FEMS Microbiology Ecology, 69, 410–424.
Orcutt, B. N., Sylvan, J. B., Knab, N. J., and Edwards, K. J., 2011.
Microbial ecology of the dark ocean above at and below the seafloor. Microbiology and Molecular Biology Reviews, 75,
361–422.
Orcutt, B. N., LaRowe, D. E., Biddle, J. F., Colwell, F. S., Glazer,
B. T., Reese, B. K., Kirkpatrick, J. B., Lapham, L. L., Mills,
H. J., Sylvan, J. B., Wankel, S. D., and Wheat, C. G., 2013a.
Microbial activity in the marine deep biosphere: progress and
prospects. Frontiers in Microbiology, 4, 189.
Orcutt, B. N., Wheat, C. G., Rouxel, O., Hulme, S., Edwards, K. J.,
and Bach, W., 2013b. Oxygen consumption rates in subseafloor
basaltic crust derived from a reaction transport model. Nature
Communications, 4, 2539.
Orsi, W. D., Biddle, J. F., and Edgcomb, V., 2013a. Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across
marine subsurface provinces. PloS One, 8, e56335.
Orsi, W. D., Edgcomb, V., Christman, G. D., and Biddle, J. F.,
2013b. Gene expression in the deep biosphere. Nature, 499,
205–208.
Parkes, R. J., and Wellsbury, P., 2004. Deep biospheres. In Bull,
A. T. (ed.), Microbial Diversity and Bioprocessing. Washington,
DC: ASM press, pp. 120–129.
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, 371, 410–413.
Parkes, R. J., Cragg, B. A., and Wellsbury, P., 2000. Recent studies
on bacterial populations and processes in subseafloor sediments:
a review. Hydrogeology Journal, 8, 11–28.
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,
436, 390–394.
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. Organic Geochemistry, 38, 845–852.
Parkes, R. J., Sellek, G., Webster, G., Martin, D., Anders, E.,
Weightman, A. J., and Sass, H., 2009. Culturable prokaryotic
diversity of deep, gas hydrate sediments: first use of a continuous
high-pressure, anaerobic, enrichment and isolation system for
subseafloor sediments (DeepIsoBUG). Environmental Microbiology, 11, 3140–3153.
Parkes, R. J., Linnane, C. D., Webster, G., Sass, H., Weightman,
A. J., Hornibrook, E. R. C., and Horsfield, B., 2011. Prokaryotes
stimulate mineral H 2 formation for the deep biosphere and subsequent thermogenic activity. Geology, 39, 219–222.
Parkes, R. J., Cragg, B., Webster, G., Roussel, E. G., Weightman,
A. J., and Sass, H., 2014. A review of prokaryotic populations
and processes in sub-seafloor sediments, including biosphere:
geosphere interactions. Marine Geology, 352, 409–425.
Pedersen, K., 1993. The deep subterranean biosphere. Earth Science Reviews, 34, 243–260.
Pedersen, K., 1997. Microbial life in deep granitic rock. FEMS
Microbiology Review, 20, 399–414.
Ravenschlag, K., Sahm, K., Knoblauch, C., Jorgensen, B. B., and
Amann, R., 2000. Community structure, cellular rRNA content,
and activity of sulfate-reducing bacteria in marine Arctic sediments. Applied and Environmental Microbiology, 66,
3592–3602.
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson,
I. J., Cheng, J. F., Darling, A., et al., 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature,
499, 431–437.
Roussel, E. G., Bonavita, M. A. C., Querellou, J., Cragg, B. A.,
Webster, G., Prieur, D., and Parkes, R. J., 2008. Extending the
sub-sea-floor biosphere. Science, 320, 1046.
Roussel, E. G., Sauvadet, A. L., Chaduteau, C., Fouquet, Y.,
Charlou, J. L., Prieur, D., and Bonavita, M. A. C., 2009.
Archaeal communities associated with shallow to deep
subseafloor sediments of the New Caledonia Basin. Environmental Microbiology, 11, 2446–2462.
Røy, H., Kallmeyer, J., Adhikari, R. R., Pockalny, R., Jørgensen,
B. B., and D’Hondt, S., 2012. Aerobic microbial respiration in
86-million-year-old deep-sea red clay. Science, 336, 922–925.
Sahm, K., MacGregor, B. J., Jørgensen, B. B., and Stahl, D. A.,
1999. Sulfate-reduction and vertical distribution of sulphatereducing bacteria quantified by rRNA slot-blot hybridization in
a coastal marine sediment. Environmental Microbiology, 1,
65–74.
Santelli, C. M., Orcutt, B. H., Banning, E., Bach, W., Moyer, C. L.,
Sogin, M. L., Staudigel, H., and Edwards, K. J., 2008. Abundance and diversity of microbial life in ocean crust. Nature,
453, 653–657.
Santelli, C. M., Edgcomb, V. P., Bach, W., and Edwards, K. J., 2009.
The diversity and abundance of bacteria inhabiting seafloor lavas
positively correlate with rock alteration. Environmental Microbiology, 11, 86–98.
Schippers, A., and Neretin, L. N., 2006. Quantification of microbial
communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environmental Microbiology, 8, 1251–1260.
Schippers, A., Neretin, L. N., Kallmeyer, J., Ferdelman, T. G.,
Cragg, B. A., Parkes, R. J., and Jørgensen, B. B., 2005. Prokaryotic cells of the deep sub-seafloor biosphere identified as living
bacteria. Nature, 433, 861–864.
Schippers, A., Köweker, G., Höft, C., and Teichert, B., 2010. Quantification of microbial communities in three forearc
sediment basins off Sumatra. Geomicrobiology Journal, 27,
170–182.
Schippers, A., Kock, D., Höft, C., Köweker, G., and Siegert, M.,
2012. Quantification of microbial communities in subsurface
marine sediments of the Black Sea and off Namibia. Frontiers
in Microbiology, 3, 16.
Schouten, S., Middelburg, J. J., Hopmans, E. C., and Sinninghe
Damste, J. S., 2010. Fossilization and degradation of intact polar
lipids in deep subsurface sediments: a theoretical approach.
Geochimica et Cosmochimica Acta, 74, 3806–3814.
154
DEEP BIOSPHERE