Schrenk, M. O., Huber, J. A., and Edwards, K. J., 2010. Microbial
provinces in the subseafloor. Annual Review of Marine Science,
2, 279–304.
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. Geomicrobiology
Journal, 17, 207–219.
Sørensen, K. B., Lauer, A., and Teske, A. P., 2004. Archaeal
phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology, 2,
151–161.
Stevens, T. O., and McKinley, J. P., 1995. Lithoautotrophic
microbial ecosystems in deep basalt aquifers. Science, 270,
450–454.
Templeton, A. S., Knowles, E. J., Eldridge, D. L., Arey, B. W.,
Dohnalkova, A. C., Webb, S. M., Bailey, B. E., Tebo, B. M.,
and Staudigel, H., 2009. A seafloor microbial biome hosted
within incipient ferromanganese crusts. Nature Geoscience, 2,
872–876.
Teske, A. P., 2005. The deep subsurface biosphere is alive and well.
Trends in Microbiology, 13, 402–404.
Teske, A. P., 2006a. Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys.
Geomicrobiology Journal, 23, 357–368.
Teske, A. P., 2006b. Microbial community composition in deep
marine subsurface sediments of ODP Leg 201: sequencing surveys and cultivations. In Jørgensen, B. B., D’Hondt, S. L., and
Miller, D. J. (eds.), Proceedings of the ODP, Scientific Results,
201. Ocean Drilling Program, College Station. http://www-odp.
tamu.edu/publications/201_SR/VOLUME/CHAPTERS/120.PDF
Teske, A. P., and Sørensen, K. B., 2008. Uncultured archaea in deep
marine subsurface sediments: have we caught them all? ISME
Journal, 2, 3–18.
Teske, A. P., Biddle, J. F., Edcomb, V. P., and Schippers, A., 2013.
Deep subsurface microbiology: a guide to the research topic
papers. Frontiers in Microbiology, 4, 122.
Toffin, L., Webster, G., Weightman, A. J., Fry, J. C., and Prieur, D.,
2004. Molecular monitoring of culturable bacteria from deep-sea
sediment of the Nankai Trough. Leg 190 Ocean Drilling Program. FEMS Microbiology Ecology, 48, 357–367.
Toffin, L., Zink, K., Kato, C., Pignet, P., Bidault, A., Bienvenu, N.,
et al., 2005. Marinilactibacillus piezotolerans sp. nov., a novel
marine lactic acid bacterium isolated from deep subseafloor sediment of the Nankai Trough. International Journal of Systematic
and Evolutionary Microbiology, 55, 345–351.
Wasmund, K., Schreiber, L., Lloyd, K. G., Petersen, D. G.,
Schramm, A., Stepanauskas, R., Jørgensen, B. B., and Adrian,
L., 2014. Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum
Chloroflexi. ISME Journal, 8, 383–397.
Webster, G., Parkes, R. J., Fry, J. C., and Weightman, A. J., 2004.
Widespread occurrence of a novel division of bacteria identified
by 16S rDNA gene sequences originally found in deep marine
sediments. Applied and Environmental Microbiology, 70,
5708–5713.
Webster, G., Parkes, R. J., Cragg, B. A., Newberry, C. J.,
Weightman, A. J., and Fry, J. C., 2006. Prokaryotic community
composition and biogeochemical processes in deep subseafloor
sediments from the Peru margin. FEMS Microbiology Ecology,
58, 65–85.
Webster, G., Yarram, L., Freese, E., Köster, J., Sass, H., Parkes,
R. J., and Weightman, A. J., 2007. Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German
Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS
Microbiology Ecology, 62, 78–89.
Webster, G., Blazejak, A., Cragg, B. A., Schippers, A., Sass, H.,
Rinna, J., Tang, X., Mathes, F., Ferdelman, T. G., Fry, J. C.,
Weightman, A. J., and Parkes, R. J., 2009. Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound
from the Porcupine Seabight (IODP Expedition 307). Environmental Microbiology, 11, 239–257.
Webster, G., Sass, H., Cragg, B. A., Gorra, R., Knab, N. J., Green,
C. J., Mathes, F., Fry, J. C., Weightman, A. J., and Parkes,
R. J., 2011. Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusioncontrolled sediments of Aarhus Bay, Denmark, under heterotrophic conditions. FEMS Microbiology Ecology, 77, 248–263.
Weinbauer, M. G., Beckmann, C., and Höfle, M. G., 1998. Utility of
green fluorescent nucleic acid dyes and aluminium oxide membrane filters for rapid epifluorescence enumeration of soil and
sediment bacteria. Applied and Environmental Microbiology,
64, 5000–5003.
Whelan, J. K., Oremland, R., Tarafa, M., Smith, R., Howarth, R.,
and Lee, C., 1986. Evidence for sulfate-reducing and methaneproducing microorganisms in sediments from Sites 618, 619,
and 622. In Bouma, A. H., Coleman, J. M., et al. (eds.), Initial
Reports of DSDP, Vol. 96, pp. 767–775.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J., 1998. Prokaryotes: the unseen majority. Proceedings of the National Academy
of Sciences of the United States of America, 95, 6578–6583.
Wilms, R., Sass, H., Köpke, B., Cypionka, H., and Engelen, B., 2007.
Methane and sulfate profiles within the subsurface of a tidal flat are
reflected by the distribution of sulfate-reducing bacteria and
methanogenic archaea. FEMS Microbiology Ecology, 59, 611–621.
Wittwer, C. T., Herrmann, M. G., Moss, A. A., and Rasmussen,
R. P., 1997. Continuous fluorescence monitoring of rapid cycle
DNA amplification. BioTechniques, 22, 130–138.
Wortmann, U. G., Bernasconi, S. M., and Böttcher, M. E., 2001.
Hypersulfidic deep biosphere indicates extreme sulfur isotope
fractionation during single-step microbial sulfate reduction.
Geology, 29, 647–650.
Xie, S., Lipp, J. S., Wegener, G., Ferdelman, T. G., and Hinrichs,
K. U., 2013. Turnover of microbial lipids in the deep biosphere
and growth of benthic archaeal populations. Proceedings of the
National Academy of Sciences of the United States of America,
110, 6010–6014.
Yanagawa, K., Nunoura, T., McAllister, S. M., Hirai, M., Breuker,
A., Brandt, L., House, C. H., Moyer, C. L., Birrien, J. L., Aoike,
K., Sunamura, M., Urabe, T., Mottl, M. J., and Takai, K., 2013.
The first contamination assessment for microbiological study
in deep-sea drilling and coring by the D/V Chikyu at the Iheya
North hydrothermal field in the Mid-Okinawa Trough (IODP
Expedition 331). Frontiers in Microbiology, 4, 327.
Ziebis, W., McManus, J., Ferdelman, T., Schmidt-Schierhorn, F.,
Bach, W., Muratli, J., et al., 2012. Interstitial fluid chemistry of
sediments underlying the North Atlantic gyre and the influence
of subsurface fluid flow. Earth and Planetary Science Letters,
323–324, 79–91.
Cross-references
Cold Seeps
Deep Biosphere
Deep-sea Sediments
Marine Sedimentary Basins
Methane in Marine Sediments
Ocean Margin Systems
Paleoceanographic Proxies
Regional Marine Geology
DEEP BIOSPHERE
155
provinces in the subseafloor. Annual Review of Marine Science,
2, 279–304.
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. Geomicrobiology
Journal, 17, 207–219.
Sørensen, K. B., Lauer, A., and Teske, A. P., 2004. Archaeal
phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology, 2,
151–161.
Stevens, T. O., and McKinley, J. P., 1995. Lithoautotrophic
microbial ecosystems in deep basalt aquifers. Science, 270,
450–454.
Templeton, A. S., Knowles, E. J., Eldridge, D. L., Arey, B. W.,
Dohnalkova, A. C., Webb, S. M., Bailey, B. E., Tebo, B. M.,
and Staudigel, H., 2009. A seafloor microbial biome hosted
within incipient ferromanganese crusts. Nature Geoscience, 2,
872–876.
Teske, A. P., 2005. The deep subsurface biosphere is alive and well.
Trends in Microbiology, 13, 402–404.
Teske, A. P., 2006a. Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys.
Geomicrobiology Journal, 23, 357–368.
Teske, A. P., 2006b. Microbial community composition in deep
marine subsurface sediments of ODP Leg 201: sequencing surveys and cultivations. In Jørgensen, B. B., D’Hondt, S. L., and
Miller, D. J. (eds.), Proceedings of the ODP, Scientific Results,
201. Ocean Drilling Program, College Station. http://www-odp.
tamu.edu/publications/201_SR/VOLUME/CHAPTERS/120.PDF
Teske, A. P., and Sørensen, K. B., 2008. Uncultured archaea in deep
marine subsurface sediments: have we caught them all? ISME
Journal, 2, 3–18.
Teske, A. P., Biddle, J. F., Edcomb, V. P., and Schippers, A., 2013.
Deep subsurface microbiology: a guide to the research topic
papers. Frontiers in Microbiology, 4, 122.
Toffin, L., Webster, G., Weightman, A. J., Fry, J. C., and Prieur, D.,
2004. Molecular monitoring of culturable bacteria from deep-sea
sediment of the Nankai Trough. Leg 190 Ocean Drilling Program. FEMS Microbiology Ecology, 48, 357–367.
Toffin, L., Zink, K., Kato, C., Pignet, P., Bidault, A., Bienvenu, N.,
et al., 2005. Marinilactibacillus piezotolerans sp. nov., a novel
marine lactic acid bacterium isolated from deep subseafloor sediment of the Nankai Trough. International Journal of Systematic
and Evolutionary Microbiology, 55, 345–351.
Wasmund, K., Schreiber, L., Lloyd, K. G., Petersen, D. G.,
Schramm, A., Stepanauskas, R., Jørgensen, B. B., and Adrian,
L., 2014. Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum
Chloroflexi. ISME Journal, 8, 383–397.
Webster, G., Parkes, R. J., Fry, J. C., and Weightman, A. J., 2004.
Widespread occurrence of a novel division of bacteria identified
by 16S rDNA gene sequences originally found in deep marine
sediments. Applied and Environmental Microbiology, 70,
5708–5713.
Webster, G., Parkes, R. J., Cragg, B. A., Newberry, C. J.,
Weightman, A. J., and Fry, J. C., 2006. Prokaryotic community
composition and biogeochemical processes in deep subseafloor
sediments from the Peru margin. FEMS Microbiology Ecology,
58, 65–85.
Webster, G., Yarram, L., Freese, E., Köster, J., Sass, H., Parkes,
R. J., and Weightman, A. J., 2007. Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German
Wadden Sea using targeted 16S rRNA gene PCR-DGGE. FEMS
Microbiology Ecology, 62, 78–89.
Webster, G., Blazejak, A., Cragg, B. A., Schippers, A., Sass, H.,
Rinna, J., Tang, X., Mathes, F., Ferdelman, T. G., Fry, J. C.,
Weightman, A. J., and Parkes, R. J., 2009. Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound
from the Porcupine Seabight (IODP Expedition 307). Environmental Microbiology, 11, 239–257.
Webster, G., Sass, H., Cragg, B. A., Gorra, R., Knab, N. J., Green,
C. J., Mathes, F., Fry, J. C., Weightman, A. J., and Parkes,
R. J., 2011. Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusioncontrolled sediments of Aarhus Bay, Denmark, under heterotrophic conditions. FEMS Microbiology Ecology, 77, 248–263.
Weinbauer, M. G., Beckmann, C., and Höfle, M. G., 1998. Utility of
green fluorescent nucleic acid dyes and aluminium oxide membrane filters for rapid epifluorescence enumeration of soil and
sediment bacteria. Applied and Environmental Microbiology,
64, 5000–5003.
Whelan, J. K., Oremland, R., Tarafa, M., Smith, R., Howarth, R.,
and Lee, C., 1986. Evidence for sulfate-reducing and methaneproducing microorganisms in sediments from Sites 618, 619,
and 622. In Bouma, A. H., Coleman, J. M., et al. (eds.), Initial
Reports of DSDP, Vol. 96, pp. 767–775.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J., 1998. Prokaryotes: the unseen majority. Proceedings of the National Academy
of Sciences of the United States of America, 95, 6578–6583.
Wilms, R., Sass, H., Köpke, B., Cypionka, H., and Engelen, B., 2007.
Methane and sulfate profiles within the subsurface of a tidal flat are
reflected by the distribution of sulfate-reducing bacteria and
methanogenic archaea. FEMS Microbiology Ecology, 59, 611–621.
Wittwer, C. T., Herrmann, M. G., Moss, A. A., and Rasmussen,
R. P., 1997. Continuous fluorescence monitoring of rapid cycle
DNA amplification. BioTechniques, 22, 130–138.
Wortmann, U. G., Bernasconi, S. M., and Böttcher, M. E., 2001.
Hypersulfidic deep biosphere indicates extreme sulfur isotope
fractionation during single-step microbial sulfate reduction.
Geology, 29, 647–650.
Xie, S., Lipp, J. S., Wegener, G., Ferdelman, T. G., and Hinrichs,
K. U., 2013. Turnover of microbial lipids in the deep biosphere
and growth of benthic archaeal populations. Proceedings of the
National Academy of Sciences of the United States of America,
110, 6010–6014.
Yanagawa, K., Nunoura, T., McAllister, S. M., Hirai, M., Breuker,
A., Brandt, L., House, C. H., Moyer, C. L., Birrien, J. L., Aoike,
K., Sunamura, M., Urabe, T., Mottl, M. J., and Takai, K., 2013.
The first contamination assessment for microbiological study
in deep-sea drilling and coring by the D/V Chikyu at the Iheya
North hydrothermal field in the Mid-Okinawa Trough (IODP
Expedition 331). Frontiers in Microbiology, 4, 327.
Ziebis, W., McManus, J., Ferdelman, T., Schmidt-Schierhorn, F.,
Bach, W., Muratli, J., et al., 2012. Interstitial fluid chemistry of
sediments underlying the North Atlantic gyre and the influence
of subsurface fluid flow. Earth and Planetary Science Letters,
323–324, 79–91.
Cross-references
Cold Seeps
Deep Biosphere
Deep-sea Sediments
Marine Sedimentary Basins
Methane in Marine Sediments
Ocean Margin Systems
Paleoceanographic Proxies
Regional Marine Geology
DEEP BIOSPHERE
155