Carbon and nitrogen assimilation in deep subseafloor microbial cells

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 45, 2011, Pages 18295-18300

  Morono, Yuki ^a   Terada, Takeshi ^b   Nishizawa, Manabu ^a   Ito, Motoo ^a   Hillion, François ^c   Takahata, Naoto ^d   Sano, Yuji ^d   Inagaki, Fumio ^a  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^b MARINE WORKS JAPAN LTD   (Japan)

^c CAMECA   (United States)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

Carbon and nitrogen fixation; Marine sedimentary habitat; Metabolic activity; Subseafloor life

Indexed keywords

ACETIC ACID; AMINO ACID; AMMONIA; BICARBONATE; CARBON 13; GLUCOSE; METHANE; NITROGEN 15; PYRUVIC ACID; TRACER;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL CELL; CARBON FIXATION; CELL GROWTH; CELL METABOLISM; CONTROLLED STUDY; IN VITRO STUDY; JAPAN; LOWER PLEISTOCENE; MASS SPECTROMETRY; NITROGEN FIXATION; NONHUMAN; PRIORITY JOURNAL; SEDIMENT;

ARCHAEA; BACTERIA; CARBON; IN SITU HYBRIDIZATION, FLUORESCENCE; NITROGEN; SEAWATER; SPECTROMETRY, MASS, SECONDARY ION; WATER MICROBIOLOGY;

EID: 81055145280     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1107763108     Document Type: Article

References (40)

1. Morita RY (1997) Bacteria in Oligotrophic Environments: Starvation-Survival Lifestyle (Chapman & Hall, New York), pp 1-529.
2. Roussel EG, et al. (2008) Extending the sub-sea-floor biosphere. Science 320:1046. (Pubitemid 351929540)
3. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: The unseen majority. Proc Natl Acad Sci USA 95:6578-6583. (Pubitemid 28278022)
4. Parkes RJ, Barry AC, Peter W (2000) Recent studies on bacterial populations and processes in subseafloor sediments: A review. Hydrogeol J 8:11-28.
5. Lipp JS, Morono Y, Inagaki F, Hinrichs K-U (2008) Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 454:991-994.
6. D'Hondt S, et al. (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306:2216-2221. (Pubitemid 40024451)
7. D'Hondt S, Rutherford S, Spivack AJ (2002) Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067-2070. (Pubitemid 34229467)
8. D'Hondt S, et al. (2009) Subseafloor sedimentary life in the South Pacific Gyre. Proc Natl Acad Sci USA 106:11651-11656.
9. Jørgensen BB, Boetius A (2007) Feast and famine-microbial life in the deep-sea bed. Nat Rev Microbiol 5:770-781. (Pubitemid 47423765)
10. Schippers A, et al. (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433:861-864. (Pubitemid 40314893)
11. Colwell FS, et al. (2008) Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin. Appl Environ Microbiol 74: 3444-3452. (Pubitemid 351812799)
12. Biddle JF, et al. (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103:3846-3851. (Pubitemid 43376643)
13. Inagaki F, et al. (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69: 7224-7235. (Pubitemid 38585373)
14. Inagaki F, et al. (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103:2815-2820.
15. Teske AP (2006) Microbial communities of deep marine subsurface sediments: Molecular and cultivation surveys. Geomicrobiol J 23:357-368.
16. Webster G, et al. (2006) Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol Ecol 58:65-85. (Pubitemid 44359309)
17. Parkes RJ, et al. (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390-394. (Pubitemid 41059048)
18. Sørensen KB, Teske A (2006) Stratified communities of active Archaea in deep marine subsurface sediments. Appl Environ Microbiol 72:4596-4603. (Pubitemid 44078783)
19. Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105:10583-10588.
20. Webster G, et al. (2009) Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307). Environ Microbiol 11:239-257.
21. Lever MA, et al. (2010) Acetogenesis in deep subseafloor sediments of the Juan de Fuca Ridge flank: A synthesis of geochemical, thermodynamic, and gene-based evidence. Geomicrobiol J 27:183-211.
22. Futagami T, Morono Y, Terada T, Kaksonen AH, Inagaki F (2009) Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments. Appl Environ Microbiol 75:6905-6909.
23. Hoehler TM (2004) Biological energy requirements as quantitative boundary conditions for life in the subsurface. Geobiology 2:205-215.
24. Price PB, Sowers T (2004) Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proc Natl Acad Sci USA 101:4631-4636. (Pubitemid 38437462)
25. Aoike K (2007) CK06-06 D/V Chikyu Shakedown Cruise Offshore Shimokita, Laboratory Operation Report (CDEX-JAMSTEC, Yokohama, Japan), pp 40-43.
26. Tomaru H, et al. (2009) Dating of dissolved iodine in pore waters from the gas hydrate occurrence offshore Shimokita Peninsula, Japan: 129I results from the D/V Chikyu shakedown cruise. Resour Geol 59:359-373.
27. Morono Y, Terada T, Masui N, Inagaki F (2009) Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J 3:503-511.
28. Treude T, et al. (2007) Consumption of methane and CO2 by methanotrophic microbial mats from gas seeps of the anoxic Black Sea. Appl Environ Microbiol 73: 2271-2283. (Pubitemid 46649519)
29. Wegener G, Niemann H, Elvert M, Hinrichs K-U, Boetius A (2008) Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane. Environ Microbiol 10:2287-2298.
30. Pernthaler A, Pernthaler J, Amann R (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68:3094-3101. (Pubitemid 34602035)
31. Pernthaler A, Amann R (2004) Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl Environ Microbiol 70:5426-5433. (Pubitemid 39279619)
32. Kubota K, et al. (2008) Evaluation of enzymatic cell treatments for application of CARD-FISH to methanogens. J Microbiol Methods 72:54-59. (Pubitemid 350309682)
33. Teske A, Sørensen KB (2008) Uncultured archaea in deep marine subsurface sediments: Have we caught them all? ISME J 2:3-18. (Pubitemid 351612350)
34. Musat N, et al. (2008) A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc Natl Acad Sci USA 105:17861-17866.
35. Toffin L, Webster G, Weightman AJ, Fry JC, Prieur D (2004) Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program. FEMS Microbiol Ecol 48:357-367. (Pubitemid 38648923)
36. Parkes RJ, et al. (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). Environ Microbiol 11:3140-3153.
37. Imachi H, et al. (2011) Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME J, 10.1038/ismej.2011.64.
38. Inagaki F, Hinrichs K-U, Kubo Y, Expedition 337 Project Team (2010) Deep coalbed biosphere off Shimokita: Microbial processes and hydrocarbon system associated with deeply buried coalbed in the ocean. The Integrated Ocean Drilling Program (IODP) Scientific Prospectus, 337, 10.2204/iodp.sp.337.2010.
39. Morono Y, Inagaki F (2010) Automatic slide-loarder fluorescence microscope for discriminative enumeration of subseafloorlife. Scientific Drilling 9:32-36.
40. Kallmeyer J, Smith DC, Spivack AJ, D'Hondt S (2008) New cell extraction procedure applied to deep subsurface sediments. Limnol Oceanogr: Methods 6:236-245. (Pubitemid 351949835)