Fluids from the Oceanic Crust Support Microbial Activities within the Deep Biosphere

REFERENCES

• Batzke , A , Engelen , B , Sass , H and Cypionka , H . 2007 . Phylogenetic and physiological diversity of cultured deep-biosphere bacteria from Equatorial Pacific Ocean and Peru Margin sediments . Geomicrobiol J , : 261 – 273 .
   Web of Science ®Google Scholar
• Biddle , J F , Lipp , J S , Lever , M A , Lloyd , K G , S⊘rensen , 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 USA , 103 : 3846 – 3851 .
   PubMed Web of Science ®Google Scholar
• Boetius , A and Lochte , K . 1996 . Effect of organic enrichments on hydrolytic potentials and growth of bacteria in deep-sea sediments . Mar Ecol-Prog Ser , 140 : 239 – 250 .
   Web of Science ®Google Scholar
• Boetius , A , Ravenschlag , K , Schubert , C J , Rickert , D , Widdel , F , Gieseke , A , Amann , R , Jorgensen , B B , Witte , U and Pfannkuche , O . 2000 . A marine microbial consortium apparently mediating anaerobic oxidation of methane . Nature , 407 : 623 – 626 .
   PubMed Web of Science ®Google Scholar
• Borowski , W S , Hoehler , T M , Alperin , M J , Rodriguez , N M and Paull , C K . 2000 . Significance of anaerobic methane oxidation in methane-rich sediments overlying the Blake Ridge gas hydrates , Edited by: Paull , C K , Matsumoto , R , Wallace , P J and Dillon , W P . 87 – 99 . College Station, TX : Ocean Drilling Program . Proc. ODP, Sci. Results, 164
   Google Scholar
• Bussmann , I , Dando , P R , Niven , S J and Suess , E . 1999 . Groundwater seepage in the marine environment: role for mass flux and bacterial activity . Mar Ecol Prog Ser , 178 : 169 – 177 .
   Web of Science ®Google Scholar
• Coolen , M JL and Overmann , J . 2000 . Functional exoenzymes as indicators of metabolically active bacteria in 124,000-year-old sapropel layers of the eastern Mediterranean Sea . Appl Environ Microbiol , 66 : 2589 – 2598 .
   PubMed Web of Science ®Google Scholar
• Cowen , J P , Giovannoni , S J , Kenig , F , Johnson , H P , Butterfield , D , Rappe , M S , Hutnak , M and Lam , P . 2003 . Fluids from aging ocean crust that support microbial life . Science , 299 : 120 – 123 .
   PubMed Web of Science ®Google Scholar
• Cowen , J P . 2004 . The microbial biosphere of sediment-buried oceanic basement . Res Microbiol , 155 : 497 – 506 .
   PubMed Web of Science ®Google Scholar
• D'Hondt , S , Jorgensen , 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 Z , 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 , Padilla , C N and Acosta , J LS . 2004 . Distributions of microbial activities in deep subseafloor sediments . Science , 306 : 2216 – 2221 .
   PubMed Web of Science ®Google Scholar
• de Man , J C . 1977 . MPN tables for more than one test . Europ J Appl Microbiol , 4 : 307 – 310 .
   Web of Science ®Google Scholar
• De Long , E F . 2004 . Microbial life breathes deep . Science , 306 : 2198 – 2200 .
   PubMed Web of Science ®Google Scholar
• Ehrhardt , C J , Haymon , R M , Lamontagne , M G and Holden , P A . 2007 . Evidence for hydrothermal Archaea within the basaltic flanks of the East Pacific Rise . Environ Microbiol , 9 : 900 – 912 .
   PubMed Web of Science ®Google Scholar
• Expedition 301 Scientists. 2005a. Site U1301. In: Fisher AT, Urabe T, Klaus A, and the Exp. 301 Scientists (Eds.). Proc. IODP, 301: College Station TX (IODP Management International, Inc.).doi:10.2204/iodp.proc.301.106.2005
   Google Scholar
• Expedition 301 Scientists. 2005b. Methods. In: Fisher AT, Urabe T, Klaus A, and the Exp. 301 Scientists (Eds.). Proc. IODP, 301: College Station TX (IODP Management International, Inc.).doi:10.2204/iodp.proc.301.105.2005
   Google Scholar
• Fisher , A T , Davis , E E , Hutnak , M , Spiess , V , Zühlsdorff , L , Cherkaoui , A , Christiansen , L , Edwards , K , Macdonald , R , Villinger , H , Mottl , M J , Wheat , C G and Becker , K . 2003 . Hydrothermal recharge and discharge across 50 km guided by seamounts on a young ridge flank . Nature , 421 : 618 – 621 .
   PubMed Web of Science ®Google Scholar
• Fisher , A T , Urabe , T , Klaus , A and the IODP Exp. 301 Scientists . 2005 . IODP Expedition 301 installs three borehole crustal observatories, prepares for three-dimensional, cross-hole experiments in the northeastern Pacific Ocean . Sci Drill , 1 : 6 – 11 .
   Google Scholar
• Fisk , M R , Giovannoni , S J and Thorseth , I H . 1998 . Alteration of oceanic volcanic glass: Textural evidence of microbial activity . Science , 281 : 978 – 980 .
   PubMed Web of Science ®Google Scholar
• Gieskes , J M , Gamo , T and Brumsack , H . 1991 . Chemical methods for interstitial water analysis aboard JOIDES Resolution http://www-odp.tamu.edu/publications/tnotes/tn15/f_chem1.htm ODP Tech. Note,15, [Online] Available from World Wide Web
   Google Scholar
• Graber , K K , Pollard , E , Jonasson , B and Schulte , E E . 2002 . Overview of Ocean Drilling Program engineering tools and hardware http://www-odp.tamu.edu/publications/tnotes/tn31/INDEX.HTM ODP Tech. Note, 31. [Online] Available from World Wide Web
   Google Scholar
• Higuchi , R , Fockler , C , Dollinger , G and Watson , R . 1993 . Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions . Bio/Technology , 11 : 1026 – 1030 .
   PubMed Web of Science ®Google Scholar
• Hinrichs , K-U and Boetius , A . 2002 . “ The anaerobic oxidation of methane: New insights in microbial ecology and biogeochemistry ” . In Ocean Margin Systems , Edited by: Wefer , G , Billett , D Hebbeln , D . 457 – 477 . Berlin-Heidelberg : Springer-Verlag .
   Google Scholar
• Holland , M E and Baross , J A . 2003 . “ Limits of life in hydrothermal systems ” . In Energy and Mass Transfer in Marine Hydrothermal Systems , Edited by: Halbach , P E , Tunnicliffe , V and Hein , J R . 235 – 248 . Berlin : Dahlem University Press .
   Google Scholar
• Huber , J A , Johnson , H P , Butterfield , D A and Baross , J A . 2006 . Microbial life in ridge flank crustal fluids . Environ Microbiol , 8 : 88 – 99 .
   PubMed Web of Science ®Google Scholar
• Hutnak , M , Fisher , A T , Zühlsdorff , L , Spiess , V , Stauffer , P H and Gable , C W . 2006 . Hydrothermal recharge and discharge guided by basement outcrops on 0.7–3.6 Ma seafloor east of the Juan de Fuca Ridge: Observations and numerical models . Geochem Geophys Geosyst , 7 : 1 – 36 .
   Web of Science ®Google Scholar
• 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 : 7224 – 7235 .
   PubMed Web of Science ®Google Scholar
• 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 J⊘rgensen , B B . 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 .
   PubMed Web of Science ®Google Scholar
• Iversen , N and Blackburn , T H . 1981 . Seasonal rates of methane oxidation in anoxic marine sediments . Appl Environ Microbiol , 41 : 1295 – 1300 .
   PubMed Web of Science ®Google Scholar
• Johnson , H P and Pruis , M J . 2003 . Fluxes of fluid and heat from the oceanic crustal reservoir . Earth Planet Sci Lett , 216 : 565 – 574 .
   Web of Science ®Google Scholar
• Johnson , H P , Baross , J A and Bjorklund , T A . 2006 . On sampling the upper crustal reservoir of the NE Pacific Ocean . Geofluids , 6 : 251 – 271 .
   Web of Science ®Google Scholar
• J⊘rgensen , B B , Weber , A and Zopfi , J . 2001 . Sulfate reduction and anaerobic methane oxidation in Black Sea sediments . Deep-Sea Res I , 48 : 2097 – 2120 .
   Google Scholar
• Joye , S B , Boetius , A , Orcutt , B N , Montoya , J P , Schulz , H N , Erickson , M J and Lugo , S K . 2004 . The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps . Chem Geol , 205 : 219 – 238 .
   Web of Science ®Google Scholar
• Kallmeyer , J , Ferdelman , T G , Weber , A , Fossing , H and J⊘rgensen , B B . 2004 . A cold chromium distillation procedure for radiolabeled sulfide applied to sulfate reduction measurements . Limnol Oceanogr Meth , 2 : 171 – 180 .
   Web of Science ®Google Scholar
• Keil , R G , Montlucon , D B , Prahl , F G and Hedges , J I . 1994 . Sorptive preservation of labile organic-matter in marine-sediments . Nature , 370 : 549 – 552 .
   Web of Science ®Google Scholar
• Köpke , B , Wilms , R , Engelen , B , Cypionka , H and Sass , H . 2005 . Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients . Appl Environ Microbiol , 71 : 7819 – 7830 .
   PubMed Web of Science ®Google Scholar
• Kormas , K A , Smith , D C , Edgcomb , V and Teske , A . 2003 . Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176) . FEMS Microbiol Ecol , 45 : 115 – 125 .
   PubMed Web of Science ®Google Scholar
• Kvenvolden , K A and McDonald , T J . 1986 . Organic geochemistry on the JOIDES Resolution—an assay ODP Tech. Note, 6
   Google Scholar
• Lane , D J . 1991 . “ 16S/23S rRNA sequencing ” . In Nucleic Acid Techniques in Bacterial Systematics , Edited by: Stackebrand , E and Goodfellow , M . 205 – 248 . Chichester, UK : Wiley .
   Google Scholar
• Lang , S Q , Butterfield , D A , Lilley , M D , Johnson , H P and Hedges , J I . 2006 . Dissolved organic carbon in ridge-axis and ridge-flank hydrothermal systems . Geochim Cosmochim Acta , 70 : 3830 – 3842 .
   Web of Science ®Google Scholar
• Lever , M A , Alperin , M , Engelen , B , Inagaki , F , Nakagawa , S , Steinsbu , B O , Teske , A and IODP Exp. 301 Scientists . 2006 . Trends in basalt and sediment core contamination during IODP Expedition 301 . Geomicrobiol J , 23 : 517 – 530 .
   Web of Science ®Google Scholar
• Lunau , M , Lemke , A , Walther , K , Martens-Habbena , W and Simon , M . 2005 . An improved method for counting bacteria from sediments and turbid environments by epifluorescence microscopy . Environ Microbiol , 7 : 961 – 968 .
   PubMed Web of Science ®Google Scholar
• Lysnes , K , Thorseth , I H , Steinsbu , B O , Ovreas , L , Torsvik , T and Pedersen , R B . 2004a . Microbial community diversity in seafloor basalt from the Arctic spreading ridges . FEMS Microbiol Ecol , 50 : 213 – 230 .
   PubMed Web of Science ®Google Scholar
• Lysnes , K , Torsvik , T , Thorseth , I H and Pedersen , R B . 2004b . Microbial populations in ocean floor basalt: results from ODP Leg 187 Edited by: Pedersen , R B and Christie , D MDJM . 1 – 27 . Proc. ODP, Sci. Results, 187
   Google Scholar
• Marchesi , J R , Weightman , A J , Cragg , B A , Parkes , R J and Fry , J C . 2001 . Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis . FEMS Microbiol Ecol , 34 : 221 – 228 .
   PubMed Web of Science ®Google Scholar
• Mather , I D and Parkes , R J . 2000 . Bacterial Profiles in sediments of the eastern flank of the Juan de Fuca Ridge, Sites 1026 and 1027 Edited by: Fisher , A , Davis , E E and Escutia , C . 161 – 165 . Proc. ODP, Sci. Results, 168
   Google Scholar
• Michaelis , W , Seifert , R , Nauhaus , K , Treude , T , Thiel , V , Blumenberg , M , Knittel , K , Gieseke , A , Peterknecht , K , Pape , T , Boetius , A , Amann , R , Jorgensen , B B , Widdel , F , Peckmann , J R , Pimenov , N V and Gulin , M B . 2002 . Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane . Science , 297 : 1013 – 1015 .
   PubMed Web of Science ®Google Scholar
• Muyzer , G , Teske , A , Wirsen , C O and Jannasch , H W . 1995 . Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments . Arch Microbiol , 164 : 165 – 172 .
   PubMed Web of Science ®Google Scholar
• Nakagawa , S , Inagaki , F , Suzuki , Y , Steinsbu , B O , Lever , M A , Takai , K , Engelen , B , Sako , Y , Wheat , C G , Horikoshi , K and IODP Exp. 301 Scientists . 2006 . Microbial community in black rust exposed to hot ridge flank crustal fluids . Appl Environ Microbiol , 72 : 6789 – 6799 .
   PubMed Web of Science ®Google Scholar
• Newberry , C J , Webster , G , Cragg , B A , Parkes , R J , Weightman , A J and Fry , J C . 2004 . Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190 . Environ Microbiol , 6 : 274 – 287 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• 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 : 11 – 28 .
   Web of Science ®Google Scholar
• Parkes , R J , Webster , G , Cragg , B A , Weightman , A J , Newberry , C J , Ferdelman , T G , Kallmeyer , J , J⊘rgensen , B B , Aiello , I W and Fry , J C . 2005 . Deep sub-seafloor prokaryotes stimulated at interfaces over geological time . Nature , 436 : 390 – 394 .
   PubMed Web of Science ®Google Scholar
• Presley , B J . 1971 . “ Techniques for analyzing interstitial water samples ” . In Appendix Part 1: Determination of selected minor and major inorganic constituents, 7. , 2nd ed. , Edited by: Winterer , E L . 1749 – 1755 . Washington, DC : U.S. Govt. Printing Office .
   Google Scholar
• Schippers , A , Neretin , L N , Kallmeyer , J , Ferdelman , T G , Cragg , B A , Parkes , R J and J⊘rgensen , B B . 2005 . Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria . Nature , 433 : 861 – 864 .
   PubMed Web of Science ®Google Scholar
• 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 . Environ Microbiol , 8 : 1251 – 1260 .
   PubMed Web of Science ®Google Scholar
• Shipboard Scientific Party . 2004 . Juan de Fuca hydrogeology: The hydrogeologic architecture of basaltic oceanic crust: compartmentalization, anisotropy, microbiology, and crustal-scale properties on the eastern flank of Juan de Fuca Ridge, eastern Pacific Ocean http://iodp.tamu.edu/publications/PR/301PR/301PR.PDF IODP Prel. Rept., 301. [Online] Available from World Wide Web
   Google Scholar
• Summit , M and Baross , J A . 2001 . A novel microbial habitat in the mid-ocean ridge subseafloor . Proc Natl Acad Sci USA , 98 : 2158 – 2163 .
   PubMed Web of Science ®Google Scholar
• Süß , J , Engelen , B , Cypionka , H and Sass , H . 2004 . Quantitative analysis of bacterial communities from Mediterranean sapropels based on cultivation-dependent methods . FEMS Microbiol Ecol , 51 : 109 – 121 .
   PubMed Web of Science ®Google Scholar
• Süß , J , Schubert , K , Sass , H , Cypionka , H , Overmann , J and Engelen , B . 2006 . Widespread distribution and high abundance of Rhizobium radiobacter within Mediterranean subsurface sediments . Environ Microbiol , 8 : 1753 – 1763 .
   PubMed Web of Science ®Google Scholar
• Thorseth , I H , Torsvik , T , Torsvik , V , Daae , F L , Pedersen , R B and Keldysh-98 Scientific Party . 2001 . Diversity of life in ocean floor basalt . Earth Planet Sci Lett , 194 : 31 – 37 .
   Web of Science ®Google Scholar
• Treude , T , Boetius , A , Knittel , K , Wallmann , K and J⊘rgensen , B B . 2003 . Anaerobic oxidation of methane above gas hydrates at Hydrate Ridge, NE Pacific Ocean . Mar Ecol Prog Ser , 264 : 1 – 14 .
   Web of Science ®Google Scholar
• Treude , T , Niggemann , J , Kallmeyer , J , Wintersteller , P , Schubert , C J , Boetius , A and J⊘rgensen , B B . 2005 . Anaerobic oxidation of methane and sulfate reduction along the Chilean continental margin . Geochim Cosmochim Acta , 69 : 2767 – 2779 .
   Web of Science ®Google Scholar
• Vetriani , C , Jannasch , H W , MacGregor , B J , Stahl , D A and Reysenbach , A L . 1999 . Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments . Appl Environ Microbiol , 65 : 4375 – 4384 .
   PubMed Web of Science ®Google Scholar
• Wakeham , S G and Canuel , E A . 2006 . Degradation and Preservation of Organic Matter in Marine Sediments . Hdb Env Chem , 2 : 1 – 27 .
   Google Scholar
• Wheat , C G , Elderfield , H , Mottl , M J and Monnins , C . 2000 . Chemical composition of basement fluids within an oceanic ridge flank: Implications for along-strike and across-strike hydrothermal circulation . J Geophys Res , 105 : 13437 – 13447 .
   Web of Science ®Google Scholar
• Whelan , J K , Oremland , R , Tarafa , M , Smith , R , Howarth , R and Lee , C . 1986 . Evidence for sulfate-reducing and methane-producing microorganisms in sediments from Site 618, Site 619, and Site 622 . Initial Reports of the Deep Sea Drilling Project , 96 : 767 – 775 .
   Google Scholar
• Whitman , W B , Coleman , D C and Wiebe , W J . 1998 . Prokaryotes: The unseen majority . Proc Natl Acad Sci USA , 95 : 6578 – 6583 .
   PubMed Web of Science ®Google Scholar
• 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 Microbiol Ecol , 59 : 611 – 621 .
   PubMed Web of Science ®Google Scholar