Mariana Forearc Serpentinite Mud Volcanoes Harbor Novel Communities of Extremophilic Archaea

References

• Altschul , F S , Gish , W , Miller , W , Myers , E W and Lipman , D J . 1990 . Basic local alignment search tool . J Mol Biol , 215 : 403 – 410 .
   PubMed Web of Science ®Google Scholar
• Ashelford , K E , Chuzhanova , N A , Fry , J C , Jones , A J and Weightman , A J . 2006 . New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras . Appl Environ Microbiol , 72 : 5734 – 5741 .
   PubMed Web of Science ®Google Scholar
• Benson , D A , Karsch-Mizrachi , I , Lipman , D J , Ostell , J , Rapp , B A and Wheeler , D L . 2000 . GenBank . Nucl Acids Res , 28 : 15 – 18 .
   PubMed Web of Science ®Google Scholar
• Biddle , J F , Lipp , J S , Lever , M A , Lloyd , K G , Sørensen , K B Anderson , R . 2006 . Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru . Proc Natl Acad Sci , 103 : 3846 – 3851 .
   PubMed Web of Science ®Google Scholar
• Boone , D R , Whitman , W B and Koga , Y . 2001 . “ Methanosarcinales ord. nov ” . In Bergey's manual of systematic bacteriology, 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria , Edited by: Boone , D R and Castenholz , R W . 268 – 289 . New York : Springer .
   Google Scholar
• Davis , R E and Moyer , C L . 2008 . Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system . J Geophys Res , 113 : B08S15 doi: 10.1029/2007JB005413
   Web of Science ®Google Scholar
• DeLong , EF. 1992 . Archaea in coastal marine environments . Proc Natl Acad Sci , 89 : 5685 – 5689 .
   PubMed Web of Science ®Google Scholar
• Dhillon , A , Lever , M , Lloyd , K G , Albert , D B , Sogin , M L and Teske , A . 2005 . Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin . Appl Environ Microbiol , 71 : 4592 – 4601 .
   PubMed Web of Science ®Google Scholar
• Emerson , D and Moyer , C L . 2010 . Microbiology of seamounts: Common patterns observed in community structure . Oceanography , 23 : 148 – 163 .
   Web of Science ®Google Scholar
• Fryer , P , Gharib , J , Ross , K , Savov , I and Mottl , M J . 2006 . Variability in serpentinite mudflow mechanisms and sources: ODP drilling results on Mariana forearc seamounts . Geochem Geophys Geosyst , 7 ( 8 ) : Q08014 doi: doi10.1029/2005GC001201
   Google Scholar
• Fryer , P and Mottl , M J . 1997 . Shinkai 6500 investigations of a resurgent mud volcano on the southeastern Mariana forearc . JAMSTEC Deep Sea Res , 13 : 103 – 114 .
   Google Scholar
• Fryer , P and Salisbury , M H . 2006 . “ Leg 195 synthesis: Site 1200 - serpentinite seamounts of the Izu-Bonin/Mariana convergent plate margin, ODP Leg 125 and 195 drilling results ” . In Proc. ODP, Sci. Results, 195 , Edited by: Shinohara , M , Salisbury , M H and Richter , C . 1 – 30 . College Station , TX : Ocean Drilling Program .
   Google Scholar
• Fryer , P , Wheat , C G and Mottl , M J . 1999 . Mariana blueschist mud volcanism: Implications for conditions within the subduction zone . Geology , 27 : 103 – 106 .
   Web of Science ®Google Scholar
• Gold , T. 1992 . The deep, hot biosphere . Proc Natl Acad Sci , 89 : 6045 – 6049 .
   PubMed Web of Science ®Google Scholar
• Hall , TA. 1999 . BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT . Nucl Acids Symp Ser , 41 : 95 – 98 .
   Google Scholar
• Häne , B G , Jäger , K and Drexler , H G . 1993 . The Pearson product-moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms . Electrophoresis , 14 : 967 – 972 .
   PubMed Web of Science ®Google Scholar
• Hartmann , M and Widmer , F . 2008 . Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling . FEMS Microbiol Ecol , 63 : 249 – 260 .
   PubMed Web of Science ®Google Scholar
• Huber , T , Faulkner , G and Hugenholtz , P . 2004 . Bellerophon: a program to detect chimeric sequences in multiple sequence alignments . Bioinformatics , 20 : 2317 – 2319 .
   PubMed Web of Science ®Google Scholar
• Hulme , S M , Wheat , C G , Fryer , P and Mottl , M J . 2010 . Pore water chemistry of the Mariana serpentinite mud volcanoes: a window to the seismogenic zone . Geochem Geophys Geosyst , 11 ( 1 ) : Q01X09 doi: 10.1029/2009GC002674
   Web of Science ®Google Scholar
• Inagaki , F , Nunoura , T , Nakagawa , S , Teske , A , Lever , M Lauer , A . 2006 . Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin . Proc Natl Acad Sci , 103 : 2815 – 2820 .
   PubMed Web of Science ®Google Scholar
• Inagaki , F , Takai , K , Komatsu , T , Kanamatsu , T , Fujioka , 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 .
   PubMed Web of Science ®Google Scholar
• Inagaki , F , Tsunogai , U , Suzuki , M , Kosaka , A , Machiyama , H Takai , K . 2004 . Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes . Appl Environ Microbiol , 70 : 7445 – 7455 .
   PubMed Web of Science ®Google Scholar
• Karner , M B , DeLong , E F and Karl , D M . 2001 . Archaeal dominance in the mesopelagic zone of the Pacific Ocean . Nature , 409 : 507 – 510 .
   PubMed Web of Science ®Google Scholar
• Kato , C , Li , L , Tamaoka , J and Horikoshi , K . 1997 . Molecular analyses of the sediment of the 11000-m deep Mariana Trench . Extremophiles , 1 : 117 – 123 .
   PubMed Web of Science ®Google Scholar
• Kishino , H and Hasegawa , M . 1989 . Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea . J Mol Evol , 29 : 170 – 179 .
   PubMed Web of Science ®Google Scholar
• Knittel , K , Lösekann , T , Boetius , A , Kort , R and Amann , R . 2005 . Diversity and distribution of methanotrophic Archaea at cold seeps . Appl Environ Microbiol , 71 : 467 – 479 .
   PubMed Web of Science ®Google Scholar
• Lloyd , K G , Lapham , L and Teske , A . 2006 . An anaerobic methane-oxidizing community of ANME-1b Archaea in hypersaline Gulf of Mexico sediments . Appl Environ Microbiol , 72 : 7218 – 7230 .
   PubMed Web of Science ®Google Scholar
• Ludwig , W , Strunk , O , Westram , R , Richter , L , Meier , H Kumar , Y . 2004 . ARB: A software environment for sequence data . Nucl Acids Res , 32 : 1363 – 1371 .
   PubMed Web of Science ®Google Scholar
• Maekawa , H , Shozui , M , Ishii , T , Fryer , P and Pearce , J A . 1993 . Blueschist metamorphism in an active subduction zone . Nature , 364 : 520 – 523 .
   Web of Science ®Google Scholar
• Marsh , TL. 2005 . Culture-independent microbial community analysis with terminal restriction fragment length polymorphism . Meth Enzymol , 397 : 308 – 329 .
   PubMed Web of Science ®Google Scholar
• Martin , W and Russell , M J . 2007 . On the origin of biochemistry at an alkaline hydrothermal vent . Phil Trans Roy Soc B , 362 : 1887 – 1926 .
   PubMed Web of Science ®Google Scholar
• McCollom , TM. 2007 . Geochemical constraints on sources of metabolic energy for chemolithoautotrophy in ultramafic-hosted deep-sea hydrothermal systems . Astrobiology , 7 : 933 – 950 .
   PubMed Web of Science ®Google Scholar
• Miller , D N , Bryant , J E , Madsen , E L and Ghiorse , W C . 1999 . Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples . Appl Environ Microbiol , 65 : 4715 – 4724 .
   PubMed Web of Science ®Google Scholar
• Mottl , M J , Komor , S C , Fryer , P and Moyer , C L . 2003 . Deep-slab fluids fuel extremophilic Archaea on a Mariana forearec serpentinite mud volcano: Ocean Drilling Program Leg 195 . Geochem Geophys Geosyst , 4 ( 11 ) : 9009 doi: 10.1029/2003GC000588
   Web of Science ®Google Scholar
• Mottl , M J , Wheat , C G , Fryer , P , Gharib , J and Martin , J B . 2004 . Chemistry of springs across the Mariana forearc shows progressive devolatilization of the subducting plate . Geochim Cosmochim Acta , 68 : 4915 – 4933 . doi: 10.1016/j.gca.2005.05.037
   Web of Science ®Google Scholar
• Moyer , CL. 2001 . Molecular phylogeny: Applications and implications for marine microbiology . Meth Microbiol , 30 : 375 – 394 .
   Web of Science ®Google Scholar
• Moyer , C L , Tiedje , J M , Dobbs , F C and Karl , D M . 1998 . Diversity of deep-sea hydrothermal vent Archaea from Loihi Seamount, Hawaii . Deep-Sea Res II , 45 : 303 – 317 .
   Web of Science ®Google Scholar
• Olsen , G J , Matsuda , H , Hagstrom , R and Overbeek , R . 1994 . fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood . Comput Appl Biosci , 10 : 41 – 48 .
   PubMedGoogle Scholar
• 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 . Microbiol Molec Biol Rev , 75 : 361 – 422 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Schloss , P D and Handelsman , J . 2005 . Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness . Appl Environ Microbiol , 71 : 1501 – 1506 .
   PubMed Web of Science ®Google Scholar
• Schrenk , M O , Kelley , D S , Bolton , S A and Baross , J A . 2004 . Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge . Environ Microbiol , 6 : 1086 – 1095 .
   PubMed Web of Science ®Google Scholar
• Schulte , M , Blake , D , Hoehler , T and McCollom , T . 2006 . Serpentinization and its implications for life on the early Earth and Mars . Astrobiology , 6 : 364 – 376 .
   PubMed Web of Science ®Google Scholar
• Shipboard Scientific Party . 2002 . Site 1200. Proc . ODP Initial Reports , 195 : 1 – 173 .
   Google Scholar
• Singh , N , Kendall , M M , Liu , Y and Boone , D R . 2005 . Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica . Int J Syst Evol Microbiol , 55 : 2531 – 2538 .
   PubMed Web of Science ®Google Scholar
• 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 . Geomicrobiol J , 17 : 207 – 219 .
   Web of Science ®Google Scholar
• Sørensen , K B and Teske , A . 2006 . Stratified communities of active Archaea in deep marine subsurface sediments . Appl Environ Microbiol , 72 : 4596 – 4603 .
   PubMed Web of Science ®Google Scholar
• Takai , K , Gamo , T , Tsunogai , U , Nakayama , N , Hirayama , H , Nealson , K H and Horikoshi , K . 2004a . Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field . Extremophiles , 8 : 269 – 282 .
   PubMed Web of Science ®Google Scholar
• Takai , K and Horikoshi , K . 1999 . Genetic diversity of Archaea in deep-sea hydrothermal vent environments . Genetics , 152 : 1285 – 1297 .
   PubMed Web of Science ®Google Scholar
• Takai , K , Moyer , C L , Miyazaki , M , Nogi , Y , Hirayama , H , Nealson , K H and Horikoshi , K . 2005 . Marinobacter alkaliphilus sp. nov., a novel alkaliphilic bacterium isolated from subseafloor alkaline serpentine mud from Ocean Drilling Program Site 1200 at South Chamorro Seamount, Mariana Forearc . Extremophiles , 9 : 17 – 27 .
   PubMed Web of Science ®Google Scholar
• Takai , K , Oida , H , Suzuki , Y , Hirayama , H , Nakagawa , S Nunoura , T . 2004b . Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems . Appl Environ Microbiol , 70 : 2404 – 2413 .
   PubMed Web of Science ®Google Scholar
• Teske , A , Dhillon , A and Sogin , M L . 2003 . Genomic markers of ancient anaerobic microbial pathways: Sulfate reduction, methanogenesis, and methane oxidation . Biol Bull , 204 : 186 – 191 .
   PubMed Web of Science ®Google Scholar
• Tourova , T P , Kolganova , T V , Kuznetsov , B B and Pimenov , N V . 2002 . Phylogenetic diversity of the archaeal component in microbial mats on coral-like structures associated with methane seeps in the Black Sea . Microbiology , 71 : 230 – 236 .
   PubMed Web of Science ®Google Scholar
• Uyeda , S. 1982 . Subduction zones: An introduction to comparative subductology . Tectonophysics , 81 : 133 – 159 .
   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
• Wang , P , Xiao , X and Wang , F . 2005 . Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool . Extremophiles , 9 : 209 – 217 .
   PubMed Web of Science ®Google Scholar
• Wheat , C G , Fryer , P , Fisher , A T , Hulme , S , Jannasch , H , Mottl , M J and Becker , K . 2008 . Borehole observations of fluid flow from South Chamorro Seamount, an active serpentinite mud volcano in the Mariana forearc . Earth Planet Sci Lett , 267 : 401 – 409 .
   Web of Science ®Google Scholar
• Whitman , W B , Coleman , D C and Wiebe , W J . 1998 . Prokaryotes: the unseen majority . Proc Natl Acad Sci , 95 : 6578 – 6583 .
   PubMed Web of Science ®Google Scholar
• Zhou , J , Bruns , M A and Tiedje , J M . 1996 . DNA recovery from soils of diverse composition . Appl Environ Microbiol , 62 : 316 – 322 .
   PubMed Web of Science ®Google Scholar