Archaeal Diversity and Spatial Distribution in the Surface Sediment of the South China Sea

References

• Barns , S M , Delwiche , C F , Palmer , J D and Pace , N R . 1996 . Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences . Proc Natl Acad Sci USA , 93 : 9188 – 9193 .
   PubMed Web of Science ®Google Scholar
• Biddle , J F , Lipp , J S , Lever , M A , Lloyd , K G , Sørensen , K B , Anderson , R , Fredricks , H F , Elvert , M , Kelly , T J and Schrag , D P . 2006 . Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru . Proc Natl Acad Sci USA , 103 : 3846 – 3851 .
   PubMed Web of Science ®Google Scholar
• Brochier-Armanet , C , Boussau , B , Gribaldo , S and Forterre , P . 2008 . Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota . Nat Rev Microbiol , 6 : 245 – 252 .
   PubMed Web of Science ®Google Scholar
• Cao , H , Hong , Y , Li , M and Gu , J-D . 2011 . Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the Western Pacific . Microb Ecol , 62 : 813 – 823 .
   PubMed Web of Science ®Google Scholar
• Cao , H , Hong , Y , Li , M and Gu , J-D . 2012 . Lower abundance of ammonia-oxidizing archaea than ammonia-oxidizing bacteria Detected in the subsurface sediments of the Northern South China Sea . Geomicrobiol J , 29 : 332 – 339 .
   Web of Science ®Google Scholar
• Dang , H , Zhang , X , Sun , J , Li , T , Zhang , Z and Yang , G . 2008 . Diversity and spatial distribution of sediment ammonia-oxidizing cenarchaeota in response to estuarine and encironmental gradients in the Changjiang Estuary and East China Sea . Environ Microbiol , 154 : 1 – 12 .
   Google Scholar
• Dawson , S , DeLong , E and Pace , N . 2001 . “ Phylogenetic and ecological perspectives on uncultured Crenarchaeota and Korarchaeota ” . In The Prokaryotes , Edited by: Dworkin , M M , Falkow , S , Rosenberg , E , Schleifer , K-H and Stackebrandt , E . 281 – 289 . New York : Springer .
   Google Scholar
• DeLong , EF. 1992 . Archaea in coastal marine environments . Proc Natl Acad Sci USA , 89 : 5685 – 5689 .
   PubMed Web of Science ®Google Scholar
• Durbin , A M and Teske , A . 2010 . Sediment-associated microdiversity within the Marine Group I Crenarchaeota . Environ Microbiol Rep , 2 : 693 – 703 .
   PubMed Web of Science ®Google Scholar
• Francis , C A , Beman , J M and Kuypers , M M . 2007 . New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation . ISME J , 1 : 19 – 27 .
   PubMed Web of Science ®Google Scholar
• Francis , C A , Roberts , K J , Beman , J M , Santoro , A E and Oakley , B B . 2005 . Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean . Proc Natl Acad Sci USA , 102 : 14683 – 14688 .
   PubMed Web of Science ®Google Scholar
• Fuhrman , J A , McCallum , K and Davis , A A . 1992 . Novel major archaebacterial group from marine plankton . Nature , 356 : 148 – 149 .
   PubMed Web of Science ®Google Scholar
• Hallam , S J , Mincer , T J , Schleper , C , Preston , C M , Roberts , K , Richardson , P M and DeLong , E F . 2006 . Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota . PLoS Biol , 4 : e95
   PubMed Web of Science ®Google Scholar
• Herndl , G J , Reinthaler , T , Teira , E , van Aken , H , Veth , C , Pernthaler , A and Pernthaler , J . 2005 . Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean . Appl Environ Microbiol , 71 : 2303 – 2309 .
   PubMed Web of Science ®Google Scholar
• Hinrichs , K U and Inagaki , F . 2012 . Downsizing the deep biosphere . Science , 338 : 204 – 205 .
   PubMed Web of Science ®Google Scholar
• Huber , H , Hohn , M J , Rachel , R , Fuchs , T , Wimmer , V C and Stetter , K O . 2002 . A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont . Nature , 417 : 63 – 67 .
   PubMed Web of Science ®Google Scholar
• Inagaki , F and Nakagawa , S . 2008 . “ Spatial distribution of the subseafloor Life: diversity and biogeography ” . In Links Between Geological Processes, Microbial Activities and Evolution of Life , Edited by: Dilek , Y , Furnes , H and Muehlenbachs , K . 135 – 158 . New York : Springer .
   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#x0060;Hondt , S and Jørgensen , 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
• 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
• Ingalls , A E , Shah , S R , Hansman , R L , Aluwihare , L I , Santos , G M , Druffel , E R and Pearson , A . 2006 . Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon . Proc Natl Acad Sci U S A , 103 : 6442 – 6447 .
   PubMed Web of Science ®Google Scholar
• Jiang , H , Dong , H , Ji , S , Ye , Y and Wu , N . 2007 . Microbial diversity in the deep marine sediments from the Qiongdongnan Basin in South China Sea . Geomicrobiol J , 24 : 505 – 517 .
   Web of Science ®Google Scholar
• Jiang , L , Peng , X , Zhou , H and Wang , F . 2008 . Vertical distribution and diversity of archaea in coastal sediments of Qi#x0060;ao Island (Zhujiang River Estuary), southern China, estimated by 16S rDNA analysis . Acta Oceanol Sin , 30 : 114 – 122 .
   Google Scholar
• Kallmeyer , J , Pockalny , R , Adhikari , R R , Smith , D C and D’Hondt , S . 2012 . Global distribution of microbial abundance and biomass in subseafloor sediment . Proc Natl Acad Sci USA Proc Natl Acad Sci USA , 109 : 16213 – 16216 .
   PubMed Web of Science ®Google Scholar
• Könneke , M , Bernhard , A E , de la Torre , J R , Walker , C B , Waterbury , J B and Stahl , D A . 2005 . Isolation of an autotrophic ammonia-oxidizing marine archaeon . Nature , 437 : 543 – 546 .
   PubMed Web of Science ®Google Scholar
• Kozubal , M A , Romine , M , Jennings , RD , Jay , Z J , Tringe , S G , Rusch , D B , Beam , J P , McCue , L A and Inskeep , W P . 2013 . Geoarchaeota: a new candidate phylum in the archaea from high-temperature acidic iron mats in Yellowstone National Park . ISME J , 7 : 622 – 634 .
   PubMed Web of Science ®Google Scholar
• Li , T and Wang , P . 2008a . Microbial diversity in surface sediments of Xisha Trough, the South China Sea . Acta Ecol Sin , 28 : 1166 – 1173 .
   Google Scholar
• Li , T , Wang , P and Wang , P X . 2008b . Bacterial and archaeal diversity in surface sediment from the south slope of the South China Sea . Acta Microbiol Sin , 48 : 323 – 329 .
   PubMedGoogle Scholar
• Li , Y , Li , F , Zhang , X , Qin , S , Zeng , Z , Dang , H and Ye , Q . 2008 . Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sampl at the East Pacific Rise (∼13°N) . Extremophiles , 12 : 573 – 585 .
   PubMed Web of Science ®Google Scholar
• Lipp , J S , Morono , Y , Inagaki , F and Hinrichs , K U . 2008 . Significant contribution of Archaea to extant biomass in marine subsurface sediments . Nature , 454 : 991 – 994 .
   PubMed Web of Science ®Google Scholar
• Morono , Y , Terada , T , Nishizawa , M , Ito , M , Hillion , F , Takahata , N , Sano , Y and Inagaki , F . 2011 . Carbon and nitrogen assimilation in deep subseafloor microbial cells . Proc Natl Acad Sci USA , 108 : 18295 – 18300 .
   PubMed Web of Science ®Google Scholar
• Nicol , G W and Schleper , C . 2006 . Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? . Trends Microbiol , 14 : 207 – 212 .
   PubMed Web of Science ®Google Scholar
• Ouverney , C C and Fuhrman , J A . 2000 . Marine planktonic archaea take up amino acids . Appl Environ Microbiol , 66 : 4829 – 4833 .
   PubMed 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 , 8 : 11 – 28 .
   Web of Science ®Google Scholar
• Prosser , J I and Nicol , G W . 2008 . Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment . Environ Microbiol , 10 : 2931 – 2941 .
   PubMed Web of Science ®Google Scholar
• Pruesse , E , Quast , C , Knittel , K , Fuchs , B M , Ludwig , W , Peplies , J and Glockner , F O . 2007 . SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB . Nucl Acids Res , 35 : 7188 – 7196 .
   PubMed Web of Science ®Google Scholar
• Schloss , P D , Westcott , S L , Ryabin , T , Hall , J R , Hartmann , M , Hollister , E B , Lesniewski , R A , Oakley , B B , Parks , D H , Robinson , C J , Sahl , J W , Stres , B , Thallinger , G G , Van , H , David , J and Weber , C F . 2009 . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities . Appl Environ Microbiol , 75 : 7537 – 7541 .
   PubMed 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
• Stahl , D A and de la Torre , J . 2012 . Physiology and diversity of ammonia-oxidizing Archaea . Annu Rev Microbiol , 66 : 83 – 101 .
   PubMed Web of Science ®Google Scholar
• ter Braak , C JF and Smilauer , P . 2002 . CANOCO Reference manual and CanoDraw for windows user#x0060;s guide: software for canonical community ordination (version 4.5) , Ithaca , NY : Microcomputer Power .
   Google Scholar
• Teske , A and Biddle , J F . 2008 . “ Analysis of deep subsurface microbial communities by functional genes and genomics ” . In Links Between Geological Processes, Microbial Activities & Evolution of Life , Edited by: Dilek , Y , Furnes , H and Muehlenbachs , K . 159 – 176 . New York : Springer .
   Google Scholar
• Valentine , D L and Reeburgh , W S . 2000 . New perspectives on anaerobic methane oxidation . Environ Microbiol , 2 : 477 – 484 .
   PubMed Web of Science ®Google Scholar
• Wang , P , Li , T , Hu , A , Wei , Y , Guo , W , Jiao , N and Zhang , C . 2010 . Community structure of archaea from deep-sea sediments of the South China Sea . Microbial Ecol , 604 : 796 – 806 .
   Web of Science ®Google Scholar
• Wei , Y , Wang , J , Liu , J , Dong , L , Li , L , Wang , H , Wang , P , Zhao , M and Zhang , C . 2011 . Spatial variations in Archaeal lipids of surface water and core-top sediments in the South China Sea and their implictions for paleoclimate studies . Appl Environ Microbiol , 77 : 7479 – 7489 .
   PubMed Web of Science ®Google Scholar
• Zhang , Y , Su , X , Chen , F , Wang , Y , Jiao , L , Dong , H , Huang , Y and Jiang , H . 2012 . Microbial diversity in cold seep sediments from the northern South China Sea . Geoscience Frontiers , 33 : 301 – 316 .
   Web of Science ®Google Scholar
• Zhao , M. 2009 . “ Productivity and nutrient dynamics in the modern South China Sea ” . In The South China Sea, Paleooceanography and sedimentology , Edited by: Wang , P and Li , Q . p439 – 457 . New York : Springer .
   Google Scholar