518
Views
33
CrossRef citations to date
0
Altmetric
Original Articles

Microbial Diversity in the Deep Marine Sediments from the Qiongdongnan Basin in South China Sea

, , , &
Pages 505-517 | Received 05 Sep 2006, Accepted 27 May 2007, Published online: 01 Oct 2007

REFERENCES

  • Acinas , S G , Sarma-Rupavtarm , R , Klepac-Ceraj , V and Polz , M F . 2005 . PCR-induced sequence artifacts and bias: Insights from comparison of two 16S rRNA clone libraries constructed from the same sample . Appl Environ Microbiol , 71 : 8966 – 8969 .
  • Biddle , J F , House , C H and Brenchley , J E . 2005 . Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles . Geobiology , 3 : 287 – 295 .
  • Bidle , K A , Kastner , M and Bartlett , D H . 1999 . A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia Margin (ODP site 892B) . FEMS Microbiol Lett , 177 : 101 – 108 .
  • 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 .
  • Brisbarre , N , Fardeau , M L , Cueff , V , Cayol , J L , Barbier , G , Cilia , V , Ravot , G , Thomas , P , Garcia , J L and Ollivier , B . 2003 . Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney . Int J Syst Evol Microbiol , 53 : 1043 – 1049 .
  • Bruns , A and Berthe-Corti , L . 1999 . Fundibacter jadensis gen. nov., sp. nov., a new slightly halophilic bacterium, isolated from intertidal sediment . Int J Syst Bacteriol , 49 : 441 – 448 .
  • Chen , D-F , Li , X and Xia , B . 2004 . Distribution of gas hydrate stable zones and resource prediction in the Qiongdongnan Basin of the South China Sea (in Chinese) . Chin J Geophy , 47 : 483 – 489 .
  • D'Hondt , S , Jorgensen , B B , Miller , D J , Batzke , A , Blake , R , Cragg , B A , Cypionka , H , Dickens , G D , Ferdelman , T , Hinrichs , K-U , Holm , N G , Mitterer , R , Spivack , A , Wang , G , Bekins , B , Engelen , B , Ford , K , Gettemy , G , Rutherford , S D , Sass , H , Skilbeck , C GI , 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 .
  • Fernandez-Martinez , J , Pujalte , M J , Garcia-Martinez , J , Mata , M , Garay , E and Rodriguez-Valera , F . 2003 . Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax . Int J Syst Evol Microbiol , 53 : 331 – 338 .
  • Franzmann , P D , Springer , N , Ludwig , W , Conway de Macario , E and Rhode , M . 1992 . A methanogenic archaeon from Ace Lake, Antarctica: Methanococcoides burtonii sp. nov . Syst Appl Microbiol , 15 : 573 – 581 .
  • Gonzalez , J M and Moran , M A . 1997 . Numerical dominance of a group of marine bacteria in the alpha-subclass of the class Proteobacteria in coastal seawater . Appl Environ Microbiol , 63 : 4237 – 4242 .
  • Gonzalez , J M and Whitman , W B . 2004 . “ Oceanospirillum and Related Genera ” . In The Prokaryotes: an evolving electronic resource for the microbiological community, , 3rd ed. , Edited by: Dworkin , M. , Rosenberg , H. , Schleifer , K.-H. and Stackebrandt , E. New York : Springer-Verlag . www.prokaryotes.com release 3.18. [online]
  • Grimberg , S J , Stringfellow , W T and Aitken , M D . 1996 . Quantifying the biodegradation of phenanthrene by Pseudomonas stutzeri P16 in the presence of a nonionic surfactant . Appl Environ Microbiol , 62 : 2387 – 2392 .
  • Grosskopf , R , Stubner , S and Liesack , W. 1998 . Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms . Appl Environ Microbiol , 64 : 4983 – 4989 .
  • Guo , T M , Wu , B H , Zhu , Y H , Fan , S S and Chen , G J . 2004 . A review on the gas hydrate research in China . J Petro Sci Eng , 41 : 11 – 20 .
  • He , J , Xia , B , Sun , D , Zhang , S and Liu , B . 2006 . Hydrocarbon accumulation, migration and play targets in the Qiongdongnan Basin, South China Sea (in Chinese) . Petrol Expl Devel , 33 : 53 – 58 .
  • Hinrichs , K U , Hayes , J M , Sylva , S P , Brewer , P G and Delong , E F . 1999 . Methane-consuming archaebacteria in marine sediments . Nature , 398 : 802 – 805 .
  • Hugenholtz , P , Goebel , B M and Pace , N R . 1998 . Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity . J Bacteriol , 180 : 4765 – 4774 .
  • Humayoun , S B , Bano , N and Hollibaugh , J T . 2003 . Depth distribution of microbial diversity in Mona Lake, A mermictic soda lake in California . Appl Environ Microbiol , 69 : 1030 – 1042 .
  • 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 Jorgensen , B B . 2006 . Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin . PNAS , 103 : 2815 – 2820 .
  • 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 .
  • Jiang , H , Dong , H , Zhang , G , Yu , B , Chapman , L R and Fields , M W . 2006 . Microbial diversity in water and sediment of Lake Chaka: an athalassohaline lake in northwestern China . Appl Environ Microbiol , 72 : 3832 – 3845 .
  • Jiang , S , Yang , T , Xue , Z , Yand , J , Ling , H , Wu , N , Huang , Y , Liu , J and Chen , D . 2005 . Chlorine and sulfate concentrations in pore waters from marine sediments in the north margin of the South China Sea and their implications for gas hydrate exploration (in Chinese) . Geoscience , 19 : 45 – 54 .
  • Joye , S B , Boetius , A , Orcutt , B , 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 .
  • Kaye , J Z , Marquez , M C , Ventosa , A and Baross , J A . 2004 . Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments . Int J Syst Evol Microbiol , 54 : 499 – 511 .
  • Kim , B S , Oh , H M , Kang , H and Chun , J . 2005 . Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis . J Microbiol , 43 : 144 – 151 .
  • Knittel , K , Losekann , T , Boetius , A , Kort , R and Amann , R . 2005 . Diversity and distribution of methanotrophic Archaea at cold seeps . Appl Environ Microbiol , 71 : 467 – 479 .
  • Kormas , K , 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 .
  • Kvenvolden , K A . 1988 . Methane hydrales and global climate . Global Biogeochemical Cycles , 2 : 221 – 229 .
  • Kwon , K K , Lee , H S , Yang , S H and Kim , S J . 2005 . Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the ‘Alphaproteobacteria’ . Int J Syst Evol Microbiol , 55 : 2033 – 2037 .
  • Lanoil , B D , Sassen , R , La Duc , M T , Sweet , S T and Nealson , K H . 2001 . Bacteria and archaea physically associated with Gulf of Mexico gas hydrates . Appl Environ Microbiol , 67 : 5143 – 5153 .
  • Liu , J and Wang , C . 2004 . Oil-gas geological implication of geothermal fluids in Yingge Sea Basin-Qingdongnan Basin (in Chinese) . Natl Gas Expl Devel , 27 : 7 – 15 .
  • 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 .
  • McDonnell , S L and Czarnecki , M . 2000 . “ A note on gas hydrate in the northern sector of the South China Sea ” . In Natural gas hydrate: in oceanic and permafrost environments , Edited by: Max , M D . 239 – 244 . Dordrecht, Boston : Kluwer Academic Publishers .
  • Milkov , A V . 2004 . Global estimates of hydrate-bound gas in marine sediments: how much is really out there? . Earth-Science Reviews , 66 : 183 – 197 .
  • Mills , H J , Hodges , C , Wilson , K , MacDonald , I R and Sobecky , P A . 2003 . Microbial diversity in sediments associated with suface-breaching gas hydrate mounds in the Gulf of Mexico . FEMS Microbiol Ecol , 46 : 39 – 52 .
  • Mills , H J , Martinez , R J , Story , S and Sobecky , P A . 2005 . Characterization of microbial community structure in Gulf of Mexico gas hydrates: comparative analysis of DNA- and RNA-derived clone libraries . Appl Environ Microbiol , 71 : 3235 – 3247 .
  • Miyazaki , M , Nogi , Y , Usami , R and Horikoshi , K . 2006 . Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan . Int J Syst Evol Microbiol , 56 : 1607 – 1613 .
  • Mullins , T D , Theresa , B B , Robin , L K and Stephen , J G . 1995 . Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities . Limnol Oceanogr , 40 : 148 – 158 .
  • 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 .
  • Niewohner , C , Hensen , C , Kasten , S , Zabel , M and Schulz , H D . 1998 . Deep sulfate reduction completely mediated by anaerobic methane oxidation in sediments of the upwelling area off Namibia . Geochim Cosmochim Acta , 62 : 455 – 464 .
  • Nunoura , T , Oida , H , Toki , T , Ashi , J , Takai , K and Horikoshi , K . 2006 . Quantification of mcrA by quantitative fluorescent PCR in sediments from methane seep of the Nankai Trough . FEMS Microbiol Ecol , 57 : 149 – 157 .
  • Orcutt , B , Boetius , A , Elvert , M , Samarkin , V and Joye , S B . 2005 . Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps . Geochim Cosmochim Acta , 69 : 4267 – 4281 .
  • Orphan , V J , House , C H , Hinrichs , K U , McKeegan , K D and De Long , E F . 2001 . Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis . Science , 293 : 484 – 487 .
  • Parkes , R J , Cragg , B A and Wellsbury , P . 2000 . Recent studies on bacterial populations and processes in marine sediments: a review . Hydrogeol J , 8 : 11 – 28 .
  • Pimenov , N V , Rusanov , I I , Poglazova , M N , Mityushina , L L , Sorokin , D Y , Khmelenina , V N and Trotsenko , Y A . 1997 . Bacterial mats on coral-like structures at methane seeps in the Black Sea . Microbiology , 66 : 354 – 360 .
  • Pinhassi , J and Berman , T . 2003 . Differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the eastern Mediterranean Sea, and the Gulf of Eilat . Appl Environ Microbiol , 69 : 199 – 211 .
  • Purdy , K J , Nedwell , D B and Embley , T M . 2003 . Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting antarctic sediments . Appl Environ Microbiol , 69 : 3181 – 3191 .
  • Reed , D W , Fujita , Y , Delwiche , M E , Blackwelder , D B , Sheridan , P P , Uchida , T and Colwell , F S . 2002 . Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin . Appl Environ Microbiol , 68 : 3759 – 3770 .
  • Sassen , R , MacDonald , I R , Requejo , A G , Guinasso , N L , Kennicutt , M C , Sweet , S T and Brooks , J M . 1994 . Organic geochemistry of sediments from chemosynthetic communities, Gulf of Mexico slope . Geo-Mar Lett , 14 : 110 – 119 .
  • Schippers , A , Neretin , L N , Kallmeyer , J , Ferdelman , T G , Cragg , B A , Parkes , R J and Jorgensen , B B . 2005 . Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria . Nature , 433 : 861 – 864 .
  • 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 .
  • 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 .
  • Sorensen , K B and Teske , A . 2006 . Stratified communities of active archaea in deep marine subsurface sediments . Appl Environ Microbiol , 72 : 4596 – 4603 .
  • Stevens , H , Stubner , M , Simon , M and Brinkhoff , T . 2005 . Phylogeny of Proteobacteria Bacteroidetes from oxic habitats of a tidal flat ecosystem . FEMS Microbiol Ecol , 54 : 351 – 365 .
  • Strous , M and Jetten , M SM . 2004 . Anaerobic oxidation of methane and ammonium . Annu Rev Microbiol , 58 : 99 – 117 .
  • Su , X , Chen , F , Yu , X and Huang , Y . 2005 . A pilot study on Miocene through Holocene dediments from the continental slope of the South China Sea in correlation with possible distribution of gas hydrates (in Chinese) . Geoscience , 19 : 1 – 13 .
  • Takai , K and Horikoshi , K . 1999 . Genetic diversity of archaea in deep-sea hydrothermal vent environments . Genetics , 152 : 1285 – 1297 .
  • Takai , K , Moser , D P , DeFlaun , M , Onstott , T C and Fredrickson , J K . 2001 . Archaeal diversity in waters from deep south African Gold Mines . Appl Environ Microbiol , 67 : 5750 – 5760 .
  • Teske , A , Brinkhoff , T , Muyzer , G , Moser , D P , Rethmeier , J and Jannasch , H W . 2000 . Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents . Appl Environ Microbiol , 66 : 3125 – 3133 .
  • Thamdrup , B , Rossello-Mora , R and Amann , R . 2000 . Microbial manganese and sulfate reduction in Black Sea shelf sediments . Appl Environ Microbiol , 66 : 2888 – 2897 .
  • Treude , T , Boetius , A , Knittel , K , Wallmann , K and JB , B. 2003 . Anaerobic oxidation of methane above gas hydrates (Hydrate Ridge, OR) . Mar Ecol Prog Ser , 264 : 1 – 14 .
  • Treude , T , Niggemann , J , Kallmeyer , J , Wintersteller , P , Schubert , C J , Boetius , A and Jorgensen , B B . 2005 . Anaerobic oxidation of methane and sulfate reduction along the Chilean continental margin . Geochim Cosmochim Acta , 69 : 2767 – 2779 .
  • Valentine , D L and Reeburgh , W S . 2000 . New perspectives on anaerobic methane oxidation . Environ Microbiol , 2 : 477 – 484 .
  • 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 .
  • Wu , B , Zhang , G , Zhu , Y , Lu , Z and Chen , B . 2003 . Progress of gas hydrate investigation in China off shore (in Chinese) . Earth Sci Front , 10 : 177 – 189 .
  • Wu , S , Zhang , G , Huang , Y , Liang , J and Wong , H K . 2005 . Gas hydrate occurrence on the continental slope of the northern South China Sea . Mar Petro Geol , 22 : 403 – 412 .
  • Zeng , R , Zhao , J , Zhang , R and Lin , N . 2005 . Bacterial community in sediment from the western Pacific Warm Pool and its relationship to environment . Science in China (Series D) , 48 : 282 – 290 .
  • Zhu , W , Wang , Z and Lv , M . 2004 . Exploration potential of atectonic oil-gas pools in the northern shelf basin of the South China Sea . Petrol Sci , 1 : 22 – 30 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.