Contrasting diversity pattern of Cytophaga–Flavobacteria in the estuarine and open ocean regions of the East China Sea

References

• Abell , GCJ and Bowman , JP . 2005a . Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean . FEMS Microbiology Ecology , 51 : 265 – 77 .
   PubMed Web of Science ®Google Scholar
• Abell , GCJ and Bowman , JP . 2005b . Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater . FEMS Microbiology Ecology , 53 : 379 – 91 .
   PubMed Web of Science ®Google Scholar
• Acinas , SG , Klepac-Ceraj , V , Hunt , DE , Pharino , C , Ceraj , I Distel , DL . 2004 . Fine-scale phylogenetic architecture of a complex bacterial community . Nature , 430 : 551 – 4 .
   PubMed Web of Science ®Google Scholar
• Alonso , C , Warnecke , F , Amann , R and Pernthaler , J . 2007 . High local and global diversity of Flavobacteria in marine plankton . Environmental Microbiology , 9 : 1253 – 66 .
   PubMed Web of Science ®Google Scholar
• Ashelford , KE , Chuzhanova , N , Fry , JC , Jones , AJ and Weightman , AJ . 2005 . At least one in twenty 16S rRNA sequence records currently held in public repositories estimated to contain substantial anomalies . Applied and Environmental Microbiology , 71 : 7724 – 36 .
   PubMed Web of Science ®Google Scholar
• Chang , P and Isobe , A . 2003 . A numerical study on the Changjiang diluted water in the Yellow and East China Seas . Journal of Geophysical Research , 108 ( C9 ) : 3299
   Google Scholar
• Chen , XH , Zeng , YH and Jiao , NZ. 2006 . Development and evaluation of a specific 16S rDNA primer pair for marine Cytophaga–Flavobacteria cluster . Molecular Ecology Notes , 6 : 1278 – 81 .
   Google Scholar
• Cole , JR , Chai , B , Farris , RJ , Wang , Q , Kulam , SA McGarrell , DM . 2005 . The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis . Nucleic Acids Research , 33 : D294 – 6 .
   PubMed Web of Science ®Google Scholar
• Cottrell , MT and Kirchman , DL . 2000a . Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization . Applied and Environmental Microbiology , 66 : 5116 – 22 .
   PubMed Web of Science ®Google Scholar
• Cottrell , MT and Kirchman , DL . 2000b . Natural assemblages of marine proteobacteria and members of the Cytophaga–Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter . Applied and Environmental Microbiology , 66 : 1692 – 7 .
   PubMed Web of Science ®Google Scholar
• Crump , BC , Armbrust , EV and Baross , JA. 1999 . Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean . Applied and Environmental Microbiology , 65 : 3192 – 204 .
   PubMed Web of Science ®Google Scholar
• Eilers , H , Pernthaler , J , Glockner , FO and Amann , R . 2000 . Culturability and in situ abundance of pelagic bacteria from the North Sea . Applied and Environmental Microbiology , 66 : 3044 – 51 .
   PubMed Web of Science ®Google Scholar
• Fuhrman , JA and Campbell , L . 1998 . Marine ecology: microbial microdiversity . Nature , 393 : 410 – 1 .
   Web of Science ®Google Scholar
• Fuhrman , JA , Comeau , DE , Hagstrom , A and Chan , AM . 1988 . Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies . Applied and Environmental Microbiology , 54 : 1426 – 9 .
   PubMed Web of Science ®Google Scholar
• Glockner , FO , Fuchs , BM and Amann , R . 1999 . Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization . Applied and Environmental Microbiology , 65 : 3721 – 6 .
   PubMed Web of Science ®Google Scholar
• Jiao , NZ , Yang , YH , Hong , N , Ma , Y , Koshikawa , H and Watanabe , M . 2005 . Dynamics of autotrophic picoplankton and heterotrophic bacteria in the East China Sea . Continental Shelf Research , 25 : 856 – 67 .
   Google Scholar
• Jiao , NZ , Yang , YH , Koshikawa , H and Watanabe , M. 2002 . Influence of hydrographic conditions on picoplankton distribution in the East China Sea, a marginal sea of the Northwest Pacific . Aquatic Microbial Ecology , 30 : 37 – 48 .
   Web of Science ®Google Scholar
• Jiao , NZ , Zhang , Y , Zeng , YH , Gardner , WD , Mishonov , AV Richardson , M . 2007 . Ecological anomalies in the East China Sea: impacts of the Three Gorges Dam? . Water Research , 41 : 1287 – 93 .
   PubMed Web of Science ®Google Scholar
• Kimura , M . 1980 . A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences . Journal of Molecular Evolution , 16 : 111 – 20 .
   PubMed Web of Science ®Google Scholar
• Kirchman , DL . 2002 . The ecology of Cytophaga–Flavobacteria in aquatic environments . FEMS Microbiology Ecology , 39 : 91 – 100 .
   PubMed Web of Science ®Google Scholar
• Kirchman , DL , Dittel , AI , Malmstrom , RR and Cottrell , MT . 2005 . Biogeography of major bacterial groups in the Delaware Estuary . Limnology and Oceanography , 50 : 1697 – 706 .
   Web of Science ®Google Scholar
• Kirchman , DL , Yu , LY and Cottrell , MT . 2003 . Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware Estuary . Applied and Environmental Microbiology , 69 : 6587 – 96 .
   PubMed Web of Science ®Google Scholar
• Koski , LB and Golding , GB . 2001 . The closest BLAST hit is often not the nearest neighbor . Journal of Molecular Evolution , 52 : 540 – 2 .
   PubMed Web of Science ®Google Scholar
• Kumar , S , Tamura , K and Nei , M. 2004 . MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment . Briefings in Bioinformatics , 5 : 150 – 63 .
   PubMed Web of Science ®Google Scholar
• McCann , KS . 2000 . The diversity–stability debate . Nature , 405 : 228 – 33 .
   PubMed Web of Science ®Google Scholar
• O'Sullivan , LA , Fuller , KE , Thomas , EM , Turley , CM , Fry , JC and Weightman , AJ . 2004 . Distribution and culturability of the uncultivated ‘AGG58 cluster’ of Bacteroidetes phylum in aquatic environments . FEMS Microbiology Ecology , 47 : 359 – 70 .
   PubMed Web of Science ®Google Scholar
• Ramette , A and Tiedje , JM . 2007 . Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology and evolution . Microbial Ecology , 53 : 197 – 207 .
   PubMed Web of Science ®Google Scholar
• Reichenbach , H and Dworkin , M . 1991 . “ The order Cytophagales ” . In The Prokaryotes , Edited by: Balows , A , Truper , HG , Dworkin , M , Harder , W and Schleifer , KH . 356 – 79 . New York : Springer .
   Google Scholar
• Thompson , JD , Gibson , TJ , Plewniak , F , Jeanmougin , F and Higgins , DG . 1997 . The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools . Nucleic Acids Research , 24 : 4876 – 82 .
   Web of Science ®Google Scholar
• Yachi , S and Loreau , M. 1999 . Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis . Proceedings of the National Academy of Sciences USA , 96 : 1463 – 8 .
   PubMed Web of Science ®Google Scholar
• Zeng , YH , Jiao , NZ , Cai , HY , Chen , XH and Wei , CL . 2004 . Phylogenetic diversity of ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit genes of bacterioplankton in the East China Sea . Acta Oceanologica Sinica , 23 : 673 – 85 .
   Web of Science ®Google Scholar
• Zhang L , Liu Z , Zhang J , Hong GH , Park Y , Zhang HF . 2007 . Reevaluation of mixing among multiple water masses in the shelf: an example from the East China Sea . Continental Shelf Research doi: 10.1016/j.csr.2007.04.002 .
   Google Scholar
• Zubkov , MV , Fuchs , BM , Archer , SD , Kiene , RP , Amann , R and Burkill , PH . 2002 . A population of the alpha-proteobacteria dominates the bacterioplankton and dimethylsulphoniopropionate uptake after an algal bloom in the North Sea. Deep-sea Research II . Topical Studies in Oceanography , 49 : 3017 – 38 .
   Google Scholar