Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis

ABSTRACT Bacterial community structure along the Changjiang River (which is more than 2,500 km long) was studied by using denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal bacterial primer sets. DGGE profiles and principal-component analysis (PCA) demonstrated that the bacterial community gradually changed from upstream to downstream in both 1998 and 1999. Bacterial diversity, as determined by the Shannon index (H′), gradually decreased from upstream to downstream. The PCA plots revealed that the differences in the bacterial communities among riverine stations were not appreciable compared with the differences in two adjacent lakes, Lake Dongting and Lake Poyang. The relative stability of the bacterial communities at the riverine stations was probably due to the buffering action of the large amount of water flowing down the river. Clone library analysis of 16S rDNA revealed that the dominant bacterial groups changed from β-proteobacteria and the Cytophaga-Flexibacter-Bacteroides group upstream to high-G+C-content gram-positive bacteria downstream and also that the bacterial community structure differed among the stations in the river and the lakes. The results obtained in this study should provide a reference for future changes caused by construction of the Three Gorges Dam.

[1]  Kazuya Watanabe,et al.  Molecular Detection, Isolation, and Physiological Characterization of Functionally Dominant Phenol-Degrading Bacteria in Activated Sludge , 1998, Applied and Environmental Microbiology.

[2]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[3]  J. Saunders,et al.  Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms , 1998, Microbial Ecology.

[4]  J. Baross,et al.  Dominance of particle-attached bacteria in the Columbia River estuary, USA , 1998 .

[5]  D. M. Ward,et al.  Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis , 1997, Applied and environmental microbiology.

[6]  J. Hobbie,et al.  Use of nuclepore filters for counting bacteria by fluorescence microscopy , 1977, Applied and environmental microbiology.

[7]  B. Forsberg,et al.  Bacterial carbon metabolism in the Amazon River system , 1995 .

[8]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[9]  D. M. Ward,et al.  Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms , 1994, Applied and environmental microbiology.

[10]  R.M.W. Amon,et al.  Seasonal Patterns of Bacterial Abundance and Production in the Mississippi River Plume and Their Importance for the Fate of Enhanced Primary Production , 1998, Microbial Ecology.

[11]  Farooq Azam,et al.  Microbial Control of Oceanic Carbon Flux: The Plot Thickens , 1998, Science.

[12]  H. Sekiguchi,et al.  A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis , 2001, Biotechnology Letters.

[13]  Gamila H. Ali,et al.  Microbiological and chemical study of the nile river water quality , 2000 .

[14]  K Kogure,et al.  A tentative direct microscopic method for counting living marine bacteria. , 1979, Canadian journal of microbiology.

[15]  S. Murakami,et al.  Bacterial Distribution and Phylogenetic Diversity in the Changjiang Estuary before the Construction of the Three Gorges Dam , 2002, Microbial Ecology.

[16]  L. Young,et al.  Unusual bacterioplankton community structure in ultra‐oligotrophic Crater Lake , 2001 .

[17]  D. M. Ward,et al.  16S rRNA sequences reveal numerous uncultured microorganisms in a natural community , 1990, Nature.

[18]  R. Wetzel.  12 – THE NITROGEN CYCLE , 2001 .

[19]  D. M. Ward,et al.  Denaturing Gradient Gel Electrophoresis Profiles of 16 S rRNA-Defined Populations Inhabiting a Hot Spring Microbial Mat Community , 1996 .

[20]  E. Stackebrandt,et al.  Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species , 1995, Applied and environmental microbiology.

[21]  John Dunbar,et al.  Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning , 1999, Applied and Environmental Microbiology.

[22]  K. Timmis,et al.  Thermal Gradient Gel Electrophoresis Analysis of Bioprotection from Pollutant Shocks in the Activated Sludge Microbial Community , 1999, Applied and Environmental Microbiology.

[23]  S. Giovannoni,et al.  Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR , 1996, Applied and environmental microbiology.

[24]  R. Amann,et al.  Predator-Specific Enrichment of Actinobacteria from a Cosmopolitan Freshwater Clade in Mixed Continuous Culture , 2001, Applied and Environmental Microbiology.

[25]  A. Ogino,et al.  Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses , 2001, Journal of applied microbiology.

[26]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[27]  J. Hejzlar,et al.  Changes in the Epilimnetic Bacterial Community Composition, Production, and Protist-Induced Mortality along the Longitudinal Axis of a Highly Eutrophic Reservoir , 2001, Microbial Ecology.

[28]  Rudolf Amann,et al.  Comparative 16S rRNA Analysis of Lake Bacterioplankton Reveals Globally Distributed Phylogenetic Clusters Including an Abundant Group of Actinobacteria , 2000, Applied and Environmental Microbiology.

[29]  Philip Hugenholtz,et al.  Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.

[30]  F. Azam,et al.  Dynamics of Bacterial Community Composition and Activity during a Mesocosm Diatom Bloom , 2000, Applied and Environmental Microbiology.

[31]  E. Virginia Armbrust,et al.  Phylogenetic Analysis of Particle-Attached and Free-Living Bacterial Communities in the Columbia River, Its Estuary, and the Adjacent Coastal Ocean , 1999, Applied and Environmental Microbiology.

[32]  A. Uitterlinden,et al.  Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.

[33]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[34]  H. Jannasch,et al.  Bacterial Populations in Sea Water as Determined by Different Methods of Enumeration1 , 1959 .

[35]  J. Antón,et al.  Diversity of Free-Living and Attached Bacteria in Offshore Western Mediterranean Waters as Depicted by Analysis of Genes Encoding 16S rRNA , 1999, Applied and Environmental Microbiology.

[36]  Christoph Humborg,et al.  Effect of Danube River dam on Black Sea biogeochemistry and ecosystem structure , 1997, Nature.

[37]  B. Methé,et al.  Contrasts between marine and freshwater bacterial community composition: Analyses of communities in Lake George and six other Adirondack lakes , 1998 .

[38]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[39]  Kitagawa,et al.  Monitoring impact of in situ biostimulation treatment on groundwater bacterial community by DGGE. , 2000, FEMS microbiology ecology.

[40]  Delwiche Cc.  The Nitrogen Cycle , 1970, Soil Microbiology.

[41]  B. Methé,et al.  Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences , 1997, Applied and environmental microbiology.