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Bacterial diversity in sediments of the eutrophic Guanting Reservoir, China, estimated by analyses of 16S rDNA sequence

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Abstract

The bacterial diversity in different layers of sediment of the eutrophic Guanting Reservoir (China) was investigated using molecular ecological techniques. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA showed presence of different bacterial communities across depths of sediments. The trend was consistent with sedimentological layers as characterized by physical and chemical parameters. Sediments were sampled at the 4–6, 34–36, and 69–72 cm depths to represent upper, middle and lower layers and used to construct three 16S rDNA clone libraries. Out of a total of 760 positive clones obtained from the three sediment layers, 148 rDNA types were identified by amplified 16S rDNA restriction analysis (ARDRA) and grouped into 42 clusters or single lineages at the similarity of 70%. We used 16S rDNA sequencing to classify 60 clones representing different ARDRA clusters into nine phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia. The diversity and distribution of rDNA types across depths were much different from the chemical profile of the sediment and pollution history of the reservoir.

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References

  • Altschul SF, Madden T, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    PubMed  CAS  Google Scholar 

  • Bissett A, Bowman J, Burke C (2006) Bacterial diversity in organically-enriched fish farm sediments. FEMS Microbiol Ecol 55:48–56

    Article  PubMed  CAS  Google Scholar 

  • Bowman JP, McCuaig RD (2003) Biodiversity, community structural shift, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69:2463–2483

    Article  PubMed  CAS  Google Scholar 

  • Fracchia L, Dohrmann AB, Martinotti MG, Tebbe CC (2006) Bacterial diversity in a finished compost and vermicompost: Differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes. Appl Microbiol Biot 5:1–11

    Google Scholar 

  • Frankowski L, Bolałek J, Szostek A (2002) Phosphorus in bottom sediments of Pomeranian Bay (Southern Baltic-Poland). Estuar Coast Shelf S 54:1027–1038

    Article  CAS  Google Scholar 

  • Gächter R, Meyer JS (1993) The role of microorganisms in mobilization and fixation of phosphorus in sediments. Hydrobiologia 253:103–121

    Article  Google Scholar 

  • Gernert C, Glockner FO, Krohne G, Hentschel U (2005) Microbial diversity of the freshwater sponge Spongilla lacustris. Microb Ecol 50:206–212

    Article  PubMed  CAS  Google Scholar 

  • Good IL (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237–264

    Google Scholar 

  • Hannen EJ, Zwart G, Agterveld MP, Gons HJ, Ebert J, Laanbroek HJ (1999) Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with virus. Appl Environ Microbiol 65:785–801

    Google Scholar 

  • Hastings RC, Saunders JR, Hall GH, Pickup RW, McCarthy AJ (1998) Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake. Appl Environ Microbiol 64:3674–3682

    PubMed  CAS  Google Scholar 

  • Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl Environ Microbiol 67:411–419

    Article  PubMed  CAS  Google Scholar 

  • Inagaki F, Nunoura T, Nakagawa S et al (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. PNAS 103:2815–2820

    Article  PubMed  CAS  Google Scholar 

  • Koizumi Y, Kojima H, Fukui M (2003) Characterization of depth-related microbial community structure in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rDNA and reversely transcribed 16S rRNA fragments. FEMS Microbiol Ecol 46:147–157

    Article  CAS  PubMed  Google Scholar 

  • Li C, Yuan HL, Huang HZ (2005) Vertical distribution of phosphorus and P-dissolving/decomposing bacteria in the sediment of Guanting Reservoir. Sci China Ser D Earth Sci 48(Supp II):285–294

    CAS  Google Scholar 

  • Liang T, Wang H, Ding SM, Xue JF, Cai CX, Zhang XM (2003) An evolution of water quality in Guanting Reservoir during the past three decades. Prog Geogr 22:38–44 (In Chinese)

    Google Scholar 

  • Liu J, Wang ET, Chen WX (2005) Diverse rhizobia associated with woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the temperate zone of China. Syst Appl Microbiol 28:465–477

    Article  PubMed  CAS  Google Scholar 

  • Liu Y, Yao T, Jiao N, Kang S, Zeng Y, Huang S (2006) Microbial community structure in moraine lakes and glacial meltwaters, Mount Everest. FEMS Microbiol Lett 265:98–105

    Article  PubMed  CAS  Google Scholar 

  • Ma DJ, Zhang FE, Gao YX, Chen H, Zhang YM (2002) The water quality rich nutrimental evaluation of Guanting Reservoir. Environ Monit China 18:41–44 (In Chinese)

    Article  Google Scholar 

  • Mills HJ, Hodges C, Wilson K, MacDonald IR, Sobecky PA (2003) Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS Microbiol Ecol 46:39–52

    Article  CAS  PubMed  Google Scholar 

  • Molles MC (2000) Ecology: concepts and applications. McGraw-Hill companies, Inc., Berlin

    Google Scholar 

  • Muyzer G, Waal ECD, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    PubMed  CAS  Google Scholar 

  • Page RDM (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358

    PubMed  CAS  Google Scholar 

  • Pielou EC (1966) The measurement of diversity in different types of biological collections. J Theor Biol 13:131–144

    Article  Google Scholar 

  • Qu JH, Yuan HL, Huang HZ, Wang ET (2005) Depth-related distribution of bacterial community in sediments of eutrophic Guanting reservoir. Sci China Ser D Earth Sci 48(Supp II):276–284

    CAS  Google Scholar 

  • Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65:3982–3989

    PubMed  CAS  Google Scholar 

  • Reed AJ, Lutz RA, Vetriani C (2006) Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida escarpment. Extremophiles 10:199–211

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning, a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York, pp 35

    Google Scholar 

  • Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain bacteria at the subphylum level. Int J Syst Evol Micr 53:1843–1851

    Article  CAS  Google Scholar 

  • Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practices of numerical classification. W. H. Freeman and Company, San Francisco

    Google Scholar 

  • Stevenson BS, Eichorst SA, Wertz JF, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748–4755

    Article  PubMed  CAS  Google Scholar 

  • Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M, Kamagata Y (2005) Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 71:2162–2169

    Article  PubMed  CAS  Google Scholar 

  • Tao QH, Tang HX (2004) Effect of dye compounds on the adsorption of atrazine by natural sediment. Chemosphere 56:31–38

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  • Thompson JR, Marcelino LA, Polz MF (2002) Heteroduplexes in mixed-template amplification: formation, consequence and elimination by ‘reconditioning PCR’. Nucleic Acids Res 30:2083–2088

    Article  PubMed  CAS  Google Scholar 

  • Vauterin L, Vauterin P (1992) Computer-aided objective comparison of electrophoresis patterns for grouping and identification of microorganisms. Eur Microbiol 1:37–41

    Google Scholar 

  • Wang RL (1997) Inspection and analysis of bacteria in the water of Guanting Reservoir. Beijing Water Conservancy 1:50–56 (In Chinese)

    Google Scholar 

  • Wang ET, van Berkum P, Sui XH, Beyene D, Chen WX, Martinez-Romero E (1999) Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. Int J Syst Bacteriol 49:51–65

    Article  PubMed  Google Scholar 

  • Wang SF, Zhao CY, Zhang PB, Zhang FJ (2003) Simultaneous determination of heavy metals and phosphorus of the sediments in Guanting Reservoir by ICP-AES. J Beijing Norm Univ (Nat Sci) 39:365–370 (In Chinese)

    CAS  Google Scholar 

  • Wilms R, Köpke B, Sass H, Chang TS, Cypionka H, Engelen B (2006) Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8:709–719

    Article  PubMed  CAS  Google Scholar 

  • Wobus A, Bleul C, Maassen S, Scheerer C, Schuppler M, Jacobs E, Rőske I (2003) Microbial diversity and functional characterization of sediments from reservoirs of different trophic state. FEMS Microbiol Ecol 46:331–347

    Article  CAS  PubMed  Google Scholar 

  • Zhang SZ, Wang SX, Shan XQ (2002) Distribution and speciation of heavy metals in surface sediments from Guanting Reservoir, Beijing. J Environ Sci Health A37:465–478

    Article  CAS  Google Scholar 

  • Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K (2003) Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating microorgnism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phy1. nov. Int J Syst Evol Micr 53:1153–1163

    Google Scholar 

  • Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322

    PubMed  CAS  Google Scholar 

Download references

Acknowledgement

This work was part of the project No. 30670071 supported by the National Natural Science Foundation of China. It was also supported by the Taihu Project (No. BK2007741) from Jiangsu Science and Technology Department.

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Authors and Affiliations

  1. College of Biological Sciences, Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture, China Agricultural University, Beijing, China

    Jian Hang Qu, Hong Li Yuan & Cui Li

  2. Department of Microbiology and Immunology, College of Biological Science, China Agricultural University, Beijing, 100094, P.R. China

    Hong Li Yuan

  3. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico, DF, Mexico

    En Tao Wang

  4. National Research Center of Geoanalysis, Beijing, China

    Huai Zeng Huang

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  1. Jian Hang Qu
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  2. Hong Li Yuan
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  3. En Tao Wang
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  4. Cui Li
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  5. Huai Zeng Huang
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Correspondence to Hong Li Yuan.

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Qu, J.H., Yuan, H.L., Wang, E.T. et al. Bacterial diversity in sediments of the eutrophic Guanting Reservoir, China, estimated by analyses of 16S rDNA sequence. Biodivers Conserv 17, 1667–1683 (2008). https://doi.org/10.1007/s10531-008-9373-9

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