Sự phong phú, đa dạng và hoạt động của vi sinh vật khử sulfát trong trầm tích ô nhiễm kim loại nặng từ một vùng đất ngập mặn tại cửa sông Medway (Vương quốc Anh)

Springer Science and Business Media LLC - Tập 14 - Trang 363-381 - 2011
Laurent Quillet1, Ludovic Besaury1, Milka Popova1, Sandrine Paissé1, Julien Deloffre1, Baghdad Ouddane2
1Faculté des Sciences, Université de Rouen-CNRS 6143-M2C, Groupe de Microbiologie, Mont Saint Aignan Cedex, France
2Laboratoire “Géosystèmes”, Equipe Chimie Analytique et Marine, UMR CNRS 8157, bâtiment C8, Université des Sciences et Technologies de Lille 1, Villeneuve d’Ascq, France

Tóm tắt

Chúng tôi đã điều tra sự đa dạng và hoạt động của vi sinh vật khử sulfát (SRP) trong lõi trầm tích sâu 3,5 m lấy từ một khu vực ô nhiễm kim loại nặng ở cửa sông Medway, Vương quốc Anh. Sự phong phú của các SRP đã được định lượng bằng qPCR của gen β-subunit giảm sulfite phân giải (dsrB) và tính đến hiệu quả chiết xuất DNA. Kết quả cho thấy rằng SRP phong phú trong toàn bộ lõi với giá trị tối đa ở 50 cm đầu tiên của lõi trầm tích, chiếm 22,4% tổng cộng cộng đồng vi khuẩn và là 13,6% ở độ sâu 250 cm. Các thư viện gen cho dsrA (α-subunit giảm sulfite phân giải) đã được xây dựng từ trầm tích bề mặt ô nhiễm nặng (20 cm đầu tiên) và từ khu vực sâu hơn ít ô nhiễm hơn và thiếu sulfát (250 cm). Một số trình tự được nhân bản có sự tương đồng với dsrA được tìm thấy trong các thành viên của Syntrophobacteraceae, Desulfobacteraceae và Desulfovibrionaceae, cũng như một tỷ lệ lớn (60%) trình tự mới hình thành một nhánh dsrA sâu. Phân tích hệ Pháp sinh học của SRP hoạt động trao đổi chất đã được thực hiện thông qua PCR phiên mã ngược và phân tích đa hình cấu trúc sợi đơn (RT-PCR–SSCP) của các gen dsrA được chiết xuất từ RNA trầm tích. Phân tích trình tự so sánh các dải SSCP đã bị cắt cho thấy hoạt động phiên mã cao của dsrA thuộc về các loài Desulfovibrio trong trầm tích bề mặt. Những kết quả này có thể cho thấy rằng các thành viên của Desulfovibrionaceae hoạt động mạnh hơn các nhóm SRP khác trong trầm tích bề mặt ô nhiễm kim loại nặng.

Từ khóa

#sulfate-reducing prokaryotes #Medway Estuary #sediment #heavy metal contamination #microbial diversity

Tài liệu tham khảo

Agrawal A, Lal B (2009) Rapid detection and quantification of bisulfite reductase genes in oil field samples using real-time PCR. FEMS Micobiol Ecol 69:301–312 Alazard D, Dukan S, Urios A, Verhé F, Bouabida N, Morel F, Thomas P, Garcia JL, Ollivier B (2003) Desulfovibrio hydrothermalis sp. nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents. Int J Syst Evol Micr 53:173–178 Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 Amann R, Fuchs B (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6:339–348 Bagwell CE, Liu X, Wu L, Zhou J (2006) Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer. FEMS Microbiol Ecol 55:424–431 Bassam BJ, Caetano-Anollés G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83 Billon G, Ouddane B, Boughriet A (2001) Chemical speciation of sulfur compounds in surface sediments from three bays (Fresnaye, Seine and Authie) in northern France, and identification of some factors controlling their generation. Talanta 53:971–981 Boyle AW, Phelps CD, Young LY (1999) Isolation from estuarine sediments of a Desulfovibrio strain which can grow on lactate coupled to the reductive dehalogenation of 2, 4, 6-tribromophenol. Appl Environ Microbiol 65:1133–1140 Brown SD, Gilmour CC, Kucken AM, Wall JD, Elias DA, Podar M, Chertkov O, Held B, Bruce DC, Detter JC, Tapia R, Han CS, Lynne A, Goodwin LA, Cheng JF, Pitluck S, Woyke T, Mikhailova N, Ivanova NN, Han J, Lucas S, Lapidus AL, Land ML, Hauser LR, Palumbo AV (2011) Genome sequence of mercury-methylating Desulfovibrio desulfuricans ND132. J Bacteriol. doi:10.1128, in press Burgmann H, Pesaro M, Widmer F, Zeyer J (2001) A strategy for optimizing quality and quantity of DNA extracted from soil. J Microbiol Methods 45:7–20 Cabrera G, Perez R, Gomez JM, Abalos A, Cantero D (2006) Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains. J Hazard Mater 135:40–46 Castro H, Reddy KR, Ogram A (2002) Composition and function of sulfate-reducing Prokaryotes in eutrophic and pristine areas of the Florida everglades. Appl Environ Microbiol 68:6129–6137 Chin KJ, Sharma ML, Russell LA, O' Neill KR, Lovley DR (2008) Quantifying expression of a dissimilatory (bi) sulfite reductase gene in petroleum-contaminated marine harbour sediments. Microbiol Ecol 55:489–499 Cundy AB, Hopkinson L, Lafite R, Spencer K, Taylor JA, Ouddane B, Heppell CM, Carey PJ, Charman R, Shell D (2005) Heavy metal distribution and accumulation in two Spartina sp.-dominated macrotidal salt marshes from the Seine estuary (France) and the Medway estuary (UK). Appl Geochem 20:1195–1208 Cundy AB, Lafite R, Taylor JA, Hopkinson L, Deloffre J, Charman R, Gilpin M, Spencer KL, Carey PJ, Heppell CM (2007) Sediment transfer and accumulation in two contrasting salt marsh/mudflat systems: the Seine estuary (France) and the Medway estuary (UK). Hydrobiologia 588:125–134 Cypionka H (2000) Oxygen respiration by Desulfovibrio species. Annu Rev Microbiol 54:827–848 Daims H, Lücker S, Wagner M (2005) Daime, a novel image analysis program for microbial ecology and biofilm research. Environ Microbiol 8:200–213 Dar SA, Yao L, van Dongen U, Kuenen JG, Muyzer G (2007) Analysis of diversity and activity of sulfate-reducing bacterial communities in sulfidogenic bioreactors using 16S rRNA and dsrB genes as molecular markers. Appl Environ Microbiol 73:594–604 De Lipthay JR, Enzinger C, Johnsen K, Aamand J, Sorensen SJ (2004) Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis. Soil Biol Biochem 36:1607–1614 Deloffre J, Verney R, Lafite R, Lesueur P, Lesourd S, Cundy AB (2007) Sedimentation on intertidal mudflats in the lower part of macrotidal estuaries: sedimentation rhythms and their preservation. Mar Geol 241:19–32 Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML (2003) Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 69:2765–2772 Duran R, Ranchou-Peyruse M, Menuet V, Monperrus M, Bareille G, Goni MS, Salvado JC, Amouroux D, Guyoneaud R, Donard OFX, Caumette P (2008) Mercury methylation by a microbial community from sediments of the Adour Estuary (Bay of Biscay, France). Environ Pollut 156:951–958 Edmonds JW, Weston NB, Joye SB, Moran MA (2008) Variation in prokaryotic community composition as a function of resource availability in tidal creek sediments. Appl Environ Microbiol 74:1836–1844 Ellis RJ, Morgan P, Weightman AD, Fry JC (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69:3223–3230 ETWB (2002) Environment, transport and work bureau technical circular. Management of dredged/excavated sediment No. 34. Government Printer, Hong Kong Foti M, Sorokin DY, Lomans B, Mussman M, Zacharova EE, Pimenov NV, Kuenen JG, Muyzer G (2007) Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Appl Environ Microbiol 73:2093–2100 Fournier M, Aubert C, Dermoun Z, Durand MC, Moinier D, Dolla A (2006) Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: proteome and transcript analysis. Biochimie 88:85–94 Geets J, Borremans B, Diels L, Springael D, Vangronsveld J, Van Der Lelie D, Vanbroekhoven K (2006) DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria. J Microbiol Methods 66:194–205 Gihring TM, Zhang G, Brandt CC, Brooks SC, Campbell JH, Carroll S, Criddle CS, Green SJ, Jardine P, Kostka JE, Lowe K, Mehlhorn TL, Overholt W, Watson DB, Yang Z, Wu WM, Schadt CW (2011) A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer. AEM Accepts, published online ahead of print on 15 July 2011 Gillan DC, Danis B, Pernet P, Joly G, Dubois P (2005) Structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment. Appl Env Microbiol 71:679–690 Gittel A, Mußmann M, Sass H, Cypionka H, Knneke M (2008) Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis. Environ Microbiol 10:2645–2658 Glavac D, Dean M (1993) Optimization of the single-strand conformation polymorphism (SSCP) technique for detection of point mutations. Hum Mutat 2:404–414 Gotelli NJ, Entsminger GL (2006) EcoSim: null models software for ecology. Version 7.0. Acquired Intelligence Inc., Kesey-Bear. http://www.garyentsminger.com/ecosim/ecosim.htm Hadas O, Pinkas R, Malinszy-Rushansky N, Markel D, Lazar B (2001) Sulfate reduction in Lake Agmon, Israel. Sci Total Environ 266:203–209 Haouari O, Fardeau ML, Casalot L, Tholozan JL, Hamdi M, Ollivier B (2006) Isolation of sulfate-reducing bacteria from Tunisian marine sediments and description of Desulfovibrio bizertensis sp. nov. Int J Syst Evol Micr 56:2909–2913 Harrison BK, Zhang H, Berelson W, Orphan VJ (2009) Variations in archaeal and bacterial diversity associated with the sulfate–methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl Environ Microbiol 75:1487–1499 He J, Xu Z, Hughes J (2005) Pre-lysis washing improves DNA extraction from a forest soil. Soil Biol Biochem 37:2337–2341 Herrmann S, Kleinsteuber S, Neu TR, Richnow HH, Vogt C (2008) Enrichment of anaerobic benzene-degrading microorganisms by in situ microcosms. FEMS Microbiol Ecol 63:94–106 Jiang W, Fan W (2008) Bioremediation of heavy metal-contaminated soils by sulfate-reducing bacteria. Ann NY Acad Sci 1140:446–454 Jiang L, Zheng Y, Peng X, Zhou H, Zhang C, Xiao X, Wang F (2009) Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China. FEMS Microbiol Ecol 70:249–262 Jin S, Fallgren PH, Bilgin AA, Morris JM, Barnes PW (2007) Bioremediation of benzene, ethylbenzene, and xylenes in groundwater under iron-amended, sulfate-reducing conditions. Environ Toxicol Chem 26:249–253 Jørgensen BB (1982) Mineralization of organic matter in the sea bed—the role of sulfate reduction. Nature 296:443–645 Jørgensen, B B, Nelson, D C (2004) Sulfide oxidation in marine sediments: geochemistry meets microbiology. In “Sulfur biogeochemistry—past and present” Publisher Geological Society of America 63–81 Joulian C, Ramsing NB, Ingvorsen K (2001) Congruent phylogenies of most common small-subunit rRNA and dissimilatory sulfite reductase gene sequences retrieved from estuarine sediments. Appl Environ Microbiol 67:3314–3318 Kaneko R, Hayashi T, Tanahashi M, Naganuma T (2007) Phylogenetic diversity and distribution of dissimilatory sulfite reductase genes from deep-sea sediment cores. Mar Biotech 9:429–436 Kawahara N, Shigematsu K, Miura S, Miyadai T, Kondo R (2008) Distribution of sulfate-reducing bacteria in fish farm sediments on the coast of southern Fukui Prefecture, Japan. Plankton Benth Res 3:42–45 Kjeldsen KU, Tang L, Jorrgensen MG, Ingvorsen K (2009) Enumeration and identification of dominant types of sulfate-reducing bacteria in pulp from a paper recycling plant: a multiphasic approach. FEMS Microbiol Ecol 69:481–494 Klappenbach JL, Saxman PH, Cole JR, Schmidt TM (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29:181–184 Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA, Wagner M (2001) Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J Bacteriol 183:6028–6035 Kondo R, Nedwell D, Purdy K, Silva S (2004) Detection and enumeration of sulfate-reducing bacteria in estuarine sediments by competitive PCR. Geomicrobiol J 21:145–157 Kondo R, Purdy KJ, Silva SQ, Nedwell DB (2007) Spatial dynamics of sulfate-reducing bacterial compositions in sediment along a salinity gradient in a UK estuary. Microbes Environ 22:11–19 Kowalchuk GA, Stephen JR, De Boer W, Prosser JI, Embley TM, Woldendorp JW (1997) Analysis of ammoniaoxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol 63:1489–1497 Kristensen E, Bodenbender J, Jensen MH, Rennenberg H, Jensen KM (2000) Sulfur cycling of intertidal Wadden Sea sediments (Konigshafen, Island of Sylt, Germany): sulfate reduction and sulfur gas emission. J Sea Res 43:93–104 Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 Labrenz M, Druschel GK, Thomsen-Ebert T, Gilbert B, Welch SA, Kemner KM, Logan GA, Summons RE, Stasio GD, Bond PL (2000) Formation of sphalerite (ZnS) deposits in natural biofilms of sulfate-reducing bacteria. Science 290:1744–1747 Lehours AC, Bardot C, Thenot A, Debroas D, Fonty G (2005) Anaerobic microbial communities in lake Pavin: a unique meromictic lake in France. Appl Environ Microbiol 71:7389–7400 Leloup J, Quillet L, Oger C, Boust D, Petit F (2004) Molecular quantification of sulfate-reducing procaryotes (carrying dsrAB genes) by competitive PCR in estuarine sediments. FEMS Microbiol Ecol 47:207–214 Leloup J, Petit F, Boust D, Deloffre J, Bally G, Clarisse O, Quillet L (2005) Dynamics of sulfate-reducing procaryotes (dsrAB genes) in two contrasting mudflats of the Seine estuary (France). Microbiol Ecol 50:307–314 Leloup J, Quillet L, Berthe T, Petit F (2006) Diversity of the dsrAB (dissimilatory sulfite reductase) gene sequences retrieved from two contrasting mudflats of the Seine estuary, France. FEMS Microbiol Ecol 55:230–238 Leloup J, Loy A, Knab NJ, Borowski C, Wagner M, Jørgensen BB (2007) Diversity and abundance of sulfate-reducing procaryotes in the sulfate and methane zones of a marine sediment, Black Sea. Environ Microbiol 9:131–142 Leloup J, Fossing H, Kohls K, Holmkvist L, Borowski C, Jørgensen BB (2009) Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation. Environ Microbiol 11:1278–1291 Liu XZ, Zhang LM, Prosser JI, He JZ (2009) Abundance and community structure of sulfate reducing prokaryotes in a paddy soil of southern China under different fertilization regimes. Soil Biol Biochem 41:687–694 Llobet-Brossa E, Rosselo-Mora R, Amann R (1998) Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microbiol 64:2691–2696 Lloyd JR, Mabbett AN, Williams DR, Macaskie LE (2001) Metal reduction by sulphate-reducing bacteria: physiological diversity and metal specificity. Hydrometall 59:327–337 Lloyd KG, MacGregor BJ, Teske A (2010a) Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition. FEMS Microbiol Ecol 72:143–151 Lloyd KG, Albert DB, Biddle JF, Chanton JP, Pizarro O, Andreas Teske (2010b) Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One 5:e8738 Lofi J, Weber O (2001) SCOPIX-digital processing of x-ray images for the enhancement of sedimentary structures in undisturbed core slabs. Geol-Mar Lett 20:182–186 Lücker S, Steger D, Kjeldsen KU, MacGregor BJ, Wagner M, Loy A (2007) Improved 16S rRNA-targeted probe set for analysis of sulfate-reducing bacteria by fluorescence in situ hybridization. J Microbiol Methods 69:523–528 Luna GM, Manini E, Danovaro R (2002) Large fraction of dead and inactive bacteria in coastal marine sediments: comparison of protocols for determination and ecological significance. Appl Environ Microbiol 68:3509–3513 Luna GM, Dell'Anno A, Danovaro R (2006) DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ Microbiol 8:308–320 Luo Q, Groh JL, Ballard JD, Krumholz LR (2007) Identification of genes that confer sediment fitness to Desulfovibrio desulfuricans G20. Appl Environ Microbiol 73:6305–6312 Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64:795–799 Mc Inerney MJ, Struchtemeyer CG, Sieber J, Mouttaki H, Stams AJM, Schink B, Rohlin L, Gunsalus RP (2008) Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann NY Acad Sci 1125:58–72 Migeon S, Weber O, Faugeres JC, Saint-Paul J (1999) SCOPIX: a new x-ray imaging system for core analysis. Geol Mar Lett 18:251–255 Miskin IP, Farrimond P, Head IM (1999) Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using rapid RNA extraction procedure and RT-PCR. Microbiology 145:1977–1987 Miyatake T, MacGregor BJ, Boschker HTS (2009) Linking microbial community function to phylogeny of sulfate-reducing Deltaproteobacteria in marine sediments by combining stable isotope probing with magnetic-bead capture hybridization of 16S rRNA. Appl Environ Microbiol 75:4927–4935 Moreau JW, Zierenberg RA, Banfield JF (2010) Diversity of dissimilatory sulfite reductase genes (dsrAB) in a salt marsh impacted by long-term acid mine drainage. Appl Environ Microbiol 76:4819–4828 Mumy KL, Findlay RH (2004) Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative–competitive PCR. J Microbiol Methods 57:259–268 Mußmann M, Ishii K, Rabus R, Amann R (2005) Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mudflat of the Wadden Sea. Environ Microbiol 7:405–418 Muyzer G, De Wall EC, Uitierlinden AG (1993) Gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700 Naz N, Young HK, Ahmed N, Gadd GM (2005) Cadmium accumulation and DNA homology with metal resistance genes in sulfate-reducing bacteria. Appl Environ Microb 71:4610–4618 Oger C, Berthe T, Quillet L, Barray S, Chiffoleau JF, Petit F (2001) Estimation of the abundance of the cadmium resistance gene cadA in microbial communities in polluted estuary water. Res Microbiol 152:671–678 Orphan VJ, Turk KA, Green AM, House CH (2009) Patterns of 15 N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS. Environ Microbiol 11:1777–1791 Ouddane B, Mikac N, Cundy AB, Quillet L, Fischer JC (2008) A comparative study of mercury distribution and methylation in mudflats from two macrotidal estuaries: the Seine (France) and the Medway (United Kingdom). Appl Geochem 23:618–631 Pavissich JP, Silva M, Gonzalez B (2010) Sulfate reduction, molecular diversity, and copper amendment effects in bacterial communities enriched from sediments exposed to copper mining residues. Environ Toxicol Chem 29:256–264 Perez-Jimenez JR, Kerkhof LJ (2005) Phylogeography of sulfate reducing bacteria among disturbed sediments, disclosed by analysis of the dissimilatory sulfite reductase genes (dsrAB). Appl Environ Microbiol 71:1004–1011 Perez-Jimenez JR, Young LY, Kerkhof LJ (2001) Molecular characterization of sulfate-reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsrAB) genes. FEMS Microbiol Ecol 35:145–150 Pernthaler A, Dekas AE, Brown CT, Goffredi SK, Embaye T, Orphan VJ (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA 105:7052–7057 Plugge CM, Scholten JCM, Culley DE, Nie L, Brockman FJ, Zhang W (2010) Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism. Microbiology 156:2746–2756 Rabus R, Hansen TA, Widdel F (2006) Dissimilatory sulfate- and sulfur-reducing prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, 3rd edition: an evolving electronic resource for the microbiological community, vol 2. Springer, New York, pp 659–768 Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394 Robador A, Brachert V, Jorgensen BB (2009) The impact of temperature change on the activity and community composition of sulfate-reducing bacteria in arctic versus temperate marine sediments. Environ Microbiol 11:1692–1703 Roose-Amsaleg CL, Garnier-Sillam E, Harry M (2001) Extraction and purification of microbial DNA from soil and sediment samples. Appl Soil Ecol 18:47–60 Rose P, Harkin JM, Hickey WJ (2003) Competitive touchdown PCR for estimation of Escherichia coli DNA recovery in soil DNA extraction. J Microbiol Methods 52:29–38 Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J (2008) Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Appl Environ Microbiol 74:2902–2907 Sahm K, Knoblauch C, Amann R (1999) Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine arctic sediments. Appl Environ Microbiol 65:3976 Saitou N, Nei M (1987) The neighbor-joining method—a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425 Sass H, Berchtold M, Branke J, König H, Cypionka H, Babenzien HD (1998) Psychrotolerant sulfate-reducing bacteria from an oxic freshwater sediment, description of Desulfovibrio cuneatus sp. nov. and Desulfovibrio litoralis sp. nov. Syst Appl Microbiol 21:212–219 Schippers A, Neretin LN (2006) Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR. Environ Microbiol 8:1251–1260 Scholten JC, Culley DE, Brockman FJ, Gang Wu G, Zhang W (2007) Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer. Biochem Biophys Res Com 352:48–54 Shao D, Liang P, Kang Y, Wanga H, Cheng Z, Wua S, Shi J, Chun Lap Lo S, Wangd W, Wong MH (2011) Mercury species of sediment and fish in freshwater fish ponds around the Pearl River Delta, PR China: human health risk assessment. Chemosphere. doi:10.1016, in press Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16SrRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67:4373–4376 Stevens H, Brinkhoff T, Rink B, Vollmers J, Simon M (2007) Diversity and abundance of Gram positive bacteria in a tidal flat ecosystem. Environ Microbiol 9:1810–1822 Suzuki D, Ueki A, Amaishi A, Ueki K (2007) Desulfobulbus japonicus sp. nov., a novel Gram-negative propionate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan. Int J Syst Evol Micr 57:849–855 Tebo BM, Obraztsova AY (1998) Sulfate-reducing bacterium grows with Cr (VI), U (VI), Mn (IV), and Fe (III) as electron acceptors. FEMS Microbiol Lett 162:193–198 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 Thomsen TR, Finster K, Ramsing NB (2001) Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Appl Environ Microbiol 67:1646–1656 Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070–1074 Tujula NA, Holmström C, Mußmann M, Amann R, Kjelleberg S, Crocetti GR (2006) A CARD–FISH protocol for the identification and enumeration of epiphytic bacteria on marine algae. J Microbiol Methods 65:604–607 Utgikar VP, Harmon SM, Chaudhary N, Tabak HH, Govind R, Haines JR (2002) Inhibition of sulfate-reducing bacteria by metal sulfide formation in bioremediation of acid mine drainage. Environ Toxicol 17:40–48 Utgikar VP, Tabak HH, Haines JR, Govind R (2003) Quantification of toxic and inhibitory impact of copper and zinc on mixed cultures of sulfate-reducing bacteria. Biotechnol Bioeng 82:306–312 Valls M, de Lorenzo V (2002) Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution. FEMS Microbiol Rev 26:327–338 Vandieken V, Knoblauch C, Jorgensen BB (2006) Desulfovibrio frigidus sp. nov. and Desulfovibrio ferrireducens sp. nov., psychrotolerant bacteria isolated from Arctic fjord sediments (Svalbard) with the ability to reduce Fe (III). Int J Syst Evol Micr 56:681–685 Villanueva L, Haveman SA, Summers ZM, Lovley DR (2008) Quantification of Desulfovibrio vulgaris dissimilatory sulfite reductase gene expression during electron donor- and electron acceptor-limited growth. Appl Environ Microbiol 74:5850–5853 Voordouw G, Walker JE, Brenner S (1985) Cloning of the gene encoding the hydrogenase from Desulfovibrio vulgaris (Hildenborough) and determination of the NH2-terminal sequence. Eur J Biochem 148:509–514 Wagner M, Roger AJ, Flax JL, Brusseau GA, Stahl DA (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180:2975–2982 Wawer C, Jetten MSM, Muyzer G (1997) Genetic diversity and expression of the [NiFe] Hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples. Appl Environ Microbiol 63:4360–4369 Webb JS, McGinness S, Lappin-Scott HM (1998) Metal removal by sulfate-reducing bacteria from natural and constructed wetlands. J Appl Microbiol 84:240–248 Webster G, Watt LC, Rinna J, Fry JC, Evershed RP, Parkes RJ, Weightman AJ (2006) A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. Environ Microbiol 9:1575–1589 Wilms R, Sass H, Köpke B, Cypionka H, Engelen B (2007) Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea. FEMS Microbiol Ecol 59:611–621 Woebken D, Fuchs BM, Kuypers MM, Amann R (2007) Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl Environ Microbiol 73:4648–4657 Zhang W, Ki JS, Qian PY (2008) Microbial diversity in polluted harbor sediments I: bacterial community assessment based on four clone libraries of 16S rDNA. Estuarine Coastal Shelf Sci 76:668–681 Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microb 62:316–322