Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology

Akkermans DL, van Elsas JD & de Bruijn FJ (1995) Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands Amann RI, Stromley J, Devereux R, Key R & Stahl DA (1992) Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58: 614-623 Amann RI, Ludwig W & Schleifer KH (1995) Phylogenetic identification and in situdetection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169 Barns SM, Fundyga RE, Jeffries MW & Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91: 1609-1613 Borneman J, Skroch PW, O'Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J & Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62: 1935-1943 Brinkhoff T & Muyzer G (1997) Increased species diversity and extended habitat range of sulfur-oxidizing Thiomicrospiraspp. Appl. Environ. Microbiol. 63: 3789-3796 Brunk CF, Avaniss-Aghajani E & Brunk CA (1996) A computer analysis of primer and probe hybridization potential with small-subunit rRNA sequences. Appl. Environ. Microbiol. 62: 872-879 Buchholz-Cleven BEE, Rattunde B & Straub KL (1997) Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst. Appl. Microbiol. 20: 301-309 Cariello NF, Keohavong P, Sanderson BJS & Thilly WG (1988) DNA damage produced by ethidium bromide staining and exposure to ultraviolet light. Nucleic Acids Res. 16: 4157 Cairns MJ & Murray V (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. BioTechniques 17: 915-919 Donner G, Schwarz K, Hoppe HG & Muyzer G (1996) Profiling the succession of bacterial populations in pelagic chemoclines. Arch. Hydrobiol. Spec. Issues Advanc. Limnol. 48: 7-14 Farrelly V, Rainey FA & Stackebrandt E (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61: 2798-2801 Ferris MJ, Muyzer G & Ward DM (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62: 340-346 Ferris MJ, Nold SC, Revsbech NP & Ward NM (1997) Population structure and physiological changes within a hot spring microbial mat community following disturbance. Appl. Environ. Microbiol. 63: 1367-1374 Ferris MJ & Ward DM (1997) Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63: 1375-1381 Felske A, Engelen B, Nübel U & Backhaus H (1996) Direct ribosomal isolation from soil to extract bacterial rRNA for community analysis. Appl. Environ. Microbiol. 62: 4162-4167 Felske A, Wolterink A, van Lis R & Akkermans ADL (1998) Screening for dominant bacterial 16S rRNA sequences in soil. Antonie van Leeuwenhoek, in press Fisher CR (1990) Chemoautotrophic and methanotrophic symbiosis in marine invertebrates. Rev. Aquat. Sci. 2: 399-436 Fischer SG & Lerman LS (1979) Length-independent separation of DNA restriction fragments in two dimensional gel electrophoresis. Cell 16: 191-200 Fischer SG & Lerman LS (1983) DNA fragments differing by single basepair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Natl. Acad. Sci. USA 80: 1579-1583 Führ A (1996) Untersuchungen zu der Biodiversität natürlicher Bakterienpopulationen im Boden mit der denaturierenden Gradientengelelectrophorese (DGGE) von 16S rDNA-Sequenzen. PhD-thesis Universitat Kaiserslautern, Kaiserslautern, Germany Fuhrman JA, McCallum K & Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59: 1294-1302 Garcia-Pichel F, Prufert-Bebout L & Muyzer G (1996) Phenotypic and phylogenetic analyses show Microcoleus chthonoplastesto be a cosmopolitan cyanobacterium. Appl. Environ. Microbiol. 62: 3284-3291 Giovannoni SJ, Britschgi TB, Moyer CL, & Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 344: 60-63 Grey JP & Herwig RP (1996) Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62: 4049-4059 Heuer H, Hartung K, Engelen B & Smalla K (1995) Studies on microbial communities associated with potato plants by BIOLOG and TGGE patterns. Med. Fac. Landbouww. Univ. Gent 60/4b: 2639-2645 Heuer H & Smalla K. (1997) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities. In: van Elsas JD, Trevors JT & Wellington EMH (Eds) Modern Soil Microbiology. Marcel Dekker, New York. pp. 353-373 Heuer H, Krsek M, Baker P, Smalla K & Wellington EMH (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63: 3233- 3241 Höfle MG (1988) Identifcation of bacteria by low molecular weight RNA profiles: a new chemotaxonomic approach. J. Microbiol. Meth. 8: 235-248 Höfle MG (1990) Transfer RNAs as genotypic fingerprints of eubacteria. Arch. Microbiol. 153: 299-304 Holben WE, Calabrese VGM, Harris D, Ka JO & Tiedje JM (1993) Analysis of structure and selection in microbial communities by molecular methods. In: Guerrero R & Pedrós-Alió C (Eds) Trends in Microbial Ecology, pp. 367-370 Holben WE & Harris D (1995) DNA-based monitoring of total bacterial community structure in environmental samples. Molecular Ecology 4: 627-631 Hollibaugh JT (1994) Relationship between thymidine metabolism bacterioplankton community metabolic capabilities and sources of organic matter used for growth. Microb. Ecol. 28: 117-131 Jaspers E & Overmann J (1997) Separation of bacterial cells by isoelectric focusing, a new method for analysis of complex microbial communities. Appl. Environ. Microbiol. 63: 3176-3181 Jeffrey WH, Nazaret S & Barkay T (1996) Detection of the merAgene and its expression in the environment. Microb. Ecol. 32: 293-303 Jensen MA & Straus N (1993) Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions. PCR Methods Applic. 3: 186-194 Karkhoff-Schweizer RR, Huber DPW, & Voordouw G (1995) Conservation of the genes for the dissimilatory sulfite reductase from Desulfovibrio vulgarisand Archaeoglobus fulgidusallows their detection by PCR. Appl. Envrion. Microbiol. 61: 290-296 Keohavong P & Thilly WG (1989) Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acid. Sci. USA 86: 9253-9257 Komatsoulis GA & Waterman MS (1997) A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations. Appl. Environ. Microbiol. 63: 2338-2346 Kopczynski ED, Bateson Mm & Ward DM (1994) Recognition of chimeric small-subunit ribosomal DNAs composed from genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60: 746-748 Kowalchuk GA, Stephen JR, de Boer W, Prosser JI, Embley TM & Woldendorp JW (1997) Analysis of ammonia-oxidizing bacteria of the β-subdivision of the class Proteobacteriain coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63: 1489-1497 Lee D-H, Zo Y-G & Kim S-J (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-Single-Strand-Conformation Polymorphism. Appl. Environ. Microbiol. 62: 3112-3120 Lerman LS & Silverstein K (1987) Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymology 155: 482-501 Liesack W, Weyland H & Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed culture of strict barophilic bacteria. Microb. Ecol. 21: 191-198 Liesack W & Stackebrandt E (1992) Occurence of novel groups of the domain Bacteriaas revealed by analysis of genetic material isolated from an Austalian terrestrial environment. J. Bacteriol. 174: 5072-5078 Liesack W, Janssen PH, Rainey FA, Ward-Rainey NL & Stackebrandt E (1997) Microbial diversity in soil: The need for a combined approach using molecular and cultivation techniques. In: van Elsas JD, Trevors JT & Wellington EMH (Eds) Modern Soil Microbiology. Marcel Dekker, New York. pp. 375-439 Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ & Woese CR (1997) The RDP (Ribosomal Database Project). Nucleic Acids Res. 25: 109-110 Martínez-Murcia AJ, Acinas SG & Rodriguez-Valera F (1995) Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiology Ecology 17: 247-256 Massol-Deya AA, Odelson DA, Hickey RF & Tiedje JM (1995) Bacterial community fingerprinting of amplified 16S and 16-23S ribosomal gene sequences and restriction endonuclease analysis (ARDRA). In: Akkermans ADL, van Elsas JD & de Bruijn FJ (Eds) Molecular Microbial Ecology Manual (3.3.2: pp. 1-8) Kluwer Academic Publishers, Dordrecht, The Netherlands. McCaig AE, Embley TM & Prosser JI (1994) Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiology Letters 120: 363-368 Moyer CL, Dobbs FC & Karl DM (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60: 871-879 Moyer CL, Dobbs FC & Karl DM (1995) Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 61: 1555-1562 Moyer CL, Tiedje JM, Dobbs FC & Karl DM (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: Efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62: 2501-2507 Murray AE, Hollibaugh JT & Orrego C (1996) Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62: 2676-2680 Muyzer G, de Waal EC & Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700 Muyzer G & deWaal EC (1994) Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rRNA. NATO ASI Series G35: 207-214 Muyzer G, Teske A, Wirsen CO & Jannasch HW (1995) Phylogenetic relationships of Thiomicrospiraspecies and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164: 165-171 Muyzer G & Ramsing NB (1995) Molecular methods to study the organization of microbial communities. Wat. Sci. Tech. 32: 1-9 Muyzer G, Hottenträger S, Teske A & Wawer C (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA - A new molecular approach to analyse the genetic diversity of mixed microbial communities. In: Akkermans ADL, van Elsas JD & de Bruijn FJ (Eds) Molecular Microbial Ecology Manual (3.4.4: pp. 1-23) Kluwer Academic Publishers, Dordrecht, The Netherlands Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H & Wawer C (1997) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Akkermans ADL, van Elsas JD & de Bruijn FJ (Eds) Molecular Microbial Ecology Manual (3.4.4: pp. 1-27) Kluwer Academic Publishers, Dordrecht, The Netherlands Myers RM, Fischer SG, Lerman LS & Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res. 13: 3131-3145 Myers RM, Maniatis T & Lerman LS (1987) Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 155: 501-527 Myers RM, Sheffield VC & Cox DR (1989) Mutation detection by PCR, GC-clamps, and denaturing gradient gel electrophoresis. In: Erlich HA (Ed) PCR-Technology- Principles and Applications for DNA amplification (pp. 71-88) Stockton Press, New York Neefs J, van de Peer Y, Hendriks L & de Wachter R (1990) Compilation of small ribosomal subunit RNA sequences. Nucleic Acid Res. 18: 2237-2242 Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W & Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxadetected by temperature gradient gel electrophoresis. J Bacteriol. 178: 5636-5643 Nübel U, Garcia-Pichel F & Muyzer G (1997) PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 63: 3327-3332 Olsen GJ, Lane DJ, Giovannoni SJ & Pace NR (1986) Microbial ecology and evolution: a ribosomal approach. Ann. Rev. Microbiol. 40: 337-365 Orita M, Iwahana H, Kanazawa H, Hayashi K & Sekiya T (1989) Detection of polymorphisms of human DNAby gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86: 2766-2770 Øvreas L, Castberg T & Torsvik V (1995) Analysis of natural microbial communities using reassociation of total DNA in combination with bisbenzimide density gradients and DGGE. In: Smalla K & Muyzer G, (Eds) Proceedings of the workshop on Application of DGGE and TGGE in Microbial Ecology Pace NA, Stahl DA, Lane DJ & Olsen G (1986) The analysis of natural microbial populations by ribosomal RNAsequences. Adv. Microb. Ecol. 9: 1-55 Paul JH (1996) Carbon cycling: molecular regulation of photosynthetic carbon fixation. Microb. Ecol. 32: 231-245 Priemé A, Sitaula JIB, Klemedtsson AK & Bakken LR (1996) Extraction of methane-oxidizing bacteria from soil particles. FEMS Microbiol. Ecol. 21: 59-68 Rainey FA, Ward N, Sly LI, & Stackebrandt E (1994) Dependence on the taxon composition of clone libraries for PCR amplified, naturally ocurring 16S rDNA, on the primer pair and the cloning system. Experientia 50: 796-797 Raskin L, Zheng D, Griffin ME, Stroot PG & Misra P (1995) Characterization of microbial communities in anaerobic bioreactors using molecular probes. Antonie van Leeuwenhoek 68: 297-308 Reysenbach A-L, Giver LJ, Wickham GS, & Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58: 3417-3418 Riesner D, Henco K & Steger G (1991) Temperature-gradient gel electrophoresis: a method for the analysis of conformational transitions and mutations in nucleic acids and proteins. In: Advances in Electrophoresis 4: 169-250 Robison-Cox JF, Bateson MM & Ward DM (1995) Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl. Environ. Microbiol. 61: 1240-1245 Rochelle PA, Cragg BA, Fry JC, Parkes RJ & Weightman AJ (1994) Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol. Ecology 15: 215-226 Rölleke S, Muyzer G, Wawer C, Wanner G & Lubitz W (1996) Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA fragments. Appl. Environ. Microbiol. 62: 2059-2065 Rosenbaum V & Riesner D (1987) Temperature-gradient gel electrophoresis; thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys. Chem. 26: 235-246 Rosset R, Julien J & Monier R (1966) Ribonucleic acid composition of bacteria as a function of growth rate. J. Mol. Biol. 18: 308-320 Saiki RK, Gelfand DH, Stoffel SJ, Scharf SJ, Higuchi R, Horn GT, Mullis KB & Erlich HA (1988) Primer-directed enzymatic amplifcation of DNA with thermostable DNA polymerase. Science 239: 487-491 Santegoeds CM, Nold SC & Ward DM (1996) Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria froma hot spring cyanobacterial mat. Appl. Environ. Microbiol. 62: 3922-3928 Santegoeds CM, Muyzer G & de Beer D (1997) Successional processes in a bacterial biofilm determined with microsensors and molecular techniques. In: Proceeding International Symposium Environmental Biotechnology '97, pp. 77-82 Schäfer H (1997) Sukzessive Veränderungen der Diversität mariner, mikrobieller Populationen, bestimmt durch 16S rDNA Klonbibliotheken und denaturierende Gradienten Gelelektrophorese (DGGE). Diplomthesis, Universität Bremen, Bremen, Germany Scheinert P, Krausse R, Ullmann U, Söller R & Krupp G (1996) Molecular differentiation of bacteria by PCR amplification of the 16S-23S rRNA spacer. J. Microbiol. Meth. 26: 103-117 Sen WH & Hohn B (1992) DMSO improves PCR amplification of DNA with complex secondary structure. Trends in Genetics 8: 227 Sheffield VC, Cox DR & Myers RM (1989) Attachment of a 40-bp G+C rich sequence (GC-clamp) to genomic DNA fragments by polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86: 232-236 Sheffield VC, Beck JS, Stone EM & Myers RM (1992) A simple and efficient method for attachment of a 40-base pair, GC-rich sequence to PCR-amplified DNA. BioTechniques 12: 386-387 Silva MC & Batt CA (1995) Effect of cellular physiology on PCR amplification efficiency. Molecular Ecology 4: 11-16 Sinigalliano CD, Kuhn DN & Jones RD (1995) Amplification of the amoAgene from diverse species of ammonium-oxidizing bacteria and from an indigenous bacterial population from seawater. Appl. Environ. Microbiol. 61: 2702-2706 Smith E, Leeflang P & Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiology Ecology 23: 249-261 Smith KT, Long CM, Bowman B & Manos MM (1990) Using cosolvents to enhance PCR amplification. Amplifications 5: 16-17 Stahl DA, Flesher B, Mansfield HR & Montgomery L (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54: 1079-1084 Suzuki MT & Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62: 625-630 Teske A, Wawer C, Muyzer G & Ramsing NB (1996a) Distribution of sulfate-reducing bacteria in a stratified Fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62: 1405-1415 Teske A, Sigalevich P, Cohen Y & Muyzer G (1996b) Molecular identification of bacteria from a coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures. Appl. Environ. Microbiol. 62: 4210-4215 Teske A (1995) Phylogenetische und Ökologische Untersuchungen an Bakterien des oxidativen und reduktiven marinen Schwefelkreislaufs mittels ribosomaler RNA. PhD-thesis. University Bremen, Bremen, Germany Torsvik V, Goksoyr J & Daale FL (1990a) High diversity in DNA of soil bacteria. Appl. Envrion. Microbiol. 56: 782-787 Torsvik V, Salte K, Sorkeim R & Goksoyr J (1990b) Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl. Environ. Microbiol. 56: 776-781 Vallaeys T, Topp E, Muyzer G, Macheret V, Laguerre G & Soulas G (1997) Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiology Ecology 24: 279-285 Varadaraj K & Skinner DM (1994) Denaturants or cosolvents improve the specificity of PCR amplification of a G+C-rich DNA using genetically engineered DNA polymerases. Gene 140: 1-5 Voytek MA & Ward BB (1995) Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteriain aquatic samples with the PCR. Appl. Environ. Microbiol. 61: 1444-1450 Ward DM, Weller R & Bateson Mm (1990) 16S rRNA sequences reveal numerous uncultivated microorganisms in a natural environment. Nature 345: 63-65 Ward DM, Bateson MM, Weller R & Ruff-Roberts (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12: 219-286 Ward DM, Santegoeds CM, Nold SC, Ramsing NB, Ferris MJ & Bateson MM (1996) Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures. Antonie van Leeuwenhoek 71: 143-150 Wawer C & Muyzer G (1995) Genetic diversity of Desulfovibriospp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments. Appl. Environ. Microbiol. 61: 2203-2210 Wawer C, Rüggeberg H, Meyer G & Muyzer G (1995) A simple and rapid electrophoresis method to detect sequence variation in PCR-amplified DNA fragments. Nucleic Acids Res. 23: 4928-4929 Wawer C (1996) Molekularbiologische Charakterisierung von sulfatreduzierenden Bakterien in Umweltproben unter den Aspekten Diversität und Aktivität. PhD-thesis, University Bremen, Bremen, Germany Wawer C, Jetten M.S.M. & Muyzer G (1997) Genetic diversity and expression of the [NiFe] hydrogenase large subunit gene of Desulfovibriospp. in environmental samples. Appl. Environ. Microbiol. 63: 4360-4369 Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP & Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464 Weller R, Weller JW & Ward DM (1991) 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl. Environ. Microbiol. 57: 1146-1151 Wheeler Alm E & Stahl DA (1996) Extraction of microbial DNA from aquatic sediments. In: Akkermans ADL, van Elsas JD & de Bruijn FJ (Eds.) Molecular Microbial Ecology Manual (1.1.5: pp.1-29) Kluwer Academic Publishers, Dordrecht, The Netherlands Wichels A (1996) Untersuchungen zur Diversität mariner Bakteriophagen und zu ihrer Verbreitung in der Nordsee. PhD-thesis, University Hamburg, Hamburg, Germany Williams JGK, Kubelik AR, Livak KJ, Rafalski JA & Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Res. 18: 6531-6535. Xia X, Bollinger J & Ogram A (1995) Molecular genetic analysis of the response of three soil microbial communities to the application of 2,4-D. Molecular Ecology 4: 17-28 Zwart G, Huismans R, van Agterveld M, van de Peer Y, de Rijk P, Eenhoorn H, Muyzer G, van Hannen E, Gons H & Laanbroek R (1997) Divergent members of the bacterial division Verrucomicrobialesin a temperate freshwater lake. FEMS Microbiology Ecology, in press.