Mikrobielle Diversität und Dynamik einer1,2-Dichlorpropan dechlorierenden Mischkultur Cord Schlötelburg111.11.21.2.121.2.23611#1831.2.3451.31.3.11.3.297891.4101.5111213580#54814151.6161.717604#4562182.1192.2202122232.3242.4252.52.62627411#444282.7292.82.8.1302.8.22.8.3312.8.4322.8.5332.8.62.8.734352.8.82.9362.9.1372.9.22.10382.11392.11.12.11.22.11.3403413.13.2423.33.3.13.3.243444849505152533.3.3545556480#4713.3.457286#4675859603.3.53.4623.4.163524#52364522#729653.4.2663.56768604#48969604#440703.671625#20872605#20473286#19174622#210286#1923.775604#3584764.14.1.1774.1.27879804.1.38182838485864.1.4874.2884.2.189904.2.2914.2.392934.2.494954.3969798510#2764.499 5 Literatur1001011021031041051061061081096 AnhangAbkürzungsverzeichnisPublikationslisteLebenslaufDanksagungEidesstattliche ErklärungdeInhaltsverzeichnisHilfe 5 Literatur Abd El Haleem, D., von Wintzingerode, F., Moter, A., Moawad, H., Göbel, U. B. (2000) . Phylogenetic analysis of rhizosphere-associated β -subclass proteobacterial ammonia oxidizers in a municipal wastewater treatment plant based on rhizoremediation technology. Lett Appl Microbiol 31:34-38. Adrian, L., Szewzyk, U., Wecke, U., Görisch, H. (2000) . Bacterial dehalorespiration with chlorinated benzenes. Nature 408:580-583. Akkermans, A. D. L., Sajjad Mirza, M., Harmsen, H. J. M., Blok, H. J., Herron, P. R., Sessitsch, A., Akkermans, W. M. (1994). Molecular ecology of microbes: A review of promises, pitfalls and true progress. FEMS Microbiol. Rev . 15:185-194. Alard, P., Lantz, O., Sebagh, M., Calvo, C. F., Weill, D., Chavanel, G., Senik, A., Charpentier, B. (1993). A versatile ELISA-PCR assay for mRNA quantitation from a few cells. Biotechniques 15:730-737. Amann, R. I., Ludwig, W., Schleifer, K. H. (1995) . Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169. Amann, R. I., Ludwig, W. (2000) . Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24:555-565. ATSDR (Agency for Toxic Substances and Disease Registry) - Public Health Statement (1989). http://atsdr1.atsdr.cdc.gov:8080/ToxProfiles/phs8912.html Barns, S. M., Fundyga, R. E., Jeffries, M. W., Pace, N. R. (1994) . Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91:1609-1613. Becker, S., Boger, P., Oehlmann, R., Ernst, A. (2000) . PCR bias in ecological analysis: A case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl Environ Microbiol 66:4945-4953. Beitz, H., Schmidt, H., Herzel, F. (1994) . Occurence, toxicological and ecotoxicological significance of pesticides in groundwater and surface water. In: Chemistry of plant protection. Pesticides in ground and surface water. Börner, H., Beitz, H. (Hrsg.).

Berlin

: Springer-Verlag, 3-56. Berliner Liste der Senatsverwaltung für Inneres, Berlin (1996) . Bewertungskriterien für die Beurteilung stofflicher Belastungen von Böden und Grundwasser in Berlin. Amtsblatt von Berlin 46 (15):957-987. Borneman, J., Skroch, P. W., O'Sullivan, K. M., Palus, J. A., Rumjanek, N. G., Jansen, J. L., Nienhuis, J., Triplett, E. W. (1996). Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935-1943. Bouchard, B., Beaudet, R., Villemur, R., McSween, G., Lepine, F., Bisaillon, J. G . (1996) . Isolation and characterization of Desulfitobacterium frappieri sp. nov., an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol. Int J Syst Bacteriol 46:1010-1015. Bouwer, E. J., Wright, J. P . (1988) . Transformations of trace halogenated aliphatics in anoxic biofilm columns. J Contam Hydrol 2:155-169. Boyle, J. S., Lew, A. M. (1995) . An inexpensive alternative to glassmilk for DNA-purification. Trends in Genetics 11:8. Brack, W., Rottler H., Frank, H. (1998) . Volatile fractions of landfill leachates and their effect on Chlamydomonas reinhardtii : In vivo chlorophyll A fluorescence. Toxicol Chem 17:1982-1991. Brockman, F. J. (1995) . Nucleic-acid-based methods for monitoring the performance of in situ bioremediation. Mol Ecol 4:567-578.

BUA (1995) . 1,2-Dichlorpropan. Beratergremium für umweltrelevante Abfallstoffe (BUA) der Gesellschaft deutscher Chemiker (GDCh), Stoffbericht 155.

Stuttgart

: S. Hirzel Verlag. Bull, A. T., Ward, A. C., Goodfellow, M. (2000) . Search and discovery strategies for biotechnology: The paradigm shift. Microbiol Mol Biol Rev 64:573-606. Cato, E. P., George, W. L., Finegold, S. M. (1986) . The genus Clostridium . In: Bergey's manual of systematic bacteriology. Sneath, H. A., Mair, N. S., Sharpe, M. E. Holt. J. G. (Edit.).

Baltimore

: The Williams & Wilkins Co ., 1141-1200. Chandler, D. P., Frederickson, J. K., Brockman, F. J. (1997) . Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol Ecol 6:475-482. Choi, B. K., Paster, B. J., Dewhirst, F. E., Göbel, U. B. (1994) . Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodontitis. Infect Immun 62:1889-1895. Christiansen, N., Ahring, B. K. (1996) . Desulfitobacterium hafniense sp. nov., an anaerobic, reductively dechlorinating bacterium. Int J Syst Bacteriol 46:442-448. Cottrell, M. T., Kirchman, D. L. (2000) . Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66:5116-5122. Criddle, C. S., McCarthy, P. L., Elliot, M. C., Barker, J. F. (1986) . Reduction of hexachloroethane to tetrachloroethylene in groundwater. J Contam Hydrol 1:133-142. DeLong, E. F., Wickham, G. S., Pace, N. R. (1989) . Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1362. Diekert, G. (1992) . The acetogenic bacteria. In: The prokaryotes. Balows, A., Trüper, H. G., Dworkin, M., Harder, W., Schleifer, K.-H. (Edit.).

New York

: Springer-Verlag, 517-533. Diekert, G. (1995) . Reduktive Dechlorierung als respiratorischer Prozeß in anaeroben Bakterien. In: Mikrobielle Eliminierung von chlororganischen Verbindungen, Schriftenreihe Biologische Abwasserreinigung, Nr. 6.

Berlin

: Technische Universität Berlin, 149-158. Dojka, M. A., Hugenholtz, P., Haack, S. K., Pace, N. R. (1998) . Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869-3877. Dojka, M. A., Harris, J. K., Pace, N. R. (2000) . Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol 66:1617-1621. Dunbar, J., Ticknor, L. O., Kuske, C. R. (2000) . Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66:2943-2950. El Fantroussi, S., Naveau, H., Agathos, S. N. (1998) . Anaerobic dechlorinating bacteria. Biotechnol Prog 14:167-188. Engelen, B., Meinken, K., von Wintzingerode, F., Heuer, H., Malkomes, H.-P., Backhaus, H. (1998) . Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures. Appl Environ Microbiol 64:2814-2821. Farrelly, V., Rainey, F. A., 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. Felsenstein, J. (1985) . Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.

Felske, A., Akkermans, A. D. L., de Vos, W. M. (1998a) . Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl Environ Microbiol 64:4581-4587. Felske, A., Akkermans, A. D. L., de Vos, W. M. (1998b) . In situ detection of an uncultured predominant bacillus in Dutch grassland soils. Appl Environ Microbiol 64:4588-4590. Ferris, M. J., Muyzer, G., Ward, D. M. (1996) . Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 62:340-346. Fetzner, S., Lingens, F. (1994) . Bacterial dehalogenases: Biochemistry, genetics, and biotechnological applications. Microbiol Rev 58:641-685. Fetzner, S. (1998) . Bacterial dehalogenation. Appl Microbiol Biotechnol 50:633-657. Field. K. G., Gordon, D., Wright, T., Rappe, M., Urback, E., Vergin, K., Giovannoni, S. J. (1997) . Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microbiol 63:63-70. Friedrich, M., Springer, N., Ludwig, W., Schink, B. (1996) . Phylogenetic positions of Desulfofustis glycolicus gen. nov., sp. nov., and Syntrophobotulus glycolicus gen. nov., sp. nov., two new strict anaerobes growing with glycolic acid. Int J Syst Bacteriol 46:1065-1069. Garrett, R. H., Grisham, C. M. (1995) . Chemistry 420 - Principles of Biochemistry, 16S rRNA Secondary Structure. http://www.nd.edu/~aseriann/rna.html . Gerritse, J., Renard, V., Gomes, T. M. P., Lawson, P. A., Collins, M. D., Gottschal, J. C. (1996) . Desulfitobacterium sp. strain PCE1, an anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethene or ortho-chlorinated phenols. Arch Microbiol 165:132-140. Glöckner, F. O., Fuchs, B. M., Amann, R. (1999) . Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65:3721-3726. Göbel, U. B. (1995) . Phylogenetic amplification for the detection of uncultured bacteria and the analysis of complex microbiota. J Microbiol Meth 23:117-128. Godon, J. J., Zumstein, E., Dabert, P., Habouzit, F., Moletta, R. (1997) . Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 63:2802-2813. Grove, G., Szeto, S. Y., Liebscher, H., Hii, B., Zebarth, B. J. (1998) . Occurrence of 1,2-dichloropropane and 1,3-dichloropropene in the Abbotsford aquifer, British Columbia. Wat Qual Res J Can 33:51-71. Grüntzig, V., Nold, S. C., Zhou, J., Tiedje, J. M. (2001) . Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR. Appl Environ Microbiol 67:760-768. Häggblom, M. M., Rivera, M. D., Young, L. Y. (1996) . Anaerobic degradation of halogenated benzoic acids coupled to denitrification observed in a variety of sediment and soil samples. FEMS Microbiol Lett 144:213-219. Hamilton, W. A. (1987) . Microbial interactions and metabolic activities. In: Ecology of microbial environments. Flechter M., Gray, T. R. G., Jones, J. G. (Hrsg.).

New York

: Cambridge University Press, 124-149. Hansen, M. C., Tolker-Nielsen, T., Givskov, M., Molin, S. (1998) . Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol Ecol 26:141-149. Harmsen, H. J., van Kuijk, B. L., Plugge, C. M., Akkermans, A. D. L., de Vos, W. M., Stams, A. J. (1998) . Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium. Int J Syst Bacteriol 48:1383-1387.

Hastings, R. C., Saunders, J. R., Hall, G. H., Pickup, R. W., McCarthy, A. J. (1998) . Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake. Appl Environ Microbiol 64:3674-3682. Hattori, T., Mitsui, H., Haga, H., Wakao, N., Shikano, S., Gorlach, K., Kasahara, Y., El-Beltagy, A., Hattori, R. (1997). Advances in soil microbial ecology and the biodiversity. Antonie Van Leeuwenhoek 72:21-28. Hauck, R., Hegemann, W. (1999) . Untersuchungen zum mikrobiellen Abbau von 1,2-Dichlorpropan im Wirbelbettreaktor. gwf Wasser Abwasser 140:843-851. Hauck, R. (2000). Entwicklung eines kontinuierlichen Verfahrens zur mikrobiellen Elimination von 1,2-Dichlorpropan in kontaminierten Wässern. Berichte zur Siedlungswasserwirtschaft, Nr. 13.

Berlin

: Technische Universität Berlin. Head, I. M., Saunders, J. R., Pickup, R. W. (1998). Microbial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Eco l 35:1-21. Heid, C. A., Stevens, J., Livak, K. J., Williams, P. M. (1996). Real time quantitative PCR. Genome Res 6:986-994. Heldal, M., Bratbak, G. (1991). Production and decay of viruses in aquatic environments. Mar Ecol Prog Ser 72:205-212. Hempel, D. C., Krull, R. (1996) . Biologische Behandlung von Abwässern mit schwerabbaubaren Inhaltsstoffen. In: Additiver Umweltschutz: Behandlung von Abwässern. Handbuch des Umweltschutzes und der Umweltschutztechnik. Brauer, H. (Hrsg.)

Berlin

: Springer-Verlag, 321-390. Hermansson, A., Lindgren, P. (2001) . Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl Environ Microbiol 67:972-976. Higuchi, R., Dollinger, G., Walsh, P. S., Griffith, R. (1992) . Simultaneous amplification and detection of specific DNA sequences. Biotechnology 10:413-417. Holden, P. W. (1986) . Pesticides and groundwater quality - issues and problems in four states. National Academy Press,

Washington, D. C

. Holliger, C., Schraa, G. (1994) . Physiological meaning and potential for application of reductive dechlorination by anaerobic bacteria. FEMS Microbiol Rev 15:297-305. Holliger, C., Hahn, D., Harmsen, H., Ludwig, W., Schuhmacher, W., Tindall, B., Vazquez, F., Weiss, N., Zehnder, A. J. B. (1998). Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration. Arch Microbiol 169:313-321. Holliger, C., Schumacher, W. (1994) . Reductive dehalogenation as a respiratory process. Antonie van Leeuwenhoek 66:239-246. Hugenholtz, P., Pitulle, C., Hershberger, K. L., Pace, N. R. (1998a) . Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366-376. Hugenholtz, P., Goebel, B. M., Pace, N. R. (1998b) . Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765-4774. Hunter-Cevera, J. C. (1998) . The value of microbial diversty. Curr Opin Microbiol 1:278-285. IARC (International Agency for Research on Cancer) (1986) . 1,2-Dichloropropane. IARC Monogr Eval Carcinog Risk Chem Hum 41:131-137. Jones, L., Owen, S. A., Horrell, P., Burns, R. G. (1998) . Bacterial inoculation of granular activated carbon filters for the removal of atrazine from surface water. Wat Res 32:2542-2549. Jukes, T. H., Cantor, C. R. (1969). Evolution of protein molecules. In: Mammalian protein metabolism. Munro, H. N. (Edit.).

New York

: Academic Press, 21-132.

Kageyama, A., Sakamoto, M., Benno, Y. (2000). Rapid indentification and quantification of Collinsella aerofaciens using PCR. FEMS Microbiol Let 183:43-47. Kahlich, D., Wiechern, U., Lindner, J. (1993). Propylene oxide. In: Ullman's encyclopedia of industrial chemistry. 5. Auflage. Vol. A22. Gerhartz, W., Elvers, B., (Hrsg.).

Weinheim

: VCH-Verlagsgesellschaft. Kengen, S. W., Breidenbach, C. G., Felske, A., Stams, A. J., Schraa G., de Vos, W. M. (1999) . Reductive dechlorination of tetrachloroethene to cis-1,2-dichloroethene by a thermophilic anaerobic enrichment culture. Appl Environ Microbiol 65:2312-2316. Kolter, R., Siegele, D. A., Tormo, A. (1993) . The stationary phase of the bacterial life cycle. Annu Rev Microbiol 47:855-874. Langer, E. (1986). Chlorinated hydrocarbons, chloropropanes.In: Ullmann's encyclopedia of industrial chemistry, 5. Auflage, Vol. A6. Gerhartz, W., Elvers, B. (Hrsg.).

Weinheim

: VCH-Verlagsgesellschaft. Larsen, N., Olsen, G. J., Maidak, B. L., McCaughey, M. J., Overbeek, R., Macke, T. J., Marsh, T. L., Woese, C. R. (1993). The ribosomal database project. Nucl Acids Res 21:3021-3023. Leclerc, M., Delbes, C., Moletta, R., Godon, J. (2001) . Single strand conformation polymorphism monitoring of 16S rDNA Archaea during start-up of an anaerobic digester. FEMS Microbiol Ecol 34:213-220. Lee D. H., Zo, Y. G., Kim, S. J. (1996) . Non-radioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ Microbiol 62:3112-3120. Leistra, M., Boesten, J. J. T. I. (1989) . Pesticide contamination of groundwater in western Europe. Agric Ecosyst Environ 26:369-389. Li, L., Kato, C., Horikoshi, K. (1999). Bacterial diversity in deep-sea sediments from different depths. Biodiv Conserv 8:659-677. 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 barophylic bacteria. Microb Ecol 21:191-198. Liesack, W., Stackebrandt, E. (1992 ). Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material from an australian terrestrial environment. J Bacteriol 174, 5072-5078. Liu, W. T., Marsh, T. L., Cheng, H., Forney, L. J. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516-4522. Livak, K. J., Flood, S. J., Marmaro, J., Giusti, W., Deetz, K. (1995). Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl 4:357-362. Löffler, F. E., Champine, J. E., Ritalahti, K. M., Sprague, S. J., Tiedje. J. M. (1997). Complete reductive dechlorination of 1,2-dichloropropane by anaerobic bacteria . Appl Environ Microbiol 63:2870-2875. Löffler, F. E., Tiedje, J. M., Sanford, R. A. (1999). Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology. Appl Environ Microbiol 65:4049-4056. Löffler, F. E., Sun, Q., Li, J., Tiedje. J. M. (2000). 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl Environ Microbiol 66:1369-1374.

Lomans, B. P., Maas, R., Luderer, R., op den Camp, H. J., Pol, A., van der Drift, C., Vogels, G. D. (1999). Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl Environ Microbiol 65:3641-3650. Ludwig, W., Schleifer, K.-H. (1994). Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15:155-173. Ludwig, W., Strunk, O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., Bachleitner, M., Schleifer, K.-H. (1998 ). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568. Lyons, S. R., Griffen, A. L., Leys, E. J. (2000). Quantitative real-time PCR for Porphyromonas gingivalis and total Bacteria. J Clin Microbiol 38:2362-2365. Mägli, A., Wendt, M., Leisinger, T. (1996) . Isolation and characterization of Dehalobacterium formicoaceticum gen. nov. sp. nov., a strictly anaerobic bacterium utilizing dichloromethane as source of carbon and energy. Arch Microbiol 166:101-108. Manz, W., Wendt-Potthoff, K., Neu, T. R., Szewzyk, U., Lawrence, J. R. (1999) . Phylogenetic composition, spatial structure, and dynamics of lotic bacterial biofilms investigated by fluorescent in situ hybridization and confocal laser scanning microscopy. Microb Ecol 37:225-237. Massol-Deyá, A., Whallon, J., Hickey, R. F., Tiedje, J. M. (1995). Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater. Appl Environ Microbiol 61:769-777. Massol-Deyá, A., Weller, R., Ríos-Hernández, L., Zhou, J.-Z., Hickey, R. F., Tiedje, J. M. (1997) . Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl Environ Microbiol 63:270-276. Mathews, S. A., Volp, K. M., Timms, P. (1999). Development of a quantitative gene expression assay for Chlamydia trachomatis identified temporal expression of σ -factors. FEBS Letters 458:354-358. Maymó-Gatell, X., Tandoi, V., Gossett, J. M., Zinder, S. H. (1995) . Characterization of an H2-utilizing enrichment culture that reductively dechlorinates tetrachloroethene to vinyl chloride and ethene in the absence of methanogenesis and acetogenesis. Appl Environ Microbiol 61:3928-3933. Maymó-Gatell, X., Chien, Y., Gossett, J. M., Zinder, S. H. (1997) . Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276:1568-1571. McGrath, J. E., Harfoot, C. G. (1997) . Reductive dehalogenation of halocarboxylic acids by the phototrophic genera Rhodospirillum and Rhodopseudomonas. Appl Environ Microbiol 63:3333-3335. Meierling, L. (1998) . Untersuchungen zur mikrobiellen Reinigung organisch belasteter Grundwässer in Kombination mit chemischen und physikalischen Verfahren, Berichte zur Siedlungswasserwirtschaft, Nr. 5.

Berlin

: Technische Universität Berlin. Meijer, W. G., Nienhuis-Kuiper, M. E., Hansen, T. A. (1999) . Fermentative bacteria from estuarine mud: phylogenetic position of Acidaminobacter hydrogenoformans and description of a new type of gram-negative, propionigenic bacterium as Propionibacter pelophilus gen. nov., sp. nov. Int J Syst Bacteriol 49:1039-1044. Merriman, J. C., Struger, J., Szawiola, R. S. (1991). Distribution of 1,3-dichloropropene and 1,2-dichloropropane in Big Creek Watershed. Bull Environ Contam Toxicol 47:572-579. Mohn, W. W., Tiedje, J. M. (1992). Microbial reductive dehalogenation. Microbiol Rev 56:482-507. Moter, A., Göbel, U. B. (2000) . Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41:85-112.

Murray, A. E., Hollibaugh, J. T., Orrego, C. (1996 ). Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol 62:2676-2680. Muyzer, G., de Waal, E. C., Uitterlinden, A. G. (1993) . Profiling of complex microbial populations by denaturating gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695-700. Muyzer, G., Smalla, K. (1998) . Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73:127-141. Muyzer, G. (1999) . DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2:317-322. Mylvaganam, S., Dennis, P. P. (1992) . Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130:399-410. Neumann, A., Scholz-Muramatsu, H., Diekert, G. (1994 ). Tetrachloroethene metabolism of Dehalospirillum multivorans . Arch Microbiol 162:295-301. Nübel, U., Engelen, B., Felske, A., Snaidr, J., Wieshuber, A., Amann, R., Ludwig, W., Backhaus, H. (1996) . Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178:5636-5643. Oldenhuis, R., Vink, R. L. J. M., Janssen, D. B., Witholt, B. (1989) . Degradation of chlorinated aliphatic hydrocarbons by Methylosinus trichosporium OB3b expressing soluble methane monooxygenase. Appl Environ Microbiol 55:2819-2826. Pillai, S. D., Josephson, K. L., Bailey, R. L., Gerba, C. P., Pepper, I. L. (1991) . Rapid method for processing soil samples for polymerase chain reaction amplification of specific gene sequences. Appl Environ Microbiol 57:2283-2286. Power, M., van der Meer, J. R., Tchelet, R., Egli, T., Eggen, R. (1998) . Molecular-based methods can contribute to assessments of toxilogical risks and bioremediation strategies . J Microbiol Meth 32:107-119. Pulliam-Holoman, T. R., Elberson, M. A., Cutter, L. A., May, H. D., Sowers, K. R. (1998) . Characterization of a defined 2,3,5,6-tetrachlorobiphenyl-ortho-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl Environ Microbiol 64:3359-3367. Qiu, X., Wu, L., Huang, H., McDonel, P. E., Palumbo, A. V., Tiedje, J. M., Zhou, J. (2001) . Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67:880-887. Rainey, F. A., Ward, N., Sly, L. I., Stackebrandt, E. (1994) . Dependence on the taxon composition of clone libraries for PCR amplified, naturally occuring 16S rDNA, on the primer pair and the cloning system used. Experientia 50:796-797. Rainey, F. A., Ward-Rainey, N. L., Janssen, P. H., Hippe, H., Stackebrandt, E. (1996) . Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiology 142:2087-2095. Rasche, M. E., Hyman, M. R., Arp, D. J. (1990) . Biodegradation of halogenated hydrocarbon fumigants by nitrifying bacteria. Appl Environ Microbiol 56:2568-2571. Ravenschlag, K., Sahm, K., Amann, R. (2001) . Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Appl Environ Microbiol 67:387-395. Reysenbach, A.-L., Giver, L. J., Wickham, G. S., Pace, N. R. (1992) . Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417-3418.

Rippen, G. (1994). Handbuch der Umweltchemikalien : Datensammlung über Umweltchemikalien, 25. Ergänzungslieferung.

Landsberg/Lech

: Ecomed Verlagsgesellschaft. Rochelle, P. A., Cragg, B. A., Fry, J. C., Parkes, R. J., Weightman, A. J. (1994) . Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol Ecol 15:215-225. Rosselló-Mora, R., Amann, R. (2001) . The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67. Roszak, D. B., Colwell, R. R. (1987) . Survival strategies of bacteria in the natural environment. Microbiol Rev 51:365-379. Saitou, N., Nei, M. (1987) . The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evo l 4:406-425. Sambrook, J., Fritsch, E. F., Maniatis, T. (1989). Molecular cloning: a laboratory manual. 2nd edition.

Cold Spring Harbour, N. Y

: Cold Spring Harbour Laboratory Press. Sanford, R. A., Cole, J. R., Löffler, F. E., Tiedje, J. M. (1996) . Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate. Appl Environ Microbiol 62:3800-3808. Schink, B. (1997) . Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61:262-280. Schlegel, H. G. (1995) . Allgemeine Mikrobiologie. 7. Auflage. Georg Thieme Verlag,

Stuttgart

. Schlötelburg, C., Gluz, M., Popovic, M., Merchuk, J. C. (1999) . Characterization of an airlift reactor with helical flow promoters. Can J Chem Eng 77:804-810. Schloter, M., Lebuhn, M., Heulin, T., Hartmann, A. (2000) . Ecology and evolution of bacterial microdiversity. FEMS Microbiol Rev 24:647-660. Schmidt, J. E., Ahring, B. K. (1999) . Immobilization patterns and dynamics of acetate-utilizing methanogens immobilized in sterile granular sludge in upflow anaerobic sludge blanket reactors. Appl Environ Microbiol 65:1050-1054. Schuppler, M., Mertens, F., Schön, G., Göbel, U. B. (1995) . Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis. Microbiology 141:513-521. Sharak-Genthner, B. R., Price, W. A., Pritchard, P. H. (1989) . Characterization of anaerobic dechlorinating consortia derived from aquatic sediments. Appl Environ Microbiol 55:1472-1476. Shelton, D. R., Tiedje, J. M. (1984) . General method for determining anaerobic biodegradation potential. Appl Environ Microbiol 48:850-857. Sienel, G., Rieth, R., Rowbottom, K. F. (1987) . Epoxides. In: Ullmanns encyclopedia of industrial chemistry. 5. Auflage, Vol. A9. Gerhartz, W., Elvers, B. (Hrsg.).

Weinheim

: VCH-Verlagsgesellschaft. Simpson, J. M., McCracken, V. J., White, B. A., Gaskins, H. R., Mackie, R. I. (1999) . Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastro-intestinal microbiota. J Microbiol Meth 36:167-179. Smidt, H., Akkermans, A. D., van der Oost, J., de Vos, W. M. (2000) . Halorespiring bacteria-molecular characterization and detection. Enzyme Microb Technol 27:812-820. Speksnijder, A. G., Kowalchuk, G. A., de Jong, S., Kline, E., Stephen, J. R., Laanbroek, H. J. (2001) . Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl Environ Microbiol 67:469-472. Squillace, P. J., Moran, M. J., Lapham, W. W., Price, C. V., Clawges, R. M., Zogorski, J. S. (1999) . Volatile organic compounds in untreated ambient groundwater of the Unites States, 1985 - 1995. Environ Science Technol 33:4176-4187.

Stackebrandt, E., Liesack, W., Goebel, B. M. (1993) . Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232-236. Stackebrandt, E. Goebel, B. M. (1994) . Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846-849. Stapleton, R. D., Ripp, S., Jimenez, L., Cheol-Koh, S., Fleming, J. T., Gregory, I. R., Sayler, G. S. (1998) . Nucleic acid analytical approaches in bioremediation: site assessment and characterization. J Microbiol Meth 32:165-178. Starnick, J. (1999) . Chlorverbindungen - Woher kommen sie? Wohin gehen sie? Eine Einschätzung des Gefährdungspotentials. In: Schriftenreihe Biologische Abwasserreinigung, Behandlung von Abwässern mit halogenorganischen Verbindungen.

Berlin

: Technische Universität Berlin, 13-28. Stuart, S. L., Woods, S. L., Lemmon, T. L., Ingle Jr., J. D. (1998) . The effect of redox potential changes on reductive dechlorination of pentachlorophenol and the degradation of acetate by a mixed methanogenic culture. Biotechnol Bioeng 63:69-78. Suzuki, M. T., Taylor, L. T., DeLong, E. F. (2000) . Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays. Appl Environ Microbiol 66:4605-4614. Suzuki, M. T., Giovannoni, S. J. (1996) . Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630. Sykes, P. J., Neoh, S. H., Brisco, M. J., Hughes, E., Condon, J., Morley, A. A. (1992) . Quantitation of targets for PCR by use of limiting dilution. Biotechniques 13:444-449. Tartakovsky, B., Hawari, J., Guiot, S. R. (2000) . Enhanced dechlorination of Aroclor 1242 in an anaerobic continuous bioreactor. Wat Res 34:85-92. Torsvik, V., Salte, K., Sorheim, R., Goksoyr, J. (1990a) . Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 56:776-781. Torsvik, V., Goksoyr, J., Daae, F. L. (1990b) . High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782-787. Traunecker, J., Preuss, A., Diekert, G. (1991) . Isolation and characterization of a methyl chloride utilizing, strictly anaerobic bacterium. Arch Microbiol 156:416-421. Tsai, Y.-L., Olson, B. H. (1991) . Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070-1074. Valentine, D. L., Reeburgh, W. S., Blanton, D. C. (2000) . A culture apparatus for maintaining H2 at sub-nanomolar concentrations. J Microbiol Methods 39:243-251. Vallaeys, T., Topp, E., Muyzer, G., Macheret, V., Laguerre, G., Rigaud A., Soulas, G. (1997) . Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol Ecol 24:279-285. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K., Swings, J. (1996) . Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407-438. Vandenbergh, P. A., Kunka, B. S. (1988) . Metabolism of volatile chlorinated aliphatic hydrocarbons by Pseudomonas fluorescens. Appl Environ Microbiol 54:2578-2579. von Wintzingerode, F., Göbel, U. B., Stackebrandt, E. (1997) . Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213-229.

von Wintzingerode, F., Selent, B., Hegemann, W. Göbel, U. B. (1999) . Phylogenetic analysis of an anaerobic, trichlorobenzene-transforming microbial consortium. Appl Environ Microbiol 65:283-286. von Wintzingerode, F., Landt, O., Ehrlich, A., Göbel, U. B. (2000) . Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity. Appl Environ Microbiol 66:549-557. von Wintzingerode, F., Schlötelburg, C., Hauck, R., Hegemann, W., Göbel, U. B. (2001) . Development of primers for amplifying genes encoding CprA- and PceA-like reductive dehalogenases in anaerobic microbial consortia, dechlorinating trichlorobenzene and 1,2-dichloropropane. FEMS Microbiol Ecol 35:189-196. Wallrabenstein, C., Gorny, N., Springer, N., Ludwig, W., Schink, B. (1995) . Pure culture of Syntrophus buswellii, definition of its phylogenitic status, and description of Syntrophus gentianae sp. nov. Syst Appl Microbiol 18:62-66. Weber, S., Stubner, S., Conrad, R. (2001) . Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. Appl Environ Microbiol 67:1318-1327. Weidner, S., Arnold, W., Pühler, A. (1996) . Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 62:766-771. Weisburg, W. G., Barns, S. M., Pelletier, D. A., Lane, D. J. (1991) . 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697-703. Whitman, W. B., Bowen, T. L., Boone, D. R. (1992) . The methanogenic bacteria. In: The prokaryotes. Balows, A., Trüper, H. G., Dworkin, M., Harder, W., Schleifer, K.-H. (Edit.).

New York, N. Y.

:Springer-Verlag, 739-745. Wild, A., Hermann, R., Leisinger, T. (1996) . Isolation of an anaerobic bacterium which reductively dechlorinates tetrachloroethene and trichloroethene. Biodegradation 7:507-511. Wind, T., Stubner, S., Conrad, R. (1999 ). Sulfate-reducing bacteria in rice field soil and on rice roots. Syst Appl Microbiol 22:269-279. Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51:221-271. Woo, T. H. S., Patel, B. K. C., Cinco, M., Smythe, L. D., Norris, M. A., Symonds, M. L., Dohnt, M. F., Piispanen, J. (1999). Identification of Leptospira biflexa by real-time homogeneous detection of rapid cycle PCR product. J Microbiol Meth 35:23-30. 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. Mol Ecol 4:17-28. Yu, Z., Martin, V. J. J., Mohn, W. W. (1999). Occurence of two resin acid-degrading bacteria and a gene encoding resin acid biodegradation in pulp and paper mill effluent biotreatment systems assayed by PCR. Microb Ecol 38:114-125. Zarda, B., Hahn, D., Chatzinotas, A., Schönhuber, W., Neef, A., Amann, R. I., Zeyer, J. (1997) . Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168:185-192. Zellner, G., Stackebrandt, E., Messner, P., Tindall, B. J., Conway de Macario, E., Kneifel, H., Sleytr, U. B., Winter, J. (1989). Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum , Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov. Arch Microbiol 151:381-390. Zou, S., Anders, K. M., Ferguson, J. F. (1999). Pentachlorophenol dechlorination in fluidized-bed reactors under methanogenic conditions. Bioremediation J 3:93-104. Zwart, G., Hiorns, W. D., Methe, B. A., van Agterveld, M. P., Huismans, R., Nold, S. C., Zehr, J. P., Laanbroek, H. J. (1998) . Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol 21:546-556.