Holler, T., F. Widdel, K. Knittel, R. Amann, M.Y. Kellermann, K.U. Hinrichs, A. Teske, A. Boetius, and G. Wegener. 2011. Thermophilic anaerobic oxidation of methane by marine microbial consortia. ISME J. 5:1946-1956.

Schauer, R., H. Røy, N. Augustin, H.H. Gennerich, M. Peters, F. Wenzhoefer, R. Amann, and A. Meyerdierks. 2011. Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field. Environ. Microbiol. 13:2633-2648.

Gómez-Pereira, P.R., M. Schüler, B.M. Fuchs, C. Bennke, H. Teeling, J. Waldmann, M. Richter, V. Barbe, E. Bataille, F.O. Glöckner, and R. Amann. 2011. Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ. Microbiol. (Epub ahead of print) doi: 10.1111/j.1462-2920.2011.02555.x.

Petersen, J.M., F.U. Zielinski, T. Pape, R. Seifert, C. Moraru, R. Amann, S. Hourdez, P.R. Girguis, S.D. Wankel, V. Barbe, E. Pelletier, D. Fink, C. Borowski, W. Bach, and N. Dubilier. 2011. Hydrogen is an energy source for hydrothermal vent symbioses. Nature. 476:176-180.

Serrano, W., R. Amann, R. Rosselló-Móra, R.A. Herbert, and U. Fischer. 2011. The genus Allochromatium (Chromatiales Chromatiaceae) revisited: A study on its intragenic structure based on multilocus sequence analysis (MLSA) and DNA-DNA hybridization (DDH). Syst. Appl. Microbiol. 34: 590-594.

Pizzetti, I., B.M. Fuchs, G. Gerdts, A. Wichels, K.H. Wiltshire, and R. Amann. 2011. Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea. Appl. Environ. Microbiol. 77:5009-5017.

Kubo, K., K. Knittel, R. Amann, M. Fukui, and K. Matsuura. 2011. Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan. Syst. Appl. Microbiol. 34:293-302.

Salman, V., R. Amann, A.C. Girnth, L. Polerecky, J.V. Bailey, S. Høgslund, G. Jessen, S. Pantoja, and H.N. Schulz-Vogt. 2011. A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. Syst. Appl. Microbiol. 34:243-259.

Suárez-Suárez, A., A. López-López, A. Tovar-Sánchez, P. Yarza, A. Orfila, J. Terrados, J. Arnds, S. Marqués, H. Niemann, P. Schmitt-Kopplin, R. Amann, and R. Rosselló-Móra. 2011. Response of sulfate-reducing bacteria to an artificial oil-spill in a coastal marine sediment. Environ. Microbiol. 13:1488-1499.

Weber, M., H. Teeling, S. Huang, J. Waldmann, M. Kassabgy, B.M. Fuchs, A. Klindworth, C. Klockow, A. Wichels, G. Gerdts, R. Amann, and F.O. Glöckner. 2011. Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. ISME J. 5:918-928.

Munoz, R., P. Yarza, W. Ludwig, J. Euzéby, R. Amann, K.H. Schleifer, F.O. Glöckner, and R. Rosselló-Móra. 2011. Release LTPs104 of the All-Species Living Tree. Syst. Appl. Microbiol. 34:169-170.

Zeder, M., A. Ellrott, and R. Amann. 2011. Automated sample area definition for high-throughput microscopy. Cytometry A. 79:306-310.

Thiele, S., B.M. Fuchs, and R.I. Amann. 2011. Identification of Microorganisms Using the Ribosomal RNA Approach and Fluorescence In Situ Hybridization. In: Treatise on Water Science, vol. 3, pp. 171–189. Peter Wilderer (ed.) Oxford: Academic Press.

Lenk, S., J. Arnds, K. Zerjatke, N. Musat, R. Amann, and M. Mussmann. 2011. Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment. Environ. Microbiol. 13:758-774.

Moraru, C., G. Moraru, B.M. Fuchs, and R. Amann. 2011. Concepts and software for a rational design of polynucleotide probes. Environ. Microbiol. Rep. 3:69–78.

Jogler, C., G. Wanner, S. Kolinko, M. Niebler, R. Amann, N. Petersen, M. Kube, R. Reinhardt, and D. Schüler. 2011. Conservation of proteobacterial magnetosome genes and structures in an uncultivated member of the deep-branching Nitrospira phylum. Proc. Natl. Acad. Sci. USA 108:1134-1139.

2010

Anton, J., R. Amann, and R. Rossello-Mora. 2010. In Bergey’s Manual. Chapter 27. Family 1. Rhodothermaceae. Genus II. Salinibacter, p. 146-151.

Yarza, P., W. Ludwig, J. Euzeby, R. Amann, K.-H. Schleifer, F.O. Glöckner, and R. Rossello-Mora. 2010. Update of the all-species Living Tree Project based on 16S and 23S rRNA sequence analyses. System. Appl. Microbiol. 33:291-299.

Alonso, C., P. Gomez-Pereira, A. Ramette, L. Ortega, B. M. Fuchs, and R. Amann. 2010. Multilevel analysis of the bacterial diversity along the environmental gradient Rio de la Plata-South Atlantic Ocean. Aquat. Microb. Ecol. 61:57-72.

Schreiber, L., T. Holler, K. Knittel, A. Meyerdierks, and R. Amann. 2010. Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ. Microbiol. 12:2327-2340.

Moraru, C., G. Moraru, B. Fuchs, and R. Amann. 2010. Concepts and software for a rational design of polynucleotide probes. Environ. Microbiol. Reports (in press).doi: 10.1111/j.1758-2229.2010.00189.x.

Moraru, C., P. Lam, B. Fuchs, M. Kuypers, and R. Amann. 2010. GeneFISH – an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environ. Microbiol. 12:3057-3073.

Thiele, S., B.M. Fuchs, and R.I. Amann. 2010. Identification of microorganisms using the ribosomal RNA approach and fluorescence in situ hybridization. In: Treatise on Water Science. Volume 1. Management of Water Resources. F. Frimmel, P. Wilderer (Eds.) Elsevier, Amsterdam, The Netherlands. in press.

Pena, A., H. Teeling, J. Huerta-Cepas, F. Santos, P. Yarza, J. Brito-Echeverria, M. Lucio, P. Schmitt-Kopplin, I. Meseguer, C. Schenowitz, C. Dossat, V. Barbe, J. Dopazo, R. Rossello-Mora, M. Schüler, F.O. Glöckner, R. Amann, T. Galbadon, and J. Anton. 2010. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two Salinibacter ruber strains simultaneously isolated from the same saltern. ISME J. 4:882-895.

Jogler, C., M. Niebler, W. Lin, M. Kube, G. Wanner, S. Kolinko, P. Stief, A.J. Beck, D. De Beer, N. Petersen, Y. Pan, R. Amann, R. Reinhard, and D. Schüler. 2010.Cultivation-independent characterization of „Candidatus Magnetobacterium bavaricum“ via ultrastructural, geochemical, ecological and metagenomic methods.Environ. Microbiol. 12:2466-2478.

Arnds, J., K. Knittel, U. Buck, M. Winkel, and R. Amann. 2010. Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake. System. Appl. Microbiol. 33:139-148.

Simonato, F., P.R. Gomez-Pereira, B.M. Fuchs, and R. Amann. 2010. Bacterioplankton diversity and community composition in the Southern Lagoon of Venice. System. Appl. Microbiol. 33:128-138.

Serrano, W., R. Amann, R. Rossello-Mora, and U. Fischer. 2010. Evaluation of the use of multilocus sequence analysis (MLSA) to resolve taxonomic conflicts with the genus Marichromatium. System. Appl. Microbiol. 33:116-121.

Gomez-Pereira, P.R., B.M. Fuchs, C. Alonso, M.J. Oliver, J.E.E. van Beusekom, and R. Amann. 2010. Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. ISME J. 4:472-487.

Meyerdierks, A., M. Kube, I. Kostadinov, H. Teeling, F. O. Glöckner, R. Reinhardt, and R. Amann. 2010. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ. Microbiol. 12:422-439.

2009

Schattenhofer, M., B. Fuchs, R. Amann, G. Tarran, M. Zubkov, and J. Pernthaler. 2009. Latitudinal distribution of bacterioplankton populations in the Atlantic Ocean. Environ. Microbiol. 11:2078-2093.

Jogler, C., W. Lin, A. Meyerdierks, M. Kube, E. Katzmann, C. Flies, Y.X. Pan, R. Amann, R. Reinhardt, and D. Schüler. 2009. Toward cloning of the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments. Appl. Environ. Microbiol. 75:3972-3979.

Buck, U., H.-P. Grossart, R. Amann, and J. Pernthaler. 2009. Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environ. Microbiol. 11:1854-1865.

Lavik, G., T. Stührmann, V. Brüchert, A. van der Plas, V. Mohrholz, P. Lam, M. Mußmann, B. M. Fuchs, R. Amann, U. Lass and & M. M.M. Kuypers. 2009. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457:581-584.

Serrano, W., R. Amann, and U. Fischer. 2009. A moderately thermophilic and high sulphide tolerant biotype of Marichromatium gracile, isolated from tidal sediments of the German Wadden Sea: Marichromatium gracile biotype thermosulphidiphilum. System. Appl. Microbiol. 32:1-7.

Yan, S., B. M. Fuchs, S. Lenk, J. Harder, J. Wulf, N.-Z. Jiao, and R. Amann. 2009. Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria. System. Appl. Microbiol. 32:124-139.

Strittmatter, A.W., H. Liesegang, R. Rabus, I. Decker, J. Amann, S. Andres, A. Henne, W.F. Fricke, R. Martinez-Arias, D. Bartels, A. Goesmann, L. Krause, A. Pühler, H.-P. Klenk, M. Richter, M. Schüler, F.O. Glöckner, A. Meyerdierks, G. Gottschalk, and R. Amann. 2009. Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ. Microbiol. 11:1038-1055.

Lam, P., G. Lavik, M.M. Jensen, J. van de Vossenberg, M. Schmid, D. Woebken, D. Guiterrez, R. Amann, M.S.M. Jetten, and M.M.M. Kuypers. 2009. Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc. Natl. Acad. Sci. USA 106:4752-4747.

2008

Amann, R., and B. Fuchs. 2008. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nature Rev. Microbiol. 6:339-348.

Hieu, C. X., B. Vogt, D. Albrecht, D. Becher, T. Lombardot, F. O. Glöckner, R. Amann, M. Hecker, and T. Schweder. 2008. Detailed proteome analysis of growing cells of the planctomycete Rhodopirellula baltica SH1T. Proteomics 8:1608-1623.

Woebken, D., P. Lam, M.M.M. Kuypers, S.W.A. Naqvi, B. Kartal, M. Strous, M.S.M. Jetten, B.M. Fuchs, and R. Amann. 2008. A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones. Environ. Microbiol. 10:3106-3119.

Yarza, P., M. Richter, J. Peplies, J. Euzeby, R. Amann, K.-H. Schleifer, W. Ludwig, F. O. Glöckner, R. Rossello-Mora. 2008. The all-species living tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. System. Appl. Microbiol. 31:241-250.

Barberyon, T., F. Carpentier, S. L’Haridon, M. Schüler, G. Michel, and R. Amann. 2008. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter. Int. J. System. Evol. Microbiol. 58:790-797.

Musat, N., H. Halm, B. Winterholler, P. Hoppe, S. Peduzzi, F. Hillon, F. Horreard, R. Amann, B.B. Jorgensen, and M.M.M. Kuypers. 2008. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc. Natl. Acad. Sci. USA 105:17861-17866.

Barberyon, T., F. Carpentier, S. L’Haridon, M. Schüler, G. Michel, and R. Amann. 2008. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from the North Sea water, and emended description of the genus Maribacter. Int. J. System. Evol. Microbiol. 58:790-797.

2007

Wakeham, S. G., R. Amann, K. H. Freeman, E. C. Hopmans, B. B. Jorgensen, I. F. Putnam, S. Schouten, J. S. Sinninghe Damste, H. M. Talbot, and D. Woebken. 2007. Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study. Organic Geochemistry. 38:2070-2097.

Prast, M., A. Bischoff, U. Waller, R. Amann, und U.-G. Berninger. 2007. Impact of ciliates on nitrification and nitrifying bacteria in Baltic Sea sediments. Marine Ecol. Progress Ser. 350:55-61.

Mussmann, M., F. Z. Hu, M. Richter, D. de Beer, A. Preisler, B. B. Jorgensen, M. Huntemann, F. O. Glöckner, R. Amann, W. J. H. Koopman, R. S. Lasken, B. Janto, J. Hogg, P. Stoodley, R. Boissy, and G. D. Ehrlich. 2007. Insights into the genomes of large sulfur bacteria revealed by analysis of single filaments. PLoS Biology 5:1923-1937 (e230).

Woebken, D., H. Teeling, P. Wecker, A. Dumitriu, I. Kostadinov, E. F. DeLong, R. Amann, and F. O. Glöckner. 2007. Fosmids of novel marine planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J. 1:419-435.

Woebken, D., B. M. Fuchs, M. M. M. Kuypers, and R. Amann. 2007. Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl. Environ. Microbiol. 73:4648-4657.

Lösekann, T., K. Knittel, T. Nadalig, B. Fuchs, H. Niemann, A. Boetius, and R. Amann. 2007. Diversity and abundance of anerobic and anaerobic methane oxidizers at the Haakon Mosby mud volcano, Barents Sea. Appl. Environ. Microbiol. 73:3348-3362.

Santos, F., A. Meyerdierks, A. Pena, R. Rossello-Mora, R. Amann, and P. Anton. 2007. Metagenomic approach to the study of halophages: the environmental halophage 1 (EHP-1). Environ. Microbiol. 9:1711-1723.

Soria-Carrasco, V., M. Valens-Vadell, A. Pena, J. Anton, R. Amann, J. Castresana, and R. Rossello-Mora. 2007. Phylogenetic position of Salinibacter ruber based on concatenated protein alignments. Syst. Appl. Microbiol. 30:171-179.

Fuchs, B. M., S. Spring, H. Teeling, C. Quast, J. Wulf, M. Schattenhofer, S. Yan, S. Ferriera, J. Johnson, F. O. Glöckner, and R. Amann. 2007. Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc. Natl. Acad. Sci. USA 104:2891-2896.

Alonso, C., F. Warnecke, R. Amann, and J. Pernthaler. 2007. High local and global diversity of Flavobacteria in marine plankton. Environ. Microbiol. 9:1253-1266.

Musat, N., O. Giere, F. Thiermann, R. Amann, and N. Dubilier. 2007 Molecular and morphological characterization of the symbiosis between bacterial endosymbionts and the nematode Astomonema sp. from the Bahamas. Environ. Microbiol. 9:1345-1353.

Lam, P., M.M. Jensen, G. Lavik, D.F. McGinnis, B. Müller, C.J. Schubert, R. Amann, B. Thamdrup, and M.M.M. Kuypers. 2007. Linking crenarchaeal and bacterial nitrification to ANAMMOX in the Black Sea. Proc. Natl. Acad. Sci. USA 104:7104-7109.

Buchkapitel:

Fuchs, B. M., J. Pernthaler, and R. Amann. 2007. Single cell identification by fluorescence in situ hybridization, pp. 886-896. In: Methods for General and Molecular Microbiology, 3rd Edition. C.A. Reddy, T. J. Beveridge, J.A. Breznak, G. Marzluf, T. M. Schmidt, and L. R. Snyder, Eds. ASM Press, Washington D.C.

2006

Musat, N., U. Werner, K. Knittel, S. Kolb, T. Dodenhof, J. E. E. van Beusekom, D. De Beer, N. Dubilier, and R. Amann. 2006. Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Romo Basin, Wadden Sea. Syst. Appl. Microbiol. 29:333-348.

MacGregor, B. J., H.T.S. Boschker, and R. Amann. 2006. Comparison of rRNA and polar-lipid-derived fatty acid biomarkers for assessing 13C-substrate incorporation by microorganisms in marine sediments. Appl. Environ. Microbiol. 72:5246-5253.

Blazejak, A., J. Kuever, C. Erseus, R. Amann, and N. Dubilier. 2006. Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5’-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (Oligochaeta) from Bermuda and the Bahamas. Appl. Environ. Microbiol. 72:5527-5536

MacGregor, B. J., and R. Amann. 2006. Single-stranded conformational polymorphism for separation of mixed rRNAs (rRNA-SSCP), a new method for profiling microbial communities. Syst. Appl. Microbiol. 29:661-670.

Niemann, H., T. Lösekann, D. de Beer, M. Elvert, T. Nadalig, K. Knittel, R. Amann, E.J. Sauter, M. Schlüter, M. Klages, J. Foucher, and A. Boetius. 2006. Novel microbial communities of the Haakon Mosby mud vulcano and their role as a methane sink. Nature (London) 443:854-858.

Woyke, T., H. Teeling, N.N. Ivanova, M. Huntemann, M. Richter, F.O. Glöckner, D. Boffelli, I.J. Anderson, K.W. Barry, H.J. Shapiro, E. Szeto, N.C. Kyrpides, M. Mussmann, R. Amann, C. Bergin, C. Ruehland, E.M. Rubin, and N. Dubilier. 2006. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (London) 443:950-956.

Bauer, M., M. Kube, H. Teeling, M. Richter, T. Lombardot, E. Allers, C.A. Würdemann, C. Quast, H. Kuhl, F. Knaust, D. Woebken, K. Bischof, M. Mussmann, J.V. Choudhuri, F. Meyer, R. Reinhardt, R.I. Amann, and F.O. Glöckner. 2006. Whole genome analysis of the marine Bacteroidetes “Gramella forsetii” reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8:2201-2213.

Mary, I., J.L. Heywood, B.M. Fuchs, R. Amann, G.A. Tarran, P.H. Burkill, and M.V. Zubkov. 2006. SAR11 dominance among metabolically active low nucleic acid bacterioplankton in surface waters along an Atlantic meridional transect. Aquat. Microb. Ecol. 45:107-113

Tujula, N. A., C. Holmström, M. Mußmann, R. Amann, S. Kjelleberg, and G. R. Crocetti. 2006. A CARD-FISH protocol for the identification and enumeration of epiphytic bacteria on marine algae. J. Microbiol. Meth. 65:604-607.

Buchkapitel:

Amann, R., J. Peplies, and D. Schüler. 2006. Diversity and taxonomy of magnetotactic bacteria. In: Magnetoreception and Magnetosomes in Bacteria, pp. 25-36. D. Schüler (Ed.). Springer-Verlag Berlin Heidelberg.

Cypionka, H., H.-D. Babenzien, F. O. Glöckner, and R. Amann. 2006. The genus Nevskia. In: The Prokaryotes. Third Edition. Volume 6: Proteobacteria: Gamma Subclass, pp. 1152-1155. M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer and E. Stackebrandt (Eds.). Springer Sciences+Business Media, LLC.

2005

Knittel, K., T. Lösekann, A. Boetius, R. Kort, and R. Amann. 2005. Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microbiol. 71:467-479

Kämpfer, P., R. Schulze, U. Jäckel, K. A. Malik, R. Amann, and S. Spring. 2005. Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 55:341-344.

Blazejak, A., C. Erseus, R. Amann, and N. Dubilier. 2005. Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru Margin. Appl. Environ. Microbiol. 71:1553-1561.

Knittel, K., J. Kuever, A. Meyerdierks, R. Meinke, R. Amann, and T. Brinkhoff. 2005. Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments. Int. J. Syst. Evol. Microbiol. 55:781-786.

Mussmann, M., K. Ishii, R. Rabus, and R. Amann. 2005. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ. Microbiol. 7:405-418.

Lombardot, T., M. Bauer, H. Teeling, R. Amann, and F.-O. Glöckner. 2005. The transcriptional regulator pool of the marine bacterium Rhodopirellula sp. strain SH 1T as revealed by whole genome comparisons. FEMS Microbiol. Lett. 242:137-145.

Duperon, S., T. Nadalig, J.-C. Caprais, M. Sibuet, A. Fiala-Medioni, R. Amann, and N. Dubilier. 2005. Dual symbiosis in a Bathymodiolus mussel from a methane seep on the Gabon continental margin (Southeast Atlantic): 16S rRNA phylogeny and distribution of the symbionts in gills. Appl. Environ. Microbiol. 71:1694-1700.

Kuypers, M.M.M., G. Lavik, D. Woebken, M. Schmid, B. M. Fuchs, R. Amann, B. B. Jorgensen, and M. S. M. Jetten. 2005. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl. Acad. Sci. USA 102:6478-6483.

Kumar, Y., R. Westram, S. Behrens, B. Fuchs, F. O. Glöckner, R. Amann, H. Meier, and W. Ludwig. 2005. Graphical representation of ribosomal RNA probe accessibility data using ARB software package. BMC Bioinformatics 6:61 (doi:10.1186/1471-2105-6-61).

Fuchs, B. M., D. Wöbken, M. V. Zubkov, P. Burkill, and R. Amann. 2005. Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquatic Microb. Ecol. 39:145-157.

Kube, M., A. Beck, A. Meyerdierks, R. Amann, R. Reinhardt, and R. Rabus. 2005. A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats. Syst. Appl. Microbiol. 28:287-294.

Pena, A., M. Valens, F. Santos, S. Buczolits, J. Anton, P. Kämpfer, H.-J. Busse, R. Amann, and R. Rossello-Mora. 2005. Intraspecific comparative analysis of the species Salinibacter ruber. Extremophiles 9:151-161.

Gieseke, A., J.L. Nielsen, R. Amann, P.H. Nielsen, and D. DeBeer. 2005. In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm. Environ. Microbiol. 7:1392-1404.

Pernthaler, J., and R. Amann. 2005. Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol. Mol. Biol. Rev. 69:440-461.

Gade, D., D. Theiss, D. Lange, E. Mirgorodskaya, T. Lombardot, F. O. Glöckner, M. Kube, R. Reinhardt, R. Amann, H. Lehrach, R. Rabus, and J. Gobom. 2005. Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins. Proteomics 5:3654-3671.

Mußmann, M., M. Richter, T. Lombardot, A. Meyerdierks, J. Kuever, M. Kube, F. O. Glöckner, and R. Amann. 2005. Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer. J. Bacteriol. 187:7126–7137.

Meyerdierks, A., M. Kube, T. Lombardot, K. Knittel, M. Bauer, F. O. Glöckner, R. Reinhardt, and R. Amann. 2005. Insights into the genomes of archaea mediating the anaerobic oxidation of methane. Environ. Microbiol. 7:1937-1951.

Beardsley, C., K. Knittel, R. Amann, and J. Pernthaler. 2005. Quantification and distinction of aplastidic and plastidic marine nanoplankton by fluorescence in situ hybridization. Aquat. Microb. Ecol. 41:163-169.

Buchkapitel:

Anton, J., A. Pena, M. Valens, F. Santos, F. O. Glöckner, M. Bauer, J. Dopazo, J. Herrero, R. Rossello-Mora, and R. Amann. 2005. Salinibacter ruber: genomics and biogeography. In: Adaptations to Life at High Salt Concentrations, p. 257-266. N. Gunde-Cimerman, A. Oren, A. Plemenitas (Eds.). Kluwer Academic Publishers BV, Dordrecht.

2004

Gade, D., H. Schlesner, F. O. Glöckner, R. Amann, S. Pfeiffer, and M. Thomm. 2004. Identification of Planctomycetes with order-, genus- and strain-specific 16S rRNA-targeted probes. Microb. Ecol. 47:243-251.

Warnecke, F., R. Amann, and J. Pernthaler. 2004. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct linages. Environ. Microbiol. 6:242-253.

Zubkov, M., L. J. Linn, R. Amann, and R. P. Kiene. 2004. Temporal patterns of biological dimethylsulfide (DMS) consumption during laboratory-induced phytoplankton bloom cycles. Mar. Ecol. Prog. Ser. 271:77-86.

Peplies, J., S. C. K. Lau, J. Pernthaler, R. Amann, and F. O. Glöckner. 2004. Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ. Microbiol. 6:638-645.

Heuchert, A., F. O. Glöckner, R. Amann, and U. Fischer. 2004. Psychrobacter nivimaris sp. nov., a heterotrophic bacterium attached to organic particles isolated from the South Atlantic (Antarctica). Syst. Appl. Microbiol. 27:399-406.

Altmann, D., P. Stief, R. Amann, and D. de Beer. 2004. Nitrification in freshwater sediments as influenced by insect larvae:quantification by microsensors and fluorescence in situ hybridization. Microb. Ecol. 48:145-153.

Brinkmeyer, R., F.-O. Glöckner, E. Helmke, and R. Amann. 2004. Predominance of betaproteobacteria in summer melt pools on Arctic pack ice. Limnol. Oceanogr. 49:1013-1021.

Rabus, R., A. Ruepp, T. Frickey, T. Rattei, B. Fartmann, M. Stark, M. Bauer, A. Zibat, T. Lombardot, I. Becker, J. Amann, K. Gellner, H. Teeling, W. D. Leuschner, F.-O, Glöckner, A. N. Lupas, R. Amann, and H.-P. Klenk. 2004. The genome of a sulphatereducing bacterium from permanently cold Arctic sediments: Desulfotalea psychrophila. Environ. Microbiol. 6:887-902.

Teeling, H., A. Meyerdierks, M. Bauer, R. Amann, and F. O. Glöckner. 2004. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol. 6:938-947.

Pernthaler, A., and R. Amann. 2004. Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 70:5426-5433.

Behrens, S., B. M. Fuchs, and R. Amann. 2004. The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes. Syst. Appl. Microbiol. 27:565-572.

Peplies, J., F. O. Glöckner, R. Amann, and W. Ludwig. 2004. Comparative sequence analysis and oligonucleotide probe design based on 23S rRNA genes of Alphaproteobacteria from North Sea bacterioplankton. Syst. Appl. Microbiol. 27:573-580.

Sekar, R., B. M. Fuchs, R. Amann, and J. Pernthaler. 2004. Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 70:6210-6219.

Ishii, K., M. Mussmann, B. J. MacGregor, and R. Amann. 2004. An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments. FEMS Microbiol. Ecol. 50:203-212.

Bauer, M., T. Lombardot, H. Teeling, N. L. Ward, R. I. Amann, and F. O. Glöckner. 2004. Archaea-like genes for C1-transfer enzymes in Planctomycetes: phylogenetic implications of their unexpected presence in this phylum. J. Mol. Evol. 59:571-586.

Buchkapitel:

Amann, R., R. Rossello-Mora, C. Flies, and D. Schüler. 2004. Phylogeny and in situ identification of magnetotactic bacteria, p. 45-60. In: Biomineralisation (2. Edition), E. Bäuerlein (Ed.), Wiley-VCH, Weinheim, Germany.

Pernthaler, A., J. Pernthaler, and R. Amann. 2004. Sensitive multi-color in situ hybridization for the identification of environmental microorganisms. In: Molecular Microbial Ecology Manual, Second Edition, 3.11, pp. 711-726. Kowalchuk, G. et al. (Eds.). Kluwer Academic Publishers, Dordrecht, The Netherlands.

Oren, A., F. Rodriguez-Valera, J. Anton, S. Benlloch, R. Rossello-Mora, R. Amann, J. Coleman, and N. J. Russell. 2004. Red, extremely halophilic, but not archaeal: the physiology and ecology of Salinibacter ruber, a bacterium isolated from saltern crystallizer ponds. In: Halophilic microorganisms, pp. 63-76. A. Ventosa. (Ed.). Springer-Verlag, Berlin Heidelberg.

2003

Zubkov, M. V., B. M. Fuchs, G. A. Tarran, P. H. Burkill, and R. Amann. 2003. High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters. Appl. Environ. Microbiol. 69:1299-1304.

Gieseke, A., L. Bjerrum, M. Wagner, and R. Amann. 2003. Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm. Environ. Microbiol. 5:355-369.

Behrens, S., C. Rühland, J. Inacio, H. Huber, A. Fonseca, I. Spencer-Martins, B. M. Fuchs, and R. Amann. 2003. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl. Environ. Microbiol. 69:1748-1758.

Peplies, J., F. O. Glöckner, and R. Amann. 2003. Optimization strategies for the DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol. 69:1397-1407.

Mußmann, M., H. N. Schulz, B. Strotmann, T. Kjaer, L. P. Nielsen, R. A. Rossello-Mora, R. I. Amann, and Bo B. Jorgensen. 2003. Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments. Environ. Microbiol. 5:523-533.

Beardsley, C., J. Pernthaler, W. Wosniok, and R. Amann. 2003. Are readily culturable bacteria in coastal North Sea wateres suppressed by selective grazing mortality? Appl. Environ. Microbiol. 69:2624-2630.

Pernthaler, J., A. Pernthaler, and R. Amann. 2003. Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 69:2631-2637.

Inacio, J., S. Behrens, B. M. Fuchs, A. Fonseca, I. Spencer-Martins, and R. Amann. 2003. In situ accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-labeled oligonucleotide probes comprising the D1 and D2 domains. Appl. Environ. Microbiol. 69:2899-2905.

Sekar, R., A. Pernthaler, J. Pernthaler, F. Warnecke, T. Posch, und R. Amann. 2003. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl. Environ. Microbiol. 69:2928-2935.

Glöckner, F.O., M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K. Borzym, K. Heitmann, R. Rabus, H. Schlesner, R. Amann, and R. Reinhardt. 2003. Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc. Natl. Acad. Sci. USA 100:8298-8303.

Neretin, L. N., A. Schippers, A. Pernthaler, K. Hamann, R. Amann, and B. B. Jorgensen. 2003. Quantification of dissimilatory (bi)sulphite reductase gene expression in Desulfobacterium autotrophicum using real-time RT-PCR. Environ. Microbiol. 5:660-671.

Gonzalez-Toril, E., E. Llobet-Brossa, E. O. Casamayor, R. Amann, and R. Amils. 2003. Microbial ecology of an extreme acidic environment, the Tinto river. Appl. Environ. Microbiol. 69:4853-4865.

Behrens, S., B. M. Fuchs, F. Müller, and R. Amann. 2003. Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a threedimensional structure model of the 30S ribosomal subunit? Appl. Environ. Microbiol. 69:4935-4941.

Knittel, K., A. Boetius, A. Lemke, H. Eilers, K. Lochte, O. Pfannkuche, P. Linke, and R. Amann. 2003. Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, Oregon). Geomicrobiol. J. 20:269-294.

Brinkmeyer, R., K. Knittel, J. Jürgens, H. Weyland, R. Amann, and E. Helmke. 2003. Diversity and structure of bacterial communities in Arctic versus Antarctic Pack Ice. Appl. Environ. Microbiol. 69:6610-6619.

Altmann, D., P. Stief, R. Amann, D. de Beer, and A. Schramm. 2003. In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environ. Microbiol. 5:798-803.

Krüger, M., A. Meyerdierks, F. O. Glöckner, R. Amann, F. Widdel, M. Kube, R. Reinhardt, J. Kahnt, R. Böcher, R. K. Thauer, and S. Shima. 2003. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature (London) 426:878-881.

2002

Gieseke, A., P. Arnz, R. Amann, and A. Schramm. 2002. Simultaneous P and N removal in a sequencing batch biofilm reactor: insights from reactor and microscale investigations. Wat. Res. 36:501-509.

Pernthaler, A., C. M. Preston, J. Pernthaler, E. F. DeLong, and R. Amann. 2002. Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Appl. Environ. Microbiol. 68:661-667.

Anton, J., A. Oren, S. Benlloch, F. Rodriguez-Valera, R. Amann, and R. Rossello-Mora. 2002. Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. Int. J. Syst. Evol. Microbiol. 52:485-491.

Casamayor, E. O., C. Pedros-Alio, G. Muyzer, and R. Amann. 2002. Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. Appl. Environ. Microbiol. 68:1706-1714.

Zubkov, M. V., B. M. Fuchs, S. D. Archer, R. P. Kiene, R. Amann, and P. H. Burkill. 2002. Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea. Deep-Sea Research II. 49:3017-3038

Pernthaler, A., J. Pernthaler, and R. Amann. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:3094-3101.

R. Rabus, D. Gade, R. Helbig, M. Bauer, F. O. Glöckner, M. Kube, H. Schlesner, R. Reinhardt, and R. Amann. 2002. Analysis of N-acetylglucosamine metabolism in the marine bacterium Pirellula sp. strain 1 by a proteomic approach. Proteomics 2:649-655.

Abed, R. M. M., W. Schönhuber, R. Amann, and F. Garcia-Pichel. 2002. Picobenthic cyanobacterial populations revealed by 16S rRNA-targeted in situ hybridization. Environ. Microbiol. 4:375-382.

Michaelis, W., R. Seifert, K. Nauhaus, T. Treude, V. Thiel, M. Blumenberg, K. Knittel, A. Gieseke, K. Peterknecht, T. Pape, A. Boetius, R. Amann, B. B. Joergensen, F. Widdel, J. Peckmann, N. V. Pimenov, and M. B. Gulin. 2002. Microbial reefs in the Black Sea fuelled by anaerobic oxidation of methane. Science 297:1013-1015.

MacGregor, B. J., V. Brüchert, S. Fleischer, and R. Amann. 2002. Isolation of smallsubunit rRNA for stable isotopic characterization. Environ. Microbiol. 4:451-464.

Llobet-Brossa, E., R. Rabus, M. E. Böttcher, M. Könneke, N. Finke, A. Schramm, R. L. Meyer, S. Grötzschel, R. Rossello-Mora, and R. Amann. 2002. Community structure and activity of sulfate-reducing bacteria in an intertidal surface-sediment: a multi-methods approach. Aquatic Microb. Ecol. 29:211-226.

Zubkov, M. V., B. M. Fuchs, G. A. Tarran, P. H. Burkill, and R. Amann. 2002. Mesoscale distribution of dominant bacterioplankton groups in the northern North Sea in early summer. Aquat. Microb. Ecol. 29:135-144.

Pernthaler, A., J. Pernthaler, M. Schattenhofer, and R. Amann. 2002. Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl. Environ. Microbiol. 68:5728-5736.

Borowski, C., O. Giere, J. Krieger, R. Amann, und N. Dubilier. 2002. New aspects of the symbiosis in the provannid snail Ifremeria nautilei from the North Fiji Back Arc Basin. Cah. Biol. Mar. 43:321-324.

Buchkapitel:

Amann, R. 2002. Molekulare Populationsanalyse von Mikroorganismen. Rundgespräche der Kommission für Ökologie, Bd. 23 “Bedeutung der Mikroorganismen für die Umwelt”, P. 31-40, Verlag Dr. Friedrich Pfeil, München.

MacGregor, B. J., K. Ravenschlag, and R. Amann. 2002. Nucleic acid-based techniques for analyzing the diversity, strucutre, and function of microbial communities in marine waters and sediments. In: Microbial systems in sedimentary environments of continental margins, pp. 419-438. G. Wefer et al. Eds. Springer-Verlag, Berlin.

Boetius, A., B. B. Jorgensen, R. Amann, J. P. Henriet, K. U. Hinrichs, K. Lochte, B. J. MacGregor, G. Voordouw. 2002. Microbial systems in sedimentary environments of continental margins. In: Microbial systems in sedimentary environments of continental margins, pp. 479-495. G. Wefer et al. Eds. Springer-Verlag, Berlin.

2001

Ravenschlag, K., K. Sahm, and R. Amann. 2001. Quantitative molecular analysis of the microbial community in marine Arctic sediments. Appl. Environ. Microbiol. 67:387-395.

Schweitzer, B., I. Huber, R. Amann, W. Ludwig, and M. Simon. 2001. Alpha- and betaproteobacteria control the consumption and release of amino acids on lake snow aggregates. Appl. Environ. Microbiol. 67:632-637.

Fuchs, B. M., K. Syutsubo, W. Ludwig, and R. Amann. 2001. In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 67:961-968.

Rossello-Mora, R., and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25:39-67.

Gieseke, A., U. Purkhold, M. Wagner, R. Amann, and A. Schramm. 2001. Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm. Appl. Environ. Microbiol. 67:1351-1362.

Nogales, B., E. R. B. Moore, E. Llobet-Brossa, R. Rossello-Mora, R. Amann, and K. N. Timmis. 2001. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl. Environ. Microbiol. 67:1874-1884.

Pernthaler, J., T. Posch, K. Simek, J. Vrba, A. Pernthaler, F. O. Glöckner, U. Nübel, R. Psenner, and R. Amann. 2001. Predator-specific enrichment of Actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl. Environ. Microbiol. 67:2145-2155.

Dubilier, N., C. Mülders, T. Ferdelman, D. De Beer, A. Pernthaler, M. Klein, M. Wagner, C. Erseus, F. Thiermann, J. Krieger, O. Giere, and R. Amann. 2001. Endosymbiotic sulphat-reducing and sulphide-oxidizing bacteria in an oligochaete worm. Nature (London) 411:298-302.

Simek, K., J. Pernthaler, M. G. Weinbauer, K. Hornak, J. R. Dolan, J. Nedoma, M. Masin, and R. Amann. 2001. Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl. Environ. Microbiol. 67:2723-2733.

Amann, R., B. M. Fuchs, and S. Behrens. 2001. The identification of microorganisms by fluorescence in situ hybridisation. Curr. Opin. Biotech. 12:231-236.

Zubkov, M. V., B. M. Fuchs, S. D. Archer, R. P. Kiene, R. Amann, and P. H. Burkill. 2001. Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ. Microbiol. 3:304-311.

West, N. J., W. A. Schönhuber, N. J. Fuller, R. I. Amann, R. Rippka, A. F. Post, and D. J. Scanlan. 2001.Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridisation using 16S rRNAtargeted oligonucleotides. Microbiol. 147:1731-1744.

Pernthaler A., J. Pernthaler, H. Eilers, and R. Amann. 2001. Growth patterns of two marine isolates: adaptations to substrate patchiness? Appl. Environ. Microbiol. 67:4077-4083.

Schönhuber, W., G. Le Bourhis, J. Tremblay, R. Amann, and S. Kulakauskas. 2001. Utilization of tm RNA sequences for bacterial identification. BMC Microbiology 1:20.

Eilers, H., J. Pernthaler, J. Peplies, F. O. Glöckner, G. Gerdts, and R. Amann. 2001. Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 67:5134-5142.

Zubkov, M. V., B. M. Fuchs, P. H. Burkill, and R. Amann. 2001. Comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the Celtic Sea. Appl. Environ. Microbiol. 67:5210-5218.

Kirchman, D. L., L. Yu, B. M. Fuchs, and R. Amann. 2001. Structure of bacterial communities in aquatic systems as revealed by filter PCR. Aquat. Microb. Ecol. 26:13-22.

Buchkapitel:

Pernthaler, J., F. O. Glöckner, W. Schönhuber, and R. Amann. 2001. Fluorescence in situ hybridization with rRNA-targeted oligonucleotide probes, p. 207-226. In: Methods in Microbiology (Vol. 30): Marine Microbiology, J. Paul (Ed.) Academic Press, San Diego, USA.

Amann, R, and R. Rossello-Mora. 2001. Mikrobiologische Aspekte der Biodiversität, p. 161-180. In: Biodiversität: Wissenschaftliche Grundlagen und gesellschaftliche Relevanz, P. Janich, M. Gutmann und K. Prieß (Ed.). Springer-Verlag, Berlin, Germany.

Amann, R., and K. H. Schleifer. 2001. Nucleic acid probes and their application in environmental microbiology, p. 67-82. In: Bergey’s Manual of Systematic Bacteriology, 2. Edition, Vol. 1, D. R. Boone and R. W. Castenholz (eds.), Springer-Verlag, New York, USA.

2000

Böttcher, M. E., B. Hespenheide, E. Llobet-Brossa, C. Beardsley, O. Larsen, A. Schramm, A. Wieland, G. Böttcher, U.-G. Berninger, and R. Amann. 2000. The biogeochemistry, stable isotope geochemistry, and microbial community structure of a temperate intertidal mudflat: An integrated study. Cont. Shelf Res. 20:1749-1769.

Amann, R. 2000. Who is out there? Microbial aspects of biodiversity. Syst. Appl. Microbiol. 23:1-8.

Groben, R., G. J. Doucette, M. Kopp, M. Kodama, R. Amann, and L. K. Medlin. 2000. 16S rRNA targeted probes for the identification of bacterial strains isolated from cultures of the toxic dinoflagellate Alexandrium tamarense. Microbiol. Ecol. 39:186-196.

Weller, R., F. O. Glöckner, and R. Amann. 2000. 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides. Syst. Appl. Microbiol. 23:107-114.

Fuchs, B. M., M. V. Zubkov, K. Sahm, P. H. Burkill and R. Amann. 2000. Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. Environ. Microbiol. 2:191-201.

Oerther, D. B., J. Pernthaler, A. Schramm, R. Amann, and L. Raskin. 2000. Monitoring precursor 16S rRNAs of Acinetobacter spp. in activated sludge wastewater treatment systems. Appl. Environ. Microbiol. 66:2154-2165.

Thamdrup, B., R. Rossello-Mora, and R. Amann. 2000. Microbial manganese and sulfate reduction in Black Sea shelf sediments. Appl. Environ. Microbiol. 66:2888-2897.

Eilers, H., J. Pernthaler, F. O. Glöckner, and R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66:3044-3051.

Anton, J., R. Rossello-Mora, F. Rodriguez-Valera, and R. Amann. 2000. Extremely halophilic Bacteria in crystallizer ponds from solar salterns. Appl. Environ. Microbiol. 66:3052-3057.

Amann, R.. 2000. Methoden zur Bestimmung der in situ-Funktion von Mikroorganismen. BIOspektrum 6:274-276.

Ravenschlag, K., K. Sahm, C. Knoblauch, B. B. Jorgensen, and R. Amann. 2000. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments. Appl. Environ. Microbiol. 66:3592-3602.

Fuchs, B. M., F. O. Glöckner, and R. Amann. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility of 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66:3603-3607.

Amann, R., and W. Ludwig. 2000. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol. Rev. 24:555-565.

Boetius, A., K. Ravenschlag, C. J. Schubert, D. Rickert, F. Widdel, A. Gieseke, R. Amann, B.B. Jorgensen, U. Witte, O. Pfannkuche. 2000. Microscopic identification of a microbial consortium apparently mediating anaerobic methane oxidation above marine gas hydrates. Nature (London) 407:623-626.

Amann, R.. 2000. Methodological Aspects of fluorescence in situ hybridization. Bioscience Microflora 19:85-91.

H. Eilers, J. Pernthaler, and R. Amann. 2000. Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Appl. Environ. Microbiol. 66:4634-4640.

Glöckner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl. Environ. Microbiol. 66:5053-5065.

Jurgens, G., F. O. Glöckner, R. Amann, A. Saano, L. Montonen, M. Likolammi, and U. Münster. 2000. Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol. Ecol. 34:45-56.

Schramm, A., D. DeBeer, A. Gieseke, and R. Amann. 2000. Microenvironments and distribution of nitrifying bacteria in a membrane-bound biofilm. Environ. Microbiol. 2:680-686.

Amann, G., K. O. Stetter, E. Llobet-Brossa, R. Amann, and J. Anton. 2000. Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui. Extremophiles 4:373-376.

Buchkapitel:

Brand, B. C., R. I. Amann, M. Steinert, D. Grimm, and J. Hacker. 2000. Identification and in situ detection of intracellular bacteria in the environment, p. 601-624. In: Subcellular Biochemistry, Volume 33: Bacterial invasion into eukaryotic cells, T. A. Oelschlaeger and J. Hacker (Eds.). Kluwer Academic/Plenum Publishers, New York, USA.

Amann, R., R. Rossello-Mora, and D. Schüler. 2000. Phylogeny and in situ identification of magnetotactic bacteria, p. 47-60. In: Biomineralisation, E. Bäuerlein (Ed.), Wiley-VCH, Weinheim, Germany.

1999

Jürgens, K., J. Pernthaler, S. Schalla, and R. Amann. 1999. Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl. Environ. Microbiol. 65:1241-1250.

Schönhuber, W., B. Zarda, S. Eix, R. Rippka, M. Herdman, W. Ludwig, and R. Amann. 1999. In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 65:1259-1267.

Juretschko, S., W. Schönhuber, S. Kulakauskas, D. S. Ehrlich, K.-H. Schleifer, and R. Amann. 1999. In situ detection of Escherichia coli cells containing ColE1-related plasmids by hybridization to regulatory RNA II. Syst. Appl. Microbiol. 22:1-8.

Glöckner, F. O., H.-D. Babenzien, J. Wulf, and R. Amann. 1999. Phylogeny and diversity of Achromatium oxaliferum. System. Appl. Microbiol. 22:28-38.

Snaidr, J., B. M. Fuchs, G. Wallner, M. Wagner, K. H. Schleifer, and R. Amann. 1999. Phylogeny and in situ identification of a morphologically conspicuous bacterium, Candidatus Magnospira bakii, present in very low frequency in activated sludge. Environ. Microbiol. 1:125-136.

Rabus, R., H. Wilkes, A. Schramm, G. Harms, A. Behrends, R. Amann, and F. Widdel. 1999. Anaerobic utilization of alkylbenzenes and n-alkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the beta-subclass of Proteobacteria. Environ. Microbiol. 1:145-158.

Dubilier, N., R. Amann, C. Erseus, G. Muyzer, S. Y. Park, O. Giere, and C. M. Cavanaugh. 1999. Phylogenetic diversity of bacterial endosymbionts in the gutless marine oligochete Olavius loisae (Annelida) Mar. Ecol. Prog. Ser. 178:271-280.

Meier, H., R. Amann, W. Ludwig, and K. H. Schleifer. 1999. Specific oligonucleotide probes for the in situ detection of a major group of Gram-positive bacteria with low DNA G+C content. Syst. Appl. Microbiol. 22:186-196.

Schulze, R., S. Spring, R. Amann, I. Huber, W. Ludwig, K.-H. Schleifer, and P. Kämpfer. 1999. Genotypic diversity of Acidovorax strains isolated from activated sludge and description of Acidovorax defluvii sp. nov. Syst. Appl. Microbiol. 22:205-214.

Rossello-Mora, R., B. Thamdrup, H. Schäfer, R. Weller, and R. Amann. 1999. The reponse of the microbial community of marine sediments to organic carbon input under anaerobic conditions. Syst. Appl. Microbiol. 22:237-248.

Zubkov, M. V., B.M. Fuchs, H. Eilers, P. H. Burkill, and R. Amann. 1999. Determination of total protein content of bacterial cells using SYPRO staining and flow cytometry. Appl. Environ. Microbiol. 65:3251-3257.

Simon, M., F. O. Glöckner, and R. Amann. 1999. Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean. Aquatic Microb. Ecol. 18:275-284.

Glöckner, F. O., B. M. Fuchs, and R. Amann. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:3721-3726.

Schramm, A., D. De Beer, J. C van den Heuvel, S. Ottengraf, and R. Amann. 1999. Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl. Environ. Microbiol. 65:3690-3696.

Sahm, K., C. Knoblauch, and R. Amann. 1999. Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine arctic sediments Appl. Environ. Microbiol. 65:3976-3981.

Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65:3882-3989.

Schramm, A., C. M. Santegoeds, H. K. Nielsen, H. Ploug, M. Wagner, M. Pribyl, J. Wanner, R. Amann, and D. De Beer. 1999. On the occurrence of anoxic microniches, denitrification, and sulfate reduction in aerated activated sludge. Appl. Environ. Microbiol. 65:4189-4196.

Anton, J., E. Llobet-Brossa, F. Rodriguez-Valera, and R. Amann. 1999. Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environ. Microbiol. 1:517-523.

Daims, H., A. Brühl, R. Amann, K.-H. Schleifer, and M. Wagner. 1999. The domainspecific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22:434-444.

Berchtold, M., A. Chatzinotas, W. Schönhuber, A. Brune, R. Amann, D. Hahn, and H. König. 1999. Differential enumeration and in situ localization of microorganisms in the hindgut of the lower termite Mastotermes darwiniensis by hybridization with rRNA-targeted probes. Arch. Microbiol. 172:407-416.

Buchkapitel:

Schramm, A., and R. Amann. 1999. Nucleic acid-based techniques for analyzing the diversity, structure, and dynamics of microbial communities in wastewater treatment, p. 85-108. In: Biotechnology: a multi volume comprehensive treatise, H.-J. Rehm, G. Reed, A. Pühler, and P.I.W. Stadler (eds.), Vol. 11a, Environmental Processes I, J. Winter (ed.), Wiley-VCH Verlag GmbH, Weinheim, Germany.

Amann, R.. 1999. FISHen im Unsichtbaren. Chemie heute. Ausgabe 1999/2000, p.118-123.

1998

Ludwig, W., R. Amann, E. Martinez-Romero, W. Schönhuber, S. Bauer, A. Neef, and K.-H. Schleifer. 1998. rRNA based identification and detection systems for rhizobia and other bacteria. Plant and Soil 204:1-19.

Spring, S., U. Lins, R. Amann, K.-H. Schleifer, L. C. S. Ferreira, D. M. S. Esquivel, and M. Farina. 1998. Phylogenetic affiliation and ultrastructure of uncultured magnetic bacteria with unusual large magnetosomes. Arch. Microbiol. 169:136-147.

Michel, R., K.-D. Müller, R. Amann, and E. N. Schmid. 1998. Legionella-like slender rods multiplying within a strain of Acanthamoeba sp. isolated from drinking water. Parasitol. Res. 60:84-88.

Stoffels, M., R. Amann, W. Ludwig, D. Hekmat, and K.-H. Schleifer. 1998. Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds. Appl. Environ. Microbiol. 64:930-939.

Amann, R., H. Lemmer, and M. Wagner. 1998. Monitoring the community structure of wastewater treatment plants: a comparison of old and new techniques. FEMS Microbiol. Ecol. 25:205-215.

Glöckner, F.O., H. D. Babenzien, and R. Amann. 1998. Phylogeny and identification in situ of Nevskia ramosa. Appl. Environ. Microbiol. 64:1895-1901.

Hekmat, D., R. Amann, A. Linn, M. Stephan, M. Stoffels, and D. Vortmeyer. 1998. Biofilm population dynamics in a trickle-bed bioreactor. Wat. Sci. Technol. 37(4-5):167-170.

Schramm, A., D. De Beer, H. van den Heuvel, S. Ottengraf, and R. Amann. 1998. In situ Structure/Function studies in wastewater treatment systems. Wat. Sci. Technol. 37(4-5):413-416.

Llobet-Brossa, E., R. Rossello-Mora, and R. Amann. 1998. Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64:2691-2696.

Amann, R., and M. Kühl. 1998. In situ methods for assessment of microorganisms and their activities. Curr. Opin. Microbiol. 1:352-358.

Hahn, D., A. Hess, R. Amann, and J. Zeyer. 1998. In situ identification of bacterial populations in terrestrial habitats without cultivation. Collana Ambiente 20:41-65.

Schramm, A., D. De Beer, M. Wagner, and R. Amann. 1998. Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl. Environ. Microbiol. 64:3480-3485.

Amann, R., and H. Lemmer. 1998. Grundlagen der in situ-Analyse von Struktur und Dynamik komplexer mikrobieller Lebensgemeinschaften mit rRNS-Sonden und ihre Bedeutung für die wasserwirtschaftliche Praxis. Münchner Beiträge zur Abwasser-, Fischerei- und Flußbiologie 52:11-24.

Lemmer, H., A. Zaglauer, A. Neef, and R. Amann. 1998. In situ-Nachweis der dominaten Denitrifikantenpopulation zur biologisch begründeten Betriebsoptimierung der methanolgestützten Denitrifikation in einem Sandfilter. Münchner Beiträge zur Abwasser-, Fischerei- und Flußbiologie 52:43-60.

Pernthaler, J., T. Posch, K. Simek, J. Vrba, R. Psenner, and R. Amann. 1998. Protisteninduzierte Populationsverschiebungen in einer experimentellen mikrobiellen Gemeinschaft. Münchner Beiträge zur Abwasser-, Fischerei- und Flußbiologie 52:117-126.

Pernthaler, J., A. Alfreider, B. Sattler, F.-O. Glöckner, R. Amann, and R. Psenner. 1998. Strukturanalyse der Bakteriengemeinschaften in einem hochalpinen See. Münchner Beiträge zur Abwasser-, Fischerei- und Flußbiologie 52:127-136.

Meier, H., C. Koob, W. Ludwig, R. Amann, E. Frahm, and K.-H. Schleifer. 1998. Nachweis von Enterokokken mit fluoreszierenden rRNS-gerichteten Sonden zur hygienischen Trinkwasserkontrolle. Münchner Beiträge zur Abwasser-, Fischerei- und Flußbiologie 52:175-200.

Pernthaler, J., F.-O. Glöckner, S. Unterholzner, A. Alfreider, R. Psenner and R. Amann. 1998. Seasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake. Appl. Environ. Microbiol. 64:4299-4306.

Frahm, E., I. Heiber, S. Hoffmann, C. Koob, H. Meier, W. Ludwig, R. Amann, K. H. Schleifer, and U. Obst. 1998. Application of 23S rDNA-targeted oligonucleotide probes specific for enterococci to water hygiene control. System. Appl. Microbiol. 21:450-453.

Neef, A., R. Amann, H. Schlesner, and K. H. Schleifer. 1998. Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144:3257-3266.

Fuchs, B., G. Wallner, W. Beisker, I. Schwippel, W. Ludwig, and R. Amann. 1998. Flow cytometric analysis of in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 64:4973-4982.

Chatzinotas, A., R. A. Sandaa, W. Schönhuber, R. Amann, F. L. Daae, V. Torsvik, J. Zeyer, and D. Hahn. 1998. Analysis of broad-scale differences in microbial community composition of two pristine forest soils. Syst. Appl. Microbiol. 21:579-587.

Michel, R., R. Hoffmann, K.-D. Müller, R. Amann, and E. N. Schmidt. 1998. Akanthamoeben, Naeglerien und andere freilebende Amöben als natürliche Dauerproduzenten von nicht kultivierbaren Bakterien. Mitt. Österr. Ges. Tropenmed. Parasitol. 20:85-92.

Buchkapitel:

Wagner, M., P. Hutzler, and R. Amann. 1998. Three dimensional analysis of complex microbial communities by combining confocal laser scanning microscopy and fluorescence in situ hybridization, p. 467-486. In: Digital image analysis of microbes: imaging, morphometry, fluorometry and motility techniques and applications. M.H.F. Wilkinson and F. Schut. (eds.). John Wiley & Sons, Ltd., Chichester, UK.

Schramm, A., and R. Amann. 1998. In situ structure and function analysis of biofilms. p.45-54 in: Technik anaerober Prozesse, (Eds.) H. Märkl, R. Stegmann, DECHEMAFachgespräche Umweltschutz, DECHEMA e.V., Frankfurt am Main, Germany.

Amann, R. 1998. Entwicklung und Einsatz von Nukleinsäuresonden für die in situ-Charakterisierung natürlicher Bakteriengemeinschaften, p. 55-72. In: Jahrbuch der Akademie der Wissenschaften zu Göttingen, Van den Hoeck & Rupprecht, Göttingen, Germany.

1997

Amann, R., N. Springer, W. Schönhuber, W. Ludwig, E.N. Schmidt, K.-D. Müller and R. Michel. 1997. Obligate intracellular bacterial parasites of acanthamoebae related to Chlamydia spp. Appl. Environ. Microbiol. 63:115-121.

Pernthaler, J., T. Posch, K. Simek, J. Vrba, R. Amann, and R. Psenner. 1997. Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage. Appl. Environ. Microbiol. 63:596-601.

Erhart, R., D. Bradford, E.M. Seviour, R.J. Seviour, R.I. Amann, and L.L. Blackall. 1997. Development and use of fluorescent in situ hybridisation probes for the identification and enumeration of "Microthrix parvicella" in activated sludge. Syst. Appl. Microbiol. 20:310-318.

Eberl, L., R. Schulze, A. Ammendola, O. Geisenberger, R. Erhart, C. Sternberg, S. Molin, and R. Amann. 1997. Use of green fluorescent protein as a marker for ecological studies of activated sludge communities. FEMS Microbiol. Lett. 149:77-83.

Amann, R., F.-O. Glöckner, and A. Neef. 1997. Modern methods in subsurface microbiology: in situ identification of microorganisms with nucleic acid probes. FEMS Microbiol. Rev. 20(3/4):191-200.

Steinert, M., L. Emödy, R. Amann, and J. Hacker. 1997. Resuscitation of viable but nonculturable Legionella pneumophila Philadelphia JR32 by Acanthamoeba castellanii. Appl. Environ. Microbiol. 63:2047-2053.

Kosse, D., H. Seiler, R. Amann, W. Ludwig, and S. Scherer. 1997. Identification of yoghurt-spoiling yeasts with 18S rRNA-targeted oligonucleotide probes. Syst. Appl. Microbiol. 20:468-480.

Snaidr, J., R. Amann, I. Huber, W. Ludwig, and K.-H. Schleifer. 1997. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63:2884-2896.

Amann, R., N. Springer, W. Schönhuber, W. Ludwig, E. N. Schmidt, K.-D. Müller and R. Michel. 1997. Coccoid obligate intracellular parasites of acanthamoebae are distantly related to the genus Chlamydia. Endocytobiosis & Cell Res. 12:99-101.

Lemmer, H., A. Zaglauer, A. Neef, H. Meier, and R. Amann. 1997. Denitrification in a methanol-fed fixed bed reactor. Part 2: Composition and ecology of the bacterial community in the biofilms. Water Res. 31:1903-1908.

Meier, H., C. Koob, W. Ludwig, R. Amann, E. Frahm, S. Hoffmann, U. Obst, and K.-H. Schleifer. 1997. Detection of enterococci with rRNA-targeted DNA probes and their use for hygienic drinking water control. Wat. Sci. Tech. 35(11-12):437-444.

Schönhuber, W., B. Fuchs, S. Juretschko, and R. Amann. 1997. Improved sensitivity of whole cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol. 63:3268-3273.

Schramm, A., L. H. Larsen, N. P. Revsbech, and R. I. Amann. 1997. Structure and function of a nitrifying biofilm as determined by microelectrodes and fluorescent oligonucleotide probes. Wat. Sci. Tech. 36(1):263-270.

Zarda, B., D. Hahn, A. Chatzinotas, W. Schönhuber, A. Neef, R. I. Amann, and J. Zeyer. 1997. Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch. Microbiol. 168:185-192.

Wallner, G., B. Fuchs, W. Beisker, S. Spring, and R. Amann. 1997. Flow cytometric sorting of microorganisms for molecular analysis. Appl. Environ. Microbiol. 63: 4223-4331.

Lischewski, A., M. Kretschmar, H. Hof, R. Amann, J. Hacker, and J. Morschhäuser. 1997. Detection and identification of Candida species in experimentally infected tissue and human blood by rRNA-specific fluorescent in situ hybridization. J. Clin. Microbiol. 35:2943-2948.

Buchkapitel:

Wagner, M., and R. Amann. 1997. Molecular techniques for determining microbial community structures in activated sludge, p. 61-72. In: Microbial community analysis: the key to the design of biological wastewater treatment systems. IAWQ Scientific and Technical Report No. 5 Eds. T.E. Cloete and N.Y.O. Muyima. University Press, Cambridge, UK.

Amann, R.. 1997. Fluorescent, rRNA-targeted oligonucleotide probes for analyzing the in situ structure and dynamics of complex microbial communities, p. 141-145. In: Proceedings of the International Symposium on Environmental Microbiology, Oostende, April 21-23, 1997. H. Verachtert and W. Verstraete (eds.). Technologisch Instituut, Universiteit Gent, Gent, Belgium.

1996

Amann, R.. 1996. In situ-Identifizierung von Mikroorganismen mit rRNS-gerichteten Oligonukleotidsonden. Biospektrum 2 (1):27-32.

Springer, N., R. Amann, W. Ludwig, K.-H. Schleifer, and H. Schmidt. 1996. Polynucleobacter necessarius, an obligate bacterial endosymbiont of the hypotrichous ciliate Euplotes ediculatus, is a member of the ß-subclass of Proteobacteria. FEMS Microb. Lett. 135:333-336.

Wagner, M., G. Rath, H.-P. Koops, J. Flood, and R. Amann. 1996. In situ analysis of nitrifying bacteria in sewage treatment plants. Wat. Sci. Tech. 34(1-2):237-244.

Kämpfer, P., R. Erhart, C. Beimfohr, J. Böhringer, M. Wagner, and R. Amann. 1996. Characterization of bacterial communities from activated sludge plant: culture-dependent numerical identification versus in situ identification using group- and genus-specific rRNAtargeted oligonucleotide probes. Microb. Ecol. 32:101-121.

Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K.-H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiol. 142:1097-1106.

Alfreider, A., J. Pernthaler, R. Amann, B. Sattler, F.-O. Glöckner, A. Wille and R. Psenner. 1996. Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake using in situ hybridization. Appl. Environ. Microbiol. 62:2138-2144.

Weiss, P., B. Schweitzer, R. Amann, and M. Simon. 1996. Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl. Environ. Microbiol. 62:1998-2005.

Glöckner, F.O., R. Amann, A. Alfreider, J. Pernthaler, R. Psenner, K. Trebesius, and K.-H. Schleifer. 1996. An optimized in situ hybridization protocol for planktonic bacteria. Syst. Appl. Microbiol. 19:403-406.

Lange, M., N. Simon, L. Guillou, D. Vaulot, R. Amann, W. Ludwig, and L. K. Medlin. 1996. Identification of the class Prymnesiophyceae and the genus Phaeocystis with rRNAtargeted nucleic acid probes. J. Phycol. 32:858-868.

Amann, R., J. Snaidr, M. Wagner, W. Ludwig and K.-H. Schleifer. 1996. In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178: 3496-3500.

Lischewski, A., R. I. Amann, D. Harmsen, H. Merkert, J. Hacker and J. Mörschenhäuser. 1996. Specific detection of Candida albicans and Candida tropicalis by fluorescent in situ ybridization with an 18S rRNA-targeted oligonucleotide probe. Microbiology 142:2731-2740.

Lloyd, D., A. G. Williams, R. Amann, A. J. Hayes, L. Durrant, and J. R. Ralphs. 1996. Intracellular prokaryotes in rumen ciliate protozoa: detection by confocal laser scanning microscopy after in situ hybridization with fluorescent 16S rRNA probes. Europ. J. Protistol. 32:523-531.

Nübel, U., B. Engelen, A. Felske, J. Snaidr, A. Wieshuber, R. I. Amann, W. Ludwig, and H. Backhaus. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:5636-5643.

Neef, A., A. Zaglauer, H. Meier, R. Amann, H. Lemmer, and K.-H. Schleifer. 1996. Population analysis in a denitrifying sand filter: conventional and in situ identification of Paracoccus sp. in methanol-fed biofilms. Appl. Environ. Microbiol. 62:4329-4339.

Schramm, A., L.H. Larsen, N. P. Revsbech, N. B. Ramsing, R. Amann, and K.-H. Schleifer. 1996. Structure and function of a nitrifying biofilm as determined by in situ hybridization and microelectrodes. Appl. Environ. Microbiol. 62:4641-4647.

Wallner, G., I. Steinmetz, D. Bitter-Suermann, and R. Amann. 1996. Combination of rRNA-targeted hybridization probes and immuno-probes for the identification of bacteria by flow cytometry. Syst. Appl. Microbiol. 19:569-576.

Amann, R., W. Ludwig, R. Schulze, S. Spring, E. Moore, and K.-H. Schleifer. 1996. rRNA-Targeted oligonucleotide probes for the identification of genuine and former pseudomonads. Syst. Appl. Microbiol. 19:501-509.

Rothemund, C., R. Amann, S. Klugbauer, W. Manz, C. Bieber, K.-H. Schleifer, and P. Wilderer. 1996. Microflora of 2,4-dichlorophenoxyacetic acid degrading biofilms on gas permeable membranes. Syst. Appl. Microbiol. 19:608-615.

Buchkapitel:

Springer, N., R. Amann, and W. Ludwig. 1996. The design and application of ribosomal RNA-targeted, fluorescent oligonucleotide probes for the identification of endosymbionts in protozoa, p. 133-144. In: Methods in Molecular Biology, Vol. 50: Species Diagnostics Protocols: PCR and other nucleic acid methods. J.P. Clapp (Ed.), Humana Press Inc., Totowa NJ, USA.

Wallner, G., and R. Amann. 1996. Durchflußzytometrische Untersuchung von Belebtschlamm mit rRNS-gerichteten Oligonukleotidsonden, p. 81-92. In H. Lemmer, T. Griebe, H.-C. Flemming (eds.), Mikrobielle Ökologie des Abwassers. Springer Verlag, Berlin.

Wagner, M., and R. Amann. 1996. Die Anwendung von in situ Hybridisierungssonden zur Aufklärung von Struktur und Dynamik der mikrobiellen Biozönosen in der Abwasserreinigung, p. 93-110. In H. Lemmer, T. Griebe, H.-C. Flemming (eds.), Mikrobielle Ökologie des Abwassers. Springer Verlag, Berlin.

1995

Manz, W., R. Szewzyk, U. Szewzyk, P. Hutzler, R. Amann and K. H. Schleifer. 1995. In situ identification of Legionellaceae using specific rRNA-targeted oligonucleotide probes and confocal laser scanning microscopy. Microbiol. 141:29-39.

Rossello-Mora, R. A., M. Wagner, R. Amann, and K. H. Schleifer. 1995. The abundance of Zoogloea ramigera in sewage treatment plants. Appl. Environ. Microbiol. 61:702-707.

Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.

Assmus, B., P. Hutzler, G. Kirchhof, R. Amann, J.R. Lawrence, and A. Hartmann. 1995. In situ localization of Azospirillum brasilense in the rhizosphere of wheat using fluorescently labeled, rRNA-targeted oligonucleotide probes and scanning confocal laser microscopy. Appl. Environ. Microbiol. 61:1013-1019.

Raskin, L., R. I. Amann, L. K. Poulsen, B. E. Rittmann, and D. A. Stahl. 1995. Use of ribosomal RNA-based molecular probes for characterization of complex microbial communities in anaerobic biofilms. Wat. Sci. Techol. 31:261-272.

Wallner, G., R. Erhart, and R. Amann. 1995. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl. Environ. Microbiol. 61:1859-1866.

Fischer, K., D. Hahn, R. I. Amann, O. Daniel, and J. Zeyer. 1995. In situ analysis of the bacterial community in the gut of the earthworm Lumbricus terrestris L. by whole-cell hybridization. Can. J. Microbiol. 41:666-673.

Wedi, D., M. Wagner, R. Amann, R. Erhart, H. Lemmer, and P. A. Wilderer. 1995. In situ-Nachweis der untergeordneten Rolle von Bakterien der Gattung Acinetobacter bei der erhöhten biologischen P-Elimination. GWF Wasser Abwasser 136:17-23.

Neef, A., R. Amann, and K.-H. Schleifer. 1995. Detection of microbial cells in aerosols using nucleic acid probes. Syst. Appl. Microbiol. 18:113-122.

Amann, R. I.. 1995. Fluorescently labelled, rRNA-targeted oligonucleotide probes in the study of microbial ecology. Mol. Ecol. 4:543-554.

Rossello-Mora, R. A., W. Ludwig, P. Kämpfer, R. Amann, and K.-H. Schleifer. 1995. Ferrimonas balearica, gen. nov., spec. nov., a new marine facultative Fe(III)-reducing bacterium. Syst. Appl. Microbiol. 17:196-202.

Wagner, M., G. Rath, R. Amann, H.-P. Koops, and K.-H. Schleifer. 1995. In situ identification of ammonia-oxidizing bacteria. Syst. Appl. Microbiol. 17:251-264.

Schleifer, K.-H., M. Ehrmann, C. Beimfohr, E. Brockmann, W. Ludwig and R. Amann. 1995. Application of molecular methods for the classification and identification of lactic acid bacteria. Int. Dairy J. 5:1081-1094.

Buchkapitel:

Amann, R. I.. 1995. In situ identification of microorganisms by whole cell hybridization with rRNA-targeted nucleic acid probes, 3.3.6., p. 1-15. In: Molecular Microbial Ecology Manual. A.D.L. Akkerman, J.D. van Elsas and F.J. de Bruijn (eds.), Kluwer Academic Publishers, Dordrecht, Netherlands.

Amann, R. I.. 1995. In situ hybridization with rRNA-targeted probes as a tool to study the compositon and dynamics of microbial communities, p. 92. In: Beijerinck Centennial. Microbial Physiology and Gene Regulation: Emerging Principles and Applications. W.A. Scheffers and J.P. van Dijken (Eds.), Delft University Press, The Netherlands.

Stahl, D. A., R. I. Amann, L. K. Poulsen, L. Raskin, and W. C. Capman. 1995. Use of fluorescent probes for determinative microscopy of methanogenic archaea, p. 111-121. In: Archaea: a laboratory manual, Vol. 2, Methanogens. K.R. Sowers & H.J. Schreier (Eds.), Cold Spring Harbor Press, Cold Spring Harbor, USA.

1994

Szewzyk, U., W. Manz, R. Amann, K.-H. Schleifer, and T.-A. Stenström. 1994. Growth and in situ detection of a pathogenic Escherichia coli in biofilms of a heterotrophic waterbacterium by use of 16S- and 23S-rRNA-directed fluorescent oligonucleotide probes. FEMS Microbiol. Ecol. 13:169-176.

Wagner, M., R. Erhart, W. Manz, R. Amann, H. Lemmer, D. Wedi, and K. H. Schleifer. 1994. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:792-800.

Aznar, R., W. Ludwig, R. I. Amann, and K.-H. Schleifer. 1994. Sequence determination of rRNA genes of pathogenic Vibrio species and whole-cell identification of Vibrio vulnificus with rRNA-targeted oligonucleotide probes. Int. J. Syst. Bacteriol. 44:330-337.

Manz, W., M. Wagner, R. Amann, and K. H. Schleifer. 1994. In situ characterization of the microbial consortia active in two wastewater treatment plants. Wat. Res. 28:1715-1723.

Amann, R., W. Ludwig, and K. H. Schleifer. 1994. Identification of nonculturable bacteria: a challenging task for the molecular taxonomist. ASM News 60:360-365.

Burggraf, S., T. Mayer, R. Amann, S. Schadhauser, C. R. Woese, and K. O. Stetter. 1994. Identifying members of the domain Archaea with rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 60:3112-3119.

Trebesius, K., R. Amann, W. Ludwig, K. Mühlegger, and K. H. Schleifer. 1994. Identification of whole fixed bacterial cells with nonradioactive 23S rRNA-targeted polynucleotide probes. Appl. Environ. Microbiol. 60:3228-3235.

Wagner, M., R. Amann, H. Lemmer, W. Manz, and K. H. Schleifer. 1994. Probing activated sludge with fluorescently labeled rRNA targeted oligonucleotides. Wat. Sci. Tech. 29:15-23.

Roller, C., M. Wagner, R. Amann, W. Ludwig, and K.-H. Schleifer. 1994. In situ probing of Gram-positive bacteria with high DNA G+C content using 23S rRNA-targeted oligonucleotides. Microbiol. 140:2849-2858.

Lin, C., B. Flesher, W. C. Capman, R. I. Amann, and D. A. Stahl. 1994. Taxon-specific hybridization probes for fiber-digesting bacteria suggest novel gut-associated Fibrobacter. Syst. Appl. Microbiol. 17:418-424.

Lloyd, D., J. Ralphs, L. Durrant, A.G. Williams, and R. Amann. 1994. Studies of the bacterial endosymbionts of "anaerobic protozoa" using fluorescently-labelled rRNA-targeted oligonucleotide probes. Biochem. Soc. Trans. 22:323S.

Wagner, M., R. Amann, P. Kämpfer, B. Assmus, A. Hartmann, P. Hutzler, N. Springer, and K. H. Schleifer. 1994. Identification and in situ detection of gram-negative filamentous bacteria in activated sludge. Syst. Appl. Microbiol. 17:405-417.

Polz, M. F., D. L. Distel, B. Zarda, R. Amann, H. Felbeck, J. A. Ott, and C. M. Cavanaugh. 1994. Phylogenetic analysis of a highly specific association between ectosymbiotic, sulfur oxidizing bacteria and a marine nematode. Appl. Environ. Microbiol. 60:4461-4467.

Ludwig, W., and R. Amann. 1994. Design and application of rRNA-targeted specific hybridization probes. Soils Newsletter 17:16.

Wagner, M., B. Aßmus, A. Hartmann, P. Hutzler, and R. Amann. 1994. In situ analysis of microbial consortia in activated sludge using fluorescently labelled, rRNA-targeted oligonucleotide probes and confocal scanning laser microscopy. J. Microscopy 176:181-187.

Spring, S., R. Amann, W. Ludwig, K.-H. Schleifer, D. Schüler, K. Poralla, and N. Petersen. 1994. Phylogenetic analysis of uncultured magnetotactic bacteria from the alphasubclass of Proteobacteria. Syst. Appl. Microbiol. 17:501-508.

Rossello-Mora, R. A., F. Caccavo, Jr., K. Osterlehner, N. Springer, S. Spring, D. Schüler, W. Ludwig, R. Amann, M. Vanncanneyt and K. H. Schleifer. 1994. Isolation and taxonomic characterization of a halotolerant, facultatively iron-reducing bacterium. Syst. Appl. Microbiol. 17:569-573.

Buchkapitel:

Amann, R., B. Zarda, K. H. Trebesius, W. Ludwig, and K. H. Schleifer. 1994. Rapid identification and in situ detection of microorganisms using fluorescent rRNA-targeted oligonucleotides, p. 237-244. In: Rapid Methods and Automation in Microbiology and Immunology. R.C. Spencer, E.P. Wright and S.W.B. Newsom (Eds.), Intercept Ltd., Andover, UK.

Amann, R., and W. Ludwig. 1994. Typing in situ with Probes, pp. 115-135. In: Bacterial Diversity and Systematics. F.G. Priest, A. Ramos-Cormenzana, and B.J. Tindall (Eds.), Plenum, New York, USA.

1993

Wallner, G., R. Amann, and W. Beisker. 1993. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143.

Wagner, M., R. Amann, H. Lemmer, and K. H. Schleifer. 1993. Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59:1520-1525.

Hahn, D., R. I. Amann, and J. Zeyer. 1993. Whole cell hybridization of Frankia strains with fluorescence- or digoxigenin-labeled, 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 59:1709-1716.

Manz, W., U. Szewzyk, P. Eriksson, R. Amann, K. H. Schleifer, and T.-A. Stenström. 1993. In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl. Environ. Microbiol. 59:2293-2298.

Spring, S., R. Amann, W. Ludwig, K. H. Schleifer, H. van Gemerden, and N. Petersen. 1993. Dominating role of an unusual magnetotactic bacterium in the microaerophilic zone of a freshwater sediment. Appl. Environ. Microbiol. 59:2397-2403.

Ludwig, W., and R. Amann. 1993. The rRNA approach: reconstruction of bacterial phylogenies, design and application of specific probes. Soils Newsletter 16:10-11.

Beimfohr, C., A. Krause, R. Amann, W. Ludwig, and K. H. Schleifer. 1993. In situ identification of lactococci, enterococci and streptococci. Syst. Appl. Microbiol. 16:450-456.

Hahn, D., R. I. Amann, and J. Zeyer. 1993. Detection of mRNA in Streptomyces cells by in situ hybridization with digoxigenin-labeled probes. Appl. Environ. Microbiol. 59:2753-2757.

Springer, N., W. Ludwig, R. Amann, H. J. Schmidt, H.-D. Görtz, and K.-H. Schleifer. 1993. Occurrence of fragmented 16S rRNA in an obligate bacterial endosymbiont of Paramecium caudatum. Proc. Natl. Acad. Sci. USA 90:9892-9895.

Buchkapitel:

Schleifer, K. H., W. Ludwig, and R. I. Amann. 1993. Nucleic acid probes, p. 463-510. In: Handbook of New Bacterial Systematics. M. Goodfellow and A.G. O'Donnell (Eds.), Academic Press Limited, London, England.

Amann, R. I., W. Ludwig, W. Manz, S. Spring, N. Springer, M. Wagner, and K. H. Schleifer. 1993. In situ identification of nonculturable bacteria with rRNA-targeted nucleic acid probes, p. 515-520. In: Trends in Microbial Ecology. R. Guerrero & C. Pedros-Alio (Eds.), Spanish Society for Microbiology, Barcelona, Spain.

Wagner, M., R. Erhart, D. Wedi, and R. Amann. 1993. In-situ-Nachweis der untergordneten Rolle von Acinetobacter in Kläranlagen mit biologisch erhöhter Phosphateliminierung, p. 91-100. In: Wechselwirkungen der biologischen und chemischen Phosphorelimination. H.H. Hahn & R. Trauth (Eds.), Veröff. Inst. Siedlungswasserbau Universität Karlsruhe, Band 68.

1992

Amann, R. I., C. Lin, R. Key, L. Montgomery, and D. A. Stahl. 1992. Diversity among Fibrobacter isolates: towards a phylogenetic and habitat-based classification. Syst. Appl. Microbiol. 15:23-31.

Spring, S., R. Amann, W. Ludwig, K.-H. Schleifer, and N. Petersen. 1992. Phylogenetic diversity and identification of nonculturable magnetotactic bacteria. Syst. Appl. Microbiol. 15:116-122.

Amann, R. I., J. Stromley, R. Devereux, R. Key, and D. A. Stahl. 1992. Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58:614-623.

Hahn, D., R. I. Amann, W. Ludwig, A. D. L. Akkermans, and K.-H. Schleifer. 1992. Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labelled oligonucleotides. J. Gen. Microbiol. 138:879-887.

Schleifer, K. H., W. Ludwig, and R. Amann. 1992. Gensonden und ihre Anwendung in der Mikrobiologie. Naturwissenschaften 79:213-219.

Amann, R., and W. Ludwig. 1992. Unbekanntem Leben auf der Spur: Stammesgeschichtliche Einordnung und Identifizierung von nichtkultivierbaren Bakterien. Naturwissenliche Rundschau 45:348-351.

Hicks, R. E., R. I. Amann, and D. A. Stahl. 1992. Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdomlevel 16S rRNA sequences. Appl. Environ. Microbiol. 58:2158-2163.

Amann, R. I., B. Zarda, D. A. Stahl, and K. H. Schleifer. 1992. Identification of individual prokaryotic cells with enzyme-labeled, rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 58:3007-3011.

Springer, N., W. Ludwig, V. Drozanski, R. Amann, and K.-H. Schleifer. 1992. The phylogenetic status of Sarcobium lyticum, an obligate intracellular bacterial parasite of small amoeba. FEMS Microbiol. Lett. 96:199-202.

Manz, W., R. Amann, W. Ludwig, M. Wagner, and K.-H. Schleifer. 1992. Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:593-600.

Schleifer, K. H., W. Ludwig, and R. Amann. 1992. Ribosomal ribonucleic acid sequence analysis and hybridization technology in the identification of microorgansims. Fresenius J. Anal. Chem. 343:47.

Amann, R., W. Ludwig, and K. H. Schleifer. 1992. Identification and in situ detection of individual bacterial cells. FEMS Microbiol. Lett. 100:45-50.

Buchkapitel:

Schleifer, K. H., W. Ludwig, and R. Amann. 1992. Einblick in eine verborgene Welt. In: TUM Forschung für Bayern 3:8-9. Technische Universität München.

Schleifer, K .H., R. Amann, W. Ludwig, C. Rothemund, N. Springer, and S. Dorn. 1992. Nucleic acid probes for the identification and in situ detection of pseudomonads, p. 127-134. In: Pseudomonas: Molecular Biology and Biotechnology. E. Galli, S. Silver and B. Witholt (Eds.), American Society for Microbiology, Washington, DC.

1991

Amann, R. I., N. Springer, W. Ludwig, H.-D. Görtz, and K.-H. Schleifer. 1991. Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature (London) 351:161-164.

Schleifer, K.-H., D. Schüler, S. Spring, M. Weizenegger, R. Amann, W. Ludwig, and M. Köhler. 1991. The genus Magnetospirillum gen. nov.. Description of Magnetospirillum gryphiswaldense sp. nov. and transfer of Aquaspirillum magnetotacticum to Magnetospirillum magnetotacticum comb. nov.. Syst. Appl. Microbiol. 14:379-385.

Zarda, B., R. Amann, G. Wallner, and K. H. Schleifer. 1991. Identification of single bacterial cells using digoxigenin-labelled, rRNA-targeted oligonucleotides. J. Gen. Microbiol. 137:2823-2830.

Buchkapitel:

Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In: Nucleic Acid Techniques in Bacterial Systematics. E. Stackebrandt and M. Goodfellow (Eds.), John Wiley and Sons, Chichester, England.

Schleifer, K. H., W. Ludwig, R. Amann, C. Hertel, M. Ehrmann, W. Köhler, and A. Krause. 1991. Phylogenetic relationships of lactic acid bacteria and their identification with nucleic acid probes. p. 23-32 In: Actes du colloque LACTIC 91. G. Novel and J.-F. Le Querler (Eds.) Caen University Press, Caen, France.

1990

Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.

Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.

1989

Buchkapitel:

Stahl, D. A., R. Devereux, R. I. Amann, B. Flesher, C. Lin, and J. Stromley. 1989. Ribosomal RNA based studies of natural microbial diversity and ecology, p. 669-673. In: Recent advances in microbial ecology. T. Hattori, Y. Ishida, Y. Maruyama, R. Morita, and A. Uchida (Eds.), Japan Scientific Societies Press, Tokio, Japan.

1988

Amann, R., P. Sostak, W. Ludwig, and K.-H. Schleifer. 1988. Cloning and sequencing of genes encoding the beta-subunits of ATP-synthases from Enterobacter aerogenes and Flavobacterium ferrugineum. FEMS Microbiol. Lett. 50:101-106.

Amann, R., W. Ludwig, and K.H. Schleifer. 1988. Beta-subunit of ATP-synthase: a useful marker for studying the phylogenetic relationship of eubacteria. J. Gen. Microbiol. 134:2815-2821.

Amann, R. I. 1988. Die beta-Untereinheit der ATP-Synthase als phylogenetischer Marker bei den Eubakterien. Dissertation. Technische Universität München.

Amann, R., W. Ludwig, W. Laubinger, P. Dimroth, and K. H. Schleifer. 1988. Cloning and sequencing of the gene encoding the beta-subunit of the sodium ion translocating ATPsynthase of Propionigenium modestum. FEMS Microbiol. Lett. 56:253-259.