Wastewater treatment: a model system for microbial ecology

Isolation of an autotrophic ammonia-oxidizing marine archaeon

Könneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., & Stahl, D. A. (2005) · Nature · doi:10.1038/nature03911 · Cited by 2,857

Missing lithotroph identified as new planctomycete

Strous, M., Fuerst, J. A., Kramer, E. H. M., Logemann, S., Muyzer, G., van de Pas-Schoonen, K. T., Webb, R., Kuenen, J. G., & Jetten, M. S. M. (1999) · Nature · doi:10.1038/22749 · Cited by 1,575

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M. W., Horn, M., Daims, H., Bartol-Mavel, D., Wincker, P., et al. (2006) · Nature · doi:10.1038/nature04647 · Cited by 1,355

Stable-isotope probing as a tool in microbial ecology

Radajewski, S., Ineson, P., Parekh, N. R., & Murrell, J. C. (2000) · Nature · doi:10.1038/35001054 · Cited by 1,252

The SHARON®-Anammox® process for treatment of ammonium rich wastewater

van Dongen, U., Jetten, M. S. M., & van Loosdrecht, M. C. M. (2001) · Water Science and Technology · doi:10.2166/wst.2001.0037 · Cited by 854

Viral metagenomics

Edwards, R. A., & Rohwer, F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1163 · Cited by 820

In Situ Characterization of Nitrospira -Like Nitrite-Oxidizing Bacteria Active in Wastewater Treatment Plants

Daims, H., Nielsen, J. L., Nielsen, P. H., Schleifer, K.-H., & Wagner, M. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.11.5273-5284.2001 · Cited by 809

Combined Molecular and Conventional Analyses of Nitrifying Bacterium Diversity in Activated Sludge: Nitrosococcus mobilis and Nitrospira -Like Bacteria as Dominant Populations

Juretschko, S., Timmermann, G., Schmid, M., Schleifer, K.-H., Pommerening-Röser, A., Koops, H.-P., & Wagner, M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.8.3042-3051.1998 · Cited by 806

Identification of Polyphosphate-Accumulating Organisms and Design of 16S rRNA-Directed Probes for Their Detection and Quantitation

Crocetti, G. R., Hugenholtz, P., Bond, P. L., Schuler, A., Keller, J., Jenkins, D., & Blackall, L. L. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.3.1175-1182.2000 · Cited by 691

Molecular Evidence for Genus Level Diversity of Bacteria Capable of Catalyzing Anaerobic Ammonium Oxidation

Schmid, M., Twachtmann, U., Klein, M., Strous, M., Juretschko, S., Jetten, M., Metzger, J. W., Schleifer, K.-H., & Wagner, M. (2000) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(00)80050-8 · Cited by 687

Combination of Fluorescent In Situ Hybridization and Microautoradiography—a New Tool for Structure-Function Analyses in Microbial Ecology

Lee, N., Nielsen, P. H., Andreasen, K. H., Juretschko, S., Nielsen, J. L., Schleifer, K.-H., & Wagner, M. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.3.1289-1297.1999 · Cited by 656

Genomic studies of uncultivated archaea

Schleper, C., Jurgens, G., & Jonuscheit, M. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1159 · Cited by 637

Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate

Egli, K., Fanger, U., Alvarez, P. J. J., Siegrist, H., van der Meer, J. R., & Zehnder, A. J. B. (2001) · Archives of Microbiology · doi:10.1007/s002030100255 · Cited by 628

RNA Stable Isotope Probing, a Novel Means of Linking Microbial Community Function to Phylogeny

Manefield, M., Whiteley, A. S., Griffiths, R. I., & Bailey, M. J. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.11.5367-5373.2002 · Cited by 595

Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea

Chain, P., Lamerdin, J., Larimer, F., Regala, W., Lao, V., Land, M., Hauser, L., Hooper, A., Klotz, M., Norton, J., et al. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.9.2759-2773.2003 · Cited by 550

Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge

Wagner, M., Erhart, R., Manz, W., Amann, R., Lemmer, H., Wedi, D., & Schleifer, K. H. (1994) · Applied and Environmental Microbiology · doi:10.1128/aem.60.3.792-800.1994 · Cited by 540

The CANON System (Completely Autotrophic Nitrogen-removal Over Nitrite) under Ammonium Limitation: Interaction and Competition between Three Groups of Bacteria

Third, K. A., Sliekers, O., Kuenen, J. G., & Jetten, M. S. M. (2001) · Systematic and Applied Microbiology · doi:10.1078/0723-2020-00077 · Cited by 481

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

Schramm, A., de Beer, D., van den Heuvel, J. C., Ottengraf, S., & Amann, R. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.8.3690-3696.1999 · Cited by 463

Genomic Islands and the Ecology and Evolution of Prochlorococcus

Coleman, M. L., Sullivan, M. B., Martiny, A. C., Steglich, C., Barry, K., DeLong, E. F., & Chisholm, S. W. (2006) · Science · doi:10.1126/science.1122050 · Cited by 458

Identification and Activities In Situ of Nitrosospira and Nitrospira spp. as Dominant Populations in a Nitrifying Fluidized Bed Reactor

Schramm, A., de Beer, D., Wagner, M., & Amann, R. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.9.3480-3485.1998 · Cited by 437

Glycogen-accumulating organisms in laboratory-scale and full-scale wastewater treatment processes b bThe GenBank accession numbers for the sequences reported in this paper are given in Methods.

Crocetti, G. R., Banfield, J. F., Keller, J., Bond, P. L., & Blackall, L. L. (2002) · Microbiology · doi:10.1099/00221287-148-11-3353 · Cited by 380

Enrichment, Phylogenetic Analysis and Detection of a Bacterium That Performs Enhanced Biological Phosphate Removal in Activated Sludge

Hesselmann, R. P. X., Werlen, C., Hahn, D., van der Meer, J. R., & Zehnder, A. J. B. (1999) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(99)80055-1 · Cited by 363

Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes

Wagner, M., Horn, M., & Daims, H. (2003) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(03)00054-7 · Cited by 363

Microbial community genomics in the ocean

DeLong, E. F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1158 · Cited by 300

Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester

Chouari, R., Le Paslier, D., Daegelen, P., Ginestet, P., Weissenbach, J., & Sghir, A. (2005) · Environmental Microbiology · doi:10.1111/j.1462-2920.2005.00795.x · Cited by 290

Identification and in situ Detection of Gram-negative Filamentous Bacteria in Activated Sludge

Wagner, M., Amann, R., Kämpfer, P., Assmus, B., Hartmann, A., Hutzler, P., Springer, N., & Schleifer, K.-H. (1994) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(11)80058-5 · Cited by 265

The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function

Adamczyk, J., Hesselsoe, M., Iversen, N., Horn, M., Lehner, A., Nielsen, P. H., Schloter, M., Roslev, P., & Wagner, M. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.11.6875-6887.2003 · Cited by 221

Nitrite concentration influences the population structure of Nitrospira ‐like bacteria

Maixner, F., Noguera, D. R., Anneser, B., Stoecker, K., Wegl, G., Wagner, M., & Daims, H. (2006) · Environmental Microbiology · doi:10.1111/j.1462-2920.2006.01033.x · Cited by 214

“Microthrix parvicella”, a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge

Rossetti, S., Tomei, M. C., Nielsen, P. H., & Tandoi, V. (2004) · FEMS Microbiology Reviews · doi:10.1016/j.femsre.2004.09.005 · Cited by 204

A review and update of the microbiology of enhanced biological phosphorus removal in wastewater treatment plants

Blackall, L. L., Crocetti, G. R., Saunders, A. M., & Bond, P. L. (2002) · Antonie van Leeuwenhoek · doi:10.1023/a:1020538429009 · Cited by 202

Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255

Starkenburg, S. R., Chain, P. S. G., Sayavedra-Soto, L. A., Hauser, L., Land, M. L., Larimer, F. W., Malfatti, S. A., Klotz, M. G., Bottomley, P. J., Arp, D. J., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.3.2050-2063.2006 · Cited by 191

Biodegradation of xenobiotics by anaerobic bacteria

Zhang, C., & Bennett, G. N. (2005) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-004-1864-3 · Cited by 177

Solved upscaling problems for implementing deammonification of rejection water

Wett, B. (2006) · Water Science & Technology · doi:10.2166/wst.2006.413 · Cited by 170

Studies on the in situ physiology of Thiothrix spp. present in activated sludge

Nielsen, P. H., de Muro, M. A., & Nielsen, J. L. (2000) · Environmental Microbiology · doi:10.1046/j.1462-2920.2000.00120.x · Cited by 147

Microbial ecology to manage processes in environmental biotechnology

Rittmann, B. E. (2006) · Trends in biotechnology · doi:10.1016/j.tibtech.2006.04.003 · Cited by 145

Microthrix parvicella, a specialized lipid consumer in anaerobic–aerobic activated sludge plants

Nielsen, P. H., Roslev, P., Dueholm, T. E., & Nielsen, J. L. (2002) · Water Science & Technology · doi:10.2166/wst.2002.0459 · Cited by 138

A Vista for Microbial Ecology and Environmental Biotechnology

Rittmann, B. E., Hausner, M., Löffler, F. E., Love, N. G., Gerard Muyzer, C., Okabe, S., Oerther, D. B., Peccia, J., Raskin, L. M., & Wagner, M. (2006) · Environmental Science & Technology · doi:10.1021/es062631k · Cited by 132

Nitrification as a source of soluble organic substrate in biological treatment

Rittmann, B. E., Regan, J. M., & Stahl, D. A. (1994) · Water Science & Technology · doi:10.2166/wst.1994.0247 · Cited by 128

A wide host‐range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase

Wexler, M., Bond, P. L., Richardson, D. J., & Johnston, A. W. B. (2005) · Environmental Microbiology · doi:10.1111/j.1462-2920.2005.00854.x · Cited by 126

Molecular, biochemical and ecological characterisation of a bio-catalytic calcification reactor

Hammes, F., Boon, N., Clément, G., de Villiers, J. D., Siciliano, S., & Verstraete, W. (2003) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-003-1287-6 · Cited by 49

Integrating economic costs into conservation planning

NAIDOO, R., BALMFORD, A., FERRARO, P., POLASKY, S., RICKETTS, T., & ROUGET, M. (2006) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.10.003 · Cited by 892

Roots, Nitrogen Transformations, and Ecosystem Services

Jackson, L. E., Burger, M., & Cavagnaro, T. R. (2008) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.59.032607.092932 · Cited by 339

Functional analysis of natural microbial consortia using community proteomics

VerBerkmoes, N. C., Denef, V. J., Hettich, R. L., & Banfield, J. F. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2080 · Cited by 269