Daniel R. Noguera

Wisconsin Distinguished Professor

3216 Engineering Hall
1415 Engineering Drive
Madison, WI 53706

Ph: (608) 263-7783
Fax: (608) 262-5199



  • PhD, University of Illinois at Urbana-Champaign, 1996
  • MS, University of Illinois at Urbana-Champaign, 1991
  • MS, University of Los Andes, Colombia, 1989
  • BS, University of Los Andes, Colombia, 1987

Awards, Honors and Societies

2010 - Fair Distinguished Engineering Educator Award, Water Environment Federation. 

2010 - Bill Boyle Educator of the Year, Central States Water Environment Association. 

2010 - Wisconsin Distinguished Professorship, University of Wisconsin System. 

2006 - Wisconsin Water Association (WWA) Research Award.

2005 - Paul L. Busch Award, Water Environment Research Foundation.

2004 - Harrison Prescott Eddy Medal, Water Environment Federation, with Sean Chaparro.

2004 - American Water Works Association (AWWA) Publications Award, with Greg Harrington, Alicia Kandou, and David van Hoven.

2004 - American Water Works Association (AWWA) Engineering & Construction Division Best Paper Award, with Greg Harrington, Alicia Kandou, and David van Hoven.

2003 - American Water Works Association (AWWA) Academic Achievement Award for Best Ph.D. Thesis, with John M. Regan.

2002 - Association of Environmental Engineering and Science Professors (AEESP) Distinguished Service Award.

2002 - Vilas Associate of the Graduate School, University of Wisconsin-Madison.

2000 - American Water Works Association (AWWA) Academic Achievement Award for Best MS Thesis, with Patrick Oldenburg.

2000 - James M. Montgomery and Association of Environmental Engineering and Science Professors (AEESP) M.S. Thesis Award, with Patrick Oldenburg.

1999 - National Science Foundation CAREER Award.

1997 - Samuel C. Johnson Distinguished Fellowship.

1992 - James M. Montgomery and Association of Environmental Engineering and Science Professors (AEESP) M.S. Thesis Award, with Bruce E. Rittmann.



Gall, D.L., J. Ralph, T.J. Donohue, and D. R. Noguera. 2013. Benzoyl-CoA pathway-mediated metabolism of meta-hydroxy-aromatic acids in Rhodopseudomonas palustris. Journal of Bacteriology, Published ahead of print, doi:10.1128/JB.00634-13.


Okten H.E., L.S. Yilmaz, and D.R. Noguera. 2012.  Exploring the In Situ Accessibility of Small Subunit Ribosomal RNA of Members of the Domains Bacteria and Eukarya to Oligonucleotide Probes.  Systematic and Applied Microbiology, 35(8): 485-495.

Kontur W., W. Shackwitz, N. Ivanova, J. Martin, K. LaButti, S. Deshpande, H. Tice, C. Pennachio, E. Sodergren, G. Weinstock, D.R. Noguera, and T.J. Donohue. 2012. Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome.  Journal of Bacteriology, 94(24):7016-7017.

Kontur W.S., D.R. Noguera, and T.J. Donohue. 2012. Maximizing reductant flow into microbial H2 production. Current Opinion in Biotechnology, 23:382-389.

Yilmaz L.S., A. Loy, E.S. Wright, M. Wagner, and D.R. Noguera. 2012. Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics, PLoS ONE 7(8): e43862.

Wright E.S., L.S. Yilmaz, and D.R. Noguera. 2012. DECIPHER: A Search-Based Approach to Chimera Identification for 16S rRNA Sequences. Applied and Environmental Microbiology, 78(3):717-725.


Kontur W.S., E.C. Ziegelhoffer, M.A. Spero, S. Imam, D.R. Noguera, and T.J. Donohue. 2011. Pathways involved in reductant distribution during photobiological H2 production by Rhodobacter sphaeroidesApplied and Environmental Microbiology, 77(20):7425-7429.


Imam S., L.S. Yilmaz, U. Sohmen, A.S. Gorzalski, J.L. Reed, D.R. Noguera, and T.J. Donohue. 2011. iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC Systems Biology, 5:116.


Yilmaz L.S., Parnerkar S., and D.R. Noguera. 2011.  mathFISH, A Web Tool for the in silico Evaluation of Oligonucleotide Probes for Fluorescence in situ Hybridization Based on Thermodynamic Models.  Applied and Environmental Microbiology, 77(3), 1118-1122.



Yilmaz L.S., W.S. Kontur, A.P. Sanders, U. Sohmen, T.J. Donohue, and D.R. Noguera. 2010. Electron Partitioning During Light- and Nutrient-Powered Hydrogen Production by Rhodobacter sphaeroides. BioEnergy Research, 3:55-66. 



Yilmaz L.S., Kang, D.W., and D.R. Noguera. 2009. Fluorescence in situ hybridization (FISH) and probe design.  In:  Microbial Ecology of Activated Sludge, Robert Seviour and Per H Nielsen (Eds), IWA Publishing. 

Noguera D.R., Yilmaz L.S., R.G. Goel, and G.W. Harrington. 2009. Identification of Heterotrophic Bacteria that Colonize Chloraminated Drinking Water Distribution Systems.  American Water Works Association Research Foundation.

Flowers J.J., S. He, L.S. Yilmaz, D. R. Noguera, K.D. McMahon. 2009. Denitrification capabilities of two biological phosphorus removal sludges dominated by different “Candidatus Accumulibacter” clades.  Environmental Microbiology Reports, 1(6), 583–588.

Perez-Roa R.E., M.A. Anderson, D. Rittschof, C.G. Hunt, and D.R. Noguera. 2009. Inhibition of Barnacle Biofouling by Electrochemical Reactive Oxygen Species (ROS) Generation. Biofouling, 25(6):563-571.


Park H.-D., and D.R. Noguera. 2008. Nitrospira Community Composition in Nitrifying Reactors Operated with Two Different Dissolved Oxygen Levels. Journal of Microbiology and Biotechnology, 18(8):1470-1474.

Perez-Roa R.E., M.A. Anderson, D. Rittschof, B. Orihuela, D. Wendt, G.L. Kowalke, and D.R. Noguera. 2008. Inhibition of barnacle (Amphibalanus amphitrite) cyprid settlement by means of localized, pulsed electric fields. Biofouling, 24(3):177-184.

Fleming K.K, G.W. Harrington, and D.R. Noguera. 2008. Nitrification potential curve evaluation of full-scale drinking water distribution systems. Journal AWWA, 100(10):92-103.

Yang J., G. W. Harrington, and D. R. Noguera. 2008. Nitrification modeling in pilot-scale chloraminated drinking water distribution systems. Journal of Environmental Engineering, 134(9):731-742

Yilmaz L.S., L.I. Bergsven, and D.R. Noguera. 2008. Single mismatch stability predictors for fluorescence in situ hybridization.  Environmental Microbiology, 10(10), 2872–2885.

Hoshino T., L.S. Yilmaz, D.R. Noguera, H. Daims, and M. Wagner. 2008. Quantification of target molecules needed to by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH, Applied and Environmental Microbiology, 74(16), 5068-5077.

Cho Y.K., T.J. Donohue, I. Tejedor, M.A. Anderson, K.D. McMahon, and D.R. Noguera. 2008. Development of a Solar Powered Microbial Fuel Cell. Journal of Applied Microbiology, 104:640-650


Yilmaz L.S., and D.R. Noguera. 2007. Development of Thermodynamic Models for Simulating Probe Dissociation Profiles in Fluorescence in situ Hybridization. Biotechnology and Bioengineering, 96(2), 349-363.

Yang J., G. W. Harrington, D. R. Noguera, and K. K. Fleming. 2007. Risk analysis of nitrification occurrence in pilot scale chloraminated distribution systems. Journal of Water Supply: Research and Technology-AQUA, 56(5):293-311.

Park H.-D., and D.R. Noguera. 2007. Characterization of Two Ammonia-Oxidizing Bacteria Isolated from Reactors Operated with Low Dissolved Oxygen Concentrations. Journal of Applied Microbiology, 102(5):1401-1417.


Yilmaz L.S., H. E. Okten, and D. R. Noguera. 2006. Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Applied and Environmental Microbiology, 72(1): 733-744.

Goel R.K., and D.R. Noguera. 2006. Evaluation of sludge yield and phosphorus removal in a Cannibal solids reduction system. Journal of Environmental Engineering, 132(10):1331-1337.

Perez-Feito R. and D.R. Noguera. 2006. Recovery of polyhydroxyalkanoate (PHA) from enhanced biological phosphorus removal (EBPR) treatment plants. Water Environment Research, 78(7):770-775.

Maixner F., D. R. Noguera, B. Anneser, K. Stoecker, G. Wegl, M. Wagner, and H. Daims. 2006. Nitrite concentration influences the population structure of Nitrospira-like bacteria. Environmental Microbiology, 8(8):1487-1495.

Park H.-D., Whang L.-M., Reusser S.R., and D. R. Noguera. 2006. Taking Advantage of Aerated-Anoxic Operation in a Full-Scale University of Cape Town (UCT) Process. Water Environment Research, 78(6):637-642.

Perez-Feito R., J. Peccia, and D. R. Noguera. 2006. Comparison between direct microscopy and flow cytometry for quantifiable RNA-based population analysis of activated sludge. Water Environment Research, 78(2):181-188.

Perez-Roa R.E., D.T. Tompkins, M. Paulose, C. A. Grimes, M.A. Anderson, and D. R. Noguera. 2006. Effects of Localized, Low-Voltage Pulsed Electric Fields on the Development and Inhibition of Pseudomonas aeruginosa Biofilms. Biofouling, 22(6):383-390.


Fleming K.K., Harrington G.W., and D. R. Noguera. 2005. Nitrification Potential Curves as a New Strategy for Nitrification Prevention. Journal AWWA, 97(8):90-99.

Pizarro G.E., J. Teixeira, M. Sepulveda, and D. R. Noguera. 2005. Bitwise implementation of a two-dimensional cellular automata biofilm model. Journal of Computing in Civil Engineering, 39(3):258-268.

Wanner O., Eberl, H., E. Morgenroth, D. R. Noguera, C. Picioreanu, B. Rittmann, M. van Loosdrecht. 2005. Mathematical Modeling of Biofilms, Scientific and Technical Report No. 18, IWA publishing, ISBN 1-84339-087-6.


Yilmaz L.S., D. R. Noguera. 2004. A mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization. Applied and Environmental Microbiology, 70(12): 7126-7139.

Drnevich M.A. and D.R. Noguera. 2004. Production of polyhydroxyalkanoate during treatment of low-phosphorus content wastewater. Water Environment Research, 76(4):380-383.

Noguera D.R. and E. Morgenroth. 2004. Introduction to the IWA Task Group on Biofilm Modeling. Water Science and Technology, 49(11-12):131-136.

Morgenroth E., H.J Eberl, M.C.M. van Loosdrecht, D.R. Noguera, G.E. Pizarro, C. Picioreanu, B.E. Rittmann, A.O. Schwartz, O. Wanner. 2004. Comparing biofilm models for a single species biofilm system. Water Science and Technology, 49(11-12):145-154.

Eberl, H.J., M.C.M. van Loosdrecht, E. Morgenroth, D.R. Noguera, C. Picioreanu, B.E. Rittmann, A.O. Schwarz, and O. Wanner. 2004. Modelling A Spatially Heterogeneous Biofilm And The Bulk Fluid: Selected Results From Benchmark Problem 2 (BM2). Water Science and Technology, 49(11-12):155-162.

Noguera D.R. and C. Picioreanu. 2004. Results from the multi-species benchmark problem 3 (BM3) using two-dimensional models. Water Science and Technology, 49(11-12):169-176.

Park H.-D. and D. R. Noguera. 2004. Evaluating the Effect of Dissolved Oxygen on Ammonia-Oxidizing Bacterial Communities in Activated Sludge. Water Research, 38(14-15):3275-3286.

Noguera, D.R., Pizarro, G.E., and Regan, J.M. 2004. Modeling Biofilms, pp. 222-249. In: Microbial Biofilms, M. Ghannoum, G. A. O\'Toole, eds., ASM Press, Washington D.C.


Chaparro S.K. and D.R. Noguera. 2003. Controlling biosolids phosphorus content in enhanced biological phosphorus removal reactors. Water Environmental Research, 73(3):254-262.

Regan J.M., P.S. Oldenburg, H.D. Park, G.W. Harrington, and D.R. Noguera. 2003. Simultaneous Determination of Bacterial Viability and Identity in Biofilms using Ethidium Monoazide and Fluorescent In Situ Hybridization. Water Science and Technology, 47(5):123-128.

Regan J.M., G.W. Harrington, H. Baribeau, R. De Leon, and D.R. Noguera. 2003. Diversity of nitrifying bacteria in full-scale chloraminated distribution systems. Water Research, 37(1):197-205.


Zilles J.L., J. Peccia, and D. R. Noguera. 2002. Microbiology of Enhanced Biological Phosphorus Removal in Aerated-Anoxic Orbal Processes. Water Environment Research, 74(5):428-436.

Harrington G.W., D.R. Noguera, A.I. Kandou, and D. J. VanHoven. 2002. Pilot-Scale Evaluation of Nitrification Control Strategies. Journal AWWA, 94(11):78-89.

Hung C.-H., J. Peccia, J.L. Zilles, and D.R. Noguera. 2002. Physical enrichment of polyphosphate-accumulating organisms in activated sludge. Water Environment Research, 74(4):354-361.

Oldenburg P. S., J. M. Regan, G. W. Harrington, and D. R. Noguera. 2002. Kinetics of Nitrosomonas europaea inactivation by chloramine. Journal AWWA, 94(10):100-110.

Zilles J.L., J. Peccia, M-W. Kim, C-H. Hung, and D.R. Noguera. 2002. Involvement of Rhodocyclus-related organisms in phosphorus removal in full-scale wastewater treatment plants. Applied and Environmental Microbiology. 68(6):2763-2769.

Zilles J.L., C.-H. Hung, and D.R. Noguera. 2002. Presence of Rhodocyclus in a full-scale wastewater treatment plant and their participation in enhanced biological phosphorus removal. Water Science and Technology. 46(1-2):123-128.

Park H.-D., J. M. Regan, and D.R. Noguera. 2002. Molecular analysis of nitrifying bacterial populations in aerated-anoxic processes. Water Science and Technology. 46(1-2):273-280.

Regan J.M., G.W. Harrington, and D.R. Noguera. 2002. Ammonia- and nitrite-oxidizing bacteria communities in a pilot-scale chloraminated drinking water distribution system. Applied and Environmental Microbiology, 68(1):73-81.


Pizarro G., D. Griffeath, D.R Noguera. 2001. Quantitative cellular automaton model for biofilms. Journal of Environmental Engineering, 127 (9): 782-789.


Pak J.W., K.L. Knoke, D.R. Noguera, B.G. Fox, G.H. Chambliss. 2000. Transformation of 2,4,6-trinitrotoluene by purified xenobiotic reductase B from Pseudomonas fluorescens I-C. Applied and Environmental Microbiology, 66:4742-4750.

Noguera D.R., G. Pizarro, L.W. Clapp. 2000. Mathematical modeling of trichloroethylene (TCE) degradation in membrane-attached biofilms. Water Science and Technology, 41:(4-5) 239-244.


Noguera D.R., S. Okabe, and C. Picioreanu. 1999. Biofilm Modeling: Present Status and Future Directions. Water Science and Technology, 39:273-278.

Noguera D. R., G. Pizarro, D. A. Stahl, and B. E. Rittmann. 1999. Simulation of Multispecies Biofilm Development in Three Dimensions. Water Science and Technology, 39:123-130.

Clapp, L. W., J. M. Regan, F. Ali, J. D. Newman, J. K. Park, and D. R. Noguera. 1999. Activity, Structure, and Stratification of Membrane-Attached Methanotrophic Biofilms Cometabolically Degrading Trichloroethylene. Water Science and Technology, 39:153-161.


Noguera D. R., G. A. Brusseau, B.E. Rittmann, and D. A. Stahl. 1998. A Unified Model Describing the Role of Hydrogen in the Growth of Desulfovibrio vulgaris under Different Environmental Conditions. Biotechnology and Bioengineering, 59:732-746.

Wagner M., D.R. Noguera, S. Juretschko, G. Rath, H-P. Koops, and K-H. Schleifer. 1998. Combining Fluorescent in Situ Hybridization (FISH) with Cultivation and Mathematical Modeling to Study Population Structure and Function of Ammonia-Oxidizing Bacteria in Activated Sludge. Water Science and Technology, 37:441-449.


Noguera D.R. and D.L. Freedman. 1997. Characterization of Products from the Biotransformation of 2,4-Dinitrotoluene by Denitrifying Enrichment Cultures. Water Environment Research, 69:260-268.

Freedman D.L., C.R. Smith, and D.R. Noguera. 1997. Dichloromethane Biodegradation under Nitrate-Reducing Conditions. Water Environment Research, 69:115-122.


Noguera D.R. and Freedman D.L. 1996. Reduction and Acetylation of 2,4-Dinitrotoluene by a Pseudomonas aeruginosa Strain. Applied and Environmental Microbiology, 62:2257-2263.


Raskin L., L.K. Poulsen, D.R. Noguera, B.E. Rittmann, and D.A. Stahl. 1994. Quantification of Methanogenic Groups in Anaerobic Biological Reactors using Oligonucleotide Probe Hybridizations. Applied and Environmental Microbiology. 60:1241-1248.

Noguera D.R., N. Araki, and B.E. Rittmann. 1994. Soluble Microbial Products (SMP) in Anaerobic Chemostats. Biotechnology and Bioengineering. 44:1040-1047.


Wirtel S.A., D.R. Noguera, D.T. Kampmeier, M.S. Heath, and B.E. Rittmann. 1992. Explaining Widely Varying Biofilm-Process Performance with Normalized-Loading Curves. Water Environment Research, 64:706-711.



We are currently looking for a postdoctoral research associate with a strong background on metabolic modeling and with great computational skills, for a bionergy-related project.  Please send inquiries with a CV to noguera@engr.wisc.edu


Summer 2014

  • CIVENGR 699 - Independent Study
  • CIVENGR 322 - Environmental Engineering Processes
  • CIVENGR 990 - Thesis
  • CIVENGR 929 - Seminar-Environmental Engineering
  • CIVENGR 890 - Pre-Dissertator\'s Research
  • CIVENGR 790 - Master\'s Research or Thesis
  • CIVENGR 629 - Special Topics in Environmental Engineering
  • CIVENGR 999 - Advanced Independent Study
  • CIVENGR 990 - Thesis
  • CIVENGR 890 - Pre-Dissertator\'s Research
  • CIVENGR 790 - Master\'s Research or Thesis
  • CIVENGR 699 - Independent Study
  • CIVENGR 699 - Independent Study
  • CIVENGR 299 - Independent Study
  • CIVENGR 999 - Advanced Independent Study
  • CIVENGR 990 - Thesis
  • CIVENGR 890 - Pre-Dissertator\'s Research
  • CIVENGR 790 - Master\'s Research or Thesis
  • Profile Summary

    My students and I work on the area of Environmental Biotechnology within Environmental Engineering. The current major areas of research are (i) bioenergy, (ii) water quality in drinking water distribution systems, (iii) biological nutrient removal during wastewater treatment, (iv) biofilms and biofouling, and (v) fundamental studies of DNA/RNA hybridizations in whole cells and bioinformatics.

    Bioenergy research is related to maximizing hydrogen production with photoheterotrophic bacteria and biological transformation of lignin to biofuel precursors.

    Our research on biological nutrient removal seeks to identify microorganisms involved in the enhanced biological phosphorus removal (EBPR) process. We are also working on nutrient recovery processes and prevention of struvite precipitation in anaerobic digesters.

    Research on the quality of drinking water focuses on the microbial ecology of the biofilms that form in chloraminated distribution systems. We are developing tools to determine the identity of the microorganisms present in the biofilm and in the bulk water, their resistance to disinfectants, and their viability.

    In the area of biofilms and biofouling we are working on developing strategies for biofouling prevention using pulse electric fields.

    Finally, our studies with in situ DNA/RNA hybridizations aim at developing a mechanistic approach for the design of fluorescent in situ hybridization (FISH). We are also engaged in the development of bioinformatic tools of relevance in microbial ecology studies within environmental engineering.


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