Katherine (Trina) McMahon

Associate Professor

Room: 5552
Microbial Sciences Building
1550 Linden Drive
Madison, WI 53706

Ph: (608) 890-2836
Fax: (608) 262-5199
tmcmahon@engr.wisc.edu


Profile Summary

Microbes possess extraordinarily diverse and sophisticated physiologies, communication strategies, and mechanisms of evolution. Scientists and engineers are only beginning to understand and exploit the metabolic potential of these organisms and their communities. The broad objective of my research program is to improve our capacity to predict and model microbial behavior, while searching for novel biologically mediated transformations that can be harnessed for engineering applications.

My students and I study the microbial ecology of both natural and engineered systems. We use molecular tools to investigate microbial community structure and function in lakes and activated sludge. We also use high-frequency environmental sensor networks to measure important variables that we know influence bacterial communities. Sensor data provided through the Global Lake Ecological Observatory Network guides our adaptive sampling efforts and provides rich contextual data for our studies of lake bacterial community ecology. We are particularly interested in phosphorus, nitrogen, and carbon cycling in lakes and how this relates to eutrophication and water quality. We are using highly resolved time series sampling of multiple lakes, combined with metagenomics and meta-trascriptomics to explore how different lineages of freshwater bacteria contribute to this cycling.

We are also engaged in metagenomic and post-genomic approaches to dissecting the metabolism of bacteria specialized in the sequestration of phosphorus in activated sludge. This information will ultimately lead to the construction of more predictive mechanistic and ecosystem-scale models to describe such processes as wastewater treatment and freshwater nutrient cycling.

Information for Prospective Students

___Interested in joining the McMahon lab?___

We are always interested in recruiting bright, motivated, and curious researchers. Undergraduates, graduate students, and postdoctoral fellows excited by our research topics should contact Trina directly by email with the information noted below. I am particularly open to helping promising applicants apply for fellowship opportunities.

___Postdoctoral Applicants___

Please submit a CV, description of past and future research interests, and the names and contact information for at least three references. In your research statement, describe why you are excited about our research, and describe the research questions you would like to pursue in our lab.

___Graduate Applicants___

Trina can advise students in a number of graduate programs on the UW-Madison campus. Please contact Trina in advance if you are unsure about which program is right for you. Note that funding to support graduate studies is extremely limited, so you should plan ahead and apply early (see note below about fellowships).

Civil and Environmental Engineering (MS and PhD) (http://www.engr.wisc.edu/cee/cee-academics-graduate.html)

Limnology and Marine Science (MS and PhD) (http://www.engr.wisc.edu/interd/limnology/)

Environmental Chemistry and Technology (MS and PhD) (http://www.engr.wisc.edu/interd/ect/)

Microbiology Doctoral Training Program (PhD) (http://microbiology.wisc.edu/)

Bacteriology (MS) (http://www.bact.wisc.edu/programs_ms.php)


We strongly encourage exceptional candidates to apply for graduate fellowships at the federal level. Note that deadlines are typically in November for the following year, so you need to plan far in advance!

US National Science Foundation Graduate Research Fellowships (http://www.nsfgrfp.org/)
US Environmental Protection Agency STAR Graduate Fellowships (http://www.epa.gov/ncer/fellow/)


___Undergraduate Applicants___

We encourage undergraduates to join our research team. Interested students should submit a list of current and planned course work, and a 1-2 paragraph statement about why you want to work in our lab. We are most interested in enthusiastic and motivated students who can commit at least two full years to research (freshmen and sophomores are encouraged to apply), with a minimum of 5-10 hours per week during the academic year.

___My mentoring philosophy___

I put a great deal of thought and effort into mentoring my students and postdocs. It is my job as a professor to help each student/postdoc achieve you personal goals during the time that you are in my lab, and beyond. I will help you tailor the courses you take, the research projects you work on, and the outreach/teaching activities you engage in, to match your goals. We meet regularly to discuss progress towards these goals and possible changes in your path.

I expect my students and postdocs to be highly independent, developing research directions and collaborations beyond their initial primary project. I provide lab members with opportunities to participate in grant proposal writing and large collaborative projects within and beyond UW-Madison. Our research group very much functions as a team and I place a high priority on best practices for \"team science\" which include open communication, mutual respect, accountability, and shared vision.

The effectiveness of my mentoring is demonstrated by the high degree of success of my former students and postdocs, several of whom have moved on to tenure-track positions at prestigious institutions.

Education

  • PhD, University of California at Berkeley, 2002
  • MS, University of Illinois at Urbana-Champaign, 1997
  • BS, University of Illinois at Urbana-Champaign, 1995

Research Interests

>>>>>>Research in the McMahon Lab <<<<<<

Note that the best way to learn about our research is to read our most recent publications (click on \"Extended Webpage\" above).

>>>>>>Enhanced Biological Phosphorus Removal <<<<<<
Enhanced Biological Phosphorus Removal (EBPR) is used worldwide to remove phosphorus from both municipal and industrial wastewaters, protecting our surface waters from excessive algal growth and the associated long-term degradation of water quality. Despite its successful use, very little is known about the naturally occurring microorganisms that carry out EBPR. These microorganisms have eluded researchers for over 30 years – they cannot be grown in pure culture. One major group of EBPR organisms was recently identified by cultivation-independent techniques and was named Accumulibacter phosphatis. The goal of this research is to learn more about the mechanism responsible for EBPR and the ecology of Accumulibacter.

We are using (meta)genomics and post-genomics methods to study how gene expression is regulated, and to discover previously unrecognized biochemical pathways that may be critically important for understanding the energy, carbon, and phosphorus budgets within the cell. We are also conducting metabolic flux modeling in an effort to link sub-cellular gene and metabolic networks to community-level dynamics.

>>>>>>Freshwater microbial ecology <<<<<<
The study of freshwater microbial ecology has matured beyond the purely descriptive phase and now represents a compelling system in which to test explicit hypotheses addressing the physical, chemical, and biological forces that structure microbial communities. Results from our prior work suggest that various drivers are acting as a system of hierarchical constraints on freshwater microbes at different temporal and spatial scales. Therefore, we now seek to determine which factors contribute to structuring communities and populations, at regional and local spatial scales. Much of the work in this area is conducted in collaboration with the scientists working through the Center for Limnology (http://limnology.wisc.edu/), the North Temperate Lakes Long Term Ecological Research site (http://lter.limnology.wisc.edu/), and the Global Lakes Ecological Observatory Network (http://www.gleon.org/).

We are using 16S rRNA gene tag sequencing, metagenomics, single-cell genomics, and transcriptomics to ask questions about the ecology and evolution of major freshwater clades. We are particularly interested in niche partitioning and compensated train loss among co-occurring clades. This has important relevance for our long-term goal of being able to quantitatively model community dynamics and associated emergent properties that influence ecosystem-level function such as production, respiration, and nutrient cycling. We are using coupled hydrodynamic-ecosystem process models to study linkages between lake physics and microbial biology, as well as predicting water quality and community dynamics.

We also maintain a long-term time series (>10 years) from several Wisconsin lakes. The sample archive is a veritable treasure trove of possible research projects just waiting for talented to students to jump on! We are currently shot-gun metagenomic sequencing 100\'s of samples using paired-end Illumina HiSeq technology in collaboration with the DOE Joint Genome Institute and the Earth Microbiome Project. This unprecedented dataset can be used to develop hypotheses that we can test using field work, lab experiments, and computational biology.

Awards, Honors and Societies

  • NSF Graduate Research Fellowship, 1996
  • EPA-STAR Graduate Fellowship, 2000
  • NSF CAREER Award, 2007
  • UW-Madison Campus Class of 1955 Distinguished Teaching Award, 2008
  • University Housing Honored Instructors Award, 2009 and 2010
  • Benjamin Smith Reynolds Award for Excellence in Teaching, 2009
  • Polygon Outstanding Instructor Award - UW-Madison College of Engineering, 2010

Publications

>>>> Note that this list may not be completely up to date. Please see \"Extended Homepage\" link above for most complete list. <<<<

64.   J. J. Flowers, S. He, S. Malfatti, T. Glavina del Rio, S. G. Tringe, P. Hugenholtz, K. D. McMahon. (2013) “Comparative genomics of two “Candidatus Accumulibacter” clades performing biological phosphorus removal.” ISME Journal, in press.

63.   J. J. Flowers, T. A. Cadkin, K. D. McMahon, (2013) “Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant.”  Water Research, in press

62.    L. J. Beversdorf, T. R. Miller, K. D. McMahon. (2013) “The role of nitrogen fixation in cyanobacterial bloom toxicity in a temperate, eutrophic lake.” PLoS One, 8(2):e56103

61.    C. A. Bareither, G. L Wolfe, K. D. McMahon, C. H. Benson. (2013) “Microbial diversity and dynamics during methane production from municipal solid waste.” Waste Management, In press.

60.    N. Youngblut, A. Shade, J. S. Read, K. D. McMahon, R. J. Whitaker, (2013) “Defining ecological units in microbial communities through cohesive response to whole ecosystem disturbance”. Applied and Environmental Microbiology, 79(1):39-47.

59.    E. L. Kara, P. C. Hanson, Y. H. Hu, L. Winslow, K. D. McMahon. (2013) “A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, Wisconsin, USA”, ISME Journal, 7(3):680-684.

58.    S. L. Garcia, K. D. McMahon, M. Martinez-Garcia, A. Srivastava, A. Sczyrba, R. Stepanauskas, H-P. Grossart, T. Woyke, F. Warnecke. (2013) “Metabolic potential of a single cell belonging to one of the most abundant lineages of freshwater bacterioplankton” ISME Journal. 7(1):137-147.

57.    A. Shade, J. S. Read, N. D. Youngblut, N. Fierer, R. Knight, T. K. Kratz, N. R. Lottig, E. E. Roden, E. H. Stanley, J. Stombaugh, R. J. Whitaker, C. H. Wu, K. D. McMahon, (2013) \"Lake microbial communities are resilient after a novel whole-ecosystem disturbance\". ISME Journal, 6:2153-2167.

56.    S. E. Jones, T. A. Cadkin, R. J. Newton, K. D. McMahon, (2012) \"Spatial and temporal scales of aquatic bacterial beta diversity\". Frontiers in Aquatic Microbiology, 3:318.

55.    E. L. Kara, P. Hanson, D. Hamilton, M. Hipsey, K. D. McMahon, J. Read, L. Winslow, J. Dedrick, K. Rose, C. Carey, S. Bertilsson, D. da Motta Marques, L. Beversdorf, T. Miller, C. Wu, Y-F. Hsieh, E. Gaiser, T. Kratz, (2012) \"Time-scale dependence in numerical simulations: Assessment of physical, chemical, and biological predictions in a stratified lake at temporal from scales of hours to months\". Environmental Modelling and Software. 35:104-121.

54.    R. Ghai, K. D. McMahon, F. Rodriguez-Valera, (2012) \"Breaking a paradigm: cosmopolitan and abundant freshwater Actinobacteria are low GC\". Environmental Microbiology Reports. 4:29-35.

53.    R. Ghai, F. Rodriguez-Valera, K. D. McMahon, D. Toyama, R. Rinke, T. Cristina Souza de Oliveira, J. Wagner Garcia, F. Pellon de Miranda, F. Henrique-Silva, (2011) \"Metagenomics of the water column in the pristine upper course of the Amazon River\". PLoS One. 6(8):e23785.

52.    R. Ghai, L. Pasic, A. Beatriz Fernandez, A.-B. Martin-Cuadrado, C. M. Mizuno, K. D. McMahon, R. T. Papke, R. Stepanauskas, B. Rodriguez-Brito, F. Rohwer, C. Sanchez-Porro, A. Ventosa, F. Rodriguez-Valera. (2011) “New abundant microbial groups in aquatic hypersaline environments” Nature Scientific Reports  Article Number 135.

51.    T. R. Miller and K. D. McMahon. (2011) \"Genetic diversity of cyanobacteria in four eutrophic lakes\". FEMS Microbiology Ecology. 78:336-348.

50.    A. Shade, J. S. Read, D. Welkie, T. K. Kratz, C. H. Wu, K. D. McMahon. (2011) \"Resistance, resilience, and recovery: aquatic bacterial dynamics after water column disturbance\". Environmental Microbiology. 13:2752-2767.

49.    S. W. Hoover, W. D. Marner II, A. K. Brownson, R. M. Lennen, T. M. Wittkopp, J. Yoshitani, S. Zulkifly, L. E. Graham, S. Chaston, K. D. McMahon, B. F. Pfleger. (2011) \"Bacterial production of free fatty acids from freshwater macroalgal cellulose\". Applied Microbiology and Biotechnology. 91(2):435-46.  

48.    C. T Skennerton, F. E. Angly, M. Breitbart, L. Bragg, S. He, K. D. McMahon, P. Hugenholtz, G. W. Tyson. (2011) \"Phage Encoded H-NS: a potential Achilles heel in the bacterial defence system\". PLoS One, 6(5): e20095.

47.    R. J. Newton, S. E. Jones, A. Eiler, K. D. McMahon, S. Bertilsson. (2011) \"A Guide to the natural history of freshwater lake bacteria\". Microbiology and Molecular Biology Reviews, 75(1):14-49.

46.    S. He and K. D. McMahon. (2011) \"Microbiology of \'Candidatus Accumulibacter\' in activated sludge\". Microbial Biotechnology. 4:603-619.

45.    R. J. Newton and K. D. McMahon. (2011) \"Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake\". Environmental Microbiology, 13(4):887-899.

44.    J. S. Read, A. Shade, C. H. Wu, K. D. McMahon. (2011) \"Gradual Entrainment Lake Inverter (GELI): A novel device for artificial lake mixing\". Limnology and Oceanography: Methods, 9: 14-28.

43.    S. He and K. D. McMahon. (2011) \"\'Candidatus Accumulibacter\' gene expression in response to dynamic EBPR conditions\". ISME Journal, 5:329-340.

42.    S. He, F. I. Bishop, K. D. McMahon. (2010). \"Bacterial community and Accumulibacter population dynamics in laboratory-scale enhanced biological phosphorus removal reactors\". Applied and Environmental Microbiology. 76:5479-5487.

41.    A. Shade, A., C.-Y. Chiu, K. D. McMahon. (2010) “Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment.” Environmental Microbiology, 12:455-466.

40.    E. E. Seyfried, R. J. Newton, K. F. Rubert IV, J. A. Pedersen, K. D. McMahon. (2010) \"Diversity of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline\" Microbial Ecology, 59(4):799.  

39.    S. He, V. Kunin, M. Haynes, H. Garcia Martin, N. Ivanova, F. Rohwer, P. Hugenholtz, K. D. McMahon. (2010) “Metatranscriptomic array analysis of “Candidatus Accumulibacter phosphatis”-enriched enhanced biological phosphorus removal sludge.” Environmental Microbiology, 12(5):1205-1217.

38.    A. Shade, C.-Y. Chiu, K. D. McMahon. (2010) “Seasonal and episodic lake mixing stimulate differential response among planktonic bacterial dynamics.” Microbial Ecology, 59:546-554.

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

36.    A. Shade, C. C. Carey, E. L. Kara, S. Bertilsson, K. D. McMahon, M. C. Smith. (2009) “Can the black box be cracked?  The augmentation of microbial ecology by high-resolution automated sensing technologies” ISME Journal, 3:881-888.

35.    S. E. Jones, R. J. Newton, K. D. McMahon. (2009) “Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes.” Environmental Microbiology, 11:2463-2472.

34.    S. E. Jones, K. D. McMahon (2009). “Species-sorting may explain an apparent minimal effect of immigration on freshwater bacterial community dynamics.” Environmental Microbiology, 11:905-913.

33.    S. E. Jones, T. K. Kratz, C.-Y. Chiu, K. D. McMahon (2009). “The influence of typhoons on annual CO2 flux from a sub-tropical, humic lake.” Global Change Biology, 15:243-254.

32.    S. B. Peterson, F. Warnecke, J. Madejska, K. D. McMahon, P. Hugenholtz. (2008) \"Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal.\" Environmental Microbiology, 10:2691-2703.

31.    G. T. Hinckley, C. J. Johnson, K. H. Jacobson, C. Bartholomay, K. D. McMahon, D. McKenzie, J. M. Aiken, J. A. Pedersen. (2008) “Persistence of pathogenic prion protein during simulated wastewater treatment processes” Environmental Science and Technology, 42:5254-5259.

30.    I. S. Gil, W. Sheldon, T. Schmidt, M. Servilla, R. Aguilar, C. Gries, T. Gray, D. Field, J. Cole, J. Y. Pan, G. Palanisamy, D. Henshaw, M. O\'Brien, L. Kinkel, K. McMahon, R. Kottman, J. Brunt, W. Michener. (2008) \"Defining linkages between the GSC and NSF\'s LTER program: how does the ecological metadata language relate to GCDML and other outcomes\" OMICS: A Journal of Integrative Biology, 12(2): 151-156.

29.    S. E. Jones, R. J. Newton, K. D. McMahon. (2008) “Potential for atmospheric deposition of bacteria to influence bacterioplankton communities” FEMS Microbiology Ecology, 64:388-394.

28.    A. Shade, S. E. Jones, K. D. McMahon. (2008) \"The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics.\" Environmental Microbiology, 10(4):1057-1067.

27.    S. E. Jones, C.-Y. Chiu, T. K. Kratz, J.-T. Wu, A. Shade, K. D. McMahon (2008)\\\"Typhoons initiate predictable change in aquatic bacterial communities” Limnology and Oceanography, 53:1319-1326.

26.    V. Kunin, S. He, F. Warnecke, S. B. Peterson, H. Garcia Martin, M. Haynes, N. Ivanova, L. L. Blackall, M. Breitbart, F. Rohwer, K. D. McMahon, P. Hugenholtz. (2008). “A bacterial metapopulation adapts locally to phage predation despite global dispersal” Genome Research, 18:293-297.

25.    S. He, A. Z. Gu, K. D. McMahon (2008) “Progress towards understanding the distribution of Accumulibacter among full-scale enhanced biological phosphorus removal systems” Microbial Ecology, 55(2):229-236.

24.    R. J. Newton, S. E. Jones, M. R. Helmus, K. D. McMahon. (2007). “Phylogenetic ecology of the freshwater acI lineage.” Applied and Environmental Microbiology, 73(22):7169-7176.

23.    S. He, D. L. Gall*, K. D. McMahon. (2007). \"’Candidatus’ Accumulibacter population structure in enhanced biological phosphorus removal sludges revealed by polyphosphate kinase genes.\" Applied and Environmental Microbiology, 73(18):5865-5874.

22.    Y. K. Cho, T. J. Donohue, I. Tejedor, M. A. Anderson, K. D. McMahon, D. R. Noguera. (2007) “Development of a solar powered microbial fuel cell” Journal of Applied Microbiology, 104:640-650.

21.    K. D. McMahon, S. Yilmaz, S. He, D. L. Gall*, D. Jenkins, J. D. Keasling. (2007). “Polyphosphate kinase genes from full-scale activated sludge plants.” Applied Microbiology and Biotechnology, 77(1):167-173.

20.    K. D. McMahon, H. Garcia Martin, P. Hugenholtz. (2007). “Integrating ecology into environmental biotechnology.” Current Opinion in Biotechnology, 18(3):287-292

19.    A. D. Kent, A. C. Yannarell, J. A. Rusak, E. W. Triplett, K. D. McMahon. (2007) “Synchrony in aquatic microbial community dynamics.” The ISME Journal, 1:38-47.

18.    S. R. Carpenter, B. J. Benson, R. Biggs, J. W. Chipman, J. A. Foley, S. A. Golding, R. B. Hammer, P. C. Hanson, P. T. J. Johnson, A. M. Kamarainen, T. K. Kratz, R. C. Lathrop, K. D. McMahon, B. Provencher, J. A. Rusak, C. T. Solomon, E. H. Stanley, M. G. Turner, M. J. Vander Zanden, C.-H. Wu and H. Yuan. (2007). “Understanding regional change:  Comparison of two lake districts.” BioScience, 57(4):323-335.

17.    E. A. Auerbach, E. E. Seyfried*, and K. D. McMahon. (2007). “Tetracycline resistance genes in activated sludge wastewater treatment plants.” Water Research, 41:1143-1151.

16.    S. E. Jones , A. L. Shade, K. D. McMahon, A. D. Kent  (2007). “Comparison of primer sets for use in automated ribosomal intergenic spacer analysis (ARISA) of aquatic bacterial communities: An ecological perspective” Applied and Environmental Microbiology, 73(2):659-662.

15.    A. Shade, A. D. Kent, E. W. Triplett, K. D. McMahon (2007). “Inter-annual dynamics and phenology of bacterial communities in a eutrophic lake.” Limnology and Oceanography, 52(2):487-494.

14.    T. C. Balser, K. D. McMahon, D. Bart, D. Bronson, D. R. Coyle, N. Craig, M. L. Flores-Mangual, K. Forshay, S. E. Jones, A. D. Kent, A. L. Shade (2006). “Bridging the gap between micro- and macro-scale perspectives on ecosystem response to disturbance” Plant and Soil. 289(1-2):59-70

13.    H. Garcia Martin, N. Ivanova, V. Kunin, F. Warnecke, K. Barry, A. C. McHardy, C. Yeates, S. He, A. Salamov, E. Szeto, E. Dalin, N. Putnam, H. J. Shapiro, J. L. Pangilinan, I. Rigoutsos, N. C. Kyrpides, L. L. Blackall, K. D. McMahon, P. Hugenholtz. (2006). “Metagenomic analysis of phosphorus removing sludge communities.” Nature Biotechnology. 24:1263-1269.

12.    R. J. Newton, A. D. Kent, E. W. Triplett, and K. D. McMahon. (2006) “Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes” Environmental Microbiology. 8(6):956-970.

11.    A. D. Kent, S. E. Jones, G. H. Lauster, J. M. Graham, R. J. Newton, K. D. McMahon. (2006) \"Experimental manipulations of microbial food web interactions in a humic lake:  shifting drivers of bacterial community structure\" Environmental Microbiology. 8(8):1448-1459.

10.    S. He, A. Z. Gu, K. D. McMahon. (2006) “Fine-scale differences between Accumulibacter-like bacteria in enhanced biological phosphorus removal activated sludge.” Water Science and Technology. 54(1):111-117.

9.      K. D. McMahon, D. Zheng, A. J. M. Stams, D. Boone, R. I. Mackie and L. Raskin. (2004) “Microbial Population Dynamics During Startup and Overload Conditions of Anaerobic Digesters Treating Municipal Solid Waste and Sewage Sludge.” Biotechnology and Bioengineering, 87(7):823-834.

8.      K. D. McMahon, M. D. Dojka, N. R. Pace, D. Jenkins, J. D. Keasling. (2002) “Polyphosphate kinase from activated sludge performing enhanced biological phosphorus removal.” Applied and Environmental Microbiology. 68 (10):4971-4978.

7.      K. D. McMahon, D. Jenkins, J. D. Keasling. (2002) “Polyphosphate kinase genes from activated sludge carrying out enhanced biological phosphorus removal” Water Science and Technology, 46 (1-2):155-162.

6.      N. Renninger, K. D. McMahon, R. Knopp, H. Nitsche, D. S. Clark, and J. D. Keasling. (2002) “Uranyl precipitation by biomass from an enhanced biological removal reactor” Biodegradation, 12:401-410.

5.      P. G. Stroot, K. D. McMahon, R. I. Mackie, L. Raskin, (2001) “Anaerobic co-digestion of municipal solid waste and biosolids under various mixing conditions – I. Performance Data” Water Research. 35 (7):1804-1816.

4.      K. D. McMahon, P. G. Stroot, R. I. Mackie, L. Raskin, (2001) “Anaerobic co-digestion of municipal solid waste and biosolids under various mixing conditions – II. Microbial population dynamics” Water Research. 35 (7):1817-1827.

3.      J. D. Keasling, S. J. Van Dien, P. Trelstad, N. Renninger, K. McMahon, (2000) \"Application of polyphosphate metabolism to environmental and biotechnological problems.\" Biochemistry (Moscow). 65 (3): 324-331.

2.      K. D. McMahon, D. A. Stahl, L. Raskin, (1998) “A comparison of in vitro transcribed rRNA and native rRNA for the quantification of microorganisms in the environment.” Microbial Ecology. 36 (3): 362-371.

1.      M. E. Griffin, K. D. McMahon, R. I. Mackie, L. Raskin, (1998) “Methanogenic population dynamics during startup of anaerobic digesters treating municipal solid waste and biosolids.” Biotechnology and Bioengineering. 57 (3): 342-355. 

Links

Courses

Fall 2014-2015

  • CIVENGR 890 - Pre-Dissertator\'s Research
  • CIVENGR 790 - Master\'s Research or Thesis
  • CIVENGR 699 - Independent Study
  • BME 399 - Independent Study
  • CIVENGR 489 - Honors in Research
  • 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 299 - Independent Study
  • BME 399 - Independent Study
  • 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
  • Secondary Contact

    3204
    Engineering Hall
    1415 Engineering Drive
    Madison, WI 53706

    Profile Summary

    Microbes possess extraordinarily diverse and sophisticated physiologies, communication strategies, and mechanisms of evolution. Scientists and engineers are only beginning to understand and exploit the metabolic potential of these organisms and their communities. The broad objective of my research program is to improve our capacity to predict and model microbial behavior, while searching for novel biologically mediated transformations that can be harnessed for engineering applications.

    My students and I study the microbial ecology of both natural and engineered systems. We use molecular tools to investigate microbial community structure and function in lakes and activated sludge. We also use high-frequency environmental sensor networks to measure important variables that we know influence bacterial communities. Sensor data provided through the Global Lake Ecological Observatory Network guides our adaptive sampling efforts and provides rich contextual data for our studies of lake bacterial community ecology. We are particularly interested in phosphorus, nitrogen, and carbon cycling in lakes and how this relates to eutrophication and water quality. We are using highly resolved time series sampling of multiple lakes, combined with metagenomics and meta-trascriptomics to explore how different lineages of freshwater bacteria contribute to this cycling.

    We are also engaged in metagenomic and post-genomic approaches to dissecting the metabolism of bacteria specialized in the sequestration of phosphorus in activated sludge. This information will ultimately lead to the construction of more predictive mechanistic and ecosystem-scale models to describe such processes as wastewater treatment and freshwater nutrient cycling.


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