Research in the McMahon Lab

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Microbial ecology and environmental engineering

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 our 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.

The McMahon Lab studies the microbial ecology of natural and engineered systems, with an emphasis on those that use microbes to remove pollutants from water. We use molecular tools to investigate microbial community structure and function in activated sludge and freshwater bodies. This information will ultimately lead to the construction of better mechanistic models to describe such processes as wastewater treatment, bioremediation, and nutrient cycling.

We also seek to understand the population ecology of microorganisms relevant to our environmental systems. Horizontal gene transfer and recombination are important mechanisms of microbial evolution. The extent to which genes are horizontally transferred between species of microbes will partially determine how populations respond to the chemicals they are exposed to in the environment. This has important implications for the capacity of microbial communities to remediate many different kinds of pollutants.

CURRENT RESEARCH PROJECTS

Jump to EBPR, Freshwater microbial ecology, or antibiotic resistance.

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.

Community and population ecology of Accumulibacter
We have identified at least five different species-like groups of Accumulibacter in lab and full-scale EBPR systems. The relative abundance of these different groups can be determined using a real-time quantitative PCR technique we have developed to target the polyphosphate kinase gene. This genetic marker allows for detection of individual groups for comparative purposes across time and space. We are currently investigating the ecology of these species-like groups to determine if their differences account for varying performance in full-scale EBPR systems.  We also were recently awarded up to twelve 454-FLX (pyrosequencing) runs to explore community and population dynamics in EBPR communities, through the Community Sequencing Program at JGI.

Students:
Shaomei He
Collaborators: 
Philip Hugenholtz, DOE Joint Genome Institute
Snow Brook Peterson, UW Microbiology
April Gu, Northeastern University
Nancy Love, Virginia Tech
Charles Bott, Virginia Military Institute
Funding:  Pending support from NSF

Genome-enabled study of metabolism
The metagenome of a highly enriched activated sludge from our bioreactor operating in Madison, Wisconsin, was sequenced at JGI in 2004. A complete reconstruction of the EBPR metabolism was possible based on established metabolic models and the genome sequence information. The study provided a much needed blueprint for a systems-level understanding of EBPR.  In follow-up studies we are now investigating factors affecting gene expression in Accumulibacter using oligonucleotide probe microarrays, whole (meta)transcriptome sequencing, and (meta)proteomics.

Students:
Shaomei He
Jason Flowers
Collaborators: 
Philip Hugenholtz, DOE Joint Genome Institute
Vincent Martin, Concordia University, Monreal, Canada
Funding:  Pending support from NSF

Recent manuscripts related to our work in enhanced biological phosphorus removal

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. 

S. He, A. 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.

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

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.

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, 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.

S. He, A. 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.

 

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 and the North Temperate Lakes Long Term Ecological Research site. Below are descriptions of the main projects we currently have related to this area.

Disturbance as a driver of community composition and dynamics
We are currently studying the influence of disturbance on bacterial community assembly. The relationship between disturbance frequency and diversity is a longstanding area of classical ecological study. Disturbances cause habitat homogenization and initiate successional trajectories that are often (but not always) predictable in macroscale communities. In our previous work, we observed recurring seasonal succession in bacterial communities which seemed to be re-set by mixing events. We hypothesize that thermal stratification and mixing are major drivers of freshwater bacterial community composition and dynamics. To explore how lake mixing regime determines bacterial community assembly, we are conducting a survey of eight bog lakes during the summer of 2007. These lakes represent a gradient of water column stability because of differences in their morphometry and exposure to climatic drivers. We are also conducting enclosure experiments to tease apart the physical and chemical factors influencing bacterial communities in a dimictic humic lake. 

Postdocs:
Todd Miller

Students:
Ashley Shade
Stuart Jones

Collaborators: 
Timothy Kratz, UW Center for Limnology and Trout Lake Station
James Rusak, UW Center for Limnology and Trout Lake Station
Chin Wu, UW Civil and Environmental Engineering
Chih-Yu Chiu, Academia Sinica, Taiwan
Funding:  NSF Microbial Observatories until September 2012

Polynucleobacter genome biology and ecology
The genome sequence of a free-living strain of Polynucleobacter, a cosmopolitan member of freshwater bacterial communities, was recently determined by the JGI. An endosymbiotic strain sharing 99.4% 16S rRNA sequence identity with the free-living strain is currently being sequenced also. Genome-enabled insights into the metabolism and ecological potential of the free-living strain will facilitate discovery of the ecological function of these numerically highly important freshwater bacteria. Comparison of genomes of the closely related free-living and endosymbiotic Polynucleobacter strains will provide unique insights in the evolutionary adaptations taking place during the early phase of endosymbiosis. Genome comparison with nonfreshwater Burkholderiaceae (Burkholderia spp., Ralstonia spp., Cupriavidus spp.) will provide first insights in evolutionary adaptations to planktonic life in freshwater.

Postdocs:
Todd Miller

Students:
None Currently

Collaborators: 
Rachel Whitaker, University of Illinois at Urbana-Champaign
Martin Hahn, Austrian Academy of Sciences
Funding:  NSF Microbial Observatories until September 2012

Freshwater Actinobacteria population ecology
The acI lineage of freshwater Actinobacteria is a cosmopolitan and often numerically dominant member of lake bacterial communities. We conducted a survey of acI 16S rRNA genes and 16S-23S rRNA internal transcribed spacer (ITS) regions from 18 Wisconsin, USA lakes; and used standard nonphylogenetic and phylogenetic statistical approaches to investigate the factors that determine acI community composition at the local (within lakes) and regional scales (across lakes). Phylogenetic reconstruction of more than 400 acI 16S rRNA genes revealed a well-defined and highly-resolved phylogeny. Eleven previously unrecognized monophyletic clades each with ≥97.9% within-clade 16S rRNA gene sequence identity were identified. Clade community similarity positively correlated with lake environmental similarity but not with geographic distance, implying that these lakes represent a single biotic region containing environmental filters for communities of similar composition. Relatively unrelated clades were the most abundant at the regional scale, but local communities were comprised of relatively related clades, with lake pH as a strong predictor of the community composition, but only when lakes with a pH below 6 were included in the dataset. In the remaining lakes (pH above 6) biogeographic patterns in the landscape were instead a predictor of the observed acI community structure. The non-random distribution of the newly defined acI clades suggests potential ecophysiological differences between the clades, with the clades acI-AI, BII, and BIII preferring acidic lakes and acI-AII, AVI, and BI preferring more alkaline lakes. We continue to study the population structure and ecology of this important freshwater group.

Students:
Ryan Newton
Stuart Jones

Collaborators: 
Matthew Helmus, UW Zoology Department
Rachel Whitaker, University of Illinois at Urbana-Champaign
Funding:  NSF Microbial Observatories until September 2012

Autonomous microbial genosensor
Microbial ecologists are currently limited in the scope of their research questions and monitoring capabilities by existing technologies for sample collection and analysis. Autonomous remote sensing devices capable of detecting bacteria at high frequency with adequate specificity are required to address these challenges. We are adapting a prototype autonomous microbial genosensor (AMG) developed at the University of South Florida Center for Ocean Technology, for use in freshwater lakes, to enable research on potentially toxic cyanobacteria and important groups of cosmopolitan heterotrophic bacteria.

Postdocs:
Todd Miller

Students:
Sheena Chaston

Collaborators: 
David Fries, University of South Florida
Matthew Smith, University of South Florida
Juli Dyble, Great Lakes Environmental Research Laboratory, NOAA, Ann Arbor, MI
Stefan Bertilsson, Uppsala University, Sweden
Funding:  Wisconsin SeaGrant starting Spring 2009

Microbial contribution to phosphorus cycling in eutrophic lakes
Accelerated eutrophication of surface waters is a well-studied but extremely complex water quality problem. Despite the research efforts expended, widely applicable viable solutions remain elusive, partly because we do not fully understand the underlying mechanisms driving the process. Phosphorus (P) is of particular concern with respect to freshwater eutrophication, as it is often the limiting nutrient in these systems. Therefore, we are investigating the relationship between bacterial community structure, function, and phosphorus cycling.  We are particularly interested in how variation in bacterial community structure across time and space relates to phosphorus dynamics. We have selected three contrasting eutrophic lakes to study: Lake Mendota, a large deep dimictic lake adjacent to Madison, WI; Lake Wingra, a small shallow polymictic lake in Madison; and Lake Taihu, a large shallow polymictic lake in China.

 It is generally accepted that microbes (primarily algae and bacteria) control P-cycling in lakes, through their actions in both the water column and sediments. However, very little is known about the biochemical mechanisms involved in microbial P-cycling, or about the contribution of different taxonomic groups to specific P transformations. Recent studies of freshwater bacterial community dynamics in eutrophic lakes suggest that community composition varies significantly over time, and that this variation is correlated with changes in nutrient availability. A better understanding of the fundamental mechanisms involved, and how these may vary with community composition, will ultimately lead to an improved ability to predict the effects of lake management practices on water quality.

Students:
Ryan Newton
Emily Kara

Collaborators: 
Chin Wu, UW Civil and Environmental Engineering
Funding:  NSF CAREER through April 2012

Recent manuscripts related to our work in freshwater microbial ecology

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

S. E. Jones, R. J. Newton, K. D. McMahon. (2008) "Potential for atmospheric deposition of bacteria to influence bacterioplankton communities." FEMS Microbiology Ecology, in press.

S. E. Jones, T. K. Kratz, C.-Y. Chiu, K. D. McMahon. (200_) "Typhoon disturbance patterns drive annual CO2 flux to the atmosphere from a sub-tropical, humic lake." In review.

A. Shade, S. E. Jones, K. D. McMahon. (2008) ."Habitat heterogeneity as a driver of aquatic bacterial community structure and dynamics." Environmental Microbiology, in press

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

A.D. Kent, A.C. Yannarell, J.A. Rusak, E.W. Triplett, K.D. McMahon. (2007) "Synchronous dynamics in aquatic microbial communities" The ISME Journal 1:38-47.

A. Shade, A.D. Kent, S. E Jones, R. J. Newton, E.W. Triplett, K.D. McMahon, (2007) "Inter-annual dynamics and phenology of bacterial communities in a eutrophic lake" Limnology and Oceanography 52:487-494.

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.

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.

 

ENVIRONMENTAL RESERVOIRS OF ANTIBIOTIC RESISTANCE
The emergence and proliferation of antibiotic resistant bacteria is a major public health concern. Recent surveys of our water resources for the presence of antibiotics have shown that these chemicals can be readily detected at microgram per liter levels in many surface and groundwater sources. The extent to which the release of these chemicals is coupled to an increase in the mobility and distribution of antibiotic resistance genes in environmental bacterial communities is unknown.  The overarching goal of this thrust area is to identify significant sources of antibiotic resistance genes to the environment and to evaluate which sources may be most easily controlled. We have studied wastewater treatment plants, septic tanks, and aquaculture as possible sources of tetracycline resistance.

Students:
Beth Pfotenhauer

Collaborators: 
Joel Pedersen, UW-Madison Soil Science and CEE
Sandra McLellan, UW-Milwaukee and Great Lakes WATER Institute
Funding:  none currently

Recent manuscripts related to our work in antibiotic resistance
E. E. Seyfried, K. F. Rubert IV, R. J. Newton, J. A. Pedersen, K. D. McMahon. (200_) "Tetracycline resistance genes and oxytetracycline use in aquaculture" In preparation.

E. E. Seyfried, R. J. Newton, K. F. Rubert IV, J. A. Pedersen, K. D. McMahon. (200_) "Diversity of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline" In review.

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




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Last Modified: February, 2008