McMahon Lab

Research Overview

Enhanced Biological Phosphorus Removal

EBPR Batch Reactors
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 and 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

Freshwater microbial ecologyThe 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 (, the North Temperate Lakes Long Term Ecological Research site (, and the Global Lakes Ecological Observatory Network (

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.

Freshwater microbial ecologyWe 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.



The best way to learn about our research is to read our most recent publications.

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McMahon Labotatory

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5552 Microbial Science Building
1550 Linden Drive
Madison, WI 53706
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Contact Info
Lab phone: (608) 890-0237
Fax: (608) 262-9865