McMahon Lab Preprints

A preprint is a sneak preview of a research article before it is published. While published articles are important because of peer review (the formal process of having other scientists outside of your research group evaluate your work), preprints have several other advantages. That formal review process can sometimes take months, so posting a preprint means that people can read, use, and credit your work earlier. You can also participate in an informal peer review in the comments section of your preprint, and you may get feedback from unexpected sources or people outside your field and find problems before you submit your research to a journal.

Preprints have been commonly used in other fields for awhile, but have recently become popular in biology as scientists seek to decrease review times and provide more open access to their research. Here in the McMahon Lab, we’ve embraced this wholeheartedly and have several preprints currently online!

Feedback is welcome! Click on the citations below to read our preprints. We’d love to hear your thoughts and answer questions before our research is officially published.


Photosynthesis + Wastewater

Microbes have been put to work in wastewater treatment for many years now. With their diverse range of metabolic processes and preferred living conditions, microbes are capable of removing many different types of compounds from our waste. Much of the research in the McMahon Lab focuses on polyphosphate accumulating organisms (PAOs), microbes that can take up and store phosphorus. To select for these organisms, a wastewater treatement process needs to alternate between aerobic (high oxygen) and anaerobic (low oxygen) conditions. However, this cycling can get expensive. That’s because we need to pump oxygen into the reactors, a process called “aeration.”

Wouldn’t it be great if there was a microbe that produced oxygen but only when you flipped on a switch? Look no further than photosynthesis, the process of producing sugar from sunlight. Photosynthetic bacteria and algae produce oxygen, but only when exposed to light. Combine this with phosphorus-storing bacteria, plus something to provide nitrogen from the wastewater (in this case, nitrifiers), and you’ve got a process that doesn’t need pumped oxygen!


Former lab member Ben Oyserman built just such a reactor as he was finishing up his PhD, and it’s pretty cool. For more info, check out his paper here.



Remember that name! One of the great things about UW-Madison is how much it encourages and helps people who want to start their own businesses, and lab members Pamela Camejo and Francisco Moya are the next entrepreneurs to come out of our graduate school. Their startup is called Pathogenomica, and the service they will provide is broad pathogen detection in water samples using DNA sequencing. Most tests for pathogenic bacteria are specific for single pathogens, while Pame and Pancho’s soon-to-be patented process will identify all currently known pathogenic bacteria at once. And this is just the beginning for Pathogenomica – they plan to expand into whole genome sequencing to detect new pathogens and antiobiotic resistance, as well as quantification of pathogens.

Keep an eye on this up-and-coming business out of UW-Madison and the McMahon Lab, and remember Pathogenomica if you need samples tested for pathogens in the near future!


Read more here:

GEODES Data Preview

We’ve been hard at work this fall processing all of the samples we collected for GEODES this summer. The RNA samples still need to be sequenced, but we’re already seeing some interesting trends in the environmental data we measured while sampling.

What have we been up to?

  • Extracting the RNA samples – we processed 108 in one day assembly-line style!
  • Measuring chlorophyll concentrations
  • Quantifying bacterial production (how much protein were the bacteria making)
  • Entering our written data into the computer. This is both more difficult and more important than it sounds.
  • Getting featured around the University of Wisconsin!


wisc_homepage homepage


The Flamingle Alumni Newsletter


What have we found? Many parameters in the lakes do show daily trends, but others do not. Sometimes a measurement was diel in one lake but not in the other! Below are some rough figures of what we’ve found -click on each plot for a larger image.

In the plots above, darker colors indicate warmer temperatures. The y axis is the depth we measured at, and the x axis is the hour the measurement was taken at. We collected our epilimnion (surface water) sample from the top to the black line. Mendota shows the strongest daily trends in temperature, and in its closely related measurement dissolved oxygen. This is also a good sanity check that we sampled at the right depth, as the black line should be at or slightly above the transition from warm to cool water.

In Lake Mendota and Trout Bog, conductivity and pH were closely correlated and changed right at the thermocline, where the temperature also sharply decreased.  Conductivity was uniformly low in Sparkling Lake, but the water does get slightly more acidic deeper down.

Chlorophyll is an interesting one. We expected this to follow diel trends because chlorophyll is produced to harvest energy from sunlight. It does in Trout Bog, but not in the other two lakes. Sparkling Lake, with its crystal clear waters doesn’t have much chlorophyll, as expected. But Mendota is notorious for its cyanobacterial blooms. What’s up with that?

Finally, the results of the bacterial production assays are pretty cool. The plots above show how much protein was being made at each time point, and is one measure of the “activity” of the microbial community. The first thing that jumps out is that there are time points with way more protein production than others, but that these high points are not at 24 hour intervals.

(Note: there can’t actually be negative protein production in Sparkling Lake. This means that the negative control for that time point was greater than the experimental samples, and that protein production was essentially zero).

What does this all mean?

It means we’re very curious about that RNA data.

  • Different process are indeed occurring in these three lakes, as shown by their differences in chlorophyll, protein production, and conductivity/pH.
  • Chlorophyll concentrations show diel trends in Trout Bog, but not Lake Mendota. Does this indicate different lifestyles or regulation strategies in photosynthetic microbes in these two lakes?
  • The timepoints with high bacterial production versus low bacterial production are very interesting. With the RNA data, we should be able to tell which taxa were active at the high time points (and not active in the low time points) AND what metabolic pathways they were using at that time.

Stay tuned for more updates as we get the RNA samples sequenced and analyzed!


Microbial Ecology in the Fall Semester

Your guide to learning about microbial ecology at UW-Madison this semester!  Here’s what’s on the McMahon Lab calendar. Click on the links for more info on each seminar series. Hope to see you there!

Bacteriology Department Seminar Thursdays at 3:30, Ebling Symposium in Microbial Sciences Building

Bess Ward, Nov. 10                   Marine nitrogen cycling

Maren Friesen, Nov. 17           Plant microbiomes

Center for Limnology SeminarWednesdays at 12:00, 102 Water Sciences

Heather Tallis, Sep. 28              The ties that bind us: Explorations of socio-ecological systems and ecosystem services in conservation

Zoology Biology ColloqiumThursdays at 3:30, Birge Hall B302

Lee Dugatkin, Dec. 15                 Altruism writ small: E. coli and antibiotic resistance

Medical Microbiology & Immunology SeminarFridays at 12:00, 6201 Microbial Sciences

Jean-Michael Ané, Nov. 11        Sweet Talks and Trade Deals in Plant-Microbe Symbioses

Qbio Seminar Series Wednesdays at 2:00, Orchard View Room in WID (3rd floor)

Shu Pan, Sep. 21                         Computational modeling and high-throughput                            experiments  for direct identification of gene functions

Ophelia Venturelli, Nov. 9      Reverse engineering synthetic ecologies from the human gut microbiome

Gheorghe Craciun, Nov. 16    Persistance, permanence, and homeostasis in biological interaction networks

Special Events:

Wisconsin Ecology Symposium, Oct. 13-14, 140 Weeks Hall

Water@UW-Madison Poster Session, Oct. 28, 3-5PM, WID

GEODES Progress Report

Last week, we began our giant experiment studying bacterial gene expression on day/night cycles. This was in many ways the most difficult week of the experiment, as it took place at UW Trout Lake Station in Minocqua, WI. While UW TLS is a fantastic research station with great facilities, we still had to figure out how to get certain reagents such as liquid nitrogen, labelled carbon isotope, and dry ice to the northwoods of Wisconsin. It was also the tightest schedule of the sampling – we only had one extra day in case of bad weather during the four days of sampling. However, I’m excited to announce that we pulled it off! We have 112 RNA samples safely stored at -80C, and only had to replace one timepoint due to a thunderstorm. Overall, it was a very successful field campaign! Anyone who does field work can tell you that things never go quite as planned once you’re out in the wilderness, so we’re pretty happy with the past week. We were even featured on Minocqua’s local news!

This week, we’re continuing GEODES by sampling Lake Mendota every 4 hours, starting Thursday at 5AM and finishing Saturday at 1AM. You may spot us coming and going from the Center for Limnology (on the start of the Lakeshore Path by Memorial Union), or at our sampling location in University Bay, directly between the tip of Picnic Point and Van Hise.

To get updates on our sampling, you can check the feed to the right of this post, or follow the Twitter hashtag #RNAGEODES. Also, lab member Sarah Stevens will be hosting a live feed of one of the sampling timepoints this Friday around 5PM – we’ll post more information about how to find that here and on Twitter earlier on Friday.

See you on the other side!