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!


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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!


RNA Field Work

After all of our planning for GEODES (Gene Expression in Oligotrophic, Dystrophic, and Eutrophic Systems), the time for field work is finally here! The goal of this experiment is to learn more about how bacterial communities process carbon in freshwater by looking at their gene expression over short time scales. Starting early Wednesday morning, we’ll be at UW Trout Lake Station collecting samples from Sparkling Lake. We’ll take samples every 4 hours for 48 hours from this lake, then start all over again from the nearby Trout Bog. Then next week, we’ll drive back to Madison to sample Lake Mendota as well. But the fun isn’t over after Mendota – we’ll still need to process all of the samples we collect, which will likely take several weeks.

We’ll be tweeting during the whole process, so follow the hashtag #RNAGEODES or check the feed to the right of this post to learn about our progress over the next few weeks. Wish us luck!


Back in the Bogs

The field season is off to a running start at UW Trout Lake Station! We’ve been maintaining our North Temperate Lakes – Microbial Observatory on a group of bog lakes near Minocqua, WI.


Crystal Bog

Bog lakes are areas of open water surrounded by mats of sphagnum moss. The bogs we study are called “quaking” bogs, meaning the edge of the mat floats on the water and moves when you walk on it! As the sphagnum dies, it falls to the bottom of the water to form peat, which accumulates over time. One day, these bog lakes will be completely filled with peat.

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A piece of sphagnum moss

But in the mean time, the sphagnum shapes the aquatic bacterial community by limiting the nitrogen and phosphorus available, lowering the pH of the water, and releasing complex carbon molecules. Bogs are hugely important for global carbon cycling because of the amount of carbon stored in their peat, and microbes are key players in carbon processing in bogs!

We’ve been observing bacterial communities in these same bogs for over a decade, and are excited to continue sampling this year. So far, we’ve placed our boats out on the bogs, cleaned and calibrated our equipment, and have collected the first samples of the year.


P.S. Check out these other sights from the bog lakes!

Distubance in Microbial Communities

One of the biggest questions in microbial ecology asks how microbial communities will respond to disturbance. Even in macro-organisms, disturbance is a hot topic. Without being able to understand how communities respond to disturbance, it’s nearly impossible to predict the composition of microbial communities. If you have ever taken an antibiotic, then you have personally experienced a disturbance in a microbial community!  Since humans live in such close association with microbes and use them for industrial purposes, we’d really like to be able to predict how a microbial community will respond to changing conditions.

In order to determine whether microbial communities show consistent responses to disturbances, Cristina grew biofilms in a lake and then disturbed them by either scouring them with water or by moving the biofilm to a different depth in the lake. These perturbations were intended to be similar to the effects of a windy day, which might scour the biofilms or move them in the lake. She then looked at species composition in diatoms and bacteria to see how much each community changed after a disturbance.


Myvatn, the lake where Cristina performed her experiments

Cristina found that disturbing microbial communities reduced their variability, meaning that populations of individual taxa were more consistent when disturbed. Communities experiencing the same type of the disturbance also became more similar to each other. Overall, Cristina’s results show that microbial communities change predictably after a disturbance.  This is great news for anyone trying to predict microbial communities!

Read the full paper here:

Herren, Cristina M., Kyle C. Webert, and Katherine D. McMahon. “Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton.” mSystems 1.3 (2016): e00013-16.



Ancestral States

Candidatus Accumulibacter phosphatis is one of our favorite bacteria in the McMahon Lab. This microbe plays a crucial role in wastewater treatment because it removes phosphorus from wastewater by accumulating polyphosphate (hence the name). The “candidatus” portion of its name means that it cannot be grown in pure culture. However, we can get it to grow in highly enriched cultures in bioreactors in the lab.


Accumulibacter is in yellow and green, representing the two of the types of Accumulibacter we see in reactors. Other bacteria are colored blue.

Accumulibacter is a fantastic microbe for wastewater treatment, but how did it become so good at its job? It’s highly unlikely that this organism evolved just to clean our wastewater, so its polyphosphate accumulating abilities must have provided an advantage in a different environment. Lab member Ben Oyserman’s paper begins to answer this question by reconstructing the ancestral genome of Accumulibacter based on modern genomes. One possibility was that Accumulibacter “copied” the genes to accumulate polyphosphate from another microbe that was already adapted to a high phosphorus environment (called horizontal gene transfer). However, Ben shows that the genes encoding the machinery for polyphosphate accumulation were most likely present in the ancestral state. Instead, the signature of horizontal gene transfer was present in pathways need to store carbon efficiently under anaerobic conditions. This analysis suggests that once these adaptations were in place, Accumulibacter could become a true polyphosphate accumulating organism.

This has implications both for other unrelated polyphosphate accumulating organisms that may have similar adaptations (called convergent evolution) and for engineering other microbes to be better at their jobs. Additionally, Ben’s methods could be used to investigate the evolution of other complex traits, or for understanding how best to engineer other microbes to have new traits.

Curious about the details? Check out Ben’s full paper here:

Oyserman, Ben O., et al. “Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria.” The ISME Journal (2016).


Introducing GEODES

In the McMahon Lab, we’ve always got something big planned. GEODES, which stands for “Gene Expression in Oligotrophic, Dystrophic, and Eutrophic Systems,” is this summer’s big sampling effort. This project stems from our earlier work on diel cycling in freshwater specifically looking at light-powered proteins called rhodopsins. The focus of GEODES is on microbially-mediated carbon cycling. We hypothesize that we will see trends in gene expression on the scale of a single day that are driven by carbon exchange between photosynthetic microbes and non-photosynthetic microbes. Check out our JGI Community Sequencing Program plan here!

We’re also expanding this project to include three lakes: Sparkling Lake and Trout Bog near Minocqua, WI, and Lake Mendota in Madison. These lakes have very different nutrient concentrations. Lake Mendota is a highly productive lake, with lots of nitrogen and phosphorus inputs from the surrounding agricultural land, resulting in large amounts of photosynthesis. Sparkling Lake has low nutrient levels, making its waters clear and, well, sparkling. It has much less microbial growth than Lake Mendota. Trout Bog is a bog lake, meaning it has very high carbon levels, but is low in other nutrients. Each of these lakes contains different types of photosynthetic microbes. While we expect that the carbon compounds exchanged between microbes in each lake will be different, we still expect to see daily trends that are similar in all three lakes. The results of this experiment will hopefully tell us more about how carbon is processed in different types of lakes, as well as help us identify reactions performed by specific bacterial groups.

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From left to right: water from Trout Bog, Sparkling Lake, and Lake Mendota. Lake Mendota usually develops a greenish tint later in the summer.

A project of this size requires a lot of preparation. The sampling is scheduled for July, but in the meantime, we’re busy getting our field equipment set up, vehicles rented, deciding what metadata to collect, and much more. Stay tuned for updates on GEODES!


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