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!

-Alex

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!

-Alex

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.

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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.

-Alex

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.

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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.

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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!

-Alex

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Ice Off Mendota

It’s been a mild winter here in Madison. Our lakes did freeze, but not for long – Mendota was covered in ice from January 11 to March 13, far less than in past years (Check out the Wisconsin State Climatology website for past records).

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One of the few pieces of ice left on Mendota on March 14

So what happens after the ice melts? Large amount of nutrients from the surrounding landscape are swept into lakes with the melting snow. Algae flourish on these extra nutrients and start off the ice-free season with rapid growth.

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Algae growing in an input to Mendota

But this only lasts for a little while. After the algae die off, the clear water phase begins. During this time, the water clarity is at its highest, and some of our favorite freshwater bacteria such as acI  become abundant.

Open water means it’s almost time for the field season. Besides our routine sampling on Mendota and the northern bog lakes, we’ve got something really big planned … stay tuned for more info!

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Ducks enjoying the open water near campus

Lab Retreat

Every spring semester, the McMahon Lab does a lab retreat. This is our designated time to do some lab team-building exercise (such as arts and crafts, hiking, and eating lots of food) as well as powering through some less-exciting lab tasks. This year, we worked on formatting our sample metadata for input into a database, and drawing maps of how everyone in the lab is connected. See below for pictures!

– Alex

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