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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Winter Microbiology

Despite a warm start to winter in Madison, Lake Mendota is definitely frozen (see pictures below from our shortcut to seminar last Friday). Frigid temperatures and snow make spring seem like a forgotten memory. But that doesn’t mean that all of the lake microbes are frozen, too. Their metabolisms may be slowed by the cold temperatures, but they are still active and impacting their environments. Here are some reviews of microbial ecology in cold environments for you to enjoy while we’re still experiencing winter!

-Alex

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Your Guide to Microbial Ecology in the Spring Semester

Although the spring semester has officially begun, it does not feel like spring here in Madison. Despite earlier concerns, the weather has cooled down enough for our lakes to freeze. Here in the McMahon Lab, we’ve had  a productive winter break! We published two new papers over the break:

We’re also looking ahead to many great seminars and events this semester! If you’d like to learn more about microbial ecology, here’s a few to get you started.
Events:
Trina is speaking at Science on Tap in Minocqua on Feb 3rd! Details and a livestream of the event here.
The College of Agricultural and Life Sciences is hosting a symposium on microbiome research on April 20th. Great line up of speakers, including Dr. Jo Handelsman, science advisor to the president! Register here.
The annual campus-wide Undergraduate Research Symposium will be held April 14th. Come see research by McMahon Lab undergraduates! Details here.
Seminars:
Environmental Engineering Graduate Seminar – Tues. 12:05 in 2535 Mechanical Engineering
  • Lab members presenting: Ben Oyserman (1/26), Chris Lawson (2/16), Pancho Moya (3/29), and Pame Camejo (4/5). The first seminar is 1/26 and it runs until 5/30.

Microbiology Doctoral Training Program Seminar – Wed. 12:05 in 1520 Microbial Sciences

  • Lab members presenting: Sarah Stevens (4/6) and Grace Shrader (5/4). Full schedule here.

Limnology and Marine Sciences Seminar – Wed. 12:00 in 102 Water Sciences and Engineering Laboratory

  • Lab member Robin Rohwer is presenting on 3/9. Full schedule here.

Dept. of Bacteriology Distinguished Lectures in Microbiology – Thurs. 3:30 in 1220 Microbial Sciences

  • Microbial ecology talks include Prof. Mark Mandel (1/28), Prof. Garret Suen (2/4), Prof. Rachel Gallery (2/18), and Prof. Nicole Koropratkin (5/5). There are many other fantastic speakers as well; see the full schedule here.

Genomics Seminar Series – Thurs. 1:30 in 1111 Biotechnology Center

  • This series has a strong start with Prof. Jack Gilbert on 1/21. Full schedule pending

Biology Colloquium – Thurs. 3:30 in 168 Noland

  • Microbial ecology talks include Prof. Linda Graham (1/28), Prof. Woei-Fuh Wang (3/31), Prof. Serita Frey (4/14), and Prof. Jason Kwan (4/21). Full schedule here.

Biodesign Biocatalyst Series – varied

  • Kathryn Fixen, “Understanding how a photosynthetic bacterium works”, Feb 2nd 3:30 in 1220 Microbial Sciences
  • Lauren Woodruff, “Programming Cells by Genetic Design”, Feb 4th 4:00 in 1610 Engineering Hall
  • Paul O’Maille, “Functional radiation and enzyme specialization in terpene biosynthesis: Origin and action of antimicrobials”, Feb 9th 3:30 in 1211 Biochemical Sciences
  • Ophelia Venturelli, “Resource trade-offs in microbial systems: from genetic circuits to multi-species communities” Feb 17th 4:00 in 1610 Engineering Hall

Qbio Lecture Series – Wed 2:00 in 3rd Floor Orchard View Room, Wisconsin Discovery Building

  • First lecture is Prof. Sailendharan Sudakaran speaking about the evolution of insect microbiomes. Full schedule here.

Medical Microbiology and Immunology Seminar – Fri 12:00in 152o Microbial Sciences

  • Speakers include Prof. David Relman (3/4) on the human microbiome and Prof. Kris Saha on CRISPR-Cas9 editing of human embroynic cells; full schedule here.