Winogradsky Columns!

For anyone who’s been following the Seagrass Microbiome Project you’ll know that we’ve had a long-running Winogradsky column side project running, courtesy of Jenna Morgan Lang who first had the idea to incorporate them into Seagrass Microbiome project and leverage the power of citizen scientists. Working with the columns over the past year has turned me into a die-hard Winogradsky fan.  Even though I’ve just changed labs for graduate school my Winogradsky adventures are just beginning.

At this point, you may be asking, “What exactly are these super-useful, super-cool Winogradsky column things?”

Sergei Winogradsky, one of the founders of microbial ecology possessed both a great brain and a great mustache. (Some people have it all).

Sergei Winogradsky, one of the founders of microbial ecology possessed both a great brain and a great mustache. (Some people have it all). (Photo credit: Wikimedia Commons)

A Winograsky column is an experimental tool invented by Sergie Wiongradsky in the late 1800s. Winogradsky was studying how microbes interact in communities and he developed these columns while studying microbial metabolism. Since their invention, Winogradsky columns have been used in numerous experiments to study microbial community interactions or to try to isolate unruly microbes through a process called enrichment culturing.

For all their usefulness, the columns are surprisingly simple. The general recipe to make one is:

  1. Fill a clear, seal-able container with a substrate (traditionally this is mud).
  2. Add some nutrients
  3. Add some microbes from the environment (these are already along for the ride if you use mud as your substrate).
  4. Top off the container with water and seal it.
  5. Wait for the microbes to grow.

That’s it!

A schematic of a typical* Winogradsky column. The sunlight bar only applies to the center core of the column since the edges are exposed to light if the container is clear. *In real life, colors may vary.

A schematic of a typical* Winogradsky column. The sunlight bar only applies to the center core of the column since the edges are exposed to light if the container is clear. *In real life, colors may vary. (Image credit: NASA Ames: http://quest.arc.nasa.gov/projects/astrobiology/fieldwork/ed.html)

The coolest part about Winogradsky columns is how those microbes grow. The bottle becomes divided into many mini-habitats based on an oxygen gradient formed from the water and oxygen. A sulfur gradient also forms, since the microbes at the bottom of the column use sulfur as a substitute for oxygen. Microbes grow only in the habitats most favorable to their particular lifestyle. Over the course of a couple of weeks, layers or patches of colorful microbes begin to grow. Ideally, each successive layer eats the waste products of the layers surrounding it and a perfectly sustainable ecosystem is established.

Since Winogradsky columns are so important and because they’re so easy to make, the outreach coordinators for my department and I decided to host a teacher workshop to train teachers to make these columns in their classrooms.

One of the perks of helping with the workshop is that I get to make example columns. Here are some pictures from our columns as they’ve established.

 

The mud columns on their first day. Each column has a different combination of nutrients, paper for a carbon source or egg yolk for a sulfur source. One is a control column which we didn't add anything to.

The mud columns on their first day. Each column has a different combination of nutrients, paper for a carbon source or egg yolk for a sulfur source. One is a control column which we didn’t add anything to.

Instead of mud, these columns have diatomaceous earth as a substrate. This will make it easier to see the microbes growing. We had two treatments, one with three times as many nutrients as the other. We used stream water mixed with stream mud to seed the columns.

Instead of mud, these columns have diatomaceous earth as a substrate. This will make it easier to see the microbes growing. We had two treatments, one with three times as many nutrients as the other. We used stream water mixed with stream mud to seed the columns.

 

 

 

 

 

 

 

We have two sets of columns, fast-growing, nutrient spiked diatomaceous earth columns and slow-growing, traditional mud columns. We added extra nutrients to the fast-growing columns, they were also in a form directly usable to the microorganisms since we were hoping to jump-start the growth process before our workshop.

The higher-nutrient column after almost 3 weeks. Layering is beginning to show on the surface.

The higher-nutrient column after almost 3 weeks. Layering is beginning to show on the surface.

The lower-nutrient column after almost 3 weeks. Layers have yet to form on the top, but the salt-and-pepper growth in the base has established.

The lower-nutrient column after almost 3 weeks. Layers have yet to form on the top, but the salt-and-pepper growth in the base has established.

The diatomaceous earth makes it easy to see the changes taking place. In mud columns, it’s often difficult to see what’s happening until quite far along in the process.

The mud columns we created are much slower to show their growth. Instead of adding the chemical compounds directly, we added common items that contain those nutrients. For carbon, we added paper scraps, for sulfur we added an egg yolk.

The mud columns are also less homogenous than the diatomaceous earth columns. Because it’s hard to completely compact mud into the water bottles, our mud columns have little pockets of empty space (and possibly oxygen) trapped at different levels in the column. These pockets are additional micro-habitats and will probably be colonized by different organisms than the surrounding soil.

The mud columns after about 5 weeks of growth. It's impossible to see in this picture but the columns show very tiny smudges of red microbes growing on the edges.

The mud columns after about 5 weeks of growth. It’s impossible to see in this picture but the columns show very tiny smudges of red microbes growing on the edges.

We know the mud columns were growing because they were producing large amounts of noxious-smelling gas, but it took a good 5 weeks for anything visible to show up. After 8 weeks of growth, the mud columns are finally beginning to show some larger visible signs of life and the microhabitats are turning green (probably with cyanobacteria).

At 8 weeks we can finally begin to see green around the edges of each pocket in the mud.

At 8 weeks we can finally begin to see green around the edges of each pocket in the mud.

At 8 weeks, the red smudges on the side of the columns have grown big enough that a cell-phone camera can capture them.

At 8 weeks, the red smudges on the side of the columns have grown big enough that a cell-phone camera can capture them.

 

 

After 6 weeks the diatomaceous earth columns have completely changed. The top of the higher-nutrient column has become dominated by red organism. The layer of green we saw at 3 weeks has completely disappeared and there is a neon-green microbe growing in a pocket partway down the column.

 

The high-nutrient column at 6 weeks.

The high-nutrient column at 6 weeks.

The low-nutrient column after 6 weeks.

The low-nutrient column after 6 weeks.

 

The low-nutrient column after 6 weeks looks like it’s on its way to the same fate. Stay tuned for more pictures as the columns mature!

 

 

 

 

 

If, after reading this, you’ve decided that you agree with me and that Winogradsky columns are the coolest, here are a couple of links explaining how you can make your own. If you make a column, don’t forget to send me pictures in the comments or on Twitter!

http://quest.arc.nasa.gov/projects/astrobiology/fieldwork/lessons/Winogradsky_5_8.pdf

http://www.scientificamerican.com/article/bring-science-home-soil-column/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416514/

 

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About Hannah Holland-Moritz

Hannah Holland-Moritz is a graduate student working in Noah Fierer’s lab. She graduated from UC Davis in June 2014 with a major in Biochemistry and Molecular Biology and minor in Bioinformatics and most recently spend a gap year working in Jonathan Eisen’s lab on the microbiome of seagrasses. Interested in Evolution, Ecology, Bioinformatics and all things microbial, she plans to pursue a career in research.
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