Adventures with Winogradskies

Often when microbiologists begin to explore an unknown (or relatively unknown) environment, they begin by using classical microbiological techniques to try to characterize the communities of microbes living in that environment. These classical techniques are often referred to as “culture-based” because they are oriented towards the goal of trying to grow (or culture) microbes in the lab. Although culture-based techniques can be limiting (it’s nearly impossible to culture every single organism in any given environment), they are very useful for laying the foundation for the non-culture-based techniques the Seagrass Microbiome project will be using.

As a result, we in the Eisen lab have been playing around with some classical microbiology techniques alongside our non-culture-based explorations. One of the coolest techniques we’re using is Winogradsky columns. Winogradsky columns are essentially microbial terrariums. The basic recipe is as follows: take a clean tube, add a few essential chemicals, spike in some wild microbes, close the lid and let natural nutrient cycles take over. If you’ve done everything right, in a couple of weeks, you should start to see layers of microbes each living in a different mini niche within your mini ecosystem.

Two weeks ago we did just that. We’ve been following the progress of the tubes on the side as we pursue other non-culture-based projects. We’ve also been exploring different ways of making the columns to figure out the best way to get clean layers while still preserving the integrity of the column. Below are some pictures of our progress to date:

Two Days in:

Two days into the experiment bubbles started to appear.

One week in:

One week into the experiment, brown patches appeared on the surface of the jars.



The smaller tubes took longer to show brown spots, at one week all they had was bubbles.

1.5 weeks in:

At a week and a half the brown mat has spread over the surface of each container.



9 Days in:

9 days into the experiment, we decided to cover one of the large flasks to simulate soil conditions.


2 weeks into the experiment: 

14 days into the experiment dark black splotches appeared under the surface of one of the large flasks.
Surprisingly, the covered flask also had the same black splotches developing.
Some of the smaller tubes had them as well.
One microcentrifuge tube had a beautiful green layer develop.


As a side experiment, we spiked new tubes with potassium nitrate and ammonium acetate to see if the presence of nitrogen changed anything about the development of the flasks. These tubes were created a week behind the others.

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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