AP Bio Winogradskies

For the Seagrass Microbiome project, one thing we’d like to do is to build a culture/reference genome collection for microbes found in association with seagrasses. For now, we are just working on this for Zostera marina, both because it is our primary experimental model organism and because we have easy year-round access to it at Bodega Bay.

However, while we hope to do more of it in the future, the Eisen lab isn’t currently set up to isolate the types of organisms that we think are likely to play an important role in seagrass adaptation to marine sediments, e.g., sulfur-oxidizing microbes (which require anaerobic conditions to grow). So, for now, we are using an enrichment tool known as a Winogradsky column to grow lots of sulfur oxidizers (and other things, but we’ll focus on sulfur oxidation here.)

In Winogradsky columns, sulfur and oxygen gradients cause microbes to stratify themselves according to their ability to utilize the available electron donors and acceptors. These microbial layers are visible to the eye, making Winogradsky columns a great classroom tool for teaching students about microbial physiology, biogeochemistry, ecological niches, succession, and much more.

Bethany Dixon is an AP Biology teacher at Western Sierra Collegiate Academy, a charter school in Rocklin, California. She has been building Winogradsky columns in her classroom for a couple of years now. We have teamed up to have her students build Winogradsky columns that have been inoculated with seagrass bed sediment. One thing we know is that we will be able to enrich for seagrass-associated microbes with a variety of metabolic capabilities. But, we don’t know much more than that. For example, how many different species will be oxidizing sulfur in these columns? Will the same microbial species perform sulfur oxidation in every column that’s made from the same sediment? What will happen if we add a bunch of elemental sulfur to the column? Will that change the makeup of the sulfur oxidizing community in the columns? Will it affect the shape of the sulfur gradient? Will it affect how quickly the layers form in the columns? Will it kill the column?

So, we arranged for Bethany’s AP Bio class to come to UC Davis’ Bodega Marine Lab (BML) to collect some sediment and inoculate some Winogradsky columns. Typically, Winogradsky columns are built by mixing sediment with a carbon source (like newspaper) and a sulfur source (like egg yolk), topping it off with water, and then sealing it. I got the idea of using diatomaceous earth as a physical matrix and laboratory chemicals for the carbon source (cellulose) and sulfur source (sodium sulfate) from Tom Benoit at McMurry University. We just make a slurry of the sediment and water, let the big particles settle, and then add the water to the columns.

This is really cool because we can control and systematically vary the chemical composition of each column. So, with the AP Bio class, we have defined 5 experimental “recipes” and each student is making two columns, with one experimental and one standard recipe. We’ll discuss the five experimental recipes in a follow-up post.

Today, the students arrived at the BML. We spent the afternoon weighing out and mixing chemicals, and loading our 50ml conical tube columns. Tomorrow, at low tide, we’ll head over to a seagrass bed, load up a bucket with sediment, and haul it back to the lab to inoculate the columns!

You can follow our progress here, or in real-time on Twitter with the hashtag #APBioGradksy

Visiting the experimental seagrass tanks. One of the experimental recipes involves substituting macerated seagrass roots for cellulose. Everyone visited the experimental tanks to grab some seagrass roots for those. They would have spent hours here, checking out the different tanks, watching the sea stars, urchins, and sea hares.
Visiting the experimental seagrass tanks.
One of the experimental recipes involves substituting macerated seagrass roots for cellulose. Everyone visited the experimental tanks to grab some seagrass roots for those. They would have spent hours here, checking out the different tanks, watching the sea stars, urchins, and sea hares.
Ecosystem engineers. Back in the lab, a classroom provided by the BML, five teams weighed out the chemicals for their experimental columns, and loaded them up.
Ecosystem engineers. Back in the lab, a classroom provided by the BML, five teams weighed out the chemicals for their experimental columns, and loaded them up.

2 thoughts on “AP Bio Winogradskies

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s